Starting phenix.real_space_refine on Thu Mar 14 18:44:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f16_31405/03_2024/7f16_31405_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f16_31405/03_2024/7f16_31405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f16_31405/03_2024/7f16_31405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f16_31405/03_2024/7f16_31405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f16_31405/03_2024/7f16_31405_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f16_31405/03_2024/7f16_31405_neut_updated.pdb" } resolution = 2.8 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= 0.001 sd= 0.023 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 58 5.16 5 C 6106 2.51 5 N 1619 2.21 5 O 1705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 75": "NH1" <-> "NH2" Residue "R ARG 127": "NH1" <-> "NH2" Residue "R TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 171": "NH1" <-> "NH2" Residue "R ARG 199": "NH1" <-> "NH2" Residue "R PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 355": "NH1" <-> "NH2" Residue "R PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 394": "NH1" <-> "NH2" Residue "P ARG 11": "NH1" <-> "NH2" Residue "P ARG 13": "NH1" <-> "NH2" Residue "P ARG 15": "NH1" <-> "NH2" Residue "P ARG 22": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9488 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3072 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 10, 'TRANS': 365} Chain breaks: 3 Chain: "P" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 282 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1905 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 220 Unusual residues: {'CLR': 4, 'PLM': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 5.70, per 1000 atoms: 0.60 Number of scatterers: 9488 At special positions: 0 Unit cell: (74.195, 101.365, 172.425, 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 58 16.00 O 1705 8.00 N 1619 7.00 C 6106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 72 " distance=2.03 Simple disulfide: pdb=" SG CYS R 63 " - pdb=" SG CYS R 103 " distance=2.03 Simple disulfide: pdb=" SG CYS R 86 " - pdb=" SG CYS R 125 " distance=2.04 Simple disulfide: pdb=" SG CYS R 236 " - pdb=" SG CYS R 306 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 3.66 Conformation dependent library (CDL) restraints added in 1.8 seconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2180 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 11 sheets defined 39.8% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'R' and resid 34 through 56 removed outlier: 3.882A pdb=" N THR R 53 " --> pdb=" O GLU R 49 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA R 54 " --> pdb=" O LEU R 50 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN R 55 " --> pdb=" O ASN R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 168 removed outlier: 3.555A pdb=" N LEU R 159 " --> pdb=" O SER R 155 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL R 161 " --> pdb=" O GLY R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 204 Processing helix chain 'R' and resid 234 through 266 removed outlier: 3.522A pdb=" N VAL R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA R 248 " --> pdb=" O ILE R 244 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN R 263 " --> pdb=" O LEU R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 301 Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 314 through 346 removed outlier: 4.802A pdb=" N ALA R 320 " --> pdb=" O ILE R 317 " (cutoff:3.500A) Proline residue: R 321 - end of helix removed outlier: 3.514A pdb=" N VAL R 339 " --> pdb=" O THR R 336 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU R 340 " --> pdb=" O VAL R 337 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU R 346 " --> pdb=" O LYS R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 354 through 372 Processing helix chain 'R' and resid 374 through 380 Processing helix chain 'R' and resid 389 through 413 removed outlier: 4.489A pdb=" N GLY R 406 " --> pdb=" O ASN R 402 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE R 407 " --> pdb=" O SER R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 418 through 433 Processing helix chain 'P' and resid 5 through 33 Processing helix chain 'A' and resid 12 through 39 