Starting phenix.real_space_refine on Tue Feb 13 12:19:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp3_30143/02_2024/7bp3_30143.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp3_30143/02_2024/7bp3_30143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp3_30143/02_2024/7bp3_30143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp3_30143/02_2024/7bp3_30143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp3_30143/02_2024/7bp3_30143.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp3_30143/02_2024/7bp3_30143.pdb" } resolution = 3.8 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= 0.021 sd= 0.104 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 42 5.16 5 C 4054 2.51 5 N 960 2.21 5 O 1024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6080 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3040 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3040 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.91, per 1000 atoms: 0.64 Number of scatterers: 6080 At special positions: 0 Unit cell: (101.905, 77.0505, 86.164, 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 42 16.00 O 1024 8.00 N 960 7.00 C 4054 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 - 3.50 Amino acid : False - 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: 2.35 Conformation dependent library (CDL) restraints added in 1.4 seconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 89.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 19 through 52 removed outlier: 4.110A pdb=" N TYR A 34 " --> pdb=" O ILE A 30 " (cutoff:3.500A) Proline residue: A 37 - end of helix removed outlier: 5.117A pdb=" N VAL A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 81 removed outlier: 3.879A pdb=" N ILE A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY A 73 " --> pdb=" O MET A 69 " (cutoff:3.500A) Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 84 through 106 removed outlier: 3.918A pdb=" N VAL A 88 " --> pdb=" O GLY A 84 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 139 Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.748A pdb=" N ASN A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 173 through 193 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 246 through 258 removed outlier: 3.556A pdb=" N GLY A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 removed outlier: 4.443A pdb=" N ILE A 265 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.511A pdb=" N ALA A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 4.577A pdb=" N ALA A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 295 removed outlier: 4.055A pdb=" N ALA A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 307 removed outlier: 4.211A pdb=" N ALA A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 312 through 328 removed outlier: 3.945A pdb=" N PHE A 316 " --> pdb=" O ARG A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 358 removed outlier: 3.776A pdb=" N LEU A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 367 Processing helix chain 'A' and resid 370 through 383 removed outlier: 3.503A pdb=" N VAL A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLY A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.641A pdb=" N LEU A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 401 removed outlier: 3.779A pdb=" N LYS A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 440 removed outlier: 3.574A pdb=" N MET A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 414 " --> pdb=" O CYS A 410 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 424 " --> pdb=" O TRP A 420 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 52 removed outlier: 4.110A pdb=" N TYR B 34 " --> pdb=" O ILE B 30 " (cutoff:3.500A) Proline residue: B 37 - end of helix removed outlier: 5.118A pdb=" N VAL B 42 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 81 removed outlier: 3.878A pdb=" N ILE B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY B 73 " --> pdb=" O MET B 69 " (cutoff:3.500A) Proline residue: B 74 - end of helix Processing helix chain 'B' and resid 84 through 106 removed outlier: 3.917A pdb=" N VAL B 88 " --> pdb=" O GLY B 84 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 139 Proline residue: B 130 - end of helix Processing helix chain 'B' and resid 143 through 154 removed outlier: 3.746A pdb=" N ASN B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 161 through 170 Processing helix chain 'B' and resid 173 through 193 Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 246 through 258 removed outlier: 3.555A pdb=" N GLY B 253 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 267 removed outlier: 4.442A pdb=" N ILE B 265 " --> pdb=" O PHE B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 276 removed outlier: 3.510A pdb=" N ALA B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 283 