Starting phenix.real_space_refine on Wed Feb 14 03:27:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv5_22493/02_2024/7jv5_22493.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv5_22493/02_2024/7jv5_22493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv5_22493/02_2024/7jv5_22493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv5_22493/02_2024/7jv5_22493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv5_22493/02_2024/7jv5_22493.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jv5_22493/02_2024/7jv5_22493.pdb" } resolution = 3.0 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= 0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians S 54 5.16 5 Cl 1 4.86 5 C 5493 2.51 5 N 1444 2.21 5 O 1539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 23": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R ARG 216": "NH1" <-> "NH2" Residue "R ARG 219": "NH1" <-> "NH2" Residue "R ARG 226": "NH1" <-> "NH2" Residue "R ARG 233": "NH1" <-> "NH2" Residue "R ARG 266": "NH1" <-> "NH2" Residue "R ARG 338": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 19": "NH1" <-> "NH2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8531 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2244 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 10, 'TRANS': 271} Chain breaks: 3 Chain: "A" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1978 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 2 Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2604 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} 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: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 296 Unusual residues: {'CLR': 6, 'PLM': 6, 'SK0': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Time building chain proxies: 5.05, per 1000 atoms: 0.59 Number of scatterers: 8531 At special positions: 0 Unit cell: (106.47, 98.358, 120.666, 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) Cl 1 17.00 S 54 16.00 O 1539 8.00 N 1444 7.00 C 5493 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " 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: 3.14 Conformation dependent library (CDL) restraints added in 1.6 seconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 44.1% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'R' and resid 21 through 51 Processing helix chain 'R' and resid 52 through 57 removed outlier: 3.826A pdb=" N LYS R 57 " --> pdb=" O HIS R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 77 removed outlier: 4.148A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 Processing helix chain 'R' and resid 94 through 127 removed outlier: 4.477A pdb=" N ILE R 98 " --> pdb=" O SER R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 135 Processing helix chain 'R' and resid 136 through 156 Processing helix chain 'R' and resid 157 through 162 Processing helix chain 'R' and resid 191 through 203 Processing helix chain 'R' and resid 203 through 240 Processing helix chain 'R' and resid 264 through 295 removed outlier: 3.998A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 296 through 298 No H-bonds generated for 'chain 'R' and resid 296 through 298' Processing helix chain 'R' and resid 309 through 332 removed outlier: 4.580A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU R 326 " --> pdb=" O ALA R 322 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 346 Processing helix chain 'A' and resid 10 through 40 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 234 through 240 removed outlier: 3.595A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 4.055A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.219A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.948A pdb=" N ASP