Starting phenix.real_space_refine on Sat Aug 23 10:03:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b9f_12103/08_2025/7b9f_12103.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b9f_12103/08_2025/7b9f_12103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7b9f_12103/08_2025/7b9f_12103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b9f_12103/08_2025/7b9f_12103.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b9f_12103/08_2025/7b9f_12103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b9f_12103/08_2025/7b9f_12103.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 7264 2.51 5 N 1985 2.21 5 O 1968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11270 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1305 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 3 Chain: "X" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3162 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 23, 'TRANS': 401} Chain breaks: 1 Chain: "C" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2679 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 28, 'TRANS': 308} Chain breaks: 2 Chain: "D" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3644 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 455} Chain: "B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Time building chain proxies: 2.83, per 1000 atoms: 0.25 Number of scatterers: 11270 At special positions: 0 Unit cell: (91.59, 143.19, 125.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1968 8.00 N 1985 7.00 C 7264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.06 Conformation dependent library (CDL) restraints added in 541.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2744 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 59.1% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'E' and resid 144 through 150 removed outlier: 4.331A pdb=" N ALA E 147 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 208 Processing helix chain 'E' and resid 209 through 215 removed outlier: 3.747A pdb=" N ALA E 215 " --> pdb=" O ALA E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 235 removed outlier: 3.785A pdb=" N LEU E 223 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 258 removed outlier: 3.639A pdb=" N ASP E 250 " --> pdb=" O SER E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 303 removed outlier: 4.331A pdb=" N ARG E 301 " --> pdb=" O GLU E 297 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 60 removed outlier: 4.540A pdb=" N ASP X 47 " --> pdb=" O SER X 43 " (cutoff:3.500A) Proline residue: X 48 - end of helix removed outlier: 3.575A pdb=" N LYS X 51 " --> pdb=" O ASP X 47 " (cutoff:3.500A) Processing helix chain 'X' and resid 117 through 130 Processing helix chain 'X' and resid 134 through 164 removed outlier: 3.697A pdb=" N GLN X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 168 through 191 removed outlier: 3.730A pdb=" N PHE X 172 " --> pdb=" O LEU X 168 " (cutoff:3.500A) Processing helix chain 'X' and resid 194 through 196 No H-bonds generated for 'chain 'X' and resid 194 through 196' Processing helix chain 'X' and resid 197 through 218 removed outlier: 4.340A pdb=" N VAL X 209 " --> pdb=" O LEU X 205 " (cutoff:3.500A) Proline residue: X 210 - end of helix Processing helix chain 'X' and resid 224 through 246 Processing helix chain 'X' and resid 249 through 272 Processing helix chain 'X' and resid 276 through 303 removed outlier: 3.720A pdb=" N HIS X 293 " --> pdb=" O VAL X 289 " (cutoff:3.500A) Proline residue: X 296 - end of helix removed outlier: 3.782A pdb=" N ARG X 300 " --> pdb=" O PRO X 296 " (cutoff:3.500A) Processing helix chain 'X' and resid 304 through 306 No H-bonds generated for 'chain 'X' and resid 304 through 306' Processing helix chain 'X' and resid 312 through 320 Processing helix chain 'X' and resid 341 through 378 removed outlier: 3.970A pdb=" N VAL X 345 " --> pdb=" O GLY X 341 " (cutoff:3.500A) Processing helix chain 'X' and resid 385 through 404 removed outlier: 3.947A pdb=" N LEU X 389 " --> pdb=" O ARG X 385 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG X 404 " --> pdb=" O ILE X 400 " (cutoff:3.500A) Processing helix chain 'X' and resid 408 through 434 removed outlier: 3.882A pdb=" N ILE X 423 " --> pdb=" O ALA X 419 " (cutoff:3.500A) Processing helix chain 'X' and resid 436 through 457 removed outlier: 3.798A pdb=" N VAL X 448 " --> pdb=" O VAL X 444 " (cutoff:3.500A) Proline residue: X 451 - end of helix Processing helix chain 'C' and resid 97 through 133 Processing helix chain 'C' and resid 136 through 141 removed outlier: 3.602A pdb=" N LEU C 139 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C 140 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA C 141 " --> pdb=" O THR C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 136 through 141' Processing helix chain 'C' and resid 156 through 161 removed outlier: 4.704A pdb=" N GLY C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 226 through 245 Processing helix chain 'C' and resid 258 through 267 removed outlier: 3.971A pdb=" N ASP C 263 " --> pdb=" O ASP C 260 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TRP C 264 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 265 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 266 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP C 267 " --> pdb=" O TRP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 295 through 300 removed outlier: 3.952A pdb=" N LEU C 300 " --> pdb=" O GLN C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 338 removed outlier: 4.132A pdb=" N