removed outlier: 4.578A pdb=" N ALA B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 295 removed outlier: 4.057A pdb=" N ALA B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 307 removed outlier: 4.210A pdb=" N ALA B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 312 through 328 removed outlier: 3.946A pdb=" N PHE B 316 " --> pdb=" O ARG B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 358 removed outlier: 3.777A pdb=" N LEU B 340 " --> pdb=" O ASP B 336 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 367 Processing helix chain 'B' and resid 370 through 383 removed outlier: 3.503A pdb=" N VAL B 375 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLY B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.641A pdb=" N LEU B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 401 removed outlier: 3.778A pdb=" N LYS B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 440 removed outlier: 3.575A pdb=" N MET B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL B 414 " --> pdb=" O CYS B 410 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 424 " --> pdb=" O TRP B 420 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG B 430 " --> pdb=" O ALA B 426 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1266 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: 2.19 Time building geometry restraints manager: 2.58 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: 1783 1.34 - 1.47: 1722 1.47 - 1.59: 2669 1.59 - 1.71: 0 1.71 - 1.84: 70 Bond restraints: 6244 Sorted by residual: bond pdb=" CB TYR B 167 " pdb=" CG TYR B 167 " ideal model delta sigma weight residual 1.512 1.460 0.052 2.20e-02 2.07e+03 5.49e+00 bond pdb=" CB TYR A 167 " pdb=" CG TYR A 167 " ideal model delta sigma weight residual 1.512 1.461 0.051 2.20e-02 2.07e+03 5.44e+00 bond pdb=" C SER A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.339 1.415 -0.076 3.40e-02 8.65e+02 5.01e+00 bond pdb=" C SER B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.339 1.415 -0.076 3.40e-02 8.65e+02 4.99e+00 bond pdb=" CB TRP A 174 " pdb=" CG TRP A 174 " ideal model delta sigma weight residual 1.498 1.430 0.068 3.10e-02 1.04e+03 4.88e+00 ... (remaining 6239 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.38: 178 106.38 - 113.53: 3257 113.53 - 120.68: 3247 120.68 - 127.84: 1732 127.84 - 134.99: 56 Bond angle restraints: 8470 Sorted by residual: angle pdb=" CA PHE A 284 " pdb=" CB PHE A 284 " pdb=" CG PHE A 284 " ideal model delta sigma weight residual 113.80 117.73 -3.93 1.00e+00 1.00e+00 1.55e+01 angle pdb=" CA PHE B 284 " pdb=" CB PHE B 284 " pdb=" CG PHE B 284 " ideal model delta sigma weight residual 113.80 117.69 -3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" N PHE B 36 " pdb=" CA PHE B 36 " pdb=" C PHE B 36 " ideal model delta sigma weight residual 112.55 117.72 -5.17 1.35e+00 5.49e-01 1.47e+01 angle pdb=" N PHE A 36 " pdb=" CA PHE A 36 " pdb=" C PHE A 36 " ideal model delta sigma weight residual 112.55 117.72 -5.17 1.35e+00 5.49e-01 1.47e+01 angle pdb=" CB LEU A 168 " pdb=" CG LEU A 168 " pdb=" CD2 LEU A 168 " ideal model delta sigma weight residual 110.70 99.32 11.38 3.00e+00 1.11e-01 1.44e+01 ... (remaining 8465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.48: 3003 15.48 - 30.96: 447 30.96 - 46.45: 122 46.45 - 61.93: 18 61.93 - 77.41: 8 Dihedral angle restraints: 3598 sinusoidal: 1342 harmonic: 2256 Sorted by residual: dihedral pdb=" CA ASN B 170 " pdb=" C ASN B 170 " pdb=" N THR B 171 " pdb=" CA THR B 171 " ideal model delta harmonic sigma weight residual 180.00 150.32 29.68 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA ASN A 170 " pdb=" C ASN A 170 " pdb=" N THR A 171 " pdb=" CA THR A 171 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA PRO B 155 " pdb=" C PRO B 155 " pdb=" N VAL B 156 " pdb=" CA VAL B 156 " ideal model delta harmonic sigma weight residual 180.00 156.27 23.73 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 3595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 515 0.038 - 0.076: 292 0.076 - 0.114: 90 0.114 - 0.152: 53 0.152 - 0.190: 10 Chirality restraints: 960 Sorted by residual: chirality pdb=" CA CYS A 331 " pdb=" N CYS A 331 " pdb=" C CYS A 331 " pdb=" CB CYS A 331 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.99e-01 chirality pdb=" CA CYS B 331 " pdb=" N CYS B 331 " pdb=" C CYS B 331 " pdb=" CB CYS B 331 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CA PHE B 36 " pdb=" N PHE B 36 " pdb=" C PHE B 36 " pdb=" CB PHE B 36 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 957 not shown) Planarity restraints: 1042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 284 " 0.036 2.00e-02 2.50e+03 2.70e-02 1.28e+01 pdb=" CG PHE B 284 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE B 284 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 284 