Starting phenix.real_space_refine on Tue Jul 29 12:27:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b9f_12103/07_2025/7b9f_12103.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b9f_12103/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7b9f_12103/07_2025/7b9f_12103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b9f_12103/07_2025/7b9f_12103.map" model { file = "/net/cci-nas-00/data/ceres_data/7b9f_12103/07_2025/7b9f_12103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b9f_12103/07_2025/7b9f_12103.cif" } resolution = 3.0 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= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.38, per 1000 atoms: 0.74 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: 2.77 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.25 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: 4.04 Time building geometry restraints manager: 3.26 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: 8.900 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.170 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:14.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.040 ------------------------------------------------------------------------------- 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 : 4.11 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 (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: -0.11 (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 TRP 0.071 0.003 TRP C 149 HIS 0.019 0.002 HIS E 102 PHE 0.027 0.003 PHE X 358 TYR 0.024 0.003 TYR C 207 ARG 0.012 0.001 ARG E 229 Details of bonding type rmsd hydrogen bonds : bond 0.15517 ( 688) hydrogen bonds : angle 5.81514 ( 2004) covalent geometry : bond 0.00775 (11529) covalent geometry : angle 1.00566 (15769) *********************** 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 : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 204 MET cc_start: 0.8959 (ttp) cc_final: 0.8729 (ttp) 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: 0.6125 (tpt170) REVERT: B 54 LEU cc_start: 0.9108 (mt) cc_final: 0.8644 (mt) outliers start: 0 outliers final: 2 residues processed: 232 average time/residue: 1.1198 time to fit residues: 282.8931 Evaluate side-chains 179 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 332 HIS C 20 ASN C 181 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.098616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.074294 restraints weight = 26785.027| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.30 r_work: 0.3037 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11529 Z= 0.164 Angle : 0.709 8.177 15769 Z= 0.356 Chirality : 0.045 0.198 1891 Planarity : 0.005 0.055 1982 Dihedral : 5.052 29.418 1605 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.12 % Allowed : 10.33 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1453 helix: 1.61 (0.18), residues: 787 sheet: -0.43 (0.41), residues: 134 loop : -0.79 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 73 HIS 0.008 0.001 HIS E 102 PHE 0.036 0.002 PHE X 396 TYR 0.016 0.001 TYR E 110 ARG 0.007 0.001 ARG C 151 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 688) hydrogen bonds : angle 4.47434 ( 2004) covalent geometry : bond 0.00372 (11529) covalent geometry : angle 0.70928 (15769) *********************** 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 218 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 GLN cc_start: 0.8692 (mp10) cc_final: 0.8474 (mm110) REVERT: X 172 PHE cc_start: 0.8521 (m-80) cc_final: 0.7935 (m-80) REVERT: X 186 MET cc_start: 0.9383 (mtp) cc_final: 0.8804 (tpt) REVERT: X 378 CYS cc_start: 0.8850 (m) cc_final: 0.8544 (m) REVERT: C 20 ASN cc_start: 0.9254 (OUTLIER) cc_final: 0.9017 (m-40) REVERT: C 180 GLN cc_start: 0.8225 (pp30) cc_final: 0.7889 (pp30) REVERT: C 201 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8781 (ttt90) REVERT: C 291 ARG cc_start: 0.8904 (ttp80) cc_final: 0.8240 (tpm170) REVERT: C 369 ASP cc_start: 0.8628 (t0) cc_final: 0.8333 (t0) REVERT: D 45 MET cc_start: 0.6248 (mmt) cc_final: 0.5966 (tpt) REVERT: D 50 LEU cc_start: 0.8727 (pt) cc_final: 0.8306 (tm) REVERT: D 164 HIS cc_start: 0.8767 (m90) cc_final: 0.8419 (m90) REVERT: D 186 MET cc_start: 0.8957 (tpt) cc_final: 0.8722 (OUTLIER) REVERT: D 381 HIS cc_start: 0.5715 (p-80) cc_final: 0.4900 (t-90) REVERT: D 399 LEU cc_start: 0.9556 (mt) cc_final: 0.9304 (mm) REVERT: D 472 LYS cc_start: 0.8250 (tptt) cc_final: 0.7198 (mptt) REVERT: B 47 GLU cc_start: 0.8880 (pm20) cc_final: 0.8631 (pm20) REVERT: B 54 LEU cc_start: 0.9229 (mt) cc_final: 0.8900 (mt) outliers start: 25 outliers final: 9 residues processed: 207 average time/residue: 1.0066 time to fit residues: 227.9476 Evaluate side-chains 179 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 399 LEU Chi-restraints excluded: chain X residue 408 ASP Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain D residue 271 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 0.0010 chunk 128 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.099094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.074773 restraints weight = 27009.527| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.32 r_work: 0.3047 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11529 Z= 0.146 Angle : 0.676 8.357 15769 Z= 0.333 Chirality : 0.045 0.358 1891 Planarity : 0.005 0.051 1982 Dihedral : 4.686 25.459 1602 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.71 % Allowed : 13.29 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.22), residues: 1453 helix: 1.93 (0.18), residues: 788 sheet: -0.48 (0.40), residues: 141 loop : -0.75 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 410 HIS 0.007 0.001 HIS E 102 PHE 0.027 0.001 PHE X 396 TYR 0.012 0.001 TYR E 110 ARG 0.005 0.000 ARG X 111 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 688) hydrogen bonds : angle 4.26440 ( 2004) covalent geometry : bond 0.00329 (11529) covalent geometry : angle 0.67558 (15769) *********************** 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 215 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 GLN cc_start: 0.8765 (mp10) cc_final: 0.8459 (mm110) REVERT: E 195 GLU cc_start: 0.7824 (pm20) cc_final: 0.7568 (pm20) REVERT: E 239 TRP cc_start: 0.7743 (p90) cc_final: 0.7540 (p90) REVERT: X 129 ARG cc_start: 0.8856 (tmt90) cc_final: 0.8647 (ttt90) REVERT: X 172 PHE cc_start: 0.8512 (m-80) cc_final: 0.7909 (m-80) REVERT: X 186 MET cc_start: 0.9381 (mtp) cc_final: 0.8808 (tpt) REVERT: X 378 CYS cc_start: 0.8697 (m) cc_final: 0.8436 (m) REVERT: C 180 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7938 (pp30) REVERT: C 291 ARG cc_start: 0.8865 (ttp80) cc_final: 0.8202 (tpm170) REVERT: C 369 ASP cc_start: 0.8559 (t0) cc_final: 0.8156 (t0) REVERT: D 45 MET cc_start: 0.6161 (mmt) cc_final: 0.5776 (tpt) REVERT: D 50 LEU cc_start: 0.8717 (pt) cc_final: 0.8262 (tm) REVERT: D 164 HIS cc_start: 0.8739 (m90) cc_final: 0.8445 (m90) REVERT: D 186 MET cc_start: 0.8956 (tpt) cc_final: 0.8721 (OUTLIER) REVERT: D 291 MET cc_start: 0.9159 (tpt) cc_final: 0.8898 (tpt) REVERT: D 381 HIS cc_start: 0.5545 (p-80) cc_final: 0.4789 (t-90) REVERT: D 472 LYS cc_start: 0.8219 (tptt) cc_final: 0.7150 (mptt) REVERT: B 47 GLU cc_start: 0.8892 (pm20) cc_final: 0.8686 (pm20) REVERT: B 54 LEU cc_start: 0.9240 (mt) cc_final: 0.8980 (mt) outliers start: 32 outliers final: 16 residues processed: 199 average time/residue: 1.0212 time to fit residues: 225.0261 Evaluate side-chains 190 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 162 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain D residue 243 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 109 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 51 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.097562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.073108 restraints weight = 26871.801| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.32 r_work: 0.3015 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2079 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= 0.198 Angle : 0.688 10.679 15769 Z= 0.338 Chirality : 0.045 0.354 1891 Planarity : 0.005 0.050 1982 Dihedral : 4.576 19.041 1602 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.90 % Allowed : 13.55 % Favored : 82.56 % 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: 1.25 (0.23), residues: 1453 helix: 2.07 (0.18), residues: 794 sheet: -0.52 (0.41), residues: 141 loop : -0.73 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP X 317 HIS 0.005 0.001 HIS E 102 PHE 0.022 0.002 PHE X 396 TYR 0.017 0.002 TYR D 466 ARG 0.006 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 688) hydrogen bonds : angle 4.20901 ( 2004) covalent geometry : bond 0.00448 (11529) covalent geometry : angle 0.68831 (15769) *********************** 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 222 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 GLU cc_start: 0.8039 (tp30) cc_final: 0.7793 (tp30) REVERT: E 113 GLN cc_start: 0.8771 (mp10) cc_final: 0.8286 (mm110) REVERT: E 195 GLU cc_start: 0.7836 (pm20) cc_final: 0.7570 (pm20) REVERT: X 172 PHE cc_start: 0.8528 (m-80) cc_final: 0.7972 (m-80) REVERT: X 186 MET cc_start: 0.9414 (mtp) cc_final: 0.8893 (tpt) REVERT: C 180 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7949 (pp30) REVERT: C 185 ASP cc_start: 0.8890 (m-30) cc_final: 0.8276 (t0) REVERT: C 201 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.9015 (tpt-90) REVERT: C 291 ARG cc_start: 0.8850 (ttp80) cc_final: 0.8271 (tpm170) REVERT: C 369 ASP cc_start: 0.8605 (t0) cc_final: 0.8214 (t0) REVERT: D 45 MET cc_start: 0.6274 (mmt) cc_final: 0.5910 (tpt) REVERT: D 74 MET cc_start: 0.8602 (ptp) cc_final: 0.8266 (ptt) REVERT: D 164 HIS cc_start: 0.8756 (m90) cc_final: 0.8493 (m90) REVERT: D 186 MET cc_start: 0.8970 (tpt) cc_final: 0.8715 (tpt) REVERT: D 291 MET cc_start: 0.9170 (tpt) cc_final: 0.8910 (tpt) REVERT: D 381 HIS cc_start: 0.5457 (p-80) cc_final: 0.4851 (t-90) REVERT: B 47 GLU cc_start: 0.9005 (pm20) cc_final: 0.8794 (pm20) outliers start: 46 outliers final: 16 residues processed: 197 average time/residue: 1.2758 time to fit residues: 276.0113 Evaluate side-chains 186 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 2.004 ------------------------------------------------------------------------------- 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 399 LEU Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 201 ARG 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 243 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 117 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 97 optimal weight: 0.0980 chunk 41 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 C 249 HIS D 31 GLN D 411 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.099006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.074730 restraints weight = 26867.678| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.32 r_work: 0.3046 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11529 Z= 0.135 Angle : 0.661 8.597 15769 Z= 0.322 Chirality : 0.044 0.308 1891 Planarity : 0.005 0.062 1982 Dihedral : 4.379 19.341 1602 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.39 % Allowed : 15.50 % Favored : 81.12 % 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: 1.33 (0.23), residues: 1453 helix: 2.17 (0.18), residues: 800 sheet: -0.60 (0.41), residues: 143 loop : -0.75 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP X 317 HIS 0.005 0.001 HIS E 102 PHE 0.020 0.001 PHE X 396 TYR 0.010 0.001 TYR E 110 ARG 0.010 0.000 ARG X 129 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 688) hydrogen bonds : angle 4.06876 ( 2004) covalent geometry : bond 0.00305 (11529) covalent geometry : angle 0.66146 (15769) *********************** 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 225 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 GLU cc_start: 0.8031 (tp30) cc_final: 0.7747 (tp30) REVERT: E 113 GLN cc_start: 0.8683 (mp10) cc_final: 0.8108 (mm110) REVERT: E 158 ASP cc_start: 0.8903 (t0) cc_final: 0.8611 (m-30) REVERT: E 195 GLU cc_start: 0.7838 (pm20) cc_final: 0.7587 (pm20) REVERT: X 91 GLU cc_start: 0.9178 (mp0) cc_final: 0.8779 (pm20) REVERT: X 172 PHE cc_start: 0.8521 (m-80) cc_final: 0.7931 (m-80) REVERT: X 186 MET cc_start: 0.9400 (mtp) cc_final: 0.8884 (tpt) REVERT: X 291 MET cc_start: 0.9300 (mmm) cc_final: 0.8878 (mmm) REVERT: C 19 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 99 LYS cc_start: 0.8744 (tmmt) cc_final: 0.8495 (pttm) REVERT: C 180 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7916 (pp30) REVERT: C 185 ASP cc_start: 0.8888 (m-30) cc_final: 0.8315 (t0) REVERT: C 291 ARG cc_start: 0.8825 (ttp80) cc_final: 0.8231 (tpm170) REVERT: C 369 ASP cc_start: 0.8611 (t0) cc_final: 0.8196 (t0) REVERT: D 50 LEU cc_start: 0.8750 (pt) cc_final: 0.8306 (tp) REVERT: D 74 MET cc_start: 0.8570 (ptp) cc_final: 0.8245 (ptt) REVERT: D 164 HIS cc_start: 0.8706 (m90) cc_final: 0.8463 (m90) REVERT: D 186 MET cc_start: 0.8972 (tpt) cc_final: 0.8715 (tpt) REVERT: D 291 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8830 (tpt) REVERT: D 381 HIS cc_start: 0.5435 (p-80) cc_final: 0.4850 (t-90) REVERT: B 47 GLU cc_start: 0.8987 (pm20) cc_final: 0.8769 (pm20) outliers start: 40 outliers final: 16 residues processed: 206 average time/residue: 1.3825 time to fit residues: 313.2825 Evaluate side-chains 184 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 447 LEU 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 229 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 138 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 135 optimal weight: 0.0670 overall best weight: 1.6126 ------------------------------------------------------------------------------- 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 ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.096795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.072361 restraints weight = 27371.658| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.34 r_work: 0.2995 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11529 Z= 0.252 Angle : 0.722 9.647 15769 Z= 0.356 Chirality : 0.046 0.270 1891 Planarity : 0.005 0.052 1982 Dihedral : 4.499 22.393 1602 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.39 % Allowed : 17.02 % Favored : 79.59 % 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: 1.27 (0.23), residues: 1453 helix: 2.14 (0.18), residues: 802 sheet: -0.81 (0.39), residues: 156 loop : -0.75 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP X 317 HIS 0.005 0.001 HIS C 414 PHE 0.017 0.002 PHE X 396 TYR 0.013 0.001 TYR E 110 ARG 0.010 0.000 ARG C 151 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 688) hydrogen bonds : angle 4.25638 ( 2004) covalent geometry : bond 0.00571 (11529) covalent geometry : angle 0.72239 (15769) *********************** 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 219 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 1.697 Fit side-chains revert: symmetry clash REVERT: E 113 GLN cc_start: 0.8677 (mp10) cc_final: 0.8261 (mp10) REVERT: E 158 ASP cc_start: 0.8906 (t0) cc_final: 0.8602 (m-30) REVERT: E 195 GLU cc_start: 0.7963 (pm20) cc_final: 0.7664 (pm20) REVERT: X 172 PHE cc_start: 0.8550 (m-80) cc_final: 0.7951 (m-80) REVERT: X 186 MET cc_start: 0.9413 (mtp) cc_final: 0.8908 (tpt) REVERT: X 291 MET cc_start: 0.9329 (mmm) cc_final: 0.8912 (mmm) REVERT: C 175 THR cc_start: 0.9575 (OUTLIER) cc_final: 0.9334 (p) REVERT: C 180 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7917 (pp30) REVERT: C 185 ASP cc_start: 0.8878 (m-30) cc_final: 0.8329 (t0) REVERT: C 291 ARG cc_start: 0.8883 (ttp80) cc_final: 0.8303 (tpm170) REVERT: C 369 ASP cc_start: 0.8710 (t0) cc_final: 0.8291 (t0) REVERT: D 74 MET cc_start: 0.8561 (ptp) cc_final: 0.8234 (ptt) REVERT: D 128 LYS cc_start: 0.9020 (pmtt) cc_final: 0.8649 (pmtt) REVERT: D 164 HIS cc_start: 0.8788 (m90) cc_final: 0.8530 (m90) REVERT: D 186 MET cc_start: 0.8969 (tpt) cc_final: 0.8706 (tpt) REVERT: D 271 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8370 (mmm) REVERT: D 291 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8918 (tpt) REVERT: D 381 HIS cc_start: 0.5492 (p-80) cc_final: 0.4821 (t-90) outliers start: 40 outliers final: 18 residues processed: 202 average time/residue: 1.0430 time to fit residues: 231.6570 Evaluate side-chains 193 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 447 LEU 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 271 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 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 113 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 142 optimal weight: 0.0000 chunk 73 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 124 optimal weight: 0.0670 chunk 96 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 121 optimal weight: 0.0970 chunk 85 optimal weight: 0.8980 overall best weight: 0.3120 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.100176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.076020 restraints weight = 27094.015| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.35 r_work: 0.3073 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2663 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= 0.127 Angle : 0.689 11.265 15769 Z= 0.332 Chirality : 0.045 0.347 1891 Planarity : 0.005 0.062 1982 Dihedral : 4.289 21.227 1602 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.88 % Allowed : 18.29 % Favored : 78.83 % 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: 1.47 (0.23), residues: 1453 helix: 2.28 (0.19), residues: 796 sheet: -0.39 (0.41), residues: 143 loop : -0.71 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP X 317 HIS 0.004 0.001 HIS C 245 PHE 0.016 0.001 PHE X 396 TYR 0.011 0.001 TYR C 207 ARG 0.007 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 688) hydrogen bonds : angle 4.04985 ( 2004) covalent geometry : bond 0.00289 (11529) covalent geometry : angle 0.68872 (15769) *********************** 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 233 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 158 ASP cc_start: 0.8893 (t0) cc_final: 0.8582 (m-30) REVERT: E 195 GLU cc_start: 0.7955 (pm20) cc_final: 0.7623 (pm20) REVERT: E 199 TRP cc_start: 0.8695 (m-90) cc_final: 0.8422 (m100) REVERT: X 91 GLU cc_start: 0.9197 (mp0) cc_final: 0.8814 (pm20) REVERT: X 145 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6189 (tpt) REVERT: X 172 PHE cc_start: 0.8494 (m-80) cc_final: 0.7914 (m-80) REVERT: X 182 THR cc_start: 0.9302 (p) cc_final: 0.9064 (p) REVERT: X 186 MET cc_start: 0.9410 (mtp) cc_final: 0.8893 (tpt) REVERT: X 291 MET cc_start: 0.9296 (mmm) cc_final: 0.8858 (mmm) REVERT: X 421 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8959 (mp) REVERT: C 148 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8159 (ptt) REVERT: C 180 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7917 (pp30) REVERT: C 185 ASP cc_start: 0.8869 (m-30) cc_final: 0.8301 (t0) REVERT: C 212 MET cc_start: 0.9239 (mpp) cc_final: 0.8990 (mpp) REVERT: C 369 ASP cc_start: 0.8622 (t0) cc_final: 0.8180 (t0) REVERT: D 50 LEU cc_start: 0.8753 (pt) cc_final: 0.8366 (tp) REVERT: D 74 MET cc_start: 0.8534 (ptp) cc_final: 0.8167 (ptt) REVERT: D 186 MET cc_start: 0.8963 (tpt) cc_final: 0.8721 (OUTLIER) REVERT: D 291 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8800 (tpt) REVERT: D 381 HIS cc_start: 0.5468 (p-80) cc_final: 0.4805 (t-90) REVERT: D 472 LYS cc_start: 0.8141 (tptt) cc_final: 0.7145 (mptt) outliers start: 34 outliers final: 16 residues processed: 218 average time/residue: 1.3913 time to fit residues: 335.9569 Evaluate side-chains 196 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.795 ------------------------------------------------------------------------------- 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 145 MET 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 148 MET 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 415 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.096594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.072197 restraints weight = 27403.578| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.33 r_work: 0.2993 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 11529 Z= 0.297 Angle : 0.781 9.990 15769 Z= 0.385 Chirality : 0.049 0.393 1891 Planarity : 0.005 0.054 1982 Dihedral : 4.500 20.939 1602 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.79 % Allowed : 20.66 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.26 (0.23), residues: 1453 helix: 2.09 (0.18), residues: 802 sheet: -0.41 (0.42), residues: 141 loop : -0.84 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP X 317 HIS 0.005 0.001 HIS C 414 PHE 0.017 0.002 PHE C 160 TYR 0.017 0.002 TYR D 253 ARG 0.015 0.001 ARG C 151 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 688) hydrogen bonds : angle 4.39260 ( 2004) covalent geometry : bond 0.00673 (11529) covalent geometry : angle 0.78143 (15769) *********************** 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 210 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 158 ASP cc_start: 0.8920 (t0) cc_final: 0.8560 (m-30) REVERT: E 195 GLU cc_start: 0.7994 (pm20) cc_final: 0.7671 (pm20) REVERT: X 145 MET cc_start: 0.6688 (mmt) cc_final: 0.6272 (tpt) REVERT: X 172 PHE cc_start: 0.8527 (m-80) cc_final: 0.7949 (m-80) REVERT: X 291 MET cc_start: 0.9337 (mmm) cc_final: 0.8907 (mmm) REVERT: X 421 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8955 (mp) REVERT: C 175 THR cc_start: 0.9695 (OUTLIER) cc_final: 0.9490 (p) REVERT: C 180 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7888 (pp30) REVERT: C 185 ASP cc_start: 0.8874 (m-30) cc_final: 0.8310 (t0) REVERT: C 212 MET cc_start: 0.9325 (mpp) cc_final: 0.9078 (mpp) REVERT: C 369 ASP cc_start: 0.8684 (t0) cc_final: 0.8323 (t0) REVERT: D 128 LYS cc_start: 0.9033 (pmtt) cc_final: 0.8635 (pmtt) REVERT: D 186 MET cc_start: 0.8967 (tpt) cc_final: 0.8700 (tpt) REVERT: D 291 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8957 (tpt) REVERT: D 381 HIS cc_start: 0.5473 (p-80) cc_final: 0.4894 (t-90) REVERT: D 418 THR cc_start: 0.9294 (m) cc_final: 0.9093 (m) outliers start: 33 outliers final: 19 residues processed: 196 average time/residue: 1.0167 time to fit residues: 219.7146 Evaluate side-chains 196 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 310 THR 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 399 LEU Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain X residue 447 LEU 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.098365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.074147 restraints weight = 27016.632| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.31 r_work: 0.3036 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11529 Z= 0.175 Angle : 0.741 10.959 15769 Z= 0.360 Chirality : 0.047 0.425 1891 Planarity : 0.005 0.057 1982 Dihedral : 4.437 24.453 1602 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.71 % Allowed : 20.83 % Favored : 76.46 % 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: 1.36 (0.23), residues: 1453 helix: 2.17 (0.18), residues: 796 sheet: -0.32 (0.43), residues: 134 loop : -0.77 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP X 317 HIS 0.004 0.001 HIS X 227 PHE 0.012 0.001 PHE D 398 TYR 0.013 0.001 TYR C 207 ARG 0.014 0.000 ARG C 151 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 688) hydrogen bonds : angle 4.26853 ( 2004) covalent geometry : bond 0.00407 (11529) covalent geometry : angle 0.74124 (15769) *********************** 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 212 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 158 ASP cc_start: 0.8913 (t0) cc_final: 0.8538 (m-30) REVERT: E 195 GLU cc_start: 0.7970 (pm20) cc_final: 0.7640 (pm20) REVERT: E 199 TRP cc_start: 0.8717 (m-90) cc_final: 0.8433 (m100) REVERT: X 37 ASP cc_start: 0.8379 (t0) cc_final: 0.7485 (t0) REVERT: X 91 GLU cc_start: 0.9236 (mp0) cc_final: 0.8871 (pm20) REVERT: X 98 ASP cc_start: 0.8698 (m-30) cc_final: 0.8490 (m-30) REVERT: X 145 MET cc_start: 0.6635 (mmt) cc_final: 0.6197 (tpt) REVERT: X 172 PHE cc_start: 0.8569 (m-80) cc_final: 0.7975 (m-80) REVERT: X 186 MET cc_start: 0.9433 (mtp) cc_final: 0.8874 (tpt) REVERT: X 291 MET cc_start: 0.9307 (mmm) cc_final: 0.8874 (mmm) REVERT: X 421 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8970 (mp) REVERT: C 175 THR cc_start: 0.9702 (OUTLIER) cc_final: 0.9488 (p) REVERT: C 180 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7882 (pp30) REVERT: C 185 ASP cc_start: 0.8865 (m-30) cc_final: 0.8315 (t0) REVERT: C 212 MET cc_start: 0.9311 (mpp) cc_final: 0.9078 (mpp) REVERT: C 369 ASP cc_start: 0.8652 (t0) cc_final: 0.8268 (t0) REVERT: D 50 LEU cc_start: 0.8809 (pt) cc_final: 0.8531 (tp) REVERT: D 74 MET cc_start: 0.8559 (ptp) cc_final: 0.8254 (ptt) REVERT: D 128 LYS cc_start: 0.9026 (pmtt) cc_final: 0.8644 (pmtt) REVERT: D 186 MET cc_start: 0.8969 (tpt) cc_final: 0.8722 (OUTLIER) REVERT: D 203 LEU cc_start: 0.9547 (mt) cc_final: 0.9327 (mm) REVERT: D 253 TYR cc_start: 0.8933 (m-80) cc_final: 0.8698 (m-80) REVERT: D 291 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8870 (tpt) REVERT: D 381 HIS cc_start: 0.5627 (p-80) cc_final: 0.5010 (t-90) REVERT: D 418 THR cc_start: 0.9270 (m) cc_final: 0.9062 (m) outliers start: 32 outliers final: 21 residues processed: 201 average time/residue: 0.9669 time to fit residues: 214.4964 Evaluate side-chains 199 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 310 THR 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 399 LEU Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain X residue 447 LEU 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 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 415 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain B residue 15 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 83 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.098745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.074434 restraints weight = 27039.450| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.33 r_work: 0.3041 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11529 Z= 0.171 Angle : 0.741 11.325 15769 Z= 0.361 Chirality : 0.047 0.430 1891 Planarity : 0.005 0.061 1982 Dihedral : 4.379 23.704 1602 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.62 % Allowed : 21.42 % Favored : 75.95 % 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: 1.37 (0.23), residues: 1453 helix: 2.17 (0.18), residues: 796 sheet: -0.46 (0.43), residues: 137 loop : -0.70 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP X 317 HIS 0.004 0.001 HIS X 227 PHE 0.012 0.001 PHE D 398 TYR 0.013 0.001 TYR C 207 ARG 0.010 0.000 ARG C 151 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 688) hydrogen bonds : angle 4.26343 ( 2004) covalent geometry : bond 0.00398 (11529) covalent geometry : angle 0.74118 (15769) ********************** REFINEMENT MACRO_CYCLE 10 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 210 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 158 ASP cc_start: 0.8912 (t0) cc_final: 0.8532 (m-30) REVERT: E 195 GLU cc_start: 0.7971 (pm20) cc_final: 0.7660 (pm20) REVERT: E 199 TRP cc_start: 0.8727 (m-90) cc_final: 0.8451 (m100) REVERT: X 29 ASP cc_start: 0.8755 (p0) cc_final: 0.8523 (p0) REVERT: X 91 GLU cc_start: 0.9228 (mp0) cc_final: 0.8861 (pm20) REVERT: X 98 ASP cc_start: 0.8685 (m-30) cc_final: 0.8456 (m-30) REVERT: X 145 MET cc_start: 0.6628 (mmt) cc_final: 0.6277 (tpt) REVERT: X 172 PHE cc_start: 0.8573 (m-80) cc_final: 0.7979 (m-80) REVERT: X 186 MET cc_start: 0.9447 (mtp) cc_final: 0.8880 (tpt) REVERT: X 291 MET cc_start: 0.9303 (mmm) cc_final: 0.8870 (mmm) REVERT: X 421 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8966 (mp) REVERT: C 175 THR cc_start: 0.9718 (OUTLIER) cc_final: 0.9510 (p) REVERT: C 180 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7882 (pp30) REVERT: C 185 ASP cc_start: 0.8838 (m-30) cc_final: 0.8317 (t0) REVERT: C 212 MET cc_start: 0.9302 (mpp) cc_final: 0.9083 (mpp) REVERT: C 335 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8486 (tp30) REVERT: C 369 ASP cc_start: 0.8664 (t0) cc_final: 0.8282 (t0) REVERT: D 50 LEU cc_start: 0.8806 (pt) cc_final: 0.8521 (tp) REVERT: D 74 MET cc_start: 0.8544 (ptp) cc_final: 0.8234 (ptt) REVERT: D 128 LYS cc_start: 0.9029 (pmtt) cc_final: 0.8643 (pmtt) REVERT: D 186 MET cc_start: 0.8966 (tpt) cc_final: 0.8719 (OUTLIER) REVERT: D 203 LEU cc_start: 0.9545 (mt) cc_final: 0.9320 (mm) REVERT: D 253 TYR cc_start: 0.8996 (m-80) cc_final: 0.8787 (m-80) REVERT: D 291 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8845 (tpt) REVERT: D 381 HIS cc_start: 0.5635 (p-80) cc_final: 0.5021 (t-90) REVERT: D 418 THR cc_start: 0.9241 (m) cc_final: 0.9025 (m) outliers start: 31 outliers final: 22 residues processed: 199 average time/residue: 0.9575 time to fit residues: 210.4898 Evaluate side-chains 202 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 310 THR 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 399 LEU Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain X residue 447 LEU 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 335 GLU 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 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 35 MET 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 ************** Weight determination summary: number of chunks: 145 random chunks: chunk 41 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.097275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072885 restraints weight = 27144.361| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.31 r_work: 0.3007 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 11529 Z= 0.250 Angle : 0.784 10.775 15769 Z= 0.385 Chirality : 0.049 0.442 1891 Planarity : 0.005 0.058 1982 Dihedral : 4.504 23.261 1602 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.46 % Allowed : 21.85 % Favored : 75.70 % 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: 1.22 (0.23), residues: 1453 helix: 2.04 (0.18), residues: 802 sheet: -0.48 (0.43), residues: 134 loop : -0.80 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP X 317 HIS 0.004 0.001 HIS E 102 PHE 0.016 0.002 PHE C 160 TYR 0.014 0.002 TYR C 207 ARG 0.011 0.001 ARG C 151 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 688) hydrogen bonds : angle 4.41917 ( 2004) covalent geometry : bond 0.00571 (11529) covalent geometry : angle 0.78444 (15769) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9060.56 seconds wall clock time: 164 minutes 49.75 seconds (9889.75 seconds total)