Starting phenix.real_space_refine on Fri Jun 6 20:25:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wcn_32425/06_2025/7wcn_32425.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wcn_32425/06_2025/7wcn_32425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wcn_32425/06_2025/7wcn_32425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wcn_32425/06_2025/7wcn_32425.map" model { file = "/net/cci-nas-00/data/ceres_data/7wcn_32425/06_2025/7wcn_32425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wcn_32425/06_2025/7wcn_32425.cif" } resolution = 2.87 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= 0.000 sd= 0.005 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 57 5.16 5 C 5232 2.51 5 N 1436 2.21 5 O 1526 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8252 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1947 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 451 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2240 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 1 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8WL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.39, per 1000 atoms: 0.65 Number of scatterers: 8252 At special positions: 0 Unit cell: (79.994, 102.971, 131.054, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 F 1 9.00 O 1526 8.00 N 1436 7.00 C 5232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 155 " distance=2.03 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: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1962 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 42.3% 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 39 removed outlier: 3.939A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 240 removed outlier: 3.781A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.763A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.508A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.738A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.860A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.230A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 37 removed outlier: 3.741A pdb=" N GLU B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 44 Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.951A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.849A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.580A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.651A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.521A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 36 removed outlier: 3.795A pdb=" N LEU R 11 " --> pdb=" O PHE R 7 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL R 25 " --> pdb=" O THR R 21 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS R 35 " --> pdb=" O LEU R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 66 removed outlier: 3.655A pdb=" N CYS R 42 " --> pdb=" O GLY R 38 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR R 63 " --> pdb=" O SER R 59 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP R 64 " --> pdb=" O GLY R 60 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 109 removed outlier: 3.819A pdb=" N CYS R 78 " --> pdb=" O GLN R 74 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL R 96 " --> pdb=" O SER R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 116 removed outlier: 3.686A pdb=" N LEU R 114 " --> pdb=" O PRO R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 138 removed outlier: 3.783A pdb=" N ALA R 122 " --> pdb=" O SER R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 143 Processing helix chain 'R' and resid 163 through 172 Processing helix chain 'R' and resid 173 through 210 removed outlier: 3.838A pdb=" N ALA R 209 " --> pdb=" O ALA R 205 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY R 210 " --> pdb=" O GLY R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 237 removed outlier: 3.544A pdb=" N THR R 226 " --> pdb=" O LYS R 222 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N CYS R 237 " --> pdb=" O SER R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 250 Processing helix chain 'R' and resid 255 through 263 removed outlier: 3.837A pdb=" N VAL R 259 " --> pdb=" O HIS R 255 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU R 261 " --> pdb=" O TYR R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 270 Processing helix chain 'R' and resid 270 through 280 removed outlier: 3.513A pdb=" N ASN R 275 " --> pdb=" O ASN R 271 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 283 through 300 