Starting phenix.real_space_refine on Sun Apr 7 02:04:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okx_16933/04_2024/8okx_16933.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okx_16933/04_2024/8okx_16933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okx_16933/04_2024/8okx_16933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okx_16933/04_2024/8okx_16933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okx_16933/04_2024/8okx_16933.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8okx_16933/04_2024/8okx_16933.pdb" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2959 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 43 5.16 5 C 4061 2.51 5 N 1093 2.21 5 O 1201 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A ARG 423": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "D ARG 8": "NH1" <-> "NH2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6399 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2966 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "B" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1737 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain: "C" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 873 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "D" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 822 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1884 SG CYS A 396 23.491 48.998 82.872 1.00 91.65 S ATOM 1890 SG CYS A 397 21.155 46.114 82.380 1.00 90.83 S ATOM 1949 SG CYS A 404 24.813 45.618 81.419 1.00 64.49 S Time building chain proxies: 3.84, per 1000 atoms: 0.60 Number of scatterers: 6399 At special positions: 0 Unit cell: (103.976, 96.368, 138.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 43 16.00 O 1201 8.00 N 1093 7.00 C 4061 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: 2.32 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 390 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 397 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 396 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 404 " Number of angles added : 3 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 33.7% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 161 through 174 removed outlier: 4.102A pdb=" N LEU A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 200 removed outlier: 3.653A pdb=" N THR A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N MET A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 289 removed outlier: 4.229A pdb=" N ASN A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 340 through 353 removed outlier: 7.702A pdb=" N ALA A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N LYS A 347 " --> pdb=" O TRP A 343 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 removed outlier: 3.592A pdb=" N LEU A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.840A pdb=" N LYS A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET A 413 " --> pdb=" O CYS A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 449 removed outlier: 4.052A pdb=" N VAL A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.192A pdb=" N ASP A 456 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 478 Processing helix chain 'A' and resid 497 through 514 Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.636A pdb=" N PHE A 522 " --> pdb=" O PHE A 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.917A pdb=" N TYR B 178 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 289 removed outlier: 4.711A pdb=" N CYS B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 319 removed outlier: 7.617A pdb=" N TRP B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 39 removed outlier: 4.080A pdb=" N SER C 39 " --> pdb=" O HIS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 47 removed outlier: 3.557A pdb=" N SER C 47 " --> pdb=" O LYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 83 Processing helix chain 'C' and resid 103 through 111 removed outlier: 3.760A pdb=" N ALA C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 36 Processing helix chain 'D' and resid 100 through 104 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.752A pdb=" N LYS A 231 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 322 " --> pdb=" O PRO A 361 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 240 " --> pdb=" O PHE A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.752A pdb=" N LYS A 231 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 308 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 309 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 112 removed outlier: 5.579A pdb=" N ARG B 139 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N LEU B 110 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 11.370A pdb=" N ALA B 137 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 256 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 