removed outlier: 4.265A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 332 through 352 removed outlier: 4.396A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.613A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.736A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'R' and resid 81 through 85 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.137A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.163A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.294A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.555A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.898A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.951A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.663A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 7.063A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.699A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 3.95 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: 3030 1.34 - 1.47: 2348 1.47 - 1.59: 4242 1.59 - 1.71: 0 1.71 - 1.83: 80 Bond restraints: 9700 Sorted by residual: bond pdb=" C PHE R 286 " pdb=" N PRO R 287 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.58e+00 bond pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.32e-02 5.74e+03 3.30e+00 bond pdb=" C5 CLR R 503 " pdb=" C6 CLR R 503 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C ALA R 320 " pdb=" N PRO R 321 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.39e+00 bond pdb=" C5 CLR R 502 " pdb=" C6 CLR R 502 " ideal model delta sigma weight residual 1.332 1.302 0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 9695 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.79: 232 106.79 - 113.59: 5342 113.59 - 120.39: 3638 120.39 - 127.19: 3798 127.19 - 134.00: 107 Bond angle restraints: 13117 Sorted by residual: angle pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " pdb=" CG TYR R 148 " ideal model delta sigma weight residual 113.90 121.73 -7.83 1.80e+00 3.09e-01 1.89e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 124.31 130.25 -5.94 1.67e+00 3.59e-01 1.27e+01 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 122.74 127.49 -4.75 1.44e+00 4.82e-01 1.09e+01 angle pdb=" N GLY B 116 " pdb=" CA GLY B 116 " pdb=" C GLY B 116 " ideal model delta sigma weight residual 111.27 116.50 -5.23 1.67e+00 3.59e-01 9.82e+00 angle pdb=" C MET R 147 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 121.14 115.67 5.47 1.75e+00 3.27e-01 9.78e+00 ... (remaining 13112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 5777 18.02 - 36.04: 127 36.04 - 54.05: 35 54.05 - 72.07: 3 72.07 - 90.09: 3 Dihedral angle restraints: 5945 sinusoidal: 2570 harmonic: 3375 Sorted by residual: dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 72 " pdb=" CB CYS R 72 " ideal model delta sinusoidal sigma weight residual -86.00 -176.09 90.09 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CA TYR R 233 " pdb=" C TYR R 233 " pdb=" N ILE R 234 " pdb=" CA ILE R 234 " ideal model delta harmonic sigma weight residual -180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ARG A 231 " pdb=" C ARG A 231 " pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 5942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1295 0.090 - 0.180: 131 0.180 - 0.270: 9 0.270 - 0.360: 4 0.360 - 0.451: 4 Chirality restraints: 1443 Sorted by residual: chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.77 0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" C14 CLR R 501 " pdb=" C13 CLR R 501 " pdb=" C15 CLR R 501 " pdb=" C8 CLR R 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.77 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" C14 CLR R 503 " pdb=" C13 CLR R 503 " pdb=" C15 CLR R 503 " pdb=" C8 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 1440 not shown) Planarity restraints: 1639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 242 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C MET R 242 " -0.049 2.00e-02 2.50e+03 pdb=" O MET R 242 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE R 243 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.46e+00 pdb=" N PRO A 332 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.043 5.00e-02 4.00e+02 6.57e-02 6.92e+00 pdb=" N PRO A 361 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.036 5.00e-02 4.00e+02 ... (remaining 1636 