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.385A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.690A pdb=" N ARG B 60 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 339 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B 329 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY B 341 " --> pdb=" O SER B 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 74 removed outlier: 3.693A pdb=" N ALA B 71 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP B 94 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LYS B 100 " --> pdb=" O ASP B 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.628A pdb=" N ARG B 148 " --> pdb=" O ILE B 134 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASN B 136 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL B 146 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 157 through 162 removed outlier: 6.749A pdb=" N SER B 171 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS B 160 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 169 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE B 168 " --> pdb=" O TRP B 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 203 removed outlier: 6.871A pdb=" N GLY B 213 " --> pdb=" O MET B 199 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU B 201 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 211 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU B 203 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU B 209 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 231 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP B 223 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS B 229 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 245 removed outlier: 6.494A pdb=" N CYS B 261 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR B 274 " --> pdb=" O CYS B 261 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B 263 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN B 270 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 284 through 289 removed outlier: 6.638A pdb=" N GLY B 299 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL B 287 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B 297 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE B 289 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 295 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N CYS B 305 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL B 318 " --> pdb=" O CYS B 305 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL B 307 " --> pdb=" O ALA B 316 " (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 11 through 12 removed outlier: 6.797A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1158 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: 2.06 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1343 1.30 - 1.43: 2221 1.43 - 1.56: 4772 1.56 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 8418 Sorted by residual: bond pdb=" C12 8WL R 401 " pdb=" N11 8WL R 401 " ideal model delta sigma weight residual 1.334 1.459 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C16 8WL R 401 " pdb=" N17 8WL R 401 " ideal model delta sigma weight residual 1.347 1.454 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C8 8WL R 401 " pdb=" C9 8WL R 401 " ideal model delta sigma weight residual 1.544 1.453 0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C34 8WL R 401 " pdb=" C8 8WL R 401 " ideal model delta sigma weight residual 1.533 1.445 0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C SER B 256 " pdb=" O SER B 256 " ideal model delta sigma weight residual 1.234 1.179 0.055 1.28e-02 6.10e+03 1.85e+01 ... (remaining 8413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 11313 3.15 - 6.30: 69 6.30 - 9.45: 10 9.45 - 12.60: 1 12.60 - 15.75: 2 Bond angle restraints: 11395 Sorted by residual: angle pdb=" N SER B 256 " pdb=" CA SER B 256 " pdb=" C SER B 256 " ideal model delta sigma weight residual 109.41 117.59 -8.18 1.52e+00 4.33e-01 2.90e+01 angle pdb=" O24 8WL R 401 " pdb=" S22 8WL R 401 " pdb=" O25 8WL R 401 " ideal model delta sigma weight residual 117.77 102.02 15.75 3.00e+00 1.11e-01 2.75e+01 angle pdb=" C7 8WL R 401 " pdb=" C8 8WL R 401 " pdb=" C9 8WL R 401 " ideal model delta sigma weight residual 111.30 96.43 14.87 3.00e+00 1.11e-01 2.46e+01 angle pdb=" N SER B 256 " pdb=" CA SER B 256 " pdb=" CB SER B 256 " ideal model delta sigma weight residual 111.43 103.96 7.47 1.59e+00 3.96e-01 2.21e+01 angle pdb=" N SER B 85 " pdb=" CA SER B 85 " pdb=" C SER B 85 " ideal model delta sigma weight residual 