119 removed outlier: 3.948A pdb=" N SER B 263 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL B 267 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 154 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG B 269 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 152 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS B 149 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP B 151 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU B 231 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL B 242 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N PHE B 233 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 240 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 32 removed outlier: 3.648A pdb=" N VAL C 31 " --> pdb=" O VAL C 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 12 through 16 removed outlier: 6.594A pdb=" N MET D 6 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU D 77 " --> pdb=" O MET D 6 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG D 8 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N PHE D 79 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 12 through 16 removed outlier: 6.594A pdb=" N MET D 6 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU D 77 " --> pdb=" O MET D 6 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG D 8 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N PHE D 79 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG D 68 " --> pdb=" O ALA D 71 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 732 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: 1.76 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.23: 18 1.23 - 1.41: 2634 1.41 - 1.59: 3818 1.59 - 1.77: 2 1.77 - 1.95: 63 Bond restraints: 6535 Sorted by residual: bond pdb=" CG PRO D 39 " pdb=" CD PRO D 39 " ideal model delta sigma weight residual 1.503 1.044 0.459 3.40e-02 8.65e+02 1.82e+02 bond pdb=" SD MET A 298 " pdb=" CE MET A 298 " ideal model delta sigma weight residual 1.791 1.950 -0.159 2.50e-02 1.60e+03 4.06e+01 bond pdb=" SD MET A 413 " pdb=" CE MET A 413 " ideal model delta sigma weight residual 1.791 1.950 -0.159 2.50e-02 1.60e+03 4.03e+01 bond pdb=" SD MET A 185 " pdb=" CE MET A 185 " ideal model delta sigma weight residual 1.791 1.949 -0.158 2.50e-02 1.60e+03 4.02e+01 bond pdb=" SD MET A 276 " pdb=" CE MET A 276 " ideal model delta sigma weight residual 1.791 1.949 -0.158 2.50e-02 1.60e+03 4.02e+01 ... (remaining 6530 not shown) Histogram of bond angle deviations from ideal: 81.45 - 92.13: 2 92.13 - 102.82: 36 102.82 - 113.50: 3617 113.50 - 124.18: 4973 124.18 - 134.86: 173 Bond angle restraints: 8801 Sorted by residual: angle pdb=" N PRO D 39 " pdb=" CD PRO D 39 " pdb=" CG PRO D 39 " ideal model delta sigma weight residual 103.20 81.45 21.75 1.50e+00 4.44e-01 2.10e+02 angle pdb=" CA PRO D 39 " pdb=" N PRO D 39 " pdb=" CD PRO D 39 " ideal model delta sigma weight residual 112.00 95.64 16.36 1.40e+00 5.10e-01 1.37e+02 angle pdb=" CA PRO D 39 " pdb=" CB PRO D 39 " pdb=" CG PRO D 39 " ideal model delta sigma weight residual 104.50 89.18 15.32 1.90e+00 2.77e-01 6.50e+01 angle pdb=" CA PRO C 97 " pdb=" N PRO C 97 " pdb=" CD PRO C 97 " ideal model delta sigma weight residual 112.00 103.77 8.23 1.40e+00 5.10e-01 3.46e+01 angle pdb=" N PRO D 39 " pdb=" CA PRO D 39 " pdb=" CB PRO D 39 " ideal model delta sigma weight residual 103.26 97.14 6.12 1.14e+00 7.69e-01 2.88e+01 ... (remaining 8796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 3462 17.38 - 34.75: 393 34.75 - 52.13: 78 52.13 - 69.50: 25 69.50 - 86.88: 8 Dihedral angle restraints: 3966 sinusoidal: 1643 harmonic: 2323 Sorted by residual: dihedral pdb=" CA GLU B 130 " pdb=" C GLU B 130 " pdb=" N TYR B 131 " pdb=" CA TYR B 131 " ideal model delta harmonic sigma weight residual -180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA VAL D 102 " pdb=" C VAL D 102 " pdb=" N MET D 103 " pdb=" CA MET D 103 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA SER A 213 " pdb=" C SER A 213 " pdb=" N TYR A 214 " pdb=" CA TYR A 214 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 3963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 775 0.057 - 0.115: 151 0.115 - 0.172: 24 0.172 - 0.229: 3 0.229 - 0.287: 5 Chirality restraints: 958 Sorted by residual: chirality pdb=" CA ASN B 122 " pdb=" N ASN B 122 " pdb=" C ASN B 122 " pdb=" CB ASN B 122 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA SER B 132 " pdb=" N SER B 132 " pdb=" C SER B 132 " pdb=" CB SER B 132 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO C 97 " pdb=" N PRO C 97 " pdb=" C PRO C 97 " pdb=" CB PRO C 97 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 955 not shown) Planarity restraints: 1127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 510 " 0.074 2.00e-02 2.50e+03 4.61e-02 4.26e+01 