VAL C 337 " --> pdb=" O GLN C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'C' and resid 401 through 413 Processing helix chain 'D' and resid 41 through 61 removed outlier: 4.647A pdb=" N ASP D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Proline residue: D 48 - end of helix removed outlier: 3.977A pdb=" N LYS D 51 " --> pdb=" O ASP D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.811A pdb=" N SER D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 164 Processing helix chain 'D' and resid 168 through 189 removed outlier: 4.089A pdb=" N PHE D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 219 removed outlier: 4.456A pdb=" N GLY D 200 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Proline residue: D 210 - end of helix removed outlier: 3.852A pdb=" N ALA D 219 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 246 removed outlier: 3.797A pdb=" N PHE D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 274 Processing helix chain 'D' and resid 276 through 303 removed outlier: 4.030A pdb=" N HIS D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) Proline residue: D 296 - end of helix Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 346 through 374 removed outlier: 3.738A pdb=" N LEU D 350 " --> pdb=" O ARG D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 385 through 403 removed outlier: 3.694A pdb=" N LEU D 389 " --> pdb=" O ARG D 385 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 406 No H-bonds generated for 'chain 'D' and resid 404 through 406' Processing helix chain 'D' and resid 408 through 434 removed outlier: 3.652A pdb=" N ILE D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 467 through 483 removed outlier: 4.147A pdb=" N GLU D 478 " --> pdb=" O VAL D 474 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR D 479 " --> pdb=" O GLU D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'B' and resid 19 through 40 Processing helix chain 'B' and resid 47 through 70 removed outlier: 3.867A pdb=" N ARG B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 96 through 97 Processing sheet with id=AA2, first strand: chain 'E' and resid 108 through 109 Processing sheet with id=AA3, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.538A pdb=" N MET E 204 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR E 198 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E 159 " --> pdb=" O ARG E 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 71 through 77 removed outlier: 8.536A pdb=" N LEU X 100 " --> pdb=" O VAL X 22 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA X 24 " --> pdb=" O LEU X 100 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU X 102 " --> pdb=" O ALA X 24 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N MET X 26 " --> pdb=" O LEU X 102 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N PHE X 104 " --> pdb=" O MET X 26 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 22 removed outlier: 7.091A pdb=" N GLU C 19 " --> pdb=" O THR C 175 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLY C 177 " --> pdb=" O GLU C 19 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE C 21 " --> pdb=" O GLY C 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 206 through 214 removed outlier: 5.694A pdb=" N GLY C 168 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY C 166 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N MET C 212 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG C 164 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER C 214 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL C 162 " --> pdb=" O SER C 214 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N MET C 169 " --> pdb=" O PHE C 394 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE C 394 " --> pdb=" O MET C 169 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N PHE C 393 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N THR C 376 " --> pdb=" O PHE C 393 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 395 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LEU C 365 " --> pdb=" O TRP C 220 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER C 222 " --> pdb=" O LEU C 365 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N PHE C 367 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C 224 " --> pdb=" O PHE C 367 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN C 251 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE C 326 " --> pdb=" O GLN C 251 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE C 253 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ASP C 328 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL C 255 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N TYR C 287 " --> pdb=" O MET C 252 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL C 254 " --> pdb=" O TYR C 287 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 272 through 277 removed outlier: 3.523A pdb=" N ALA C 283 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 30 through 37 Processing sheet with id=AA9, first strand: chain 'D' and resid 327 through 328 690 hydrogen bonds defined for protein. 