109.41 114.94 -5.53 1.52e+00 4.33e-01 1.32e+01 ... (remaining 11390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 4508 17.57 - 35.15: 417 35.15 - 52.72: 72 52.72 - 70.30: 23 70.30 - 87.87: 10 Dihedral angle restraints: 5030 sinusoidal: 1992 harmonic: 3038 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -157.91 -22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ASP A 310 " pdb=" C ASP A 310 " pdb=" N TYR A 311 " pdb=" CA TYR A 311 " ideal model delta harmonic sigma weight residual 180.00 160.57 19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA MET B 273 " pdb=" C MET B 273 " pdb=" N THR B 274 " pdb=" CA THR B 274 " ideal model delta harmonic sigma weight residual 180.00 161.23 18.77 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1133 0.070 - 0.141: 141 0.141 - 0.211: 6 0.211 - 0.281: 1 0.281 - 0.351: 1 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA SER B 85 " pdb=" N SER B 85 " pdb=" C SER B 85 " pdb=" CB SER B 85 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA TYR B 70 " pdb=" N TYR B 70 " pdb=" C TYR B 70 " pdb=" CB TYR B 70 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB THR A 325 " pdb=" CA THR A 325 " pdb=" OG1 THR A 325 " pdb=" CG2 THR A 325 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 1279 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 70 " -0.034 2.00e-02 2.50e+03 2.54e-02 1.30e+01 pdb=" CG TYR B 70 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR B 70 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 70 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 70 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 70 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 70 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 70 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 246 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO B 247 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO N 88 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.028 5.00e-02 4.00e+02 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1825 2.79 - 3.31: 7440 3.31 - 3.84: 13192 3.84 - 4.37: 15664 4.37 - 4.90: 27342 Nonbonded interactions: 65463 Sorted by model distance: nonbonded pdb=" OE1 GLU B 226 " pdb=" NH2 ARG B 230 " model vdw 2.257 3.120 nonbonded pdb=" OD2 ASP R 64 " pdb=" NH2 ARG R 81 " model vdw 2.327 3.120 nonbonded pdb=" NH1 ARG N 67 " pdb=" O SER N 85 " model vdw 2.333 3.120 nonbonded pdb=" OG SER B 85 " pdb=" OD1 ASP B 87 " model vdw 2.360 3.040 nonbonded pdb=" O ASP B 174 " pdb=" OG1 THR B 175 " model vdw 2.381 3.040 ... (remaining 65458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.140 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.005 0.125 8420 Z= 0.250 Angle : 0.703 15.746 11399 Z= 0.358 Chirality : 0.047 0.351 1282 Planarity : 0.004 0.063 1450 Dihedral : 14.765 87.874 3062 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.10 % 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 (0.27), residues: 1033 helix: 1.82 (0.28), residues: 390 sheet: -0.10 (0.35), residues: 208 loop : -1.04 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 282 HIS 0.012 0.001 HIS A 357 PHE 0.019 0.002 PHE B 245 TYR 0.062 0.002 TYR B 70 ARG 0.008 0.001 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.14134 ( 407) hydrogen bonds : angle 5.53889 ( 1158) SS BOND : bond 0.00393 ( 2) SS BOND : angle 0.92676 ( 4) covalent geometry : bond 0.00499 ( 8418) covalent geometry : angle 0.70316 (11395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.952 Fit side-chains REVERT: A 27 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6641 (mm-30) REVERT: R 145 MET cc_start: 0.6431 (ptt) cc_final: 0.6230 (ptm) outliers start: 0 outliers final: 1 residues processed: 119 average time/residue: 1.5726 time to fit residues: 196.8025 Evaluate side-chains 96 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 202 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN B 241 ASN N 5 GLN R 147 GLN R 197 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.151370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111992 restraints weight = 8948.708| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.05 r_work: 0.3131 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8420 Z= 0.126 Angle : 0.554 10.228 11399 Z= 0.292 Chirality : 0.043 0.155 1282 Planarity : 0.004 0.063 1450 Dihedral : 6.283 53.118 1172 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.13 % Allowed : 8.90 % Favored : 89.98 % 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: 0.72 (0.27), residues: 