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1354 2.77 - 3.30: 8772 3.30 - 3.84: 15539 3.84 - 4.37: 17974 4.37 - 4.90: 31555 Nonbonded interactions: 75194 Sorted by model distance: nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.240 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.267 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.292 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.301 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.307 2.440 ... (remaining 75189 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 2.850 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.560 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 0.004 0.049 9700 Z= 0.251 Angle : 0.844 8.843 13117 Z= 0.470 Chirality : 0.060 0.451 1443 Planarity : 0.006 0.068 1639 Dihedral : 8.872 77.994 3747 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 0.51 (0.22), residues: 1141 helix: 1.29 (0.20), residues: 464 sheet: 0.82 (0.36), residues: 211 loop : -0.84 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 281 HIS 0.022 0.003 HIS A 220 PHE 0.032 0.003 PHE R 290 TYR 0.024 0.002 TYR R 178 ARG 0.006 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 33 THR cc_start: 0.8198 (m) cc_final: 0.6786 (m) REVERT: R 70 LEU cc_start: 0.8501 (tp) cc_final: 0.8227 (pt) REVERT: R 86 CYS cc_start: 0.3613 (m) cc_final: 0.3144 (m) REVERT: R 371 VAL cc_start: 0.8306 (t) cc_final: 0.7947 (p) REVERT: R 410 SER cc_start: 0.8490 (t) cc_final: 0.8211 (p) REVERT: A 221 MET cc_start: 0.7304 (ttp) cc_final: 0.7027 (ttp) REVERT: A 344 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7065 (tp30) REVERT: B 280 LYS cc_start: 0.8534 (tttp) cc_final: 0.8268 (tttp) REVERT: N 11 LEU cc_start: 0.8565 (tp) cc_final: 0.8222 (tm) REVERT: N 73 ASP cc_start: 0.7387 (t0) cc_final: 0.6774 (t0) REVERT: N 78 THR cc_start: 0.6547 (m) cc_final: 0.6237 (m) REVERT: N 95 TYR cc_start: 0.8595 (m-10) cc_final: 0.8372 (m-80) outliers start: 0 outliers final: 1 residues processed: 340 average time/residue: 1.0773 time to fit residues: 392.6556 Evaluate side-chains 204 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 0.0470 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 GLN R 204 HIS R 250 ASN R 396 HIS A 23 ASN A 59 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS B 88 ASN B 91 HIS ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9700 Z= 0.161 Angle : 0.562 7.879 13117 Z= 0.297 Chirality : 0.042 0.259 1443 Planarity : 0.005 0.059 1639 Dihedral : 6.691 57.198 1615 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.83 % Allowed : 18.20 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.24), residues: 1141 helix: 2.22 (0.22), residues: 462 sheet: 0.82 (0.35), residues: 223 loop : -0.46 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 281 HIS 0.006 0.001 HIS R 180 PHE 0.031 0.002 PHE R 290 TYR 0.028 0.002 TYR R 148 ARG 0.008 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 217 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8493 (mp0) cc_final: 0.8082 (pm20) REVERT: R 421 GLN cc_start: 0.8804 (mt0) cc_final: 0.8537 (mt0) REVERT: P 16 LEU cc_start: 0.8325 (tm) cc_final: 0.8095 (tm) REVERT: P 20 LEU cc_start: 0.9062 (mt) cc_final: 0.8778 (mt) REVERT: A 292 ASN cc_start: 0.9036 (m110) cc_final: 0.8437 (m-40) REVERT: B 155 ASN cc_start: 0.7402 (t0) cc_final: 0.6789 (t0) REVERT: B 220 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8409 (mt0) REVERT: B 280 LYS cc_start: 0.8665 (tttp) cc_final: 0.8407 (tttp) REVERT: B 298 ASP cc_start: 0.7960 (t0) cc_final: 0.7745 (t0) REVERT: G 21 MET cc_start: 0.7286 (tmm) cc_final: 0.6972 (tmm) REVERT: N 11 LEU cc_start: 0.8440 (tp) cc_final: 0.8229 (tm) REVERT: N 73 ASP cc_start: 0.7432 (t0) cc_final: 0.6840 (t0) REVERT: N 82 GLN cc_start: 0.8035 (tp-100) cc_final: 0.7795 (tp40) REVERT: N 87 LYS cc_start: 0.8891 (mmtp) cc_final: 0.8589 (mttp) REVERT: N 95 TYR cc_start: 0.8531 (m-10) cc_final: 0.8304 (m-80) outliers start: 28 outliers final: 7 residues processed: 232 average time/residue: 1.1649 time to fit residues: 289.3536 Evaluate side-chains 177 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 169 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 84 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 396 HIS A 23 ASN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 HIS B 88 