2004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3589 1.34 - 1.46: 2171 1.46 - 1.58: 5678 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 11529 Sorted by residual: bond pdb=" CB TRP C 149 " pdb=" CG TRP C 149 " ideal model delta sigma weight residual 1.498 1.415 0.083 3.10e-02 1.04e+03 7.24e+00 bond pdb=" CG1 ILE D 473 " pdb=" CD1 ILE D 473 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.89e+00 bond pdb=" CG1 ILE D 477 " pdb=" CD1 ILE D 477 " ideal model delta sigma weight residual 1.513 1.427 0.086 3.90e-02 6.57e+02 4.84e+00 bond pdb=" CA GLN C 203 " pdb=" C GLN C 203 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.80e-02 3.09e+03 4.49e+00 bond pdb=" CG ARG C 304 " pdb=" CD ARG C 304 " ideal model delta sigma weight residual 1.520 1.457 0.063 3.00e-02 1.11e+03 4.38e+00 ... (remaining 11524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 14980 2.00 - 4.00: 626 4.00 - 6.01: 104 6.01 - 8.01: 49 8.01 - 10.01: 10 Bond angle restraints: 15769 Sorted by residual: angle pdb=" N VAL X 309 " pdb=" CA VAL X 309 " pdb=" C VAL X 309 " ideal model delta sigma weight residual 106.55 114.16 -7.61 1.45e+00 4.76e-01 2.76e+01 angle pdb=" CA TRP C 149 " pdb=" CB TRP C 149 " pdb=" CG TRP C 149 " ideal model delta sigma weight residual 113.60 104.93 8.67 1.90e+00 2.77e-01 2.08e+01 angle pdb=" CA THR C 320 " pdb=" C THR C 320 " pdb=" N PRO C 321 " ideal model delta sigma weight residual 118.44 125.62 -7.18 1.59e+00 3.96e-01 2.04e+01 angle pdb=" C ALA X 28 " pdb=" N ASP X 29 " pdb=" CA ASP X 29 " ideal model delta sigma weight residual 121.54 130.07 -8.53 1.91e+00 2.74e-01 1.99e+01 angle pdb=" N GLU D 353 " pdb=" CA GLU D 353 " pdb=" CB GLU D 353 " ideal model delta sigma weight residual 110.28 116.83 -6.55 1.55e+00 4.16e-01 1.78e+01 ... (remaining 15764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6359 17.86 - 35.72: 414 35.72 - 53.58: 41 53.58 - 71.44: 9 71.44 - 89.30: 9 Dihedral angle restraints: 6832 sinusoidal: 2600 harmonic: 4232 Sorted by residual: dihedral pdb=" CA GLY D 224 " pdb=" C GLY D 224 " pdb=" N ALA D 225 " pdb=" CA ALA D 225 " ideal model delta harmonic sigma weight residual 180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" C THR C 320 " pdb=" N THR C 320 " pdb=" CA THR C 320 " pdb=" CB THR C 320 " ideal model delta harmonic sigma weight residual -122.00 -133.62 11.62 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" CA GLY C 161 " pdb=" C GLY C 161 " pdb=" N VAL C 162 " pdb=" CA VAL C 162 " ideal model delta harmonic sigma weight residual 180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 6829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1525 0.072 - 0.145: 321 0.145 - 0.217: 38 0.217 - 0.290: 6 0.290 - 0.362: 1 Chirality restraints: 1891 Sorted by residual: chirality pdb=" CA THR C 320 " pdb=" N THR C 320 " pdb=" C THR C 320 " pdb=" CB THR C 320 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CB ILE D 133 " pdb=" CA ILE D 133 " pdb=" CG1 ILE D 133 " pdb=" CG2 ILE D 133 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CG LEU C 241 " pdb=" CB LEU C 241 " pdb=" CD1 LEU C 241 " pdb=" CD2 LEU C 241 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1888 not shown) Planarity restraints: 1982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 149 " 0.044 2.00e-02 2.50e+03 2.76e-02 1.91e+01 pdb=" CG TRP C 149 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP C 149 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 149 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 149 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 149 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 149 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 149 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 149 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 149 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP X 317 " -0.030 2.00e-02 2.50e+03 2.43e-02 1.47e+01 pdb=" CG TRP X 317 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP X 317 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP X 317 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP X 317 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP X 317 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP X 317 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 317 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 317 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP X 317 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 152 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO C 153 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 153 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 153 " -0.039 5.00e-02 4.00e+02 ... (remaining 1979 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2321 2.78 - 3.31: 11255 3.31 - 3.84: 18435 3.84 - 4.37: 20643 4.37 - 4.90: 35988 Nonbonded interactions: 88642 Sorted by model distance: nonbonded pdb=" O PHE C 160 " pdb=" NE2 HIS C 245 " model vdw 2.247 3.120 nonbonded pdb=" OG SER X 88 " pdb=" OE1 GLU X 91 " model vdw 2.247 3.040 nonbonded pdb=" NE ARG D 190 " pdb=" O THR D 193 " model vdw 2.257 3.120 nonbonded pdb=" OG1 THR E 307 " pdb=" O ALA E 309 " model vdw 2.270 3.040 nonbonded pdb=" O ILE D 187 " pdb=" OG1 THR D 193 " model vdw 2.284 3.040 ... (remaining 88637 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 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 18 through 323 or resid 339 through 457)) selection = chain 'X' } 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: 6.440 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.210 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.008 0.095 11529 Z= 0.329 Angle : 1.006 10.009 15769 Z= 0.530 Chirality : 0.060 0.362 1891 Planarity : 0.007 0.072 1982 Dihedral : 12.028 89.296 4088 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.21), residues: 1453 helix: 0.70 (0.18), residues: 781 sheet: -0.53 (0.41), residues: 140 loop : -1.01 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 229 TYR 0.024 0.003 TYR C 207 PHE 