1033 helix: 2.17 (0.28), residues: 398 sheet: 0.17 (0.36), residues: 208 loop : -1.02 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 93 HIS 0.008 0.001 HIS A 357 PHE 0.017 0.001 PHE A 212 TYR 0.012 0.001 TYR A 339 ARG 0.003 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04883 ( 407) hydrogen bonds : angle 4.21197 ( 1158) SS BOND : bond 0.00298 ( 2) SS BOND : angle 0.85419 ( 4) covalent geometry : bond 0.00271 ( 8418) covalent geometry : angle 0.55358 (11395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 1.001 Fit side-chains REVERT: A 60 MET cc_start: 0.4914 (mmp) cc_final: 0.4500 (mmp) REVERT: B 208 ARG cc_start: 0.7608 (mmm160) cc_final: 0.7316 (mtp180) REVERT: N 5 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6513 (mp-120) REVERT: R 141 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6628 (mp) REVERT: R 145 MET cc_start: 0.6729 (ptt) cc_final: 0.6385 (ptm) REVERT: R 175 PHE cc_start: 0.6489 (m-10) cc_final: 0.6189 (m-80) outliers start: 10 outliers final: 5 residues processed: 109 average time/residue: 1.3748 time to fit residues: 158.8623 Evaluate side-chains 96 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 147 GLN Chi-restraints excluded: chain R residue 172 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 7 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN B 279 ASN N 5 GLN R 46 ASN R 197 GLN R 289 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.148360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.108193 restraints weight = 9152.028| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.13 r_work: 0.3088 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8420 Z= 0.169 Angle : 0.601 11.549 11399 Z= 0.315 Chirality : 0.045 0.157 1282 Planarity : 0.004 0.063 1450 Dihedral : 6.245 52.167 1169 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.48 % Allowed : 11.49 % Favored : 86.04 % 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 (0.27), residues: 1033 helix: 2.04 (0.27), residues: 398 sheet: 0.21 (0.37), residues: 202 loop : -1.10 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 93 HIS 0.010 0.001 HIS A 357 PHE 0.017 0.002 PHE A 212 TYR 0.018 0.002 TYR R 185 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.05377 ( 407) hydrogen bonds : angle 4.21964 ( 1158) SS BOND : bond 0.00474 ( 2) SS BOND : angle 0.92972 ( 4) covalent geometry : bond 0.00390 ( 8418) covalent geometry : angle 0.60082 (11395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.970 Fit side-chains REVERT: A 60 MET cc_start: 0.4937 (mmp) cc_final: 0.4554 (mmp) REVERT: B 70 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.7709 (m-80) REVERT: B 72 MET cc_start: 0.8965 (ppp) cc_final: 0.8684 (pp-130) REVERT: R 112 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7600 (ptp90) REVERT: R 141 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6604 (mp) REVERT: R 145 MET cc_start: 0.6811 (ptt) cc_final: 0.6145 (ptp) REVERT: R 175 PHE cc_start: 0.6599 (m-10) cc_final: 0.6245 (m-10) outliers start: 22 outliers final: 8 residues processed: 110 average time/residue: 1.6976 time to fit residues: 197.5604 Evaluate side-chains 102 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 112 ARG Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 94 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 83 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN R 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.154269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.114616 restraints weight = 9088.669| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.09 r_work: 0.3157 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8420 Z= 0.098 Angle : 0.499 8.327 11399 Z= 0.263 Chirality : 0.041 0.164 1282 Planarity : 0.004 0.060 1450 Dihedral : 5.676 45.003 1169 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.03 % Allowed : 14.86 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.94 (0.27), residues: 1033 helix: 2.50 (0.27), residues: 394 sheet: 0.42 (0.38), residues: 201 loop : -1.09 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 93 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE R 181 TYR 0.010 0.001 TYR A 37 ARG 0.002 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 407) hydrogen bonds : angle 3.83526 ( 1158) SS BOND : bond 0.00279 ( 2) SS BOND : angle 0.60777 ( 4) covalent geometry : bond 0.00199 ( 8418) covalent geometry : angle 0.49867 (11395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7028 (mm-30) REVERT: A 60 MET cc_start: 0.4787 (mmp) cc_final: 0.4406 (mmp) REVERT: A 314 GLU cc_start: 0.7623 (pt0) cc_final: 0.7156 (pm20) REVERT: B 70 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: B 72 MET cc_start: 0.8947 (ppp) cc_final: 0.8737 (pp-130) REVERT: B 208 ARG cc_start: 0.7654 (mtp180) cc_final: 0.7383 (mmm160) REVERT: B 230 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7861 (mmt-90) REVERT: R 132 VAL cc_start: 0.7465 (t) cc_final: 0.7227 (p) REVERT: R 141 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6600 (mp) REVERT: R 145 MET cc_start: 0.6785 (ptt) cc_final: 0.6394 (ptm) REVERT: R 175 PHE cc_start: 0.6342 (m-10) cc_final: 0.6003 (m-10) outliers start: 18 outliers final: 6 residues processed: 114 average time/residue: 1.3911 time to fit residues: 167.5715 Evaluate side-chains 98 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 48 optimal weight: 0.0980 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 279 ASN R 147 GLN R 197 GLN R 289 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108561 restraints weight = 8968.859| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.04 r_work: 0.3075 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8420 Z= 0.182 Angle : 0.614 11.847 11399 Z= 0.322 Chirality : 0.045 0.180 1282 Planarity : 0.004 0.060 1450 Dihedral : 6.076 45.714 1169 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.70 % Allowed : 15.43 % Favored : 81.87 % 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: 1033 helix: 2.15 (0.27), residues: 397 sheet: 0.35 (0.37), residues: 201 loop : -1.10 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 74 HIS 0.008 0.001 HIS A 357 PHE 0.019 0.002 PHE A 212 TYR 0.018 0.002 TYR R 185 ARG 0.005 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.05431 ( 407) hydrogen bonds : angle 4.17099 ( 1158) SS BOND : bond 0.00439 ( 2) SS BOND : angle 1.14447 ( 4) covalent geometry : bond 0.00424 ( 8418) covalent geometry : angle 0.61403 (11395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.893 Fit side-chains REVERT: A 27 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7052 (mm-30) REVERT: A 317 ARG cc_start: 0.7882 (ptp90) cc_final: 0.7665 (ptt-90) REVERT: B 70 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: B 72 MET cc_start: 0.8968 (ppp) cc_final: 0.8652 (pp-130) REVERT: R 145 MET cc_start: 0.6836 (ptt) cc_final: 0.6465 (ptm) REVERT: R 170 SER cc_start: 0.7766 (t) cc_final: 0.7489 (t) outliers start: 24 outliers final: 12 residues processed: 120 average time/residue: 1.3638 time to fit residues: 172.9769 Evaluate side-chains 112 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 147 GLN Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 3 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN R 197 GLN R 289 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.109041 restraints weight = 9040.105| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.08 r_work: 0.3072 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8420 Z= 0.170 Angle : 0.602 11.666 11399 Z= 0.315 Chirality : 0.045 0.175 1282 Planarity : 0.004 0.059 1450 Dihedral : 6.113 46.051 1169 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.25 % Allowed : 17.23 % Favored : 80.52 % 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: 0.65 (0.27), residues: 1033 helix: 2.04 (0.27), residues: 401 sheet: 0.31 (0.37), residues: 201 loop : -1.09 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 93 HIS 0.008 0.001 HIS A 357 PHE 0.018 0.002 PHE A 212 TYR 0.017 0.002 TYR R 185 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.05303 ( 407) hydrogen bonds : angle 4.16287 ( 1158) SS BOND : bond 0.00450 ( 2) SS BOND : angle 1.13345 ( 4) covalent geometry : bond 0.00395 ( 8418) covalent geometry : angle 0.60214 (11395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.979 Fit side-chains REVERT: A 27 GLU cc_start: 0.7561 (mm-30) cc_final: 0.6964 (mm-30) REVERT: A 317 ARG cc_start: 0.7907 (ptp90) cc_final: 0.7703 (ptt-90) REVERT: B 70 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: B 72 MET cc_start: 0.8979 (ppp) cc_final: 0.8654 (pp-130) REVERT: N 5 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6159 (mp-120) REVERT: R 145 MET cc_start: 0.6771 (ptt) cc_final: 0.6428 (ptm) REVERT: R 175 PHE cc_start: 0.6611 (m-10) cc_final: 0.6253 (m-10) outliers start: 20 outliers final: 13 residues processed: 111 average time/residue: 1.3513 time to fit residues: 159.0515 Evaluate side-chains 110 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 60 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN R 147 GLN R 197 GLN R 289 