Starting phenix.real_space_refine on Fri Mar 14 03:00:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xwr_10636/03_2025/6xwr_10636.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xwr_10636/03_2025/6xwr_10636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xwr_10636/03_2025/6xwr_10636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xwr_10636/03_2025/6xwr_10636.map" model { file = "/net/cci-nas-00/data/ceres_data/6xwr_10636/03_2025/6xwr_10636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xwr_10636/03_2025/6xwr_10636.cif" } resolution = 3.22 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= 0.021 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 48 5.16 5 C 6309 2.51 5 N 1551 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9564 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3189 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Conformer: "B" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} bond proxies already assigned to first conformer: 3225 Chain: "B" Number of atoms: 3187 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Conformer: "B" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} bond proxies already assigned to first conformer: 3227 Chain: "C" Number of atoms: 3188 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Conformer: "B" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} bond proxies already assigned to first conformer: 3225 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 8 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 8 " occ=0.50 residue: pdb=" N ALYS B 86 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 86 " occ=0.50 residue: pdb=" N AHIS C 334 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 334 " occ=0.50 Time building chain proxies: 10.21, per 1000 atoms: 1.07 Number of scatterers: 9564 At special positions: 0 Unit cell: (82.984, 102.212, 116.38, 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 48 16.00 O 1656 8.00 N 1551 7.00 C 6309 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: 2.53 Conformation dependent library (CDL) restraints added in 2.4 seconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 removed outlier: 3.541A pdb=" N TYR A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 36 Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.907A pdb=" N GLY A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 75 Processing helix chain 'A' and resid 81 through 110 removed outlier: 3.813A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 152 through 172 removed outlier: 3.787A pdb=" N VAL A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 222 Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 226 through 255 removed outlier: 3.529A pdb=" N ALA A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 267 Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.615A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 removed outlier: 4.109A pdb=" N THR A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.627A pdb=" N GLY A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 350 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 360 through 374 removed outlier: 3.507A pdb=" N GLY A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 420 removed outlier: 3.813A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ALA A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLY A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'B' and resid 13 through 35 Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 45 through 59 removed outlier: 3.740A pdb=" N GLY B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 75 removed outlier: 3.761A pdb=" N ILE B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 109 removed outlier: 4.056A pdb=" N ALYS B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE B 109 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.528A pdb=" N THR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 152 through 171 removed outlier: 3.762A pdb=" N VAL B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 222 removed outlier: 3.739A pdb=" N GLN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Proline residue: B 208 - end of helix removed outlier: 3.837A pdb=" N PHE B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 257 removed outlier: 3.702A pdb=" N VAL B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 278 removed outlier: 5.672A pdb=" N ASP B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 removed outlier: 3.891A pdb=" N GLU B 293 " --> pdb=" O ARG B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.842A pdb=" N VAL B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 327 " --> pdb=" O VAL B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 348 Processing helix chain 'B' and resid 360 through 373 removed outlier: 3.530A pdb=" N SER B 372 " --> pdb=" O MET B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 393 removed outlier: 3.712A pdb=" N LEU B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 402 removed outlier: 4.290A pdb=" N GLY B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 420 