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 284 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 284 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 284 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 284 " -0.036 2.00e-02 2.50e+03 2.68e-02 1.26e+01 pdb=" CG PHE A 284 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 284 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 284 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 284 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 284 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 284 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 331 " 0.052 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO A 332 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.043 5.00e-02 4.00e+02 ... (remaining 1039 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1444 2.77 - 3.30: 5739 3.30 - 3.83: 10425 3.83 - 4.37: 11498 4.37 - 4.90: 18879 Nonbonded interactions: 47985 Sorted by model distance: nonbonded pdb=" O SER A 281 " pdb=" OH TYR A 337 " model vdw 2.235 2.440 nonbonded pdb=" O SER B 281 " pdb=" OH TYR B 337 " model vdw 2.236 2.440 nonbonded pdb=" O ASP B 336 " pdb=" OG SER B 339 " model vdw 2.277 2.440 nonbonded pdb=" O ASP A 336 " pdb=" OG SER A 339 " model vdw 2.277 2.440 nonbonded pdb=" OG SER B 160 " pdb=" OG SER B 287 " model vdw 2.279 2.440 ... (remaining 47980 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.920 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: 3.200 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.040 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 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 : 0.007 0.076 6244 Z= 0.462 Angle : 1.051 11.380 8470 Z= 0.557 Chirality : 0.057 0.190 960 Planarity : 0.008 0.077 1042 Dihedral : 16.157 77.409 2166 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 12.81 % Favored : 87.19 % 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: -4.77 (0.22), residues: 780 helix: -2.93 (0.15), residues: 600 sheet: None (None), residues: 0 loop : -3.11 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 174 HIS 0.006 0.002 HIS A 328 PHE 0.060 0.002 PHE B 284 TYR 0.017 0.002 TYR A 271 ARG 0.005 0.001 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.6772 (p-80) cc_final: 0.5737 (m-70) REVERT: A 127 ASN cc_start: 0.9268 (t0) cc_final: 0.8963 (t0) REVERT: A 129 GLN cc_start: 0.8367 (tp-100) cc_final: 0.8159 (tp40) REVERT: A 143 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7612 (mtt180) REVERT: A 147 ASN cc_start: 0.7600 (m-40) cc_final: 0.7151 (m110) REVERT: A 151 MET cc_start: 0.7229 (mmp) cc_final: 0.6387 (mmt) REVERT: A 166 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8172 (mm-40) REVERT: A 169 PHE cc_start: 0.8186 (m-10) cc_final: 0.7759 (m-80) REVERT: A 175 LYS cc_start: 0.5891 (mptt) cc_final: 0.5529 (pttt) REVERT: A 274 ASP cc_start: 0.8702 (t0) cc_final: 0.8440 (t0) REVERT: A 284 PHE cc_start: 0.5441 (p90) cc_final: 0.5181 (p90) REVERT: A 289 MET cc_start: 0.8593 (ppp) cc_final: 0.7752 (ppp) REVERT: A 404 LYS cc_start: 0.7735 (mptt) cc_final: 0.7457 (mtpt) REVERT: A 430 ARG cc_start: 0.7978 (mtt-85) cc_final: 0.7224 (ptm160) REVERT: B 20 TRP cc_start: 0.8799 (p-90) cc_final: 0.8184 (p-90) REVERT: B 52 HIS cc_start: 0.7031 (p-80) cc_final: 0.6149 (m-70) REVERT: B 57 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7512 (mp0) REVERT: B 68 VAL cc_start: 0.9114 (t) cc_final: 0.8899 (p) REVERT: B 79 LEU cc_start: 0.8824 (tp) cc_final: 0.8562 (tp) REVERT: B 127 ASN cc_start: 0.9383 (t0) cc_final: 0.8684 (t0) REVERT: B 166 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8183 (mm-40) REVERT: B 184 LEU cc_start: 0.8655 (mp) cc_final: 0.8372 (mt) REVERT: B 241 LEU cc_start: 0.8100 (tp) cc_final: 0.7892 (tp) REVERT: B 242 PHE cc_start: 0.7886 (m-10) cc_final: 0.7040 (p90) REVERT: B 248 LEU cc_start: 0.8777 (tp) cc_final: 0.8558 (tp) REVERT: B 330 LEU cc_start: 0.7730 (mt) cc_final: 0.7455 (tt) REVERT: B 331 CYS cc_start: 0.7744 (p) cc_final: 0.7331 (p) REVERT: B 359 PHE cc_start: 0.8639 (m-80) cc_final: 0.8355 (m-10) REVERT: B 365 LEU cc_start: 0.8983 (mt) cc_final: 0.8542 (tt) REVERT: B 408 MET cc_start: 0.5932 (ttp) cc_final: 0.5422 (tmm) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1755 time to fit residues: 59.2961 Evaluate side-chains 169 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.0370 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 129 GLN A 166 GLN A 234 ASN A 254 ASN A 275 GLN A 305 ASN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN B 234 ASN B 244 HIS B 275 GLN B 305 ASN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6244 Z= 0.235 Angle : 0.743 10.651 8470 Z= 0.376 Chirality : 0.045 0.201 960 Planarity : 0.006 0.060 1042 Dihedral : 5.731 22.434 850 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.69 % Allowed : 20.62 % Favored : 74.69 % 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: -2.33 (0.28), residues: 780 helix: -0.96 (0.19), residues: 642 sheet: None (None), residues: 0 loop : -3.67 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 420 HIS 0.005 0.002 HIS B 328 PHE 0.047 0.002 PHE B 284 TYR 0.018 0.001 TYR B 343 ARG 0.003 0.000 ARG B 297 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 193 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8900 (t) cc_final: 0.8519 (t) REVERT: A 34 TYR cc_start: 0.8376 (t80) cc_final: 0.7992 (t80) REVERT: A 48 GLN cc_start: 0.7341 (tm-30) cc_final: 0.7129 (tm-30) REVERT: A 52 HIS cc_start: 0.6832 (p-80) cc_final: 0.5509 (m-70) REVERT: A 65 MET cc_start: 0.8572 (ttm) cc_final: 0.8334 (ttm) REVERT: A 127 ASN cc_start: 0.9305 (t0) cc_final: 0.9038 (t0) REVERT: A 129 GLN cc_start: 0.8498 (tp40) cc_final: 0.8060 (tp40) REVERT: A 151 MET cc_start: 0.7271 (mmp) cc_final: 0.6228 (mmt) REVERT: A 166 GLN cc_start: 0.8418 (mm110) cc_final: 0.8125 (mm110) REVERT: A 169 PHE cc_start: 0.8090 (m-10) cc_final: 0.7791 (m-80) REVERT: A 175 LYS cc_start: 0.5818 (mptt) cc_final: 0.5301 (pttt) REVERT: A 196 ARG cc_start: 0.5650 (mtt180) cc_final: 0.4738 (mmm160) REVERT: A 244 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7288 (t70) REVERT: A 274 ASP cc_start: 0.8705 (t0) cc_final: 0.8456 (t0) REVERT: A 289 MET cc_start: 0.8326 (ppp) cc_final: 0.7677 (tmm) REVERT: A 294 MET cc_start: 0.8984 (tmm) cc_final: 0.8668 (tmm) REVERT: A 404 LYS cc_start: 0.8020 (mptt) cc_final: 0.7483 (mtpt) REVERT: A 430 ARG cc_start: 0.7905 (mtt-85) cc_final: 0.7357 (tmt170) REVERT: B 52 HIS cc_start: 0.7058 (p-80) cc_final: 0.5963 (m-70) REVERT: B 68 VAL cc_start: 0.9060 (t) cc_final: 0.8836 (p) REVERT: B 120 THR cc_start: 0.8606 (m) cc_final: 0.8394 (t) REVERT: B 127 ASN cc_start: 0.9437 (t0) cc_final: 0.9229 (t0) REVERT: B 134 ILE cc_start: 0.9032 (mm) cc_final: 0.8827 (tp) REVERT: B 196 ARG cc_start: 0.5993 (ttt180) cc_final: 0.5024 (tpt170) REVERT: B 242 PHE cc_start: 0.7914 (m-10) cc_final: 0.6968 (p90) REVERT: B 248 LEU cc_start: 0.8558 (tp) cc_final: 0.8353 (tp) REVERT: B 279 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7989 (tm-30) REVERT: B 315 TYR cc_start: 0.8279 (m-10) cc_final: 0.7992 (m-10) REVERT: B 319 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.8146 (m-80) REVERT: B 330 LEU cc_start: 0.7697 (mt) cc_final: 0.7378 (tt) REVERT: B 392 LEU cc_start: 0.8250 (tp) cc_final: 0.7774 (mp) REVERT: B 408 MET cc_start: 0.6017 (ttp) cc_final: 0.5398 (tmm) outliers start: 30 outliers final: 14 residues processed: 208 average time/residue: 0.1526 time to fit residues: 43.1488 Evaluate side-chains 175 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 159 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 76 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6244 Z= 0.199 Angle : 0.711 10.535 8470 Z= 0.348 Chirality : 0.043 0.202 960 Planarity : 0.005 0.053 1042 Dihedral : 5.412 24.568 850 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.53 % Allowed : 22.50 % Favored : 72.97 % 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: -1.38 (0.29), residues: 780 helix: -0.17 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -3.95 (0.42), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 60 HIS 0.004 0.001 HIS A 328 PHE 0.046 0.002 PHE B 284 TYR 0.014 0.001 TYR B 140 ARG 0.003 0.000 ARG B 297 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 176 time to evaluate : 0.671 Fit side-chains REVERT: A 34 TYR cc_start: 0.8326 (t80) cc_final: 0.8053 (t80) REVERT: A 52 HIS cc_start: 0.6768 (p-80) cc_final: 0.5132 (m-70) REVERT: A 65 MET cc_start: 0.8561 (ttm) cc_final: 0.8272 (ttp) REVERT: A 69 MET cc_start: 0.7999 (tpp) cc_final: 0.7777 (tpt) REVERT: A 127 ASN cc_start: 0.9313 (t0) cc_final: 0.9069 (t0) REVERT: A 129 GLN cc_start: 0.8471 (tp40) cc_final: 0.7984 (tp40) REVERT: A 151 MET cc_start: 0.7210 (mmp) cc_final: 0.5930 (mmt) REVERT: A 169 PHE cc_start: 0.8045 (m-10) cc_final: 0.7716 (m-80) REVERT: A 175 LYS cc_start: 0.5789 (mptt) cc_final: 0.5250 (pttt) REVERT: A 196 ARG cc_start: 0.5317 (mtt180) cc_final: 0.4473 (mmm160) REVERT: A 244 HIS cc_start: 0.7727 (OUTLIER) cc_final: 0.7334 (t-90) REVERT: A 274 ASP cc_start: 0.8734 (t0) cc_final: 0.8478 (t0) REVERT: A 289 MET cc_start: 0.8264 (ppp) cc_final: 0.7736 (tmm) REVERT: A 312 ARG cc_start: 0.7644 (mmt180) cc_final: 0.6991 (mtt180) REVERT: A 404 LYS cc_start: 0.8026 (mptt) cc_final: 0.7493 (mtpt) REVERT: A 413 ILE cc_start: 0.8879 (tt) cc_final: 0.8668 (tt) REVERT: A 430 ARG cc_start: 0.7843 (mtt-85) cc_final: 0.7421 (tmt170) REVERT: A 431 LEU cc_start: 0.8843 (pp) cc_final: 0.8500 (mt) REVERT: B 52 HIS cc_start: 0.7096 (p-80) cc_final: 0.5866 (m-70) REVERT: B 127 ASN cc_start: 0.9429 (t0) cc_final: 0.8810 (t0) REVERT: B 196 ARG cc_start: 