0.027 0.003 PHE X 358 TRP 0.071 0.003 TRP C 149 HIS 0.019 0.002 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00775 (11529) covalent geometry : angle 1.00566 (15769) hydrogen bonds : bond 0.15517 ( 688) hydrogen bonds : angle 5.81514 ( 2004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 204 MET cc_start: 0.8959 (ttp) cc_final: 0.8729 (ttp) REVERT: E 235 ASN cc_start: 0.8920 (t0) cc_final: 0.8711 (t0) REVERT: X 172 PHE cc_start: 0.8477 (m-80) cc_final: 0.7945 (m-80) REVERT: X 205 LEU cc_start: 0.8820 (tp) cc_final: 0.8606 (tm) REVERT: X 378 CYS cc_start: 0.9234 (m) cc_final: 0.8897 (m) REVERT: C 148 MET cc_start: 0.8429 (ptt) cc_final: 0.8177 (ptt) REVERT: C 291 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7958 (tpm170) REVERT: D 164 HIS cc_start: 0.8720 (m90) cc_final: 0.8352 (m90) REVERT: D 186 MET cc_start: 0.8746 (tpt) cc_final: 0.8492 (OUTLIER) REVERT: D 381 HIS cc_start: 0.5555 (p-80) cc_final: 0.4938 (t-90) REVERT: D 472 LYS cc_start: 0.8120 (tptt) cc_final: 0.7074 (mptt) REVERT: B 50 ARG cc_start: 0.6652 (tpt170) cc_final: 0.6126 (tpt170) REVERT: B 54 LEU cc_start: 0.9108 (mt) cc_final: 0.8644 (mt) outliers start: 0 outliers final: 1 residues processed: 232 average time/residue: 0.5802 time to fit residues: 145.6717 Evaluate side-chains 179 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS E 332 HIS C 20 ASN C 181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.098912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.074578 restraints weight = 26888.687| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.32 r_work: 0.3044 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11529 Z= 0.156 Angle : 0.705 7.843 15769 Z= 0.353 Chirality : 0.045 0.197 1891 Planarity : 0.005 0.055 1982 Dihedral : 4.971 22.895 1602 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.12 % Allowed : 10.08 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.22), residues: 1453 helix: 1.60 (0.18), residues: 787 sheet: -0.41 (0.41), residues: 134 loop : -0.81 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 39 TYR 0.016 0.001 TYR E 110 PHE 0.036 0.002 PHE X 396 TRP 0.024 0.002 TRP B 73 HIS 0.009 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00353 (11529) covalent geometry : angle 0.70531 (15769) hydrogen bonds : bond 0.04626 ( 688) hydrogen bonds : angle 4.46282 ( 2004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 GLN cc_start: 0.8690 (mp10) cc_final: 0.8481 (mm110) REVERT: E 195 GLU cc_start: 0.7712 (pm20) cc_final: 0.7506 (pm20) REVERT: X 172 PHE cc_start: 0.8518 (m-80) cc_final: 0.7928 (m-80) REVERT: X 186 MET cc_start: 0.9381 (mtp) cc_final: 0.8803 (tpt) REVERT: X 378 CYS cc_start: 0.8855 (m) cc_final: 0.8546 (m) REVERT: C 19 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: C 20 ASN cc_start: 0.9268 (OUTLIER) cc_final: 0.9029 (m-40) REVERT: C 180 GLN cc_start: 0.8239 (pp30) cc_final: 0.7917 (pp30) REVERT: C 201 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8789 (ttt90) REVERT: C 291 ARG cc_start: 0.8899 (ttp80) cc_final: 0.8231 (tpm170) REVERT: C 369 ASP cc_start: 0.8615 (t0) cc_final: 0.8308 (t0) REVERT: D 45 MET cc_start: 0.6250 (mmt) cc_final: 0.5843 (tpt) REVERT: D 50 LEU cc_start: 0.8748 (pt) cc_final: 0.8347 (tm) REVERT: D 164 HIS cc_start: 0.8764 (m90) cc_final: 0.8417 (m90) REVERT: D 186 MET cc_start: 0.8952 (tpt) cc_final: 0.8715 (OUTLIER) REVERT: D 291 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8897 (tpt) REVERT: D 381 HIS cc_start: 0.5709 (p-80) cc_final: 0.4903 (t-90) REVERT: D 399 LEU cc_start: 0.9552 (mt) cc_final: 0.9302 (mm) REVERT: D 472 LYS cc_start: 0.8253 (tptt) cc_final: 0.7200 (mptt) REVERT: B 47 GLU cc_start: 0.8865 (pm20) cc_final: 0.8640 (pm20) REVERT: B 50 ARG cc_start: 0.6735 (tpt170) cc_final: 0.6198 (tpt170) REVERT: B 54 LEU cc_start: 0.9211 (mt) cc_final: 0.8888 (mt) outliers start: 25 outliers final: 11 residues processed: 208 average time/residue: 0.5491 time to fit residues: 124.5998 Evaluate side-chains 186 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 317 TRP Chi-restraints excluded: chain X residue 399 LEU Chi-restraints excluded: chain X residue 408 ASP Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 291 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 2 optimal weight: 0.0370 chunk 46 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.099646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.075297 restraints weight = 27003.180| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.34 r_work: 0.3059 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11529 Z= 0.137 Angle : 0.666 8.119 15769 Z= 0.328 Chirality : 0.044 0.328 1891 Planarity : 0.005 0.052 1982 Dihedral : 4.645 25.710 1602 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.79 % Allowed : 12.87 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.22), residues: 1453 helix: 1.95 (0.18), residues: 788 sheet: -0.43 (0.40), residues: 141 loop : -0.74 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 39 TYR 0.017 0.001 TYR D 253 PHE 0.028 0.001 PHE X 396 TRP 0.016 0.001 TRP X 410 HIS 0.007 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00305 (11529) covalent geometry : angle 0.66610 (15769) hydrogen bonds : bond 0.04125 ( 688) hydrogen bonds : angle 4.22280 ( 2004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 109 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7829 (tp30) REVERT: E 113 GLN cc_start: 0.8803 (mp10) cc_final: 0.8506 (mm110) REVERT: E 195 GLU cc_start: 0.7713 (pm20) cc_final: 0.7451 (pm20) REVERT: X 172 PHE cc_start: 0.8509 (m-80) cc_final: 