A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.554A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.191A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.736A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.979A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.600A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.599A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.157A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.904A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.773A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.681A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.780A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.590A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1308 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: 2.29 Time building geometry restraints manager: 3.39 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: 2419 1.34 - 1.46: 1815 1.46 - 1.58: 4404 1.58 - 1.70: 0 1.70 - 1.83: 74 Bond restraints: 8712 Sorted by residual: bond pdb=" C MET R 78 " pdb=" N PRO R 79 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.76e+00 bond pdb=" C ILE R 157 " pdb=" N PRO R 158 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.20e-02 6.94e+03 3.59e+00 bond pdb=" CA PHE R 297 " pdb=" C PHE R 297 " ideal model delta sigma weight residual 1.523 1.557 -0.033 1.80e-02 3.09e+03 3.42e+00 bond pdb=" C LEU R 295 " pdb=" N PRO R 296 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.36e-02 5.41e+03 3.35e+00 bond pdb=" C ASN R 327 " pdb=" N PRO R 328 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.27e+00 ... (remaining 8707 not shown) Histogram of bond angle deviations from ideal: 100.02 - 107.06: 255 107.06 - 114.10: 5025 114.10 - 121.14: 4149 121.14 - 128.19: 2292 128.19 - 135.23: 75 Bond angle restraints: 11796 Sorted by residual: angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 122.08 128.51 -6.43 1.47e+00 4.63e-01 1.91e+01 angle pdb=" N MET R 78 " pdb=" CA MET R 78 " pdb=" C MET R 78 " ideal model delta sigma weight residual 109.81 119.30 -9.49 2.21e+00 2.05e-01 1.84e+01 angle pdb=" N GLU A 16 " pdb=" CA GLU A 16 " pdb=" C GLU A 16 " ideal model delta sigma weight residual 111.11 116.04 -4.93 1.20e+00 6.94e-01 1.69e+01 angle pdb=" N ILE B 33 " pdb=" CA ILE B 33 " pdb=" C ILE B 33 " ideal model delta sigma weight residual 110.62 115.17 -4.55 1.14e+00 7.69e-01 1.59e+01 angle pdb=" N LYS A 17 " pdb=" CA LYS A 17 " pdb=" C LYS A 17 " ideal model delta sigma weight residual 111.37 117.33 -5.96 1.65e+00 3.67e-01 1.31e+01 ... (remaining 11791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 5177 15.04 - 30.07: 282 30.07 - 45.11: 46 45.11 - 60.15: 4 60.15 - 75.18: 2 Dihedral angle restraints: 5511 sinusoidal: 2469 harmonic: 3042 Sorted by residual: dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 153.14 26.86 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA SER N 49 " pdb=" C SER N 49 " pdb=" N ASP N 50 " pdb=" CA ASP N 50 " ideal model delta harmonic sigma weight residual 180.00 -153.23 -26.77 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA LEU B 198 " pdb=" C LEU B 198 " pdb=" N PHE B 199 " pdb=" CA PHE B 199 " ideal model delta harmonic sigma weight residual 180.00 154.33 25.67 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 5508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1127 0.085 - 0.170: 169 0.170 - 0.254: 24 0.254 - 0.339: 7 0.339 - 0.424: 7 Chirality restraints: 1334 Sorted by residual: chirality pdb=" C14 CLR R 502 " pdb=" C13 CLR R 502 " pdb=" C15 CLR R 502 " pdb=" C8 CLR R 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" C14 CLR R 507 " pdb=" C13 CLR R 507 " pdb=" C15 CLR R 507 " pdb=" C8 CLR R 507 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.45e+00 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 -2.72 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 1331 not shown) Planarity restraints: 1453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 207 " 0.022 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C VAL R 207 " -0.074 