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.149175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109564 restraints weight = 9013.848| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.06 r_work: 0.3090 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8420 Z= 0.154 Angle : 0.581 11.097 11399 Z= 0.305 Chirality : 0.044 0.173 1282 Planarity : 0.004 0.059 1450 Dihedral : 6.010 44.846 1169 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.36 % Allowed : 17.34 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.27), residues: 1033 helix: 2.14 (0.27), residues: 401 sheet: 0.32 (0.37), residues: 201 loop : -1.07 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 93 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.002 PHE A 212 TYR 0.016 0.002 TYR R 185 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.05037 ( 407) hydrogen bonds : angle 4.09447 ( 1158) SS BOND : bond 0.00424 ( 2) SS BOND : angle 1.03804 ( 4) covalent geometry : bond 0.00354 ( 8418) covalent geometry : angle 0.58063 (11395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.893 Fit side-chains REVERT: A 27 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6982 (mm-30) REVERT: A 60 MET cc_start: 0.4964 (mmp) cc_final: 0.4645 (mmp) REVERT: A 317 ARG cc_start: 0.7821 (ptp90) cc_final: 0.7602 (ptt-90) REVERT: B 70 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: B 72 MET cc_start: 0.8970 (ppp) cc_final: 0.8717 (pp-130) REVERT: R 145 MET cc_start: 0.6765 (ptt) cc_final: 0.6413 (ptm) REVERT: R 175 PHE cc_start: 0.6639 (m-10) cc_final: 0.6230 (m-10) outliers start: 21 outliers final: 14 residues processed: 113 average time/residue: 1.2619 time to fit residues: 151.5953 Evaluate side-chains 111 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 147 GLN Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 279 ASN R 147 GLN R 197 GLN R 289 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109575 restraints weight = 9123.561| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.08 r_work: 0.3077 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8420 Z= 0.146 Angle : 0.574 10.951 11399 Z= 0.301 Chirality : 0.044 0.171 1282 Planarity : 0.004 0.059 1450 Dihedral : 5.976 44.050 1169 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.36 % Allowed : 17.57 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.74 (0.27), residues: 1033 helix: 2.17 (0.27), residues: 401 sheet: 0.34 (0.37), residues: 201 loop : -1.08 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 93 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.002 PHE A 212 TYR 0.015 0.001 TYR R 185 ARG 0.003 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 407) hydrogen bonds : angle 4.08189 ( 1158) SS BOND : bond 0.00402 ( 2) SS BOND : angle 1.01798 ( 4) covalent geometry : bond 0.00332 ( 8418) covalent geometry : angle 0.57424 (11395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.045 Fit side-chains REVERT: A 27 GLU cc_start: 0.7584 (mm-30) cc_final: 0.6982 (mm-30) REVERT: A 60 MET cc_start: 0.4959 (mmp) cc_final: 0.4645 (mmp) REVERT: A 317 ARG cc_start: 0.7856 (ptp90) cc_final: 0.7656 (ptt-90) REVERT: B 70 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: B 72 MET cc_start: 0.8972 (ppp) cc_final: 0.8716 (pp-130) REVERT: N 5 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6140 (mp-120) REVERT: R 145 MET cc_start: 0.6835 (ptt) cc_final: 0.6498 (ptm) REVERT: R 175 PHE cc_start: 0.6663 (m-10) cc_final: 0.6215 (m-10) outliers start: 21 outliers final: 13 residues processed: 111 average time/residue: 1.3612 time to fit residues: 160.7840 Evaluate side-chains 109 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 99 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 279 ASN R 147 GLN R 197 GLN R 289 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.148380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.108530 restraints weight = 9099.962| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.08 r_work: 0.3097 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8420 Z= 0.146 Angle : 0.575 10.885 11399 Z= 0.301 Chirality : 0.044 0.170 1282 Planarity : 0.004 0.058 1450 Dihedral : 5.950 43.033 1169 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.59 % Allowed : 18.02 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.77 (0.27), residues: 1033 helix: 2.27 (0.27), residues: 397 sheet: 0.35 (0.37), residues: 201 loop : -1.13 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 93 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.002 PHE A 212 TYR 0.015 