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9700 Z= 0.205 Angle : 0.539 7.069 13117 Z= 0.289 Chirality : 0.041 0.255 1443 Planarity : 0.004 0.038 1639 Dihedral : 6.432 57.108 1613 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.04 % Allowed : 19.11 % Favored : 76.85 % 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: 1.32 (0.24), residues: 1141 helix: 2.13 (0.23), residues: 468 sheet: 0.73 (0.35), residues: 224 loop : -0.38 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 281 HIS 0.004 0.001 HIS R 180 PHE 0.028 0.002 PHE R 290 TYR 0.025 0.002 TYR P 29 ARG 0.010 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 176 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 33 THR cc_start: 0.8311 (m) cc_final: 0.8023 (m) REVERT: R 35 GLU cc_start: 0.8539 (mp0) cc_final: 0.8133 (pm20) REVERT: R 273 THR cc_start: 0.7355 (m) cc_final: 0.7143 (t) REVERT: R 309 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7737 (mm) REVERT: R 357 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7730 (pp30) REVERT: R 397 CYS cc_start: 0.8572 (m) cc_final: 0.8329 (m) REVERT: R 421 GLN cc_start: 0.8774 (mt0) cc_final: 0.8457 (mt0) REVERT: R 423 GLU cc_start: 0.7943 (tp30) cc_final: 0.7615 (tp30) REVERT: P 20 LEU cc_start: 0.8981 (mt) cc_final: 0.8584 (mt) REVERT: A 281 TRP cc_start: 0.7750 (m100) cc_final: 0.7491 (m100) REVERT: B 19 ARG cc_start: 0.8081 (ttm110) cc_final: 0.7869 (ttp-110) REVERT: B 280 LYS cc_start: 0.8778 (tttp) cc_final: 0.8573 (tttp) REVERT: G 21 MET cc_start: 0.7310 (tmm) cc_final: 0.7010 (tmm) REVERT: N 11 LEU cc_start: 0.8492 (tp) cc_final: 0.8268 (tm) REVERT: N 73 ASP cc_start: 0.7526 (t0) cc_final: 0.7003 (t0) REVERT: N 76 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8168 (ttmm) REVERT: N 82 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7662 (tp40) REVERT: N 87 LYS cc_start: 0.8901 (mmtp) cc_final: 0.8572 (mttp) REVERT: N 89 GLU cc_start: 0.8504 (pp20) cc_final: 0.8017 (tm-30) REVERT: N 105 ARG cc_start: 0.8077 (mtm180) cc_final: 0.7729 (mtp85) outliers start: 40 outliers final: 17 residues processed: 195 average time/residue: 1.1434 time to fit residues: 239.4139 Evaluate side-chains 175 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 357 GLN Chi-restraints excluded: chain R residue 393 ILE Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 396 HIS ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 390 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9700 Z= 0.216 Angle : 0.530 7.982 13117 Z= 0.281 Chirality : 0.040 0.234 1443 Planarity : 0.004 0.037 1639 Dihedral : 6.143 59.715 1613 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.04 % Allowed : 19.92 % Favored : 76.04 % 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: 1.32 (0.24), residues: 1141 helix: 2.14 (0.23), residues: 463 sheet: 0.47 (0.33), residues: 231 loop : -0.19 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 431 HIS 0.007 0.001 HIS P 31 PHE 0.027 0.002 PHE R 290 TYR 0.023 0.002 TYR P 29 ARG 0.007 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 179 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8617 (mp0) cc_final: 0.8394 (mp0) REVERT: R 273 THR cc_start: 0.7486 (m) cc_final: 0.7275 (t) REVERT: R 309 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7698 (mm) REVERT: R 397 CYS cc_start: 0.8660 (m) cc_final: 0.8335 (m) REVERT: R 421 GLN cc_start: 0.8653 (mt0) cc_final: 0.8337 (mt0) REVERT: R 427 MET cc_start: 0.8349 (tmm) cc_final: 0.8073 (tmt) REVERT: P 12 GLU cc_start: 0.8255 (tp30) cc_final: 0.8047 (tp30) REVERT: P 16 LEU cc_start: 0.8391 (tm) cc_final: 0.8074 (tm) REVERT: P 20 LEU cc_start: 0.8990 (mt) cc_final: 0.8592 (mt) REVERT: A 220 HIS cc_start: 0.7164 (m170) cc_final: 0.6835 (m170) REVERT: A 344 GLU cc_start: 0.7173 (tt0) cc_final: 0.6925 (mt-10) REVERT: A 346 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7567 (mm) REVERT: B 19 ARG cc_start: 0.8087 (ttm110) cc_final: 0.7838 (ttp-110) REVERT: B 226 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7896 (mm-30) REVERT: B 268 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8125 (p0) REVERT: B 308 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8412 (mt) REVERT: G 21 MET cc_start: 0.7453 (tmm) cc_final: 0.7206 (tmm) REVERT: N 11 LEU cc_start: 0.8605 (tp) cc_final: 0.8336 (tm) REVERT: N 46 GLU cc_start: 