0.5838 (ttt180) cc_final: 0.5189 (tpp-160) REVERT: B 279 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7310 (tm-30) REVERT: B 315 TYR cc_start: 0.8248 (m-10) cc_final: 0.7987 (m-10) REVERT: B 322 MET cc_start: 0.7665 (tmm) cc_final: 0.7395 (tmm) REVERT: B 330 LEU cc_start: 0.7559 (mt) cc_final: 0.7348 (tp) REVERT: B 363 MET cc_start: 0.9042 (tpp) cc_final: 0.8545 (tpp) REVERT: B 408 MET cc_start: 0.5978 (ttp) cc_final: 0.5335 (tmm) outliers start: 29 outliers final: 15 residues processed: 192 average time/residue: 0.1566 time to fit residues: 40.8261 Evaluate side-chains 168 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 418 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6244 Z= 0.282 Angle : 0.727 9.052 8470 Z= 0.370 Chirality : 0.045 0.225 960 Planarity : 0.005 0.052 1042 Dihedral : 5.468 24.186 850 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 5.94 % Allowed : 26.25 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.30), residues: 780 helix: 0.11 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -4.04 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 60 HIS 0.005 0.002 HIS B 328 PHE 0.046 0.002 PHE B 284 TYR 0.018 0.002 TYR B 167 ARG 0.002 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8374 (t80) cc_final: 0.8098 (t80) REVERT: A 52 HIS cc_start: 0.6963 (p-80) cc_final: 0.4930 (m-70) REVERT: A 57 GLU cc_start: 0.8578 (mp0) cc_final: 0.8368 (mp0) REVERT: A 65 MET cc_start: 0.8651 (ttm) cc_final: 0.8287 (ttp) REVERT: A 127 ASN cc_start: 0.9290 (t0) cc_final: 0.9044 (t0) REVERT: A 129 GLN cc_start: 0.8625 (tp40) cc_final: 0.8328 (tp40) REVERT: A 168 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6032 (tt) REVERT: A 169 PHE cc_start: 0.8413 (m-10) cc_final: 0.8188 (m-80) REVERT: A 175 LYS cc_start: 0.5793 (mptt) cc_final: 0.5203 (pttt) REVERT: A 244 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7433 (t-90) REVERT: A 274 ASP cc_start: 0.8742 (t0) cc_final: 0.8488 (t0) REVERT: A 289 MET cc_start: 0.8299 (ppp) cc_final: 0.7843 (tmm) REVERT: A 312 ARG cc_start: 0.7715 (mmt180) cc_final: 0.7206 (mtt180) REVERT: A 404 LYS cc_start: 0.7997 (mptt) cc_final: 0.7457 (mtpt) REVERT: A 430 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7521 (tmt170) REVERT: A 431 LEU cc_start: 0.8756 (pp) cc_final: 0.8536 (mt) REVERT: B 120 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8440 (t) REVERT: B 127 ASN cc_start: 0.9484 (t0) cc_final: 0.8963 (t0) REVERT: B 129 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8233 (tm-30) REVERT: B 168 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6560 (tt) REVERT: B 196 ARG cc_start: 0.5982 (ttt180) cc_final: 0.5300 (tpt170) REVERT: B 279 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7491 (tm-30) REVERT: B 315 TYR cc_start: 0.8252 (m-10) cc_final: 0.7928 (m-10) REVERT: B 322 MET cc_start: 0.7775 (tmm) cc_final: 0.7528 (tmm) REVERT: B 363 MET cc_start: 0.9103 (tpp) cc_final: 0.8603 (tpp) REVERT: B 408 MET cc_start: 0.6039 (ttp) cc_final: 0.5342 (tmm) outliers start: 38 outliers final: 22 residues processed: 187 average time/residue: 0.1681 time to fit residues: 42.8496 Evaluate side-chains 176 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.1980 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 0.0040 chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6244 Z= 0.205 Angle : 0.687 8.956 8470 Z= 0.337 Chirality : 0.043 0.222 960 Planarity : 0.005 0.050 1042 Dihedral : 5.228 26.782 850 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.38 % Allowed : 30.62 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.31), residues: 780 helix: 0.36 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -3.81 (0.42), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 60 HIS 0.004 0.001 HIS A 328 PHE 0.038 0.002 PHE B 139 TYR 0.014 0.001 TYR A 343 ARG 0.002 0.000 ARG B 297 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 0.700 Fit side-chains REVERT: A 34 TYR cc_start: 0.8378 (t80) cc_final: 0.8016 (t80) REVERT: A 52 HIS cc_start: 0.6815 (p-80) cc_final: 0.4688 (m-70) REVERT: A 57 GLU cc_start: 0.8523 (mp0) cc_final: 0.8321 (mp0) REVERT: A 65 MET cc_start: 0.8578 (ttm) cc_final: 0.8326 (ttt) REVERT: A 129 GLN cc_start: 0.8577 (tp40) cc_final: 0.8129 (tp40) REVERT: A 169 PHE cc_start: 0.8286 (m-10) cc_final: 0.7978 (m-80) REVERT: A 175 LYS cc_start: 0.5750 (mptt) cc_final: 0.5188 (pttt) REVERT: A 274 ASP cc_start: 0.8704 (t0) cc_final: 0.8437 (t0) REVERT: A 289 MET cc_start: 0.8152 (ppp) cc_final: 0.7830 (ppp) REVERT: A 312 ARG cc_start: 0.7624 (mmt180) cc_final: 0.7159 (mtt180) REVERT: A 404 LYS cc_start: 0.7922 (mptt) cc_final: 0.7386 (mtpt) REVERT: A 430 ARG cc_start: 0.7871 (mtt-85) cc_final: 0.7492 (tmt170) REVERT: A 431 LEU cc_start: 0.8693 (pp) cc_final: 0.8408 (mm) REVERT: B 52 HIS cc_start: 0.7219 (p-80) cc_final: 0.5770 (m-70) REVERT: B 127 ASN cc_start: 0.9471 (t0) cc_final: 0.9094 (t0) REVERT: B 168 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.5925 (tt) REVERT: B 196 ARG cc_start: 0.5998 (ttt180) cc_final: 0.5444 (tpt170) REVERT: B 266 ILE cc_start: 0.9554 (OUTLIER) cc_final: 0.9244 (mp) REVERT: B 279 GLU cc_start: 0.8551 (tm-30) cc_final: 0.7619 (tm-30) REVERT: B 280 TYR cc_start: 0.8261 (m-80) cc_final: 0.7942 (m-80) REVERT: B 289 MET cc_start: 0.8694 (ppp) cc_final: 0.8198 (ppp) REVERT: B 315 TYR cc_start: 0.8121 (m-10) cc_final: 0.7899 (m-10) REVERT: B 322 MET cc_start: 0.7765 (tmm) cc_final: 0.7500 (tmm) REVERT: B 363 MET cc_start: 0.9138 (tpp) cc_final: 0.8819 (tpt) REVERT: B 406 MET cc_start: 0.7921 (tmm) cc_final: 0.7201 (tmm) REVERT: B 408 MET cc_start: 0.6097 (ttp) cc_final: 0.5349 (tmm) outliers start: 28 outliers final: 17 residues processed: 176 average time/residue: 0.1507 time to fit residues: 35.8739 Evaluate side-chains 164 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6244 Z= 0.302 Angle : 0.759 9.580 8470 Z= 0.381 Chirality : 0.046 0.241 960 Planarity : 0.005 0.046 1042 Dihedral : 5.421 24.506 850 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 5.47 % Allowed : 31.56 % Favored : 62.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.31), residues: 780 helix: 0.27 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -3.48 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 18 HIS 0.005 0.001 HIS A 328 PHE 0.040 0.002 PHE B 284 TYR 0.021 0.002 TYR B 167 ARG 0.003 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8380 (t80) cc_final: 0.7855 (t80) REVERT: A 52 HIS cc_start: 0.7009 (p-80) cc_final: 0.4504 (m-70) REVERT: A 57 GLU cc_start: 0.8632 (mp0) cc_final: 0.8357 (mp0) REVERT: A 65 MET cc_start: 0.8677 (ttm) cc_final: 0.8399 (ttt) REVERT: A 129 GLN cc_start: 0.8601 (tp40) cc_final: 0.8332 (tp40) REVERT: A 147 ASN cc_start: 0.7961 (m-40) cc_final: 0.7608 (m110) REVERT: A 166 GLN cc_start: 0.8440 (mm110) cc_final: 0.7728 (mm110) REVERT: A 168 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6348 (tt) REVERT: A 169 PHE cc_start: 0.8525 (m-10) cc_final: 0.8317 (m-80) REVERT: A 175 LYS cc_start: 0.5889 (mptt) cc_final: 0.5227 (pttt) REVERT: A 274 ASP cc_start: 0.8782 (t0) cc_final: 0.8533 (t0) REVERT: A 289 MET cc_start: 0.8363 (ppp) cc_final: 0.7884 (tmm) REVERT: A 312 ARG cc_start: 0.7685 (mmt180) cc_final: 0.7179 (mtt180) REVERT: A 404 LYS cc_start: 0.7973 (mptt) cc_final: 0.7454 (mtpt) REVERT: A 406 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.6624 (tpp) REVERT: A 430 ARG cc_start: 0.7966 (mtt-85) cc_final: 0.7643 (tmt170) REVERT: B 102 LEU cc_start: 0.8354 (tt) cc_final: 0.7854 (tt) REVERT: B 112 LEU cc_start: 0.5751 (OUTLIER) cc_final: 0.5347 (mt) REVERT: B 126 PHE cc_start: 0.8301 (t80) cc_final: 0.7910 (t80) REVERT: B 127 ASN cc_start: 0.9485 (t0) cc_final: 0.9162 (t0) REVERT: B 169 PHE cc_start: 0.8349 (m-10) cc_final: 0.8110 (m-10) REVERT: B 196 ARG cc_start: 0.6170 (ttt180) cc_final: 0.5493 (tpt170) REVERT: B 279 GLU cc_start: 0.8565 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 280 TYR cc_start: 0.8372 (m-80) cc_final: 0.8029 (m-80) REVERT: B 289 MET cc_start: 0.8840 (ppp) cc_final: 0.8434 (ppp) REVERT: B 315 TYR cc_start: 0.8232 (m-10) cc_final: 0.7950 (m-10) REVERT: B 363 MET cc_start: 0.9205 (tpp) cc_final: 0.8844 (tpt) REVERT: B 408 MET cc_start: 0.6009 (ttp) cc_final: 0.5303 (tmm) outliers start: 35 outliers final: 24 residues processed: 182 average time/residue: 0.1547 time to fit residues: 38.0578 Evaluate side-chains 178 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6244 Z= 0.226 Angle : 0.714 9.574 8470 Z= 0.352 Chirality : 0.045 0.242 960 Planarity : 0.005 0.047 1042 Dihedral : 5.274 26.386 850 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.53 % Allowed : 34.22 % Favored : 61.25 % 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: -0.43 (0.31), residues: 780 helix: 0.49 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -3.52 (0.46), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 60 HIS 0.003 0.001 HIS A 328 PHE 0.042 0.002 PHE A 284 TYR 0.015 0.001 TYR A 337 ARG 0.001 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 0.637 Fit side-chains REVERT: A 20 TRP cc_start: 0.8730 (p-90) cc_final: 0.8523 (p-90) REVERT: A 34 TYR cc_start: 0.8402 (t80) cc_final: 0.7739 (t80) REVERT: A 52 HIS cc_start: 0.6963 (p-80) cc_final: 0.4355 (m-70) REVERT: A 57 GLU cc_start: 0.8593 (mp0) cc_final: 0.8344 (mp0) REVERT: A 129 GLN cc_start: 0.8578 (tp40) cc_final: 0.8300 (tp40) REVERT: A 147 ASN cc_start: 0.7918 (m-40) cc_final: 0.7542 (m110) REVERT: A 166 GLN cc_start: 0.8281 (mm110) cc_final: 0.7572 (mm110) REVERT: A 168 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.5685 (tt) REVERT: A 169 PHE cc_start: 0.8383 (m-10) cc_final: 0.8125 (m-80) REVERT: A 175 LYS