pdb=" CG TYR A 510 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 510 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 510 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 510 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 510 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A 510 " -0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 510 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 38 " -0.110 5.00e-02 4.00e+02 1.50e-01 3.58e+01 pdb=" N PRO D 39 " 0.258 5.00e-02 4.00e+02 pdb=" CA PRO D 39 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO D 39 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 128 " 0.060 2.00e-02 2.50e+03 4.47e-02 2.99e+01 pdb=" CG HIS B 128 " -0.071 2.00e-02 2.50e+03 pdb=" ND1 HIS B 128 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS B 128 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 HIS B 128 " 0.029 2.00e-02 2.50e+03 pdb=" NE2 HIS B 128 " 0.034 2.00e-02 2.50e+03 ... (remaining 1124 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 27 2.47 - 3.07: 4344 3.07 - 3.68: 9749 3.68 - 4.29: 13163 4.29 - 4.90: 21836 Nonbonded interactions: 49119 Sorted by model distance: nonbonded pdb=" CE LYS A 171 " pdb=" CE1 PHE A 522 " model vdw 1.857 3.740 nonbonded pdb=" CE LYS A 171 " pdb=" CD1 PHE A 522 " model vdw 1.944 3.740 nonbonded pdb=" OD2 ASP A 465 " pdb=" NH2 ARG A 512 " model vdw 2.208 2.520 nonbonded pdb=" OH TYR C 79 " pdb=" O PRO C 91 " model vdw 2.227 2.440 nonbonded pdb=" OD1 ASP D 40 " pdb=" NH2 ARG D 80 " model vdw 2.254 2.520 ... (remaining 49114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 5.230 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.200 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5347 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 : 0.010 0.459 6535 Z= 0.661 Angle : 0.988 21.749 8801 Z= 0.581 Chirality : 0.051 0.287 958 Planarity : 0.009 0.150 1127 Dihedral : 16.065 86.877 2462 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.32 % Favored : 93.17 % Rotamer: Outliers : 0.42 % Allowed : 19.55 % Favored : 80.03 % 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: -1.03 (0.30), residues: 791 helix: -0.16 (0.33), residues: 247 sheet: -0.35 (0.47), residues: 124 loop : -1.06 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 107 HIS 0.010 0.002 HIS B 283 PHE 0.044 0.002 PHE B 127 TYR 0.085 0.004 TYR A 510 ARG 0.007 0.001 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 MET cc_start: -0.2069 (ttm) cc_final: -0.2326 (mmm) REVERT: C 77 PHE cc_start: 0.7584 (m-10) cc_final: 0.7209 (m-10) outliers start: 3 outliers final: 0 residues processed: 97 average time/residue: 0.2331 time to fit residues: 28.5497 Evaluate side-chains 69 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.0570 chunk 61 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 0.0170 chunk 71 optimal weight: 9.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5377 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6535 Z= 0.195 Angle : 0.718 12.121 8801 Z= 0.359 Chirality : 0.043 0.181 958 Planarity : 0.007 0.134 1127 Dihedral : 5.109 62.254 862 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.80 % Favored : 95.07 % Rotamer: Outliers : 2.25 % Allowed : 21.38 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.30), residues: 791 helix: 0.29 (0.34), residues: 246 sheet: -0.28 (0.46), residues: 131 loop : -0.98 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 107 HIS 0.019 0.002 HIS B 283 PHE 0.020 0.001 PHE B 210 TYR 0.015 0.001 TYR C 18 ARG 0.014 0.001 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 LYS cc_start: 0.8224 (pttp) cc_final: 0.7946 (tppt) REVERT: D 6 MET cc_start: 0.3928 (tmm) cc_final: 0.3642 (tpp) outliers start: 16 outliers final: 9 residues processed: 88 average time/residue: 0.2015 time to fit residues: 23.3363 Evaluate side-chains 79 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 52 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 77 optimal weight: 30.0000 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 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 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5428 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6535 Z= 0.193 Angle : 0.670 12.026 8801 Z= 0.334 Chirality : 0.042 0.184 958 Planarity : 0.005 0.068 1127 Dihedral : 5.036 60.305 862 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.69 % Favored : 94.18 % Rotamer: Outliers : 3.66 % Allowed : 20.68 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.30), residues: 791 helix: 0.35 (0.34), residues: 242 sheet: -0.14 (0.46), residues: 131 loop : -0.95 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 193 HIS 0.022 0.002 HIS B 283 PHE 0.025 0.001 PHE D 4 TYR 0.016 0.001 TYR C 83 ARG 0.004 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 75 