0.8340 (pt0) cc_final: 0.8058 (pt0) REVERT: N 73 ASP cc_start: 0.7646 (t0) cc_final: 0.7218 (t0) REVERT: N 76 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8229 (tptp) REVERT: N 77 ASN cc_start: 0.7861 (t0) cc_final: 0.7434 (t0) REVERT: N 82 GLN cc_start: 0.8266 (tp-100) cc_final: 0.7793 (tp40) REVERT: N 87 LYS cc_start: 0.9037 (mmtp) cc_final: 0.8731 (mttp) REVERT: N 89 GLU cc_start: 0.8605 (pp20) cc_final: 0.8019 (tm-30) REVERT: N 105 ARG cc_start: 0.8145 (mtm180) cc_final: 0.7842 (mtm-85) outliers start: 40 outliers final: 19 residues processed: 205 average time/residue: 1.1210 time to fit residues: 247.0154 Evaluate side-chains 178 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 75 optimal weight: 0.0570 chunk 0 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN R 396 HIS ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9700 Z= 0.188 Angle : 0.517 8.526 13117 Z= 0.274 Chirality : 0.040 0.215 1443 Planarity : 0.004 0.038 1639 Dihedral : 6.011 59.414 1613 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.74 % Allowed : 21.44 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1141 helix: 2.31 (0.23), residues: 460 sheet: 0.44 (0.33), residues: 230 loop : -0.26 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 119 HIS 0.006 0.001 HIS P 31 PHE 0.032 0.002 PHE B 292 TYR 0.025 0.002 TYR P 29 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 172 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 273 THR cc_start: 0.7488 (m) cc_final: 0.7275 (t) REVERT: R 309 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7661 (mm) REVERT: R 397 CYS cc_start: 0.8665 (m) cc_final: 0.8356 (m) REVERT: R 421 GLN cc_start: 0.8674 (mt0) cc_final: 0.8348 (mt0) REVERT: R 423 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: P 20 LEU cc_start: 0.9044 (mt) cc_final: 0.8690 (mt) REVERT: A 344 GLU cc_start: 0.7172 (tt0) cc_final: 0.6935 (mt-10) REVERT: A 346 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7695 (mm) REVERT: B 19 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7895 (ttp-110) REVERT: B 226 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7866 (mm-30) REVERT: B 267 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: B 268 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8097 (p0) REVERT: B 292 PHE cc_start: 0.7895 (m-80) cc_final: 0.7666 (m-80) REVERT: B 308 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8426 (mt) REVERT: G 21 MET cc_start: 0.7573 (tmm) cc_final: 0.7236 (tmm) REVERT: G 38 MET cc_start: 0.7602 (mtm) cc_final: 0.6939 (mtt) REVERT: N 11 LEU cc_start: 0.8637 (tp) cc_final: 0.8369 (tm) REVERT: N 46 GLU cc_start: 0.8354 (pt0) cc_final: 0.8049 (pt0) REVERT: N 73 ASP cc_start: 0.7720 (t0) cc_final: 0.7246 (t0) REVERT: N 76 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8288 (tptp) REVERT: N 77 ASN cc_start: 0.7795 (t0) cc_final: 0.7399 (t0) REVERT: N 89 GLU cc_start: 0.8639 (pp20) cc_final: 0.8023 (tm-30) REVERT: N 105 ARG cc_start: 0.8157 (mtm180) cc_final: 0.7737 (mtm180) outliers start: 37 outliers final: 19 residues processed: 193 average time/residue: 1.1570 time to fit residues: 238.7770 Evaluate side-chains 184 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain R residue 423 GLU Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 204 HIS R 319 GLN R 396 HIS ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 44 GLN B 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9700 Z= 0.201 Angle : 0.522 7.553 13117 Z= 0.279 Chirality : 0.040 0.163 1443 Planarity : 0.004 0.042 1639 Dihedral : 5.902 59.669 1613 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.65 % Allowed : 20.93 % Favored : 74.42 % 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: 1.37 (0.25), residues: 1141 helix: 2.30 (0.24), residues: 462 sheet: 0.35 (0.33), residues: 236 loop : -0.22 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 431 HIS 0.007 0.001 HIS P 31 PHE 0.024 0.001 PHE R 290 TYR 0.026 0.002 TYR P 29 ARG 0.008 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 33 THR cc_start: 0.8209 (m) cc_final: 0.8002 (m) REVERT: R 35 GLU cc_start: 0.8446 (mp0) cc_final: 0.8133 (pm20) REVERT: R 273 THR cc_start: 0.7552 (m) cc_final: 0.7323 (t) REVERT: R 309 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7618 (mm) REVERT: R 319 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7596 (tp40) REVERT: R 397 CYS cc_start: 0.8668 (m) cc_final: 0.8356 (m) REVERT: R 421 GLN cc_start: 0.8618 (mt0) cc_final: 0.8285 (mt0) REVERT: P 12 GLU cc_start: 0.8320 (tp30) cc_final: 0.8055 (tp30) REVERT: P 16 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8112 (tm) REVERT: P 20 LEU cc_start: 0.9046 (mt) cc_final: 0.8684 (mt) REVERT: P 21 GLU cc_start: 0.8507 (pp20) cc_final: 0.8123 (pp20) REVERT: A 344 GLU cc_start: 0.7190 (tt0) cc_final: 0.6948 (mt-10) REVERT: A 346 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8006 (mm) REVERT: A 365 CYS cc_start: 0.7528 (m) cc_final: 0.7228 (t) REVERT: A 389 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7924 (ttp80) REVERT: B 19 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7954 (ttp-110) REVERT: B 226 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7838 (mt-10) REVERT: B 230 ASN cc_start: 0.8553 (m-40) cc_final: 0.8198 (m110) REVERT: B 301 LYS cc_start: 0.8538 (mmmm) cc_final: 0.8284 (mmmt) REVERT: B 308 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8447 (mt) REVERT: G 21 MET cc_start: 0.7563 (tmm) cc_final: 0.7248 (tmm) REVERT: N 35 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.7180 (p0) REVERT: N 46 GLU cc_start: 0.8323 (pt0) cc_final: 0.8008 (pt0) REVERT: N 73 ASP cc_start: 0.7794 (t0) cc_final: 0.7301 (t0) REVERT: N 76 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8299 (tptp) REVERT: N 77 ASN cc_start: 0.7822 (t0) cc_final: 0.7437 (t0) REVERT: N 83 MET cc_start: 0.8792 (mtm) cc_final: 0.8485 (ptp) REVERT: N 89 GLU cc_start: 0.8620 (pp20) cc_final: 0.7941 (tm-30) REVERT: N 105 ARG cc_start: 0.8168 (mtm180) cc_final: 0.7779 (mtm180) outliers start: 46 outliers final: 24 residues processed: 204 average time/residue: 1.1645 time to fit residues: 254.3969 Evaluate side-chains 191 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 319 GLN Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN R 396 HIS ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9700 Z= 0.231 Angle : 0.548 8.137 13117 Z= 0.292 Chirality : 0.040 0.141 1443 Planarity : 0.004 0.037 1639 Dihedral : 5.897 59.656 1613 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.75 % Allowed : 21.13 % 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: 1.38 (0.25), residues: 1141 helix: 2.30 (0.24), residues: 462 sheet: 0.20 (0.32), residues: 246 loop : -0.11 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 119 HIS 0.008 0.001 HIS P 31 PHE 0.044 0.002 PHE B 292 TYR 0.026 0.002 TYR P 29 ARG 0.006 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 162 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 273 THR cc_start: 0.7699 (m) cc_final: 0.7418 (t) REVERT: R 309 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7574 (mm) REVERT: R 397 CYS cc_start: 0.8626 (m) cc_final: 0.8338 (m) REVERT: R 421 GLN cc_start: 0.8634 (mt0) cc_final: 0.8286 (mt0) REVERT: P 16 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8128 (tm) REVERT: P 20 LEU cc_start: 0.9023 (mt) cc_final: 0.8646 (mt) REVERT: A 344 GLU cc_start: 0.7292 (tt0) cc_final: 0.7041 (mt-10) REVERT: A 365 CYS cc_start: 0.7543 (m) cc_final: 0.7275 (t) REVERT: A 389 ARG cc_start: 0.8185 (tpp80) cc_final: 0.7953 (ttp80) REVERT: B 19 ARG cc_start: 0.8212 (ttm110) cc_final: 0.7960 (ttp-110) REVERT: B 226 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7827 (mt-10) REVERT: B 230 ASN cc_start: 0.8555 (m-40) cc_final: 0.8244 (m110) REVERT: B 267 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8144 (m-30) REVERT: G 21 MET cc_start: 0.7535 (tmm) cc_final: 0.7257 (tmm) REVERT: G 38 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6814 (mtm) REVERT: N 46 GLU cc_start: 0.8320 (pt0) cc_final: 0.7996 (pt0) REVERT: N 73 ASP cc_start: 0.7830 (t0) cc_final: 0.7337 (t0) REVERT: N 76 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8360 (tptp) REVERT: N 83 MET cc_start: 0.8832 (mtm) cc_final: 0.8557 (ptp) outliers start: 47 outliers final: 25 residues processed: 190 average time/residue: 1.1837 time to fit residues: 241.8260 Evaluate side-chains 185 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 358 TYR Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 396 HIS A 19 GLN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 44 GLN B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9700 Z= 0.213 Angle : 