Starting phenix.real_space_refine on Wed Sep 25 04:27:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwr_10636/09_2024/6xwr_10636.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwr_10636/09_2024/6xwr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwr_10636/09_2024/6xwr_10636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwr_10636/09_2024/6xwr_10636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwr_10636/09_2024/6xwr_10636.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwr_10636/09_2024/6xwr_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-5461/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: 10.45, per 1000 atoms: 1.09 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: 2.50 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: 0.88 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: 2.91 Time building geometry restraints manager: 2.86 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: 1.080 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.780 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.900 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.967 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: 0.2028 time to fit residues: 37.3120 Evaluate side-chains 95 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1596 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 fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 393 ILE cc_start: 0.9206 (tp) cc_final: 0.8896 (tp) REVERT: B 50 ASP cc_start: 0.7811 (m-30) cc_final: 0.7501 (m-30) REVERT: B 259 ASP cc_start: 0.8319 (t0) cc_final: 0.7899 (t0) REVERT: B 295 MET cc_start: 0.8204 (mmm) cc_final: 0.7889 (mmt) REVERT: B 424 ASP cc_start: 0.8541 (t0) cc_final: 0.8304 (p0) outliers start: 5 outliers final: 1 residues processed: 129 average time/residue: 0.1838 time to fit residues: 34.9933 Evaluate side-chains 110 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 91 optimal weight: 0.0470 overall best weight: 1.3480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 138 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9745 Z= 0.235 Angle : 0.605 7.611 13268 Z= 0.305 Chirality : 0.041 0.185 1650 Planarity : 0.004 0.054 1632 Dihedral : 4.187 23.711 1369 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.80 % Allowed : 12.74 % Favored : 86.47 % 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: 1032 sheet: None (None), residues: 0 loop : -1.67 (0.40), residues: 249 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 0.013 0.001 TYR A 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 121 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 393 ILE cc_start: 0.9220 (tp) cc_final: 0.8901 (tp) REVERT: B 259 ASP cc_start: 0.8284 (t0) cc_final: 0.8018 (t0) outliers start: 7 outliers final: 5 residues processed: 118 average time/residue: 0.1731 time to fit residues: 31.0060 Evaluate side-chains 104 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 323 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.0570 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 0.0970 chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.1298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 138 ASN B 134 GLN B 138 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9745 Z= 0.218 Angle : 0.589 7.732 13268 Z= 0.297 Chirality : 0.041 0.145 1650 Planarity : 0.004 0.054 1632 Dihedral : 4.127 25.061 1369 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.60 % Allowed : 14.03 % Favored : 85.37 % 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: 0.39 (0.24), residues: 1281 helix: 0.73 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -1.51 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 20 HIS 0.004 0.001 HIS B 334 PHE 0.023 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 116 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 393 ILE cc_start: 0.9197 (tp) cc_final: 0.8879 (tp) REVERT: B 259 ASP cc_start: 0.8270 (t0) cc_final: 0.7987 (t0) outliers start: 5 outliers final: 4 residues processed: 113 average time/residue: 0.1748 time to fit residues: 29.8764 Evaluate side-chains 105 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 323 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9745 Z= 0.229 Angle : 0.614 10.878 13268 Z= 0.306 Chirality : 0.041 0.176 1650 Planarity : 0.004 0.055 1632 Dihedral : 4.099 26.648 1369 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.60 % Allowed : 15.62 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1281 helix: 0.88 (0.17), residues: 1035 sheet: None (None), residues: 0 loop : -1.37 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 20 HIS 0.003 0.001 HIS B 334 PHE 0.018 0.001 PHE A 302 TYR 0.015 0.001 TYR A 320 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 5 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 108 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.001 Fit side-chains REVERT: A 219 MET cc_start: 0.8239 (mmm) cc_final: 0.7852 (mmm) REVERT: B 150 LYS cc_start: 0.8829 (mtmm) cc_final: 0.8488 (mtmm) REVERT: B 295 MET cc_start: 0.8353 (mmm) cc_final: 0.8065 (mmp) outliers start: 5 outliers final: 4 residues processed: 106 average time/residue: 0.1666 time to fit residues: 27.2661 Evaluate side-chains 108 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 323 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 30 optimal weight: 0.0870 chunk 121 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 138 ASN B 321 GLN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9745 Z= 0.216 Angle : 0.605 9.161 13268 Z= 0.301 Chirality : 0.041 0.200 1650 Planarity : 0.004 0.053 1632 Dihedral : 4.072 26.064 1369 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.90 % Allowed : 16.02 % Favored : 83.08 % 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: 0.82 (0.24), residues: 1281 helix: 1.02 (0.17), residues: 1033 sheet: None (None), residues: 0 loop : -1.25 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 20 HIS 0.003 0.001 HIS B 334 PHE 0.020 0.001 PHE B 242 TYR 0.014 0.001 TYR A 320 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 6 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 110 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.044 Fit side-chains REVERT: A 219 MET cc_start: 0.8211 (mmm) cc_final: 0.7850 (mmm) REVERT: C 314 MET cc_start: 