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.6670 (p) REVERT: D 6 MET cc_start: 0.4572 (tmm) cc_final: 0.4172 (tpp) outliers start: 26 outliers final: 15 residues processed: 91 average time/residue: 0.1981 time to fit residues: 24.0470 Evaluate side-chains 84 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 84 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 40.0000 chunk 68 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5514 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6535 Z= 0.260 Angle : 0.720 11.957 8801 Z= 0.360 Chirality : 0.044 0.226 958 Planarity : 0.005 0.063 1127 Dihedral : 5.240 63.316 862 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.19 % Favored : 93.68 % Rotamer: Outliers : 4.50 % Allowed : 21.38 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.30), residues: 791 helix: 0.09 (0.33), residues: 248 sheet: -0.08 (0.44), residues: 138 loop : -0.93 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 193 HIS 0.019 0.002 HIS B 283 PHE 0.013 0.002 PHE A 280 TYR 0.014 0.001 TYR C 18 ARG 0.003 0.001 ARG B 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 71 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 286 ARG cc_start: 0.7063 (tpt170) cc_final: 0.6627 (tpp-160) REVERT: C 41 THR cc_start: 0.7229 (OUTLIER) cc_final: 0.6609 (p) REVERT: D 6 MET cc_start: 0.4737 (tmm) cc_final: 0.4167 (tpp) outliers start: 32 outliers final: 22 residues processed: 92 average time/residue: 0.2016 time to fit residues: 24.4269 Evaluate side-chains 91 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 68 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 84 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 ASN ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6535 Z= 0.281 Angle : 0.736 12.999 8801 Z= 0.366 Chirality : 0.043 0.176 958 Planarity : 0.004 0.061 1127 Dihedral : 5.437 67.528 862 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.50 % Allowed : 22.22 % Favored : 73.28 % 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: -1.02 (0.29), residues: 791 helix: -0.06 (0.33), residues: 243 sheet: -0.27 (0.43), residues: 141 loop : -1.17 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 227 HIS 0.020 0.002 HIS B 283 PHE 0.013 0.002 PHE A 280 TYR 0.015 0.002 TYR C 18 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 67 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 6 MET cc_start: 0.4834 (tmm) cc_final: 0.4186 (tpp) outliers start: 32 outliers final: 21 residues processed: 89 average time/residue: 0.2187 time to fit residues: 25.6555 Evaluate side-chains 84 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 63 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 84 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 73 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5574 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6535 Z= 0.247 Angle : 0.742 12.627 8801 Z= 0.364 Chirality : 0.043 0.158 958 Planarity : 0.004 0.060 1127 Dihedral : 5.471 69.464 862 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.64 % Allowed : 21.80 % Favored : 73.56 % 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: -0.99 (0.29), residues: 791 helix: -0.11 (0.32), residues: 254 sheet: -0.28 (0.44), residues: 137 loop : -1.11 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 227 HIS 0.019 0.002 HIS B 283 PHE 0.013 0.001 PHE A 280 TYR 0.019 0.002 TYR C 83 ARG 0.002 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 66 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6992 (mmmt) REVERT: D 6 MET cc_start: 0.4912 (tmm) cc_final: 0.4320 (tpp) outliers start: 33 outliers final: 19 residues processed: 90 average time/residue: 0.2086 time to fit residues: 24.6293 Evaluate side-chains 85 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 52 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5553 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 : 0.003 0.047 6535 Z= 0.217 Angle : 0.752 14.584 8801 Z= 0.367 Chirality : 0.043 0.164 958 Planarity : 0.004 0.059 1127 Dihedral : 5.416 69.522 862 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.66 % Allowed : 23.35 % Favored : 73.00 % 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: -0.97 (0.29), residues: 791 helix: -0.12 (0.32), residues: 254 sheet: -0.34 (0.43), residues: 137 loop : -1.03 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 227 HIS 0.018 0.001 HIS B 283 PHE 0.011 0.001 PHE A 280 TYR 0.022 0.002 TYR C 76 ARG 0.002 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 63 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7044 (mmmt) REVERT: B 285 LEU cc_start: 0.8978 (pp) cc_final: 0.8606 (mt) REVERT: D 6 MET cc_start: 0.4831 (tmm) cc_final: 0.4367 (tpp) outliers start: 26 outliers final: 24 residues processed: 83 average time/residue: 0.2342 time to fit residues: 25.5764 Evaluate side-chains 86 