0.7902 (m-80) REVERT: X 186 MET cc_start: 0.9385 (mtp) cc_final: 0.8811 (tpt) REVERT: X 378 CYS cc_start: 0.8681 (m) cc_final: 0.8429 (m) REVERT: C 19 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7642 (mm-30) REVERT: C 99 LYS cc_start: 0.8689 (tmmt) cc_final: 0.8477 (pttm) REVERT: C 151 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.7366 (mmm-85) REVERT: C 180 GLN cc_start: 0.8238 (pp30) cc_final: 0.7879 (pp30) REVERT: C 369 ASP cc_start: 0.8534 (t0) cc_final: 0.8123 (t0) REVERT: D 45 MET cc_start: 0.6159 (mmt) cc_final: 0.5777 (tpt) REVERT: D 50 LEU cc_start: 0.8705 (pt) cc_final: 0.8253 (tm) REVERT: D 164 HIS cc_start: 0.8735 (m90) cc_final: 0.8445 (m90) REVERT: D 186 MET cc_start: 0.8977 (tpt) cc_final: 0.8735 (OUTLIER) REVERT: D 291 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8869 (tpt) REVERT: D 381 HIS cc_start: 0.5524 (p-80) cc_final: 0.4775 (t-90) REVERT: D 472 LYS cc_start: 0.8199 (tptt) cc_final: 0.7147 (mptt) REVERT: B 47 GLU cc_start: 0.8940 (pm20) cc_final: 0.8731 (pm20) REVERT: B 50 ARG cc_start: 0.6774 (tpt170) cc_final: 0.6213 (tpt170) REVERT: B 54 LEU cc_start: 0.9256 (mt) cc_final: 0.8923 (mt) outliers start: 33 outliers final: 16 residues processed: 204 average time/residue: 0.5096 time to fit residues: 113.9858 Evaluate side-chains 184 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 203 LEU Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 315 SER Chi-restraints excluded: chain X residue 399 LEU Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 72 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 0.0470 chunk 103 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS E 102 HIS D 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.098742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.074364 restraints weight = 27194.676| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.35 r_work: 0.3039 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11529 Z= 0.164 Angle : 0.665 8.652 15769 Z= 0.327 Chirality : 0.044 0.301 1891 Planarity : 0.005 0.050 1982 Dihedral : 4.499 18.759 1602 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.81 % Allowed : 13.80 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.23), residues: 1453 helix: 2.10 (0.18), residues: 794 sheet: -0.48 (0.40), residues: 143 loop : -0.69 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG X 129 TYR 0.012 0.001 TYR E 110 PHE 0.023 0.001 PHE X 396 TRP 0.026 0.001 TRP X 317 HIS 0.005 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00372 (11529) covalent geometry : angle 0.66526 (15769) hydrogen bonds : bond 0.03991 ( 688) hydrogen bonds : angle 4.13940 ( 2004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 GLN cc_start: 0.8783 (mp10) cc_final: 0.8378 (mm110) REVERT: E 195 GLU cc_start: 0.7720 (pm20) cc_final: 0.7466 (pm20) REVERT: X 109 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8571 (tm-30) REVERT: X 129 ARG cc_start: 0.9011 (ttt90) cc_final: 0.8741 (mtp-110) REVERT: X 145 MET cc_start: 0.7009 (mmt) cc_final: 0.6565 (tpt) REVERT: X 172 PHE cc_start: 0.8534 (m-80) cc_final: 0.7954 (m-80) REVERT: X 186 MET cc_start: 0.9408 (mtp) cc_final: 0.8883 (tpt) REVERT: C 19 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: C 180 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7892 (pp30) REVERT: C 185 ASP cc_start: 0.8898 (m-30) cc_final: 0.8281 (t0) REVERT: C 369 ASP cc_start: 0.8611 (t0) cc_final: 0.8220 (t0) REVERT: D 45 MET cc_start: 0.6307 (mmt) cc_final: 0.5976 (tpt) REVERT: D 50 LEU cc_start: 0.8717 (pt) cc_final: 0.8246 (tm) REVERT: D 74 MET cc_start: 0.8589 (ptp) cc_final: 0.8270 (ptt) REVERT: D 164 HIS cc_start: 0.8753 (m90) cc_final: 0.8491 (m90) REVERT: D 186 MET cc_start: 0.9001 (tpt) cc_final: 0.8759 (OUTLIER) REVERT: D 291 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8880 (tpt) REVERT: D 381 HIS cc_start: 0.5388 (p-80) cc_final: 0.4795 (t-90) REVERT: D 472 LYS cc_start: 0.8221 (tptt) cc_final: 0.7191 (mptt) REVERT: B 47 GLU cc_start: 0.8976 (pm20) cc_final: 0.8736 (pm20) REVERT: B 50 ARG cc_start: 0.6802 (tpt170) cc_final: 0.6299 (tpt170) REVERT: B 54 LEU cc_start: 0.9245 (mt) cc_final: 0.9039 (mt) outliers start: 45 outliers final: 17 residues processed: 203 average time/residue: 0.5350 time to fit residues: 118.8861 Evaluate side-chains 189 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain X residue 109 GLU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 315 SER Chi-restraints excluded: chain X residue 399 LEU Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 72 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS E 102 HIS C 249 HIS D 31 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.098166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.073806 restraints weight = 26976.256| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.32 r_work: 0.3025 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11529 Z= 0.178 Angle : 0.681 8.775 15769 Z= 0.334 Chirality : 0.044 0.242 1891 Planarity : 0.005 0.067 1982 Dihedral : 4.417 19.987 1602 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.64 % Allowed : 15.92 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.23), residues: 1453 helix: 2.13 (0.18), residues: 802 sheet: -0.54 (0.40), residues: 143 loop : -0.76 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 151 TYR 0.010 0.001 TYR E 110 PHE 0.019 0.001 PHE X 396 TRP 0.033 0.001 TRP X 317 HIS 0.004 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00404 (11529) covalent geometry : angle 0.68112 (15769) hydrogen bonds : bond 0.03993 ( 688) hydrogen