cc_start: 0.5896 (mptt) cc_final: 0.5293 (pttt) REVERT: A 274 ASP cc_start: 0.8737 (t0) cc_final: 0.8452 (t0) REVERT: A 289 MET cc_start: 0.8162 (ppp) cc_final: 0.7933 (ppp) REVERT: A 312 ARG cc_start: 0.7637 (mmt180) cc_final: 0.7108 (mtt180) REVERT: A 404 LYS cc_start: 0.7927 (mptt) cc_final: 0.7436 (mtpt) REVERT: A 430 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7651 (tmt170) REVERT: B 126 PHE cc_start: 0.8333 (t80) cc_final: 0.8005 (t80) REVERT: B 129 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8447 (tm-30) REVERT: B 166 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8281 (mm-40) REVERT: B 167 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.6913 (m-10) REVERT: B 196 ARG cc_start: 0.6097 (ttt180) cc_final: 0.5574 (tpt170) REVERT: B 279 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8441 (tp30) REVERT: B 289 MET cc_start: 0.8744 (ppp) cc_final: 0.8386 (ppp) REVERT: B 315 TYR cc_start: 0.8216 (m-10) cc_final: 0.7932 (m-10) REVERT: B 363 MET cc_start: 0.9178 (tpp) cc_final: 0.8820 (tpt) REVERT: B 406 MET cc_start: 0.7949 (tmm) cc_final: 0.7688 (tmm) REVERT: B 408 MET cc_start: 0.5930 (ttp) cc_final: 0.5217 (tmm) REVERT: B 443 GLN cc_start: 0.6163 (OUTLIER) cc_final: 0.5591 (mm110) outliers start: 29 outliers final: 20 residues processed: 174 average time/residue: 0.1631 time to fit residues: 38.0729 Evaluate side-chains 176 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 443 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6244 Z= 0.220 Angle : 0.717 9.032 8470 Z= 0.350 Chirality : 0.045 0.263 960 Planarity : 0.004 0.047 1042 Dihedral : 5.209 25.240 850 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.69 % Allowed : 34.38 % Favored : 60.94 % 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: -0.36 (0.31), residues: 780 helix: 0.54 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -3.52 (0.45), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 20 HIS 0.003 0.001 HIS A 328 PHE 0.040 0.002 PHE A 284 TYR 0.016 0.001 TYR A 343 ARG 0.002 0.000 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 0.767 Fit side-chains REVERT: A 34 TYR cc_start: 0.8195 (t80) cc_final: 0.7669 (t80) REVERT: A 52 HIS cc_start: 0.6911 (p-80) cc_final: 0.4292 (m-70) REVERT: A 57 GLU cc_start: 0.8553 (mp0) cc_final: 0.8316 (mp0) REVERT: A 129 GLN cc_start: 0.8587 (tp40) cc_final: 0.8309 (tp40) REVERT: A 147 ASN cc_start: 0.7888 (m-40) cc_final: 0.7522 (m110) REVERT: A 166 GLN cc_start: 0.8256 (mm110) cc_final: 0.7515 (mm110) REVERT: A 169 PHE cc_start: 0.8310 (m-10) cc_final: 0.8009 (m-80) REVERT: A 175 LYS cc_start: 0.5906 (mptt) cc_final: 0.5337 (pttt) REVERT: A 274 ASP cc_start: 0.8735 (t0) cc_final: 0.8443 (t0) REVERT: A 289 MET cc_start: 0.8086 (ppp) cc_final: 0.7769 (ppp) REVERT: A 312 ARG cc_start: 0.7611 (mmt180) cc_final: 0.7084 (mtt180) REVERT: A 404 LYS cc_start: 0.7918 (mptt) cc_final: 0.7423 (mtpt) REVERT: A 430 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7680 (tmt170) REVERT: B 126 PHE cc_start: 0.8383 (t80) cc_final: 0.8013 (t80) REVERT: B 196 ARG cc_start: 0.6052 (ttt180) cc_final: 0.5553 (tpt90) REVERT: B 254 ASN cc_start: 0.8514 (m-40) cc_final: 0.8214 (m110) REVERT: B 279 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8057 (tm-30) REVERT: B 289 MET cc_start: 0.8716 (ppp) cc_final: 0.8360 (ppp) REVERT: B 315 TYR cc_start: 0.8208 (m-10) cc_final: 0.7935 (m-10) REVERT: B 363 MET cc_start: 0.9163 (tpp) cc_final: 0.8784 (tpt) REVERT: B 406 MET cc_start: 0.7912 (tmm) cc_final: 0.7652 (tmm) REVERT: B 408 MET cc_start: 0.5880 (ttp) cc_final: 0.5254 (tmm) REVERT: B 443 GLN cc_start: 0.6184 (OUTLIER) cc_final: 0.5624 (mm110) outliers start: 30 outliers final: 21 residues processed: 177 average time/residue: 0.1567 time to fit residues: 37.5943 Evaluate side-chains 171 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 443 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6244 Z= 0.256 Angle : 0.787 15.415 8470 Z= 0.381 Chirality : 0.046 0.248 960 Planarity : 0.005 0.047 1042 Dihedral : 5.303 27.782 850 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.38 % Allowed : 35.16 % Favored : 60.47 % 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: -0.41 (0.31), residues: 780 helix: 0.52 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -3.62 (0.43), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 60 HIS 0.003 0.001 HIS A 328 PHE 0.043 0.002 PHE A 284 TYR 0.016 0.001 TYR A 343 ARG 0.002 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8228 (t80) cc_final: 0.7589 (t80) REVERT: A 129 GLN cc_start: 0.8594 (tp40) cc_final: 0.8337 (tp40) REVERT: A 147 ASN cc_start: 0.7951 (m-40) cc_final: 0.7578 (m110) REVERT: A 166 GLN cc_start: 0.8289 (mm110) cc_final: 0.7745 (mm110) REVERT: A 168 LEU cc_start: 0.5937 (tp) cc_final: 0.4861 (tt) REVERT: A 169 PHE cc_start: 0.8350 (m-10) cc_final: 