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 61 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 52 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.0060 chunk 69 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5529 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6535 Z= 0.193 Angle : 0.752 15.376 8801 Z= 0.361 Chirality : 0.043 0.172 958 Planarity : 0.004 0.059 1127 Dihedral : 5.346 68.014 862 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.94 % Allowed : 23.77 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.30), residues: 791 helix: 0.08 (0.33), residues: 254 sheet: -0.34 (0.44), residues: 137 loop : -0.97 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 227 HIS 0.018 0.001 HIS B 283 PHE 0.011 0.001 PHE C 77 TYR 0.014 0.001 TYR C 18 ARG 0.009 0.000 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 65 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6994 (mmmt) REVERT: D 6 MET cc_start: 0.4833 (tmm) cc_final: 0.4435 (tpp) outliers start: 28 outliers final: 22 residues processed: 86 average time/residue: 0.2587 time to fit residues: 28.7864 Evaluate side-chains 85 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 62 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 52 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5638 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6535 Z= 0.363 Angle : 0.860 12.985 8801 Z= 0.427 Chirality : 0.046 0.164 958 Planarity : 0.005 0.060 1127 Dihedral : 5.896 73.210 862 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.08 % Allowed : 24.61 % Favored : 71.31 % 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: -1.21 (0.29), residues: 791 helix: -0.25 (0.32), residues: 247 sheet: -0.60 (0.43), residues: 137 loop : -1.18 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 227 HIS 0.017 0.002 HIS B 283 PHE 0.019 0.002 PHE C 109 TYR 0.023 0.002 TYR C 76 ARG 0.008 0.001 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 62 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6990 (mmmt) REVERT: C 77 PHE cc_start: 0.7497 (m-10) cc_final: 0.7273 (m-10) REVERT: D 6 MET cc_start: 0.5414 (tmm) cc_final: 0.4816 (tpp) outliers start: 29 outliers final: 23 residues processed: 83 average time/residue: 0.2218 time to fit residues: 23.9035 Evaluate side-chains 84 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 60 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 52 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 62 optimal weight: 0.0970 chunk 6 optimal weight: 7.9990 chunk 48 optimal weight: 0.2980 chunk 38 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 19 optimal weight: 0.0040 chunk 57 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5514 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6535 Z= 0.190 Angle : 0.832 16.104 8801 Z= 0.395 Chirality : 0.045 0.184 958 Planarity : 0.004 0.060 1127 Dihedral : 5.499 68.905 862 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.67 % Allowed : 25.74 % Favored : 71.59 % 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: -0.91 (0.30), residues: 791 helix: -0.04 (0.32), residues: 254 sheet: -0.43 (0.43), residues: 137 loop : -0.97 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 227 HIS 0.018 0.001 HIS B 283 PHE 0.027 0.001 PHE C 109 TYR 0.013 0.001 TYR C 18 ARG 0.005 0.000 ARG B 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 286 ARG cc_start: 0.6621 (tpt170) cc_final: 0.6284 (tpp-160) REVERT: D 6 MET cc_start: 0.5278 (tmm) cc_final: 0.4832 (tpp) outliers start: 19 outliers final: 15 residues processed: 76 average time/residue: 0.2326 time to fit residues: 22.7858 Evaluate side-chains 74 residues out of total 711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 PHE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.087463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.062032 restraints weight = 53608.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.061917 restraints weight = 39559.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.062311 restraints weight = 28321.206| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6535 Z= 0.251 Angle : 0.847 13.465 8801 Z= 0.405 Chirality : 0.045 0.286 958 Planarity : 0.004 0.059 1127 Dihedral : 5.593 70.043 862 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 22.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.95 % Allowed : 25.60 % Favored : 71.45 % 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: -0.97 (0.29), residues: 791 helix: 0.02 (0.32), residues: 248 sheet: -0.53 (0.42), residues: 137 loop : -1.05 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 227 HIS 0.017 0.002 HIS B 283 PHE 0.012 0.001 PHE A 280 TYR 0.016 0.001 TYR C 18 ARG 0.006 0.000 ARG B 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1653.63 seconds wall clock time: 30 minutes 50.11 seconds (1850.11 seconds total)