0.001 TYR R 185 ARG 0.003 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04934 ( 407) hydrogen bonds : angle 4.07329 ( 1158) SS BOND : bond 0.00403 ( 2) SS BOND : angle 1.00810 ( 4) covalent geometry : bond 0.00332 ( 8418) covalent geometry : angle 0.57465 (11395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.888 Fit side-chains REVERT: A 27 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7000 (mm-30) REVERT: A 60 MET cc_start: 0.4962 (mmp) cc_final: 0.4643 (mmp) REVERT: A 317 ARG cc_start: 0.7874 (ptp90) cc_final: 0.7643 (ptt-90) REVERT: B 70 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: B 72 MET cc_start: 0.8979 (ppp) cc_final: 0.8685 (pp-130) REVERT: N 5 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6158 (mp-120) REVERT: R 132 VAL cc_start: 0.7478 (OUTLIER) cc_final: 0.7259 (p) REVERT: R 145 MET cc_start: 0.6858 (ptt) cc_final: 0.6516 (ptm) REVERT: R 175 PHE cc_start: 0.6705 (m-10) cc_final: 0.6237 (m-10) outliers start: 23 outliers final: 14 residues processed: 115 average time/residue: 1.3067 time to fit residues: 159.5614 Evaluate side-chains 110 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 147 GLN Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 279 ASN R 147 GLN R 197 GLN R 289 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.151667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.112164 restraints weight = 9002.880| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.07 r_work: 0.3131 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8420 Z= 0.112 Angle : 0.528 9.263 11399 Z= 0.276 Chirality : 0.042 0.170 1282 Planarity : 0.004 0.058 1450 Dihedral : 5.654 39.554 1169 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.91 % Allowed : 18.69 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.96 (0.27), residues: 1033 helix: 2.53 (0.27), residues: 395 sheet: 0.41 (0.37), residues: 201 loop : -1.10 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 93 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE A 212 TYR 0.012 0.001 TYR A 37 ARG 0.003 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 407) hydrogen bonds : angle 3.90848 ( 1158) SS BOND : bond 0.00315 ( 2) SS BOND : angle 0.74171 ( 4) covalent geometry : bond 0.00237 ( 8418) covalent geometry : angle 0.52788 (11395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.889 Fit side-chains REVERT: A 27 GLU cc_start: 0.7626 (mm-30) cc_final: 0.6990 (mm-30) REVERT: A 60 MET cc_start: 0.4874 (mmp) cc_final: 0.4536 (mmp) REVERT: A 314 GLU cc_start: 0.7613 (pt0) cc_final: 0.7129 (pm20) REVERT: A 317 ARG cc_start: 0.7856 (ptp90) cc_final: 0.7630 (ptt-90) REVERT: B 70 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.7515 (m-80) REVERT: B 226 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7022 (mt-10) REVERT: N 5 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6136 (mp-120) REVERT: R 145 MET cc_start: 0.6873 (ptt) cc_final: 0.6493 (ptm) REVERT: R 175 PHE cc_start: 0.6562 (m-10) cc_final: 0.6143 (m-10) outliers start: 17 outliers final: 12 residues processed: 107 average time/residue: 1.3106 time to fit residues: 148.7422 Evaluate side-chains 104 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 147 GLN Chi-restraints excluded: chain R residue 224 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 57 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 279 ASN R 147 GLN R 197 GLN R 289 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109921 restraints weight = 9136.164| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.10 r_work: 0.3099 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8420 Z= 0.149 Angle : 0.577 10.668 11399 Z= 0.301 Chirality : 0.044 0.170 1282 Planarity : 0.004 0.059 1450 Dihedral : 5.779 38.352 1169 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.91 % Allowed : 18.92 % Favored : 79.17 % 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: 0.84 (0.27), residues: 1033 helix: 2.38 (0.27), residues: 396 sheet: 0.34 (0.37), residues: 201 loop : -1.10 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 93 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.002 PHE A 212 TYR 0.015 0.002 TYR R 185 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04895 ( 407) hydrogen bonds : angle 4.04026 ( 1158) SS BOND : bond 0.00409 ( 2) SS BOND : angle 0.95517 ( 4) covalent geometry : bond 0.00340 ( 8418) covalent geometry : angle 0.57714 (11395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6800.41 seconds wall clock time: 119 minutes 47.76 seconds (7187.76 seconds total)