0.7626 (mtm) cc_final: 0.7298 (mtm) outliers start: 8 outliers final: 4 residues processed: 104 average time/residue: 0.1811 time to fit residues: 28.8238 Evaluate side-chains 101 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 323 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 89 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 0.0010 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9745 Z= 0.179 Angle : 0.610 9.994 13268 Z= 0.299 Chirality : 0.041 0.369 1650 Planarity : 0.004 0.053 1632 Dihedral : 4.015 27.182 1369 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.60 % Allowed : 16.72 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.24), residues: 1281 helix: 1.12 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -1.28 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 20 HIS 0.003 0.001 HIS B 334 PHE 0.016 0.001 PHE B 302 TYR 0.014 0.001 TYR A 320 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 7 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 122 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.052 Fit side-chains REVERT: B 365 MET cc_start: 0.8391 (tpp) cc_final: 0.7937 (tpp) outliers start: 5 outliers final: 2 residues processed: 119 average time/residue: 0.1612 time to fit residues: 30.1680 Evaluate side-chains 110 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 323 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 0.0020 chunk 95 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 138 ASN B 134 GLN B 138 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9745 Z= 0.185 Angle : 0.627 12.964 13268 Z= 0.303 Chirality : 0.041 0.369 1650 Planarity : 0.004 0.051 1632 Dihedral : 4.003 27.030 1369 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.40 % Allowed : 17.91 % Favored : 81.69 % 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: 1.01 (0.24), residues: 1281 helix: 1.14 (0.17), residues: 1029 sheet: None (None), residues: 0 loop : -1.09 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 20 HIS 0.003 0.001 HIS B 334 PHE 0.020 0.001 PHE B 242 TYR 0.015 0.001 TYR A 320 ARG 0.002 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 8 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 112 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 259 ASP cc_start: 0.8256 (t0) cc_final: 0.7925 (t0) REVERT: B 365 MET cc_start: 0.8351 (tpp) cc_final: 0.7938 (tpp) REVERT: C 314 MET cc_start: 0.7556 (mtm) cc_final: 0.7344 (mtm) outliers start: 3 outliers final: 2 residues processed: 111 average time/residue: 0.1703 time to fit residues: 28.7967 Evaluate side-chains 110 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain C residue 20 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 119 optimal weight: 0.0870 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 321 GLN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9745 Z= 0.192 Angle : 0.634 12.747 13268 Z= 0.305 Chirality : 0.042 0.391 1650 Planarity : 0.004 0.051 1632 Dihedral : 3.991 27.411 1369 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.40 % Allowed : 18.21 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1281 helix: 1.16 (0.17), residues: 1035 sheet: None (None), residues: 0 loop : -1.03 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 20 HIS 0.003 0.001 HIS B 334 PHE 0.016 0.001 PHE A 302 TYR 0.019 0.001 TYR A 320 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 9 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 112 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: B 365 MET cc_start: 0.8321 (tpp) cc_final: 0.7891 (tpp) REVERT: C 314 MET cc_start: 0.7601 (mtm) cc_final: 0.7386 (mtm) outliers start: 3 outliers final: 2 residues processed: 111 average time/residue: 0.1792 time to fit residues: 30.2675 Evaluate side-chains 112 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain C residue 20 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 125 optimal weight: 0.0980 chunk 115 optimal weight: 0.8980 chunk 99 optimal weight: 0.0370 chunk 10 optimal weight: 0.3980 chunk 77 optimal weight: 0.0050 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.2072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9745 Z= 0.172 Angle : 0.638 12.733 13268 Z= 0.308 Chirality : 0.041 0.401 1650 Planarity : 0.004 0.051 1632 Dihedral : 3.978 27.540 1369 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.50 % Allowed : 18.41 % Favored : 81.09 % 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: 1.14 (0.24), residues: 1281 helix: 1.20 (0.17), residues: 1033 sheet: None (None), residues: 0 loop : -0.90 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 20 HIS 0.003 0.001 HIS B 334 PHE 0.018 0.001 PHE B 242 TYR 0.019 0.001 TYR A 320 ARG 0.003 0.000 ARG B 289 ********************** REFINEMENT MACRO_CYCLE 10 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 124 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: B 219 MET cc_start: 0.8337 (mmp) cc_final: 0.8033 (mmp) REVERT: B 259 ASP cc_start: 0.8222 (t0) cc_final: 0.7910 (t0) REVERT: C 314 MET cc_start: 0.7523 (mtm) cc_final: 0.7304 (mtm) outliers start: 4 outliers final: 4 residues processed: 121 average time/residue: 0.1745 time to fit residues: 31.9696 Evaluate side-chains 123 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain C residue 20 TRP Chi-restraints excluded: chain C residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.1980 chunk 92 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.062856 restraints weight = 78557.845| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 5.66 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 9745 Z= 0.243 Angle : 0.949 59.196 13268 Z= 0.515 Chirality : 0.048 0.924 1650 Planarity : 0.004 0.051 1632 Dihedral : 3.971 27.520 1369 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.80 % Allowed : 18.21 % Favored : 81.00 % Cbeta Deviations : 0.09 % 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: 1.12 (0.24), residues: 1281 helix: 1.18 (0.17), residues: 1033 sheet: None (None), residues: 0 loop : -0.91 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 428 HIS 0.003 0.001 HIS B 334 PHE 0.016 0.001 PHE B 302 TYR 0.019 0.001 TYR A 320 ARG 0.003 0.000 ARG B 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1893.25 seconds wall clock time: 34 minutes 38.63 seconds (2078.63 seconds total)