0.8101 (m-80) REVERT: A 175 LYS cc_start: 0.5948 (mptt) cc_final: 0.5329 (pttt) REVERT: A 274 ASP cc_start: 0.8731 (t0) cc_final: 0.8436 (t0) REVERT: A 289 MET cc_start: 0.8098 (ppp) cc_final: 0.7773 (ppp) REVERT: A 312 ARG cc_start: 0.7708 (mmt180) cc_final: 0.7156 (mtt180) REVERT: A 404 LYS cc_start: 0.7957 (mptt) cc_final: 0.7454 (mtpt) REVERT: A 430 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7693 (tmt170) REVERT: B 126 PHE cc_start: 0.8334 (t80) cc_final: 0.8097 (t80) REVERT: B 167 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.7273 (m-10) REVERT: B 168 LEU cc_start: 0.6459 (tp) cc_final: 0.5478 (tt) REVERT: B 196 ARG cc_start: 0.6158 (ttt180) cc_final: 0.5697 (tpt170) REVERT: B 279 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8329 (tm-30) REVERT: B 289 MET cc_start: 0.8793 (ppp) cc_final: 0.8372 (ppp) REVERT: B 315 TYR cc_start: 0.8228 (m-10) cc_final: 0.7920 (m-10) REVERT: B 363 MET cc_start: 0.9203 (tpp) cc_final: 0.8872 (tpt) REVERT: B 406 MET cc_start: 0.7920 (tmm) cc_final: 0.7683 (tmm) REVERT: B 408 MET cc_start: 0.5926 (ttp) cc_final: 0.5274 (tmm) REVERT: B 443 GLN cc_start: 0.6241 (OUTLIER) cc_final: 0.5638 (mm110) outliers start: 28 outliers final: 22 residues processed: 172 average time/residue: 0.1561 time to fit residues: 36.2780 Evaluate side-chains 175 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 443 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6244 Z= 0.264 Angle : 0.805 14.475 8470 Z= 0.390 Chirality : 0.046 0.279 960 Planarity : 0.005 0.047 1042 Dihedral : 5.372 32.232 850 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.53 % Allowed : 35.16 % Favored : 60.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.35 (0.31), residues: 780 helix: 0.63 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -3.72 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 20 HIS 0.003 0.001 HIS A 328 PHE 0.044 0.002 PHE A 284 TYR 0.017 0.001 TYR A 343 ARG 0.002 0.000 ARG A 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 0.693 Fit side-chains REVERT: A 34 TYR cc_start: 0.8235 (t80) cc_final: 0.7508 (t80) REVERT: A 52 HIS cc_start: 0.7042 (OUTLIER) cc_final: 0.4291 (m-70) REVERT: A 57 GLU cc_start: 0.8557 (mp0) cc_final: 0.8288 (mp0) REVERT: A 129 GLN cc_start: 0.8524 (tp40) cc_final: 0.8256 (tp40) REVERT: A 147 ASN cc_start: 0.7995 (m-40) cc_final: 0.7619 (m110) REVERT: A 166 GLN cc_start: 0.8229 (mm110) cc_final: 0.7756 (mm110) REVERT: A 169 PHE cc_start: 0.8423 (m-10) cc_final: 0.8205 (m-80) REVERT: A 175 LYS cc_start: 0.6017 (mptt) cc_final: 0.5393 (pttt) REVERT: A 289 MET cc_start: 0.8118 (ppp) cc_final: 0.7799 (ppp) REVERT: A 312 ARG cc_start: 0.7773 (mmt180) cc_final: 0.7187 (mtt180) REVERT: A 404 LYS cc_start: 0.7948 (mptt) cc_final: 0.7472 (mtpt) REVERT: B 126 PHE cc_start: 0.8358 (t80) cc_final: 0.8055 (t80) REVERT: B 164 PHE cc_start: 0.6441 (OUTLIER) cc_final: 0.6134 (m-80) REVERT: B 167 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.7247 (m-10) REVERT: B 168 LEU cc_start: 0.6606 (tp) cc_final: 0.5599 (tt) REVERT: B 169 PHE cc_start: 0.8289 (m-10) cc_final: 0.7995 (m-10) REVERT: B 196 ARG cc_start: 0.6212 (ttt180) cc_final: 0.5744 (tpt170) REVERT: B 279 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8332 (tm-30) REVERT: B 289 MET cc_start: 0.8794 (ppp) cc_final: 0.8396 (ppp) REVERT: B 315 TYR cc_start: 0.8243 (m-10) cc_final: 0.7962 (m-10) REVERT: B 363 MET cc_start: 0.9215 (tpp) cc_final: 0.8921 (tpt) REVERT: B 408 MET cc_start: 0.5928 (ttp) cc_final: 0.5275 (tmm) REVERT: B 443 GLN cc_start: 0.6282 (OUTLIER) cc_final: 0.5673 (mm110) outliers start: 29 outliers final: 24 residues processed: 169 average time/residue: 0.1575 time to fit residues: 36.1316 Evaluate side-chains 173 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 443 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.141141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.129402 restraints weight = 14216.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.132596 restraints weight = 7994.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.134767 restraints weight = 5006.893| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6244 Z= 0.213 Angle : 0.790 14.258 8470 Z= 0.377 Chirality : 0.046 0.260 960 Planarity : 0.005 0.047 1042 Dihedral : 5.211 32.315 850 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.06 % Allowed : 35.62 % Favored : 60.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.09 (0.31), residues: 780 helix: 0.82 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -3.67 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 20 HIS 0.003 0.001 HIS B 328 PHE 0.031 0.001 PHE A 284 TYR 0.015 0.001 TYR A 343 ARG 0.001 0.000 ARG B 297 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1465.38 seconds wall clock time: 27 minutes 21.35 seconds (1641.35 seconds total)