bonds : angle 4.13885 ( 2004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 GLN cc_start: 0.8778 (mp10) cc_final: 0.8304 (mm110) REVERT: E 158 ASP cc_start: 0.8906 (t0) cc_final: 0.8609 (m-30) REVERT: E 195 GLU cc_start: 0.7746 (pm20) cc_final: 0.7471 (pm20) REVERT: X 91 GLU cc_start: 0.9189 (mp0) cc_final: 0.8795 (pm20) REVERT: X 172 PHE cc_start: 0.8527 (m-80) cc_final: 0.7938 (m-80) REVERT: X 186 MET cc_start: 0.9407 (mtp) cc_final: 0.8890 (tpt) REVERT: X 291 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8754 (mmm) REVERT: C 19 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: C 175 THR cc_start: 0.9671 (OUTLIER) cc_final: 0.9425 (p) REVERT: C 180 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7878 (pp30) REVERT: C 185 ASP cc_start: 0.8894 (m-30) cc_final: 0.8297 (t0) REVERT: C 369 ASP cc_start: 0.8649 (t0) cc_final: 0.8233 (t0) REVERT: D 45 MET cc_start: 0.6225 (mmt) cc_final: 0.5905 (tpt) REVERT: D 74 MET cc_start: 0.8598 (ptp) cc_final: 0.8271 (ptt) REVERT: D 164 HIS cc_start: 0.8707 (m90) cc_final: 0.8460 (m90) REVERT: D 186 MET cc_start: 0.9009 (tpt) cc_final: 0.8751 (tpt) REVERT: D 190 ARG cc_start: 0.8213 (mmp80) cc_final: 0.7843 (tpp80) REVERT: D 205 LEU cc_start: 0.9176 (tp) cc_final: 0.8974 (tm) REVERT: D 291 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8849 (tpt) REVERT: D 381 HIS cc_start: 0.5427 (p-80) cc_final: 0.4848 (t-90) REVERT: B 47 GLU cc_start: 0.8999 (pm20) cc_final: 0.8784 (pm20) outliers start: 43 outliers final: 19 residues processed: 200 average time/residue: 0.5207 time to fit residues: 113.8716 Evaluate side-chains 194 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 291 MET Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 315 SER Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 72 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 52 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS E 102 HIS E 196 HIS D 31 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.099075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.074874 restraints weight = 27098.408| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.36 r_work: 0.3052 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11529 Z= 0.143 Angle : 0.672 9.279 15769 Z= 0.326 Chirality : 0.044 0.319 1891 Planarity : 0.005 0.084 1982 Dihedral : 4.324 19.396 1602 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.39 % Allowed : 16.77 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.23), residues: 1453 helix: 2.23 (0.18), residues: 802 sheet: -0.49 (0.40), residues: 143 loop : -0.75 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 151 TYR 0.010 0.001 TYR X 292 PHE 0.018 0.001 PHE X 396 TRP 0.041 0.001 TRP X 317 HIS 0.004 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00327 (11529) covalent geometry : angle 0.67190 (15769) hydrogen bonds : bond 0.03817 ( 688) hydrogen bonds : angle 4.05339 ( 2004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 GLU cc_start: 0.8019 (tp30) cc_final: 0.7721 (tp30) REVERT: E 113 GLN cc_start: 0.8680 (mp10) cc_final: 0.8095 (mm110) REVERT: E 158 ASP cc_start: 0.8899 (t0) cc_final: 0.8578 (m-30) REVERT: E 195 GLU cc_start: 0.7790 (pm20) cc_final: 0.7580 (pm20) REVERT: E 199 TRP cc_start: 0.8703 (m-90) cc_final: 0.8347 (m100) REVERT: X 145 MET cc_start: 0.6738 (mmp) cc_final: 0.6255 (tpt) REVERT: X 172 PHE cc_start: 0.8547 (m-80) cc_final: 0.7929 (m-80) REVERT: X 186 MET cc_start: 0.9404 (mtp) cc_final: 0.8889 (tpt) REVERT: X 291 MET cc_start: 0.9195 (mmm) cc_final: 0.8726 (mmm) REVERT: C 19 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7881 (mm-30) REVERT: C 99 LYS cc_start: 0.8747 (tmmt) cc_final: 0.8506 (pttm) REVERT: C 115 ARG cc_start: 0.8941 (ttm110) cc_final: 0.7970 (ttp80) REVERT: C 175 THR cc_start: 0.9710 (OUTLIER) cc_final: 0.9481 (p) REVERT: C 180 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7861 (pp30) REVERT: C 185 ASP cc_start: 0.8880 (m-30) cc_final: 0.8313 (t0) REVERT: C 369 ASP cc_start: 0.8660 (t0) cc_final: 0.8237 (t0) REVERT: D 50 LEU cc_start: 0.8745 (pt) cc_final: 0.8428 (tp) REVERT: D 74 MET cc_start: 0.8570 (ptp) cc_final: 0.8241 (ptt) REVERT: D 164 HIS cc_start: 0.8768 (m90) cc_final: 0.8519 (m90) REVERT: D 186 MET cc_start: 0.9001 (tpt) cc_final: 0.8761 (OUTLIER) REVERT: D 203 LEU cc_start: 0.9512 (mt) cc_final: 0.9289 (mm) REVERT: D 253 TYR cc_start: 0.8871 (m-80) cc_final: 0.8655 (m-80) REVERT: D 291 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8791 (tpt) REVERT: D 381 HIS cc_start: 0.5389 (p-80) cc_final: 0.4745 (t-90) REVERT: D 472 LYS cc_start: 0.8172 (tptt) cc_final: 0.7157 (mptt) REVERT: B 47 GLU cc_start: 0.8988 (pm20) cc_final: 0.8787 (pm20) outliers start: 40 outliers final: 19 residues processed: 212 average time/residue: 0.5205 time to fit residues: 120.7269 Evaluate side-chains 203 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 315 SER Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 72 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS E 102 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.098616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.074445 restraints weight = 27071.437| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.32 r_work: 0.3045 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11529 Z= 0.170 Angle : 0.695 9.038 15769 Z= 0.337 Chirality : 0.045 0.289 1891 Planarity : 0.004 0.047 1982 Dihedral : 4.318 20.241 1602 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.96 % Allowed : 18.29 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.23), residues: 1453 helix: 2.21 (0.19), residues: 802 sheet: -0.51 (0.41), residues: 143 loop : -0.76 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 151 TYR 0.011 0.001 TYR E 110 PHE 0.011 0.001 PHE D 398 TRP 0.041 0.001 TRP X 317 HIS 0.003 0.001 HIS X 227 Details of bonding type rmsd covalent geometry : bond 0.00390 (11529) covalent geometry : angle 0.69457 (15769) hydrogen bonds : bond 0.03866 ( 688) hydrogen bonds : angle 4.10831 ( 2004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 GLU cc_start: 0.8076 (tp30) cc_final: 0.7812 (tp30) REVERT: E 113 GLN cc_start: 0.8624 (mp10) cc_final: 0.8017 (mm110) REVERT: E 158 ASP cc_start: 0.8876 (t0) cc_final: 0.8577 (m-30) REVERT: E 195 GLU cc_start: 0.7899 (pm20) cc_final: 0.7691 (pm20) REVERT: E 199 TRP cc_start: 0.8713 (m-90) cc_final: 0.8377 (m100) REVERT: X 91 GLU cc_start: 0.9192 (mp0) cc_final: 0.8821 (pm20) REVERT: X 145 MET cc_start: 0.6783 (mmp) cc_final: 0.6354 (tpt) REVERT: X 172 PHE cc_start: 0.8500 (m-80) cc_final: 0.7899 (m-80) REVERT: X 291 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8735 (mmm) REVERT: C 19 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: C 99 LYS cc_start: 0.8765 (tmmt) cc_final: 0.8517 (pttm) REVERT: C 115 ARG cc_start: 0.8918 (ttm110) cc_final: 0.7937 (ttp80) REVERT: C 148 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8029 (ptt) REVERT: C 180 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7860 (pp30) REVERT: C 185 ASP cc_start: 0.8879 (m-30) cc_final: 0.8320 (t0) REVERT: C 212 MET cc_start: 0.9297 (mpp) cc_final: 0.9049 (mpp) REVERT: C 369 ASP cc_start: 0.8688 (t0) cc_final: 0.8267 (t0) REVERT: D 74 MET cc_start: 0.8546 (ptp) cc_final: 0.8187 (ptt) REVERT: D 186 MET cc_start: 0.9017 (tpt) cc_final: 0.8779 (OUTLIER) REVERT: D 291 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8831 (tpt) REVERT: D 336 GLN cc_start: 0.8573 (mp10) cc_final: 0.8324 (pm20) REVERT: D 381 HIS cc_start: 0.5432 (p-80) cc_final: 0.4782 (t-90) REVERT: D 493 MET cc_start: 0.8574 (mtm) cc_final: 0.8346 (mpp) outliers start: 35 outliers final: 21 residues processed: 199 average time/residue: 0.5149 time to fit residues: 112.1214 Evaluate side-chains 197 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 291 MET Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 315 SER Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 72 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS E 102 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.099470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.075208 restraints weight = 26924.128| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.35 r_work: 0.3053 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11529 Z= 0.152 Angle : 0.695 10.159 15769 Z= 0.336 Chirality : 0.045 0.313 1891 Planarity : 0.004 0.053 1982 Dihedral : 4.276 21.201 1602 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.96 % Allowed : 19.39 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.23), residues: 1453 helix: 2.27 (0.19), residues: 797 sheet: -0.23 (0.42), residues: 136 loop : -0.68 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 151 TYR 0.011 0.001 TYR C 207 PHE 0.012 0.001 PHE D 398 TRP 0.047 0.001 TRP X 317 HIS 0.003 0.001 HIS X 227 Details of bonding type rmsd covalent geometry : bond 0.00352 (11529) covalent geometry : angle 0.69470 (15769) hydrogen bonds : bond 0.03791 ( 688) hydrogen bonds : angle 4.08600 ( 2004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 GLU cc_start: 0.8004 (tp30) cc_final: 0.7448 (tp30) REVERT: E 113 GLN cc_start: 0.8591 (mp10) cc_final: 0.8157 (mp10) REVERT: E 158 ASP cc_start: 0.8880 (t0) cc_final: 0.8564 (m-30) REVERT: E 195 GLU cc_start: 0.7869 (pm20) cc_final: 0.7566 (pm20) REVERT: E 199 TRP cc_start: 0.8718 (m-90) cc_final: 0.8405 (m100) REVERT: X 91 GLU cc_start: 0.9194 (mp0) cc_final: 0.8808 (pm20) REVERT: X 145 MET cc_start: 0.6745 (mmp) cc_final: 0.6273 (tpt) REVERT: X 172 PHE cc_start: 0.8508 (m-80) cc_final: 0.7931 (m-80) REVERT: X 186 MET cc_start: 0.9461 (mtp) cc_final: 0.8866 (tpt) REVERT: X 291 MET cc_start: 0.9206 (mmm) cc_final: 0.8721 (mmm) REVERT: C 19 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7904 (mm-30) REVERT: C 99 LYS cc_start: 0.8745 (tmmt) cc_final: 0.8508 (pttm) REVERT: C 115 ARG cc_start: 0.8901 (ttm110) cc_final: 0.7962 (ttp80) REVERT: C 180 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7848 (pp30) REVERT: C 185 ASP cc_start: 0.8891 (m-30) cc_final: 0.8324 (t0) REVERT: C 212 MET cc_start: 0.9314 (mpp) cc_final: 0.9074 (mpp) REVERT: C 369 ASP cc_start: 0.8714 (t0) cc_final: 0.8279 (t0) REVERT: D 50 LEU cc_start: 0.8766 (pt) cc_final: 0.8351 (tp) REVERT: D 74 MET cc_start: 0.8527 (ptp) cc_final: 0.8159 (ptt) REVERT: D 186 MET cc_start: 0.8988 (tpt) cc_final: 0.8744 (OUTLIER) REVERT: D 253 TYR cc_start: 0.8841 (m-80) cc_final: 0.8573 (m-80) REVERT: D 291 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8828 (tpt) REVERT: D 336 GLN cc_start: 0.8589 (mp10) cc_final: 0.8271 (pm20) REVERT: D 381 HIS cc_start: 0.5446 (p-80) cc_final: 0.4786 (t-90) outliers start: 35 outliers final: 17 residues processed: 200 average time/residue: 0.5063 time to fit residues: 111.5534 Evaluate side-chains 195 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 315 SER Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 72 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 68 optimal weight: 0.3980 chunk 94 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS E 102 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.100501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.076394 