2.00e-02 2.50e+03 pdb=" O VAL R 207 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA R 208 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 218 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C TYR R 218 " 0.073 2.00e-02 2.50e+03 pdb=" O TYR R 218 " -0.027 2.00e-02 2.50e+03 pdb=" N ARG R 219 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 272 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C LYS R 272 " -0.072 2.00e-02 2.50e+03 pdb=" O LYS R 272 " 0.027 2.00e-02 2.50e+03 pdb=" N THR R 273 " 0.025 2.00e-02 2.50e+03 ... (remaining 1450 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1224 2.77 - 3.30: 7752 3.30 - 3.84: 13286 3.84 - 4.37: 15683 4.37 - 4.90: 27429 Nonbonded interactions: 65374 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.240 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.276 2.440 nonbonded pdb=" O TRP N 47 " pdb=" OG1 THR N 61 " model vdw 2.329 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.339 2.440 nonbonded pdb=" NE2 GLN B 75 " pdb=" O VAL B 100 " model vdw 2.345 2.520 ... (remaining 65369 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: 0.640 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: 0.000 Extract box with map and model: 2.090 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 25.590 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 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 : 0.005 0.051 8712 Z= 0.308 Angle : 1.087 10.230 11796 Z= 0.624 Chirality : 0.070 0.424 1334 Planarity : 0.009 0.076 1453 Dihedral : 9.419 75.182 3523 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: -3.02 (0.22), residues: 1024 helix: -2.90 (0.18), residues: 413 sheet: -0.01 (0.33), residues: 232 loop : -2.01 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP N 36 HIS 0.010 0.003 HIS B 183 PHE 0.040 0.003 PHE B 234 TYR 0.020 0.002 TYR R 331 ARG 0.008 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.7224 (mmmt) cc_final: 0.5561 (tttm) REVERT: A 317 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.8225 (ptt-90) REVERT: A 392 GLU cc_start: 0.8387 (tt0) cc_final: 0.7943 (tp30) REVERT: B 46 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7486 (mtp-110) REVERT: B 134 ARG cc_start: 0.7338 (mtm-85) cc_final: 0.6768 (pmt170) REVERT: B 163 ASP cc_start: 0.8713 (p0) cc_final: 0.8502 (p0) REVERT: B 175 GLN cc_start: 0.8563 (mt0) cc_final: 0.7951 (mm-40) REVERT: B 217 MET cc_start: 0.8622 (ptt) cc_final: 0.8300 (ppp) REVERT: B 226 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8540 (mt-10) REVERT: B 239 ASN cc_start: 0.8036 (m-40) cc_final: 0.7240 (t0) REVERT: B 303 ASP cc_start: 0.7805 (t0) cc_final: 0.7469 (p0) REVERT: B 315 VAL cc_start: 0.8675 (t) cc_final: 0.8259 (p) REVERT: G 21 MET cc_start: 0.8095 (mtt) cc_final: 0.7405 (tmm) REVERT: G 61 PHE cc_start: 0.8183 (m-80) cc_final: 0.7903 (m-80) REVERT: N 72 ARG cc_start: 0.8322 (ptm160) cc_final: 0.8062 (ppp80) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 1.2761 time to fit residues: 253.9586 Evaluate side-chains 106 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 0.0980 chunk 42 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 0.0060 chunk 91 optimal weight: 0.6980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 323 ASN R 327 ASN A 14 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 HIS B 75 GLN B 88 ASN B 142 HIS B 176 GLN B 259 GLN N 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8712 Z= 0.147 Angle : 0.528 6.310 11796 Z= 0.280 Chirality : 0.041 0.155 1334 Planarity : 0.005 0.047 1453 Dihedral : 6.459 53.380 1625 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.23 % Allowed : 10.93 % Favored : 86.85 % 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: -0.26 (0.25), residues: 1024 helix: 0.52 (0.23), residues: 427 sheet: 0.60 (0.35), residues: 220 loop : -1.41 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS R 53 PHE 0.014 