0.541 6.588 13117 Z= 0.289 Chirality : 0.040 0.142 1443 Planarity : 0.004 0.036 1639 Dihedral : 5.836 59.289 1613 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.94 % Allowed : 22.55 % Favored : 73.51 % 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: 1.34 (0.25), residues: 1141 helix: 2.31 (0.24), residues: 462 sheet: 0.15 (0.33), residues: 234 loop : -0.17 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 431 HIS 0.007 0.001 HIS P 31 PHE 0.029 0.002 PHE B 292 TYR 0.027 0.002 TYR P 29 ARG 0.006 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 167 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 70 LEU cc_start: 0.8364 (pt) cc_final: 0.7866 (tm) REVERT: R 273 THR cc_start: 0.7721 (m) cc_final: 0.7440 (t) REVERT: R 303 ASP cc_start: 0.7334 (t0) cc_final: 0.7116 (t70) REVERT: R 309 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7646 (mm) REVERT: R 397 CYS cc_start: 0.8621 (m) cc_final: 0.8333 (m) REVERT: R 421 GLN cc_start: 0.8647 (mt0) cc_final: 0.8286 (mt0) REVERT: P 16 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8126 (tm) REVERT: P 20 LEU cc_start: 0.9060 (mt) cc_final: 0.8697 (mt) REVERT: P 21 GLU cc_start: 0.8555 (pp20) cc_final: 0.8170 (pp20) REVERT: A 344 GLU cc_start: 0.7316 (tt0) cc_final: 0.7069 (mt-10) REVERT: A 389 ARG cc_start: 0.8174 (tpp80) cc_final: 0.7970 (ttp80) REVERT: B 19 ARG cc_start: 0.8269 (ttm110) cc_final: 0.8013 (ttp-110) REVERT: B 226 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7803 (mt-10) REVERT: B 292 PHE cc_start: 0.8261 (m-10) cc_final: 0.7843 (m-80) REVERT: G 21 MET cc_start: 0.7543 (tmm) cc_final: 0.7263 (tmm) REVERT: N 43 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7926 (ttmm) REVERT: N 46 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8042 (pt0) REVERT: N 73 ASP cc_start: 0.7762 (t0) cc_final: 0.7170 (t0) REVERT: N 76 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8482 (ttmm) REVERT: N 83 MET cc_start: 0.8844 (mtm) cc_final: 0.8598 (ptp) outliers start: 39 outliers final: 25 residues processed: 190 average time/residue: 1.1168 time to fit residues: 227.9003 Evaluate side-chains 186 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.0980 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 396 HIS ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 230 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9700 Z= 0.215 Angle : 0.560 8.540 13117 Z= 0.298 Chirality : 0.040 0.137 1443 Planarity : 0.004 0.037 1639 Dihedral : 5.808 58.588 1613 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.15 % Allowed : 21.94 % Favored : 73.91 % 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: 1.28 (0.25), residues: 1141 helix: 2.24 (0.24), residues: 466 sheet: 0.17 (0.33), residues: 233 loop : -0.23 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 119 HIS 0.007 0.001 HIS A 220 PHE 0.023 0.001 PHE R 290 TYR 0.028 0.002 TYR P 29 ARG 0.006 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 165 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 70 LEU cc_start: 0.8454 (pt) cc_final: 0.8006 (tm) REVERT: R 273 THR cc_start: 0.7749 (m) cc_final: 0.7476 (t) REVERT: R 303 ASP cc_start: 0.7483 (t0) cc_final: 0.7264 (t70) REVERT: R 309 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7735 (mm) REVERT: R 397 CYS cc_start: 0.8622 (m) cc_final: 0.8330 (m) REVERT: R 421 GLN cc_start: 0.8615 (mt0) cc_final: 0.8229 (mt0) REVERT: P 16 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8091 (tm) REVERT: P 20 LEU cc_start: 0.9032 (mt) cc_final: 0.8668 (mt) REVERT: A 27 GLU cc_start: 0.8149 (tp30) cc_final: 0.7540 (tp30) REVERT: A 344 GLU cc_start: 0.7349 (tt0) cc_final: 0.7101 (mt-10) REVERT: B 19 ARG cc_start: 0.8254 (ttm110) cc_final: 0.8003 (ttp-110) REVERT: B 226 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7825 (mt-10) REVERT: B 292 PHE cc_start: 0.8357 (m-10) cc_final: 0.7912 (m-80) REVERT: G 21 MET cc_start: 0.7537 (tmm) cc_final: 0.7263 (tmm) REVERT: N 3 GLN cc_start: 0.8334 (tt0) cc_final: 0.7927 (tt0) REVERT: N 43 LYS cc_start: 0.8291 (ttmt) cc_final: 0.8057 (ttmm) REVERT: N 46 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8044 (pt0) REVERT: N 73 ASP cc_start: 0.7793 (t0) cc_final: 0.7241 (t0) REVERT: N 76 LYS cc_start: 0.8855 (ttmm) cc_final: 0.8262 (tptp) REVERT: N 83 MET cc_start: 0.8877 (mtm) cc_final: 0.8673 (ptp) outliers start: 41 outliers final: 21 residues processed: 192 average time/residue: 1.1274 time to fit residues: 232.5442 Evaluate side-chains 182 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 71 optimal weight: 0.0070 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 396 HIS ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 230 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9700 Z= 0.200 Angle : 0.576 11.945 13117 Z= 0.303 Chirality : 0.040 0.139 1443 Planarity : 0.004 0.062 1639 Dihedral : 5.741 58.524 1613 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.03 % Allowed : 23.56 % Favored : 73.41 % 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: 1.32 (0.25), residues: 1141 helix: 2.25 (0.24), residues: 461 sheet: 0.20 (0.32), residues: 240 loop : -0.15 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 431 HIS 0.007 0.001 HIS P 31 PHE 0.023 0.001 PHE R 290 TYR 0.027 0.002 TYR R 168 ARG 0.006 0.000 ARG A 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 70 LEU cc_start: 0.8498 (pt) cc_final: 0.8054 (tm) REVERT: R 273 THR cc_start: 0.7733 (m) cc_final: 0.7459 (t) REVERT: R 303 ASP cc_start: 0.7495 (t0) cc_final: 0.7267 (t70) REVERT: R 309 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7706 (mm) REVERT: R 397 CYS cc_start: 0.8615 (m) cc_final: 0.8325 (m) REVERT: R 421 GLN cc_start: 0.8505 (mt0) cc_final: 0.8215 (mt0) REVERT: R 423 GLU cc_start: 0.6806 (tt0) cc_final: 0.6565 (tt0) REVERT: P 16 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8107 (tm) REVERT: P 20 LEU cc_start: 0.9043 (mt) cc_final: 0.8710 (mt) REVERT: P 21 GLU cc_start: 0.8656 (pp20) cc_final: 0.8373 (pp20) REVERT: A 27 GLU cc_start: 0.8147 (tp30) cc_final: 0.7541 (tp30) REVERT: A 344 GLU cc_start: 0.7317 (tt0) cc_final: 0.7073 (mt-10) REVERT: B 19 ARG cc_start: 0.8274 (ttm110) cc_final: 0.7909 (ttp-110) REVERT: B 226 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7848 (mt-10) REVERT: B 262 MET cc_start: 0.7502 (mtp) cc_final: 0.7271 (mtt) REVERT: B 292 PHE cc_start: 0.8357 (m-10) cc_final: 0.7887 (m-80) REVERT: G 21 MET cc_start: 0.7529 (tmm) cc_final: 0.7252 (tmm) REVERT: N 3 GLN cc_start: 0.8323 (tt0) cc_final: 0.7976 (tt0) REVERT: N 43 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7884 (ttmm) REVERT: N 46 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8025 (pt0) REVERT: N 73 ASP cc_start: 0.7748 (t0) cc_final: 0.7222 (t0) REVERT: N 76 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8217 (tptp) REVERT: N 85 SER cc_start: 0.8941 (m) cc_final: 0.8639 (p) outliers start: 30 outliers final: 20 residues processed: 185 average time/residue: 1.1257 time to fit residues: 223.8178 Evaluate side-chains 181 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 309 LEU Chi-restraints excluded: chain R residue 337 VAL Chi-restraints excluded: chain R residue 411 ILE Chi-restraints excluded: chain P residue 6 ASP Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 23 ARG Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 89 optimal weight: 0.0170 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 0.0370 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 0.0770 chunk 5 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 overall best weight: 0.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 396 HIS ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 44 GLN B 230 ASN B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.144419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.104599 restraints weight = 14847.108| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.93 r_work: 0.3279 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9700 Z= 0.162 Angle : 0.562 9.851 13117 Z= 0.296 Chirality : 0.040 0.158 1443 Planarity : 0.004 0.059 1639 Dihedral : 5.546 58.810 1613 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.33 % Allowed : 24.37 % Favored : 73.31 % 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: 1.34 (0.25), residues: 1141 helix: 2.34 (0.24), residues: 460 sheet: 0.26 (0.33), residues: 225 loop : -0.24 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.007 0.001 HIS P 31 PHE 0.024 0.001 PHE R 290 TYR 0.028 0.002 TYR P 29 ARG 0.012 0.000 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4339.64 seconds wall clock time: 76 minutes 49.93 seconds (4609.93 seconds total)