Starting phenix.real_space_refine on Mon Nov 13 22:49:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp3_30143/11_2023/7bp3_30143.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp3_30143/11_2023/7bp3_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_30143/11_2023/7bp3_30143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp3_30143/11_2023/7bp3_30143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp3_30143/11_2023/7bp3_30143.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bp3_30143/11_2023/7bp3_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 3.57, per 1000 atoms: 0.59 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: 2.30 Conformation dependent library (CDL) restraints added in 1.2 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: 0.59 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: 1.77 Time building geometry restraints manager: 2.51 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: 0.810 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: 3.160 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.320 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.650 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1803 time to fit residues: 61.1119 Evaluate side-chains 163 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8928 ------------------------------------------------------------------------------- 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: 0.0020 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 0.0050 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN A 254 ASN A 305 ASN B 127 ASN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 244 HIS B 275 GLN B 305 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6244 Z= 0.213 Angle : 0.766 11.608 8470 Z= 0.381 Chirality : 0.044 0.190 960 Planarity : 0.006 0.060 1042 Dihedral : 5.782 23.661 850 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.38 % Allowed : 22.03 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.28), residues: 780 helix: -0.95 (0.19), residues: 628 sheet: None (None), residues: 0 loop : -3.58 (0.48), residues: 152 *********************** 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 219 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 204 average time/residue: 0.1395 time to fit residues: 39.1717 Evaluate side-chains 164 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0740 time to fit residues: 2.7651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 147 ASN A 166 GLN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN B 425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6244 Z= 0.220 Angle : 0.736 10.122 8470 Z= 0.366 Chirality : 0.044 0.199 960 Planarity : 0.005 0.054 1042 Dihedral : 5.552 24.322 850 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.12 % Allowed : 24.53 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.48 (0.29), residues: 780 helix: -0.20 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -3.99 (0.41), residues: 154 *********************** 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 185 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 0.705 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 177 average time/residue: 0.1425 time to fit residues: 35.4123 Evaluate side-chains 149 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0603 time to fit residues: 1.5735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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** B 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4917 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= 0.210 Angle : 0.718 9.232 8470 Z= 0.355 Chirality : 0.044 0.209 960 Planarity : 0.004 0.051 1042 Dihedral : 5.376 24.250 850 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.97 % Allowed : 28.12 % Favored : 68.91 % 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: -1.00 (0.30), residues: 780 helix: 0.13 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -3.95 (0.42), residues: 146 *********************** 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 180 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 0.722 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 169 average time/residue: 0.1316 time to fit residues: 31.7774 Evaluate side-chains 154 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0733 time to fit residues: 1.8681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.6980 chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 0 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.7514 moved from start: 0.5201 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= 0.212 Angle : 0.722 9.081 8470 Z= 0.354 Chirality : 0.044 0.211 960 Planarity : 0.004 0.049 1042 Dihedral : 5.327 26.668 850 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.66 % Allowed : 31.25 % Favored : 66.09 % 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: -0.68 (0.31), residues: 780 helix: 0.38 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -3.97 (0.43), residues: 148 *********************** 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 163 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 0.712 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 155 average time/residue: 0.1402 time to fit residues: 30.6412 Evaluate side-chains 145 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 0.701 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0706 time to fit residues: 1.9798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.7545 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6244 Z= 0.236 Angle : 0.727 9.346 8470 Z= 0.359 Chirality : 0.045 0.226 960 Planarity : 0.005 0.047 1042 Dihedral : 5.315 26.251 850 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.19 % Allowed : 31.25 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.31), residues: 780 helix: 0.46 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -3.68 (0.48), residues: 144 *********************** 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 160 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 0.772 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 152 average time/residue: 0.1367 time to fit residues: 29.3960 Evaluate side-chains 142 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0688 time to fit residues: 2.0531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- 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: 0.7481 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6244 Z= 0.209 Angle : 0.772 14.469 8470 Z= 0.367 Chirality : 0.044 0.245 960 Planarity : 0.005 0.048 1042 Dihedral : 5.227 28.189 850 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.56 % Allowed : 34.06 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.31), residues: 780 helix: 0.57 (0.22), residues: 632 sheet: None (None), residues: 0 loop : -4.03 (0.41), residues: 148 *********************** 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 161 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 0.670 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 153 average time/residue: 0.1383 time to fit residues: 30.0894 Evaluate side-chains 145 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 0.691 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0938 time to fit residues: 1.1869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 0.0270 chunk 42 optimal weight: 0.7980 overall best weight: 1.1440 ------------------------------------------------------------------------------- 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: 0.7472 moved from start: 0.5928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6244 Z= 0.228 Angle : 0.792 13.077 8470 Z= 0.377 Chirality : 0.044 0.251 960 Planarity : 0.005 0.047 1042 Dihedral : 5.296 30.716 850 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.41 % Allowed : 36.09 % Favored : 62.50 % 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: -0.41 (0.31), residues: 780 helix: 0.57 (0.22), residues: 634 sheet: None (None), residues: 0 loop : -3.92 (0.43), residues: 146 *********************** 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 164 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 0.716 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 160 average time/residue: 0.1377 time to fit residues: 31.0079 Evaluate side-chains 148 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 0.685 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0738 time to fit residues: 1.5116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7519 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6244 Z= 0.261 Angle : 0.807 13.042 8470 Z= 0.391 Chirality : 0.046 0.274 960 Planarity : 0.005 0.048 1042 Dihedral : 5.422 30.395 850 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 1.09 % Allowed : 36.56 % Favored : 62.34 % 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: -0.41 (0.31), residues: 780 helix: 0.62 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -4.06 (0.41), residues: 150 *********************** 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 154 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.683 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 148 average time/residue: 0.1354 time to fit residues: 28.8499 Evaluate side-chains 147 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0762 time to fit residues: 1.2227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 18 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7446 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6244 Z= 0.219 Angle : 0.813 12.925 8470 Z= 0.385 Chirality : 0.044 0.262 960 Planarity : 0.005 0.047 1042 Dihedral : 5.317 31.773 850 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.94 % Allowed : 36.72 % Favored : 62.34 % 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: -0.07 (0.32), residues: 780 helix: 0.86 (0.22), residues: 626 sheet: None (None), residues: 0 loop : -3.81 (0.46), residues: 154 ********************** 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 155 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 0.717 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 151 average time/residue: 0.1310 time to fit residues: 28.4310 Evaluate side-chains 144 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 0.677 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0704 time to fit residues: 1.3764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 254 ASN ** 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 = 0.3981 r_free = 0.3981 target = 0.139415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.127122 restraints weight = 14905.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.130317 restraints weight = 8429.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.132471 restraints weight = 5318.792| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6244 Z= 0.235 Angle : 0.825 13.612 8470 Z= 0.391 Chirality : 0.045 0.265 960 Planarity : 0.004 0.048 1042 Dihedral : 5.352 31.230 850 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.31 % Allowed : 37.03 % Favored : 62.66 % 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: -0.15 (0.32), residues: 780 helix: 0.85 (0.22), residues: 624 sheet: None (None), residues: 0 loop : -4.03 (0.43), residues: 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1383.71 seconds wall clock time: 26 minutes 0.04 seconds (1560.04 seconds total)