0.001 PHE B 199 TYR 0.015 0.001 TYR B 105 ARG 0.008 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.8544 (ttm) cc_final: 0.8227 (ttp) REVERT: A 307 LYS cc_start: 0.7360 (mmmt) cc_final: 0.5814 (tttm) REVERT: A 317 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8257 (ptt-90) REVERT: A 392 GLU cc_start: 0.8404 (tt0) cc_final: 0.7977 (tp30) REVERT: B 46 ARG cc_start: 0.7885 (ttm-80) cc_final: 0.7583 (mtp-110) REVERT: B 134 ARG cc_start: 0.7339 (mtm-85) cc_final: 0.6776 (pmt170) REVERT: B 175 GLN cc_start: 0.8598 (mt0) cc_final: 0.7962 (mm-40) REVERT: B 205 ASP cc_start: 0.7731 (p0) cc_final: 0.7287 (p0) REVERT: B 217 MET cc_start: 0.8694 (ptt) cc_final: 0.8296 (ppp) REVERT: B 219 ARG cc_start: 0.8245 (mtp180) cc_final: 0.7659 (mtt90) REVERT: B 226 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8659 (mt-10) REVERT: B 239 ASN cc_start: 0.7996 (m-40) cc_final: 0.7080 (t0) REVERT: B 303 ASP cc_start: 0.7794 (t0) cc_final: 0.7459 (p0) REVERT: B 315 VAL cc_start: 0.8649 (t) cc_final: 0.8268 (p) REVERT: G 21 MET cc_start: 0.8175 (mtt) cc_final: 0.7368 (tmm) REVERT: G 61 PHE cc_start: 0.8183 (m-80) cc_final: 0.7893 (m-80) outliers start: 20 outliers final: 6 residues processed: 134 average time/residue: 1.1420 time to fit residues: 163.7717 Evaluate side-chains 105 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain N residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 ASN R 323 ASN R 327 ASN A 14 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8712 Z= 0.216 Angle : 0.545 6.482 11796 Z= 0.283 Chirality : 0.042 0.168 1334 Planarity : 0.004 0.043 1453 Dihedral : 6.373 56.975 1625 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.01 % Allowed : 12.26 % Favored : 84.73 % 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: 0.86 (0.26), residues: 1024 helix: 2.10 (0.25), residues: 422 sheet: 0.39 (0.33), residues: 234 loop : -1.15 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 36 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.002 PHE B 199 TYR 0.013 0.001 TYR B 59 ARG 0.008 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 0.962 Fit side-chains REVERT: A 34 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7873 (tppt) REVERT: A 221 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8221 (ttp) REVERT: A 265 ARG cc_start: 0.8663 (mmt180) cc_final: 0.8122 (mtm-85) REVERT: A 314 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8097 (mt-10) REVERT: A 317 ARG cc_start: 0.8701 (mtm-85) cc_final: 0.8323 (ptt90) REVERT: A 392 GLU cc_start: 0.8552 (tt0) cc_final: 0.8012 (tp30) REVERT: B 75 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: B 134 ARG cc_start: 0.7681 (mtm-85) cc_final: 0.6897 (pmt170) REVERT: B 175 GLN cc_start: 0.8574 (mt0) cc_final: 0.7991 (mm-40) REVERT: B 205 ASP cc_start: 0.7920 (p0) cc_final: 0.7464 (p0) REVERT: B 217 MET cc_start: 0.8799 (ptt) cc_final: 0.8470 (ppp) REVERT: B 226 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8590 (mt-10) REVERT: B 239 ASN cc_start: 0.8124 (m-40) cc_final: 0.7558 (t0) REVERT: B 303 ASP cc_start: 0.7789 (t0) cc_final: 0.7518 (p0) REVERT: B 339 TRP cc_start: 0.8692 (m100) cc_final: 0.8350 (m-10) REVERT: G 21 MET cc_start: 0.8080 (mtt) cc_final: 0.7323 (tmm) outliers start: 27 outliers final: 14 residues processed: 127 average time/residue: 1.3837 time to fit residues: 186.1263 Evaluate side-chains 109 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8712 Z= 0.254 Angle : 0.556 6.479 11796 Z= 0.287 Chirality : 0.043 0.169 1334 Planarity : 0.004 0.042 1453 Dihedral : 6.584 57.293 1625 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.12 % Allowed : 13.15 % Favored : 82.72 % 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: 0.93 (0.26), residues: 1024 helix: 2.21 (0.25), residues: 435 sheet: 0.35 (0.34), residues: 222 loop : -1.20 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.002 PHE B 199 TYR 0.015 0.001 