restraints weight = 26759.253| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.33 r_work: 0.3079 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11529 Z= 0.131 Angle : 0.722 13.074 15769 Z= 0.342 Chirality : 0.046 0.401 1891 Planarity : 0.004 0.060 1982 Dihedral : 4.169 19.437 1602 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.86 % Allowed : 20.24 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.23), residues: 1453 helix: 2.27 (0.19), residues: 799 sheet: -0.19 (0.42), residues: 136 loop : -0.66 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 39 TYR 0.011 0.001 TYR C 207 PHE 0.013 0.001 PHE D 398 TRP 0.051 0.001 TRP X 317 HIS 0.004 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00303 (11529) covalent geometry : angle 0.72192 (15769) hydrogen bonds : bond 0.03664 ( 688) hydrogen bonds : angle 4.07886 ( 2004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 109 GLU cc_start: 0.7909 (tp30) cc_final: 0.7378 (tp30) REVERT: E 113 GLN cc_start: 0.8630 (mp10) cc_final: 0.8225 (mp10) REVERT: E 158 ASP cc_start: 0.8868 (t0) cc_final: 0.8518 (m-30) REVERT: E 195 GLU cc_start: 0.7950 (pm20) cc_final: 0.7711 (pm20) REVERT: E 199 TRP cc_start: 0.8716 (m-90) cc_final: 0.8416 (m100) REVERT: E 239 TRP cc_start: 0.7728 (p90) cc_final: 0.7314 (p90) REVERT: X 29 ASP cc_start: 0.8719 (p0) cc_final: 0.8497 (p0) REVERT: X 91 GLU cc_start: 0.9174 (mp0) cc_final: 0.8645 (pm20) REVERT: X 98 ASP cc_start: 0.8704 (m-30) cc_final: 0.8459 (m-30) REVERT: X 145 MET cc_start: 0.6612 (mmp) cc_final: 0.6262 (tpt) REVERT: X 172 PHE cc_start: 0.8543 (m-80) cc_final: 0.7947 (m-80) REVERT: X 182 THR cc_start: 0.9274 (p) cc_final: 0.8978 (p) REVERT: X 186 MET cc_start: 0.9462 (mtp) cc_final: 0.8854 (tpt) REVERT: X 291 MET cc_start: 0.9161 (mmm) cc_final: 0.8671 (mmm) REVERT: C 19 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7959 (mm-30) REVERT: C 99 LYS cc_start: 0.8722 (tmmt) cc_final: 0.8503 (pttm) REVERT: C 180 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7343 (pp30) REVERT: C 181 ASN cc_start: 0.9224 (m-40) cc_final: 0.8314 (m110) REVERT: C 185 ASP cc_start: 0.8871 (m-30) cc_final: 0.8350 (t0) REVERT: C 212 MET cc_start: 0.9254 (mpp) cc_final: 0.9028 (mpp) REVERT: C 369 ASP cc_start: 0.8690 (t0) cc_final: 0.8261 (t0) REVERT: D 50 LEU cc_start: 0.8745 (pt) cc_final: 0.8317 (tm) REVERT: D 74 MET cc_start: 0.8491 (ptp) cc_final: 0.8125 (ptt) REVERT: D 186 MET cc_start: 0.8973 (tpt) cc_final: 0.8725 (OUTLIER) REVERT: D 253 TYR cc_start: 0.8918 (m-80) cc_final: 0.8717 (m-80) REVERT: D 291 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8812 (tpt) REVERT: D 298 LEU cc_start: 0.9510 (tp) cc_final: 0.9273 (tp) REVERT: D 336 GLN cc_start: 0.8513 (mp10) cc_final: 0.8296 (pm20) REVERT: D 381 HIS cc_start: 0.5448 (p-80) cc_final: 0.4798 (t-90) REVERT: D 415 LEU cc_start: 0.9450 (mp) cc_final: 0.9236 (mp) REVERT: D 418 THR cc_start: 0.9212 (m) cc_final: 0.8908 (p) REVERT: D 449 LEU cc_start: 0.8959 (mm) cc_final: 0.8716 (mm) REVERT: D 483 MET cc_start: 0.8820 (mtt) cc_final: 0.8613 (tpp) REVERT: D 493 MET cc_start: 0.8641 (mtm) cc_final: 0.8438 (mpp) REVERT: B 50 ARG cc_start: 0.6748 (tpt170) cc_final: 0.6479 (tpt170) outliers start: 22 outliers final: 16 residues processed: 218 average time/residue: 0.5072 time to fit residues: 121.3007 Evaluate side-chains 200 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 315 SER Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 72 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.3164 > 50: distance: 5 - 10: 22.649 distance: 10 - 11: 11.289 distance: 10 - 16: 21.242 distance: 11 - 12: 27.221 distance: 11 - 14: 39.076 distance: 12 - 17: 40.551 distance: 14 - 15: 13.946 distance: 15 - 16: 6.761 distance: 17 - 18: 52.122 distance: 18 - 19: 61.561 distance: 18 - 21: 50.453 distance: 19 - 26: 63.825 distance: 22 - 23: 39.790 distance: 23 - 24: 20.437 distance: 26 - 27: 59.571 distance: 27 - 28: 42.017 distance: 28 - 29: 14.352 distance: 28 - 30: 35.818 distance: 30 - 31: 18.043 distance: 31 - 32: 3.469 distance: 31 - 34: 59.149 distance: 32 - 33: 21.185 distance: 32 - 39: 41.726 distance: 34 - 35: 37.407 distance: 35 - 36: 61.454 distance: 36 - 37: 14.824 distance: 37 - 38: 40.069 distance: 39 - 40: 29.966 distance: 39 - 45: 21.690 distance: 40 - 41: 43.511 distance: 40 - 43: 40.248 distance: 41 - 42: 16.951 distance: 44 - 45: 41.187 distance: 46 - 47: 24.912 distance: 47 - 48: 28.206 distance: 47 - 50: 14.358 distance: 48 - 49: 21.646 distance: 48 - 52: 15.497 distance: 50 - 51: 5.730 distance: 52 - 53: 16.558 distance: 53 - 54: 25.071 distance: 53 - 56: 17.502 distance: 54 - 55: 25.190 distance: 54 - 63: 12.532 distance: 55 - 87: 22.254 distance: 56 - 57: 24.007 distance: 57 - 58: 9.885 distance: 58 - 59: 25.505 distance: 59 - 60: 15.095 distance: 60 - 61: 14.940 distance: 60 - 62: 5.396 distance: 63 - 64: 20.681 distance: 63 - 69: 38.736 distance: 64 - 65: 29.277 distance: 64 - 67: 29.574 distance: 65 - 66: 13.968 distance: 65 - 70: 28.805 distance: 66 - 95: 29.258 distance: 67 - 68: 4.337 distance: 68 - 69: 30.925 distance: 70 - 71: 18.390 distance: 71 - 72: 33.107 distance: 71 - 74: 18.659 distance: 72 - 73: 40.981 distance: 72 - 79: 12.874 distance: 73 - 100: 30.159 distance: 74 - 75: 12.071 distance: 75 - 76: 40.486 distance: 76 - 77: 9.114 distance: 77 - 78: 32.856 distance: 79 - 80: 20.618 distance: 80 - 81: 34.607 distance: 80 - 83: 32.432 distance: 81 - 82: 24.391 distance: 81 - 87: 22.036 distance: 82 - 108: 25.556 distance: 83 - 84: 37.775 distance: 84 - 85: 19.529 distance: 84 - 86: 20.178