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 16 through 34 Processing helix chain 'C' and resid 37 through 45 Processing helix chain 'C' and resid 45 through 76 removed outlier: 3.938A pdb=" N GLY C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N MET C 61 " --> pdb=" O LYS C 57 " (cutoff:3.500A) Proline residue: C 62 - end of helix Processing helix chain 'C' and resid 81 through 108 removed outlier: 3.882A pdb=" N VAL C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 153 through 171 Processing helix chain 'C' and resid 175 through 223 Proline residue: C 208 - end of helix removed outlier: 4.156A pdb=" N GLN C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 236 through 255 removed outlier: 4.593A pdb=" N PHE C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 278 removed outlier: 5.742A pdb=" N ASP C 269 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA C 270 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 294 removed outlier: 3.649A pdb=" N GLU C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 313 removed outlier: 5.347A pdb=" N PHE C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 306 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Proline residue: C 307 - end of helix removed outlier: 3.937A pdb=" N THR C 311 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 removed outlier: 4.229A pdb=" N GLN C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 325 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 351 removed outlier: 3.550A pdb=" N VAL C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 removed outlier: 3.590A pdb=" N ALA C 361 " --> pdb=" O GLY C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 374 removed outlier: 3.771A pdb=" N ALA C 367 " --> pdb=" O ALA C 363 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 393 removed outlier: 3.594A pdb=" N LEU C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 420 removed outlier: 4.504A pdb=" N GLY C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N MET C 403 " --> pdb=" O MET C 399 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 428 removed outlier: 3.537A pdb=" N LYS C 427 " --> pdb=" O ASP C 424 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 2086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 2.82 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: 2975 1.34 - 1.46: 1451 1.46 - 1.57: 5223 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 9745 Sorted by residual: bond pdb=" CG LEU C 68 " pdb=" CD1 LEU C 68 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.76e+00 bond pdb=" C ILE A 75 " pdb=" N SER A 76 " ideal model delta sigma weight residual 1.332 1.313 0.018 1.21e-02 6.83e+03 2.32e+00 bond pdb=" CB THR C 168 " pdb=" CG2 THR C 168 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.85e+00 bond pdb=" CB TRP A 20 " pdb=" CG TRP A 20 " ideal model delta sigma weight residual 1.498 1.456 0.042 3.10e-02 1.04e+03 1.82e+00 bond pdb=" CB VAL A 200 " pdb=" CG2 VAL A 200 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.80e+00 ... (remaining 9740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 12695 1.59 - 3.18: 466 3.18 - 4.77: 77 4.77 - 6.36: 25 6.36 - 7.95: 5 Bond angle restraints: 13268 Sorted by residual: angle pdb=" N GLY C 235 " pdb=" CA GLY C 235 " pdb=" C GLY C 235 " ideal model delta sigma weight residual 114.69 109.10 5.59 1.19e+00 7.06e-01 2.21e+01 angle pdb=" C VAL A 246 " pdb=" N ILE A 247 " pdb=" CA ILE A 247 " ideal model delta sigma weight residual 122.97 119.16 3.81 9.80e-01 1.04e+00 1.51e+01 angle pdb=" N ILE B 301 " pdb=" CA ILE B 301 " pdb=" C ILE B 301 " ideal model delta sigma weight residual 111.48 108.67 2.81 9.40e-01 1.13e+00 8.92e+00 angle pdb=" N THR B 378 " pdb=" CA THR B 378 " pdb=" C THR B 378 " ideal model delta sigma weight residual 109.81 116.29 -6.48 2.21e+00 2.05e-01 8.61e+00 angle pdb=" N ALA C 207 " pdb=" CA ALA C 207 " pdb=" C ALA C 207 " ideal model delta sigma weight residual 109.81 116.17 -6.36 2.21e+00 2.05e-01 8.27e+00 ... (remaining 13263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5287 18.00 - 36.00: 400 36.00 - 53.99: 48 53.99 - 71.99: 6 71.99 - 89.99: 6 Dihedral angle restraints: 5747 sinusoidal: 2132 harmonic: 3615 Sorted by residual: dihedral pdb=" CA LEU B 342 " pdb=" C LEU B 342 " pdb=" N VAL B 343 " pdb=" CA VAL B 343 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEU C 59 " pdb=" C LEU C 59 " pdb=" N VAL C 60 " pdb=" CA VAL C 60 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN C 110 " pdb=" C ASN C 110 " pdb=" N VAL C 111 " pdb=" CA VAL C 111 " ideal model delta harmonic sigma weight residual -180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 814 0.031 - 0.062: 585 0.062 - 0.094: 177 0.094 - 0.125: 61 0.125 - 0.156: 13 Chirality restraints: 1650 Sorted by residual: chirality pdb=" CA THR B 378 " pdb=" N THR B 378 " pdb=" C THR B 378 " pdb=" CB THR B 378 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CB VAL B 105 " pdb=" CA VAL B 105 " pdb=" CG1 VAL B 105 " pdb=" CG2 VAL B 105 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA PRO B 47 " pdb=" N PRO B 47 " pdb=" C PRO B 47 " pdb=" CB PRO B 47 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1647 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 64 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C VAL A 64 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 64 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 65 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 245 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C ILE A 245 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE A 245 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 246 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 381 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO B 382 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 382 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 382 " 0.027 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 167 2.68 - 3.23: 10503 3.23 - 3.79: 15341 3.79 - 4.34: 20170 4.34 - 4.90: 33962 Nonbonded interactions: 80143 Sorted by model distance: nonbonded pdb=" OG1 THR C 305 " pdb=" OG1 THR C 413 " model vdw 2.122 3.040 nonbonded pdb=" O THR A 283 " pdb=" OG1 THR A 287 " model vdw 2.183 3.040 nonbonded pdb=" OH TYR A 249 " pdb=" OD2 ASP A 315 " model vdw 2.197 3.040 nonbonded pdb=" O THR A 378 " pdb=" OG SER A 381 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR C 249 " pdb=" OD2 ASP C 315 " model vdw 2.224 3.040 ... (remaining 80138 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 'A' and (resid 5 through 7 or resid 9 through 85 or resid 87 through 333 \ or resid 335 through 430)) selection = (chain 'B' and (resid 5 through 7 or resid 9 through 85 or resid 87 through 333 \ or resid 335 through 430)) selection = (chain 'C' and (resid 5 through 7 or resid 9 through 85 or resid 87 through 333 \ or resid 335 through 430)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.130 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 0.055 9745 Z= 0.539 Angle : 0.754 7.950 13268 Z= 0.406 Chirality : 0.046 0.156 1650 Planarity : 0.005 0.049 1632 Dihedral : 12.807 89.991 3455 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % 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: -2.71 (0.21), residues: 1281 helix: -1.38 (0.15), residues: 997 sheet: None (None), residues: 0 loop : -2.70 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 20 HIS 0.002 0.001 HIS C 34 PHE 0.020 0.002 PHE A 302 TYR 0.016 0.002 TYR A 320 ARG 0.003 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8686 (mmt) cc_final: 0.8448 (mmm) REVERT: A 393 ILE cc_start: 0.9333 (tp) cc_final: 0.8994 (tp) REVERT: B 259 ASP cc_start: 0.8312 (t0) cc_final: 0.8105 (t0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2170 time to fit residues: 40.1969 Evaluate side-chains 95 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 138 ASN B 321 GLN B 340 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.079134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.058649 restraints weight = 82985.881| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 5.63 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9745 Z= 0.221 Angle : 0.619 7.853 13268 Z= 0.312 Chirality : 0.041 0.166 1650 Planarity : 0.005 0.053 1632 Dihedral : 4.338 21.970 1369 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.60 % Allowed : 9.65 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.76 (0.23), residues: 1281 helix: -0.05 (0.16), residues: 1025 sheet: None (None), residues: 0 loop : -1.89 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 20 HIS 0.003 0.001 HIS A 34 PHE 0.024 0.001 PHE A 302 TYR 0.013 0.001 TYR B 320 ARG 0.004 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ASN cc_start: 0.9344 (m110) cc_final: 0.9082 (m110) REVERT: A 219 MET cc_start: 0.9022 (mmm) cc_final: 0.8808 (mmm) REVERT: A 321 GLN cc_start: 0.8138 (mt0) cc_final: 0.7930 (mt0) REVERT: A 365 MET cc_start: 0.9323 (ttm) cc_final: 0.9009 (ttt) REVERT: A 393 ILE cc_start: 0.9112 (tp) cc_final: 0.8696 (tp) REVERT: B 46 LYS cc_start: 0.8713 (tptt) cc_final: 0.8451 (tptp) REVERT: B 50 ASP cc_start: 0.8598 (m-30) cc_final: 0.8214 (m-30) REVERT: B 150 LYS cc_start: 0.9501 (mtmm) cc_final: 0.9158 (mtmm) REVERT: B 259 ASP cc_start: 0.8642 (t0) cc_final: 0.8138 (t0) REVERT: B 295 MET cc_start: 0.8440 (mmm) cc_final: 0.8138 (mmt) REVERT: B 424 ASP cc_start: 0.8813 (t0) cc_final: 0.7827 (p0) REVERT: C 340 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7634 (pm20) REVERT: C 403 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7179 (tpp) outliers start: 5 outliers final: 1 residues processed: 129 average time/residue: 0.1864 time to fit residues: 35.5304 Evaluate side-chains 115 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 403 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 121 optimal weight: 0.0770 chunk 118 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.079579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.058884 restraints weight = 91265.557| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 5.90 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9745 Z= 0.213 Angle : 0.595 7.675 13268 Z= 0.299 Chirality : 0.041 0.185 1650 Planarity : 0.004 0.054 1632 Dihedral : 4.140 23.731 1369 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.00 % Allowed : 12.34 % Favored : 86.67 % 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: -0.04 (0.24), residues: 1281 helix: 0.44 (0.17), residues: 1039 sheet: None (None), residues: 0 loop : -1.72 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 20 HIS 0.003 0.001 HIS B 334 PHE 0.020 0.001 PHE A 302 TYR 0.012 0.001 TYR B 320 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.9314 (ttm) cc_final: 0.8915 (ttm) REVERT: A 393 ILE cc_start: 0.9095 (tp) cc_final: 0.8671 (tp) REVERT: B 46 LYS cc_start: 0.8716 (tptt) cc_final: 0.8387 (tptp) REVERT: B 50 ASP cc_start: 0.8647 (m-30) cc_final: 0.8210 (m-30) REVERT: B 150 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.9011 (mtmm) REVERT: B 238 TYR cc_start: 0.8864 (m-80) cc_final: 0.8649 (m-80) REVERT: B 259 ASP cc_start: 0.8599 (t0) cc_final: 0.8258 (t0) REVERT: C 340 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: C 403 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7042 (tpp) outliers start: 9 outliers final: 4 residues processed: 124 average time/residue: 0.1776 time to fit residues: 33.2490 Evaluate side-chains 109 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 403 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 83 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 138 ASN ** B 334 HIS ** 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 = 0.3366 r_free = 0.3366 target = 0.080253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060069 restraints weight = 73632.835| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 5.35 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9745 Z= 0.195 Angle : 0.581 7.760 13268 Z= 0.292 Chirality : 0.040 0.141 1650 Planarity : 0.004 0.054 1632 Dihedral : 4.064 25.145 1369 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.90 % Allowed : 13.23 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.24), residues: 1281 helix: 0.77 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -1.47 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 20 HIS 0.004 0.001 HIS B 334 PHE 0.026 0.001 PHE B 242 TYR 0.014 0.001 TYR B 320 ARG 0.003 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.9128 (ttm) cc_final: 0.8781 (ttm) REVERT: A 393 ILE cc_start: 0.9082 (tp) cc_final: 0.8681 (tp) REVERT: B 46 LYS cc_start: 0.8763 (tptt) cc_final: 0.8445 (tptp) REVERT: B 50 ASP cc_start: 0.8750 (m-30) cc_final: 0.8327 (m-30) REVERT: B 150 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.8982 (mtmm) REVERT: B 219 MET cc_start: 0.9446 (tpp) cc_final: 0.9229 (mmp) REVERT: B 238 TYR cc_start: 0.8846 (m-80) cc_final: 0.8574 (m-80) REVERT: B 259 ASP cc_start: 0.8609 (t0) cc_final: 0.8253 (t0) REVERT: C 314 MET cc_start: 0.8538 (mtp) cc_final: 0.8132 (mtm) REVERT: C 340 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: C 403 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7005 (tpp) outliers start: 8 outliers final: 4 residues processed: 114 average time/residue: 0.2385 time to fit residues: 40.7372 Evaluate side-chains 110 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 403 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9036 > 50: distance: 44 - 68: 31.820 distance: 63 - 68: 31.154 distance: 64 - 90: 36.432 distance: 68 - 69: 18.449 distance: 69 - 70: 33.303 distance: 69 - 72: 41.586 distance: 70 - 71: 30.970 distance: 70 - 75: 32.530 distance: 71 - 101: 49.261 distance: 72 - 73: 20.229 distance: 72 - 74: 37.055 distance: 75 - 76: 22.712 distance: 76 - 77: 34.408 distance: 76 - 79: 41.735 distance: 77 - 78: 29.414 distance: 77 - 82: 32.883 distance: 79 - 80: 30.186 distance: 82 - 83: 13.179 distance: 83 - 86: 19.231 distance: 84 - 85: 37.905 distance: 85 - 113: 41.256 distance: 86 - 87: 23.353 distance: 87 - 88: 5.355 distance: 87 - 89: 39.674 distance: 91 - 92: 41.833 distance: 91 - 94: 30.096 distance: 92 - 93: 9.457 distance: 92 - 101: 25.016 distance: 93 - 121: 41.361 distance: 94 - 95: 40.055 distance: 95 - 96: 9.936 distance: 95 - 97: 17.030 distance: 97 - 99: 8.684 distance: 98 - 100: 14.809 distance: 99 - 100: 23.745 distance: 101 - 102: 25.316 distance: 102 - 103: 38.513 distance: 102 - 105: 23.940 distance: 103 - 104: 6.785 distance: 103 - 108: 6.999 distance: 104 - 126: 43.153 distance: 105 - 106: 32.642 distance: 105 - 107: 12.995 distance: 108 - 109: 5.401 distance: 111 - 134: 44.231 distance: 113 - 114: 5.923 distance: 114 - 115: 34.465 distance: 114 - 117: 8.794 distance: 115 - 116: 38.361 distance: 115 - 121: 10.469 distance: 118 - 119: 4.734 distance: 121 - 122: 19.801 distance: 122 - 123: 35.242 distance: 122 - 125: 31.173 distance: 123 - 126: 45.202 distance: 126 - 127: 30.015 distance: 127 - 128: 34.264 distance: 127 - 130: 24.106 distance: 128 - 129: 63.088 distance: 128 - 134: 22.570 distance: 130 - 131: 41.164 distance: 130 - 132: 34.102 distance: 131 - 133: 6.938 distance: 134 - 135: 18.337 distance: 135 - 136: 63.139 distance: 136 - 137: 12.928 distance: 136 - 138: 28.753 distance: 136 - 147: 28.729