TYR B 59 ARG 0.008 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 99 time to evaluate : 0.869 Fit side-chains REVERT: R 132 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8233 (mt-10) REVERT: R 154 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.6542 (tt) REVERT: A 34 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7840 (ttpt) REVERT: A 221 MET cc_start: 0.8546 (ttm) cc_final: 0.8200 (mtp) REVERT: A 229 ASP cc_start: 0.8894 (t0) cc_final: 0.8618 (t70) REVERT: A 230 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8165 (mt-10) REVERT: A 265 ARG cc_start: 0.8622 (mmt180) cc_final: 0.8115 (mtm-85) REVERT: A 314 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7714 (pm20) REVERT: A 317 ARG cc_start: 0.8799 (mtm-85) cc_final: 0.8363 (ptt-90) REVERT: A 392 GLU cc_start: 0.8574 (tt0) cc_final: 0.7947 (tp30) REVERT: B 46 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7602 (mtp-110) REVERT: B 68 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7989 (mmm160) REVERT: B 75 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7697 (mp-120) REVERT: B 134 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.6630 (pmt170) REVERT: B 175 GLN cc_start: 0.8708 (mt0) cc_final: 0.8126 (mm110) REVERT: B 180 PHE cc_start: 0.5859 (OUTLIER) cc_final: 0.3636 (p90) REVERT: B 205 ASP cc_start: 0.8015 (p0) cc_final: 0.7599 (p0) REVERT: B 217 MET cc_start: 0.8806 (ptt) cc_final: 0.8597 (ppp) REVERT: B 226 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8600 (mt-10) REVERT: B 239 ASN cc_start: 0.8205 (m-40) cc_final: 0.7740 (t0) REVERT: B 325 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8556 (tpp) REVERT: B 339 TRP cc_start: 0.8741 (m100) cc_final: 0.8379 (m-10) REVERT: G 21 MET cc_start: 0.7992 (mtt) cc_final: 0.7263 (tmm) REVERT: N 105 ARG cc_start: 0.7903 (mtm180) cc_final: 0.7396 (mtm180) outliers start: 37 outliers final: 14 residues processed: 123 average time/residue: 1.2837 time to fit residues: 167.8452 Evaluate side-chains 115 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 185 ASN A 23 ASN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8712 Z= 0.209 Angle : 0.528 7.186 11796 Z= 0.271 Chirality : 0.042 0.151 1334 Planarity : 0.004 0.045 1453 Dihedral : 6.477 57.633 1625 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.01 % Allowed : 14.94 % Favored : 82.05 % 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 (0.26), residues: 1024 helix: 2.45 (0.25), residues: 429 sheet: 0.21 (0.33), residues: 226 loop : -1.19 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE B 199 TYR 0.010 0.001 TYR A 339 ARG 0.009 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: R 154 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.6525 (tt) REVERT: R 185 ASN cc_start: 0.6576 (OUTLIER) cc_final: 0.6274 (m-40) REVERT: A 34 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7802 (ttpt) REVERT: A 60 MET cc_start: 0.6957 (mpt) cc_final: 0.6570 (mpt) REVERT: A 221 MET cc_start: 0.8485 (ttm) cc_final: 0.8213 (mtp) REVERT: A 229 ASP cc_start: 0.8796 (t0) cc_final: 0.8541 (t0) REVERT: A 265 ARG cc_start: 0.8605 (mmt180) cc_final: 0.8124 (mtm-85) REVERT: A 314 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7750 (pm20) REVERT: A 317 ARG cc_start: 0.8840 (mtm-85) cc_final: 0.8386 (ptt-90) REVERT: A 392 GLU cc_start: 0.8558 (tt0) cc_final: 0.7962 (tp30) REVERT: B 68 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7948 (mmm160) REVERT: B 134 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.6627 (pmt170) REVERT: B 175 GLN cc_start: 0.8649 (mt0) cc_final: 0.8089 (mp10) REVERT: B 180 PHE cc_start: 0.6143 (OUTLIER) cc_final: 0.4249 (p90) REVERT: B 189 SER cc_start: 0.8189 (t) cc_final: 0.7896 (m) REVERT: B 205 ASP cc_start: 0.8121 (p0) cc_final: 0.7316 (t0) REVERT: B 217 MET cc_start: 0.8810 (ptt) cc_final: 0.8593 (ppp) REVERT: B 239 ASN cc_start: 0.8197 (m-40) cc_final: 0.7761 (t0) REVERT: B 339 TRP cc_start: 0.8745 (m100) cc_final: 0.8380 (m-10) REVERT: G 21 MET cc_start: 0.7856 (mtt) cc_final: 0.7089 (tmm) REVERT: N 90 ASP cc_start: 0.7857 (p0) cc_final: 0.7498 (p0) REVERT: N 105 ARG cc_start: 0.7998 (mtm180) cc_final: 0.7399 (mtm180) outliers start: 27 outliers final: 11 residues processed: 113 average time/residue: 1.2765 time to fit residues: 153.5181 Evaluate side-chains 104 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 185 ASN Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 185 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8712 Z= 0.227 Angle : 0.533 8.068 11796 Z= 0.274 Chirality : 0.042 0.150 1334 Planarity : 0.003 0.044 1453 Dihedral : 6.534 59.682 1625 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.01 % Allowed : 15.16 % Favored : 81.83 % 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: 1.05 (0.27), residues: 1024 helix: 2.59 (0.25), residues: 421 sheet: 0.05 (0.33), residues: 226 loop : -1.12 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE B 199 TYR 0.012 0.001 TYR A 339 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: R 154 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.6565 (tt) REVERT: A 34 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7776 (ttpt) REVERT: A 60 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6671 (mpt) REVERT: A 229 ASP cc_start: 0.8786 (t0) cc_final: 0.8517 (t0) REVERT: A 265 ARG cc_start: 0.8601 (mmt180) cc_final: 0.8128 (mtm-85) REVERT: A 314 GLU cc_start: 0.8504 (mt-10) cc_final: 0.7755 (pm20) REVERT: A 317 ARG cc_start: 0.8880 (mtm-85) cc_final: 0.8383 (ptt-90) REVERT: A 392 GLU cc_start: 0.8565 (tt0) cc_final: 0.7967 (tp30) REVERT: B 68 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.8024 (mmm160) REVERT: B 134 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.6658 (pmt170) REVERT: B 175 GLN cc_start: 0.8629 (mt0) cc_final: 0.8088 (mp10) REVERT: B 180 PHE cc_start: 0.6301 (OUTLIER) cc_final: 0.4772 (p90) REVERT: B 189 SER cc_start: 0.8196 (t) cc_final: 0.7875 (m) REVERT: B 205 ASP cc_start: 0.8168 (p0) cc_final: 0.7751 (p0) REVERT: B 214 ARG cc_start: 0.9211 (tpp80) cc_final: 0.8678 (mmt180) REVERT: B 217 MET cc_start: 0.8828 (ptt) cc_final: 0.8600 (ppp) REVERT: B 239 ASN cc_start: 0.8271 (m-40) cc_final: 0.7829 (t0) REVERT: B 339 TRP cc_start: 0.8782 (m100) cc_final: 0.8379 (m-10) REVERT: G 21 MET cc_start: 0.7772 (mtt) cc_final: 0.7028 (tmm) REVERT: N 38 ARG cc_start: 0.9017 (ptt180) cc_final: 0.8537 (ptm-80) REVERT: N 90 ASP cc_start: 0.7884 (p0) cc_final: 0.7591 (p0) REVERT: N 105 ARG cc_start: 0.8021 (mtm180) cc_final: 0.7413 (mtm180) outliers start: 27 outliers final: 14 residues processed: 114 average time/residue: 1.2877 time to fit residues: 156.4283 Evaluate side-chains 109 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.0040 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 185 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8712 Z= 0.230 Angle : 0.533 8.773 11796 Z= 0.274 Chirality : 0.042 0.148 1334 Planarity : 0.004 0.045 1453 Dihedral : 6.539 58.690 1625 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.01 % Allowed : 15.27 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.27), residues: 1024 helix: 2.60 (0.25), residues: 422 sheet: -0.07 (0.33), residues: 225 loop : -1.14 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 80 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.002 PHE B 199 TYR 0.014 0.001 TYR B 59 ARG 0.011 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: R 154 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.6608 (tt) REVERT: R 185 ASN cc_start: 0.6408 (OUTLIER) cc_final: 0.6162 (m-40) REVERT: A 60 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6767 (mpt) REVERT: A 229 ASP cc_start: 0.8783 (t0) cc_final: 0.8511 (t0) REVERT: A 265 ARG cc_start: 0.8605 (mmt180) cc_final: 0.8173 (mtm180) REVERT: A 314 GLU cc_start: 0.8623 (mt-10) cc_final: 0.7901 (pm20) REVERT: A 317 ARG cc_start: 0.8939 (mtm-85) cc_final: 0.8407 (ptt-90) REVERT: A 392 GLU cc_start: 0.8534 (tt0) cc_final: 0.7913 (tp30) REVERT: B 134 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.6554 (pmt170) REVERT: B 138 GLU cc_start: 0.8948 (tp30) cc_final: 0.8713 (tp30) REVERT: B 175 GLN cc_start: 0.8615 (mt0) cc_final: 0.8101 (mp10) REVERT: B 180 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.5436 (p90) REVERT: B 189 SER cc_start: 0.8248 (t) cc_final: 0.7959 (m) REVERT: B 205 ASP cc_start: 0.8133 (p0) cc_final: 0.7735 (p0) REVERT: B 214 ARG cc_start: 0.9218 (tpp80) cc_final: 0.8690 (mmt180) REVERT: B 217 MET cc_start: 0.8832 (ptt) cc_final: 0.8589 (ppp) REVERT: B 239 ASN cc_start: 0.8317 (m-40) cc_final: 0.7974 (t0) REVERT: B 339 TRP cc_start: 0.8744 (m100) cc_final: 0.8372 (m-10) REVERT: G 21 MET cc_start: 0.7711 (mtt) cc_final: 0.6977 (tmm) REVERT: N 38 ARG cc_start: 0.9030 (ptt180) cc_final: 0.8563 (ptm-80) REVERT: N 90 ASP cc_start: 0.7855 (p0) cc_final: 0.7533 (p0) REVERT: N 105 ARG cc_start: 0.8029 (mtm180) cc_final: 0.7424 (mtm180) outliers start: 27 outliers final: 15 residues processed: 116 average time/residue: 1.2276 time to fit residues: 151.7582 Evaluate side-chains 111 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 185 ASN Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 0.0970 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 88 optimal weight: 0.2980 chunk 93 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8712 Z= 0.133 Angle : 0.495 9.510 11796 Z= 0.253 Chirality : 0.040 0.164 1334 Planarity : 0.003 0.047 1453 Dihedral : 6.047 58.369 1625 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.12 % Allowed : 16.61 % Favored : 81.27 % 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 (0.27), residues: 1024 helix: 2.91 (0.25), residues: 421 sheet: -0.00 (0.33), residues: 227 loop : -1.06 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 123 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE B 199 TYR 0.007 0.001 TYR N 80 ARG 0.004 0.000 ARG R 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: R 136 THR cc_start: 0.6164 (OUTLIER) cc_final: 0.5809 (p) REVERT: R 154 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.6581 (tt) REVERT: A 60 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6824 (mpt) REVERT: A 221 MET cc_start: 0.7969 (tpt) cc_final: 0.7295 (tpt) REVERT: A 229 ASP cc_start: 0.8771 (t0) cc_final: 0.8489 (t0) REVERT: A 265 ARG cc_start: 0.8576 (mmt180) cc_final: 0.8177 (mtm-85) REVERT: A 314 GLU cc_start: 0.8622 (mt-10) cc_final: 0.7889 (pm20) REVERT: A 317 ARG cc_start: 0.8930 (mtm-85) cc_final: 0.8424 (ptt-90) REVERT: A 392 GLU cc_start: 0.8505 (tt0) cc_final: 0.7898 (tp30) REVERT: B 134 ARG cc_start: 0.7620 (mtm-85) cc_final: 0.6494 (pmt170) REVERT: B 138 GLU cc_start: 0.8952 (tp30) cc_final: 0.8719 (tp30) REVERT: B 175 GLN cc_start: 0.8629 (mt0) cc_final: 0.8112 (mp10) REVERT: B 180 PHE cc_start: 0.6590 (OUTLIER) cc_final: 0.4952 (p90) REVERT: B 189 SER cc_start: 0.8222 (t) cc_final: 0.7956 (m) REVERT: B 205 ASP cc_start: 0.7999 (p0) cc_final: 0.7205 (t0) REVERT: B 214 ARG cc_start: 0.9228 (tpp80) cc_final: 0.8706 (mmt180) REVERT: B 217 MET cc_start: 0.8829 (ptt) cc_final: 0.8595 (ppp) REVERT: B 239 ASN cc_start: 0.8193 (m-40) cc_final: 0.7878 (t0) REVERT: B 339 TRP cc_start: 0.8818 (m100) cc_final: 0.8370 (m-10) REVERT: G 21 MET cc_start: 0.7659 (mtt) cc_final: 0.6984 (tmm) REVERT: N 90 ASP cc_start: 0.7712 (p0) cc_final: 0.7378 (p0) outliers start: 19 outliers final: 9 residues processed: 108 average time/residue: 1.1904 time to fit residues: 137.9742 Evaluate side-chains 102 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 9.9990 chunk 93 optimal weight: 0.5980 chunk 54 optimal weight: 0.0570 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8712 Z= 0.157 Angle : 0.498 9.244 11796 Z= 0.255 Chirality : 0.040 0.148 1334 Planarity : 0.003 0.049 1453 Dihedral : 5.848 58.386 1625 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.67 % Allowed : 17.17 % Favored : 81.16 % 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: 1.36 (0.27), residues: 1024 helix: 2.98 (0.25), residues: 421 sheet: 0.03 (0.33), residues: 229 loop : -1.02 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 123 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE B 199 TYR 0.008 0.001 TYR A 339 ARG 0.004 0.000 ARG R 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: R 154 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.6531 (tt) REVERT: A 60 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6787 (mpt) REVERT: A 221 MET cc_start: 0.7866 (tpt) cc_final: 0.7216 (tpt) REVERT: A 229 ASP cc_start: 0.8771 (t0) cc_final: 0.8484 (t0) REVERT: A 265 ARG cc_start: 0.8569 (mmt180) cc_final: 0.8182 (mtm-85) REVERT: A 300 LYS cc_start: 0.8945 (mttt) cc_final: 0.8667 (ttpp) REVERT: A 314 GLU cc_start: 0.8671 (mt-10) cc_final: 0.7911 (pm20) REVERT: A 317 ARG cc_start: 0.8929 (mtm-85) cc_final: 0.8410 (ptt-90) REVERT: A 392 GLU cc_start: 0.8508 (tt0) cc_final: 0.7914 (tp30) REVERT: B 134 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.6493 (pmt170) REVERT: B 138 GLU cc_start: 0.8931 (tp30) cc_final: 0.8694 (tp30) REVERT: B 175 GLN cc_start: 0.8610 (mt0) cc_final: 0.8109 (mp10) REVERT: B 180 PHE cc_start: 0.6592 (OUTLIER) cc_final: 0.4898 (p90) REVERT: B 189 SER cc_start: 0.8259 (t) cc_final: 0.7996 (m) REVERT: B 205 ASP cc_start: 0.8010 (p0) cc_final: 0.7187 (t0) REVERT: B 214 ARG cc_start: 0.9230 (tpp80) cc_final: 0.8708 (mmt180) REVERT: B 217 MET cc_start: 0.8823 (ptt) cc_final: 0.8587 (ppp) REVERT: B 239 ASN cc_start: 0.8200 (m-40) cc_final: 0.7879 (t0) REVERT: B 339 TRP cc_start: 0.8804 (m100) cc_final: 0.8368 (m-10) REVERT: G 21 MET cc_start: 0.7664 (mtt) cc_final: 0.6995 (tmm) REVERT: N 90 ASP cc_start: 0.7779 (p0) cc_final: 0.7430 (p0) outliers start: 15 outliers final: 12 residues processed: 98 average time/residue: 1.2501 time to fit residues: 130.7189 Evaluate side-chains 102 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 185 ASN Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8712 Z= 0.235 Angle : 0.545 9.572 11796 Z= 0.279 Chirality : 0.042 0.149 1334 Planarity : 0.003 0.047 1453 Dihedral : 6.094 57.935 1625 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.78 % Allowed : 16.83 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 1024 helix: 2.62 (0.25), residues: 429 sheet: 0.01 (0.34), residues: 221 loop : -1.22 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 80 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE B 199 TYR 0.013 0.001 TYR A 339 ARG 0.004 0.000 ARG R 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 136 THR cc_start: 0.6699 (OUTLIER) cc_final: 0.6449 (p) REVERT: R 154 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.6671 (tt) REVERT: A 60 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6865 (mpt) REVERT: A 221 MET cc_start: 0.8123 (tpt) cc_final: 0.7459 (tpt) REVERT: A 229 ASP cc_start: 0.8778 (t0) cc_final: 0.8469 (t0) REVERT: A 265 ARG cc_start: 0.8587 (mmt180) cc_final: 0.8327 (ptt180) REVERT: A 300 LYS cc_start: 0.9000 (mttt) cc_final: 0.8731 (ttpp) REVERT: A 314 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8016 (pm20) REVERT: A 317 ARG cc_start: 0.9018 (mtm-85) cc_final: 0.8543 (ptt-90) REVERT: A 392 GLU cc_start: 0.8514 (tt0) cc_final: 0.7881 (tp30) REVERT: B 45 MET cc_start: 0.7976 (mtt) cc_final: 0.7654 (mtt) REVERT: B 134 ARG cc_start: 0.7647 (mtm-85) cc_final: 0.6482 (pmt170) REVERT: B 138 GLU cc_start: 0.8945 (tp30) cc_final: 0.8707 (tp30) REVERT: B 175 GLN cc_start: 0.8594 (mt0) cc_final: 0.8089 (mp10) REVERT: B 180 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.5753 (p90) REVERT: B 189 SER cc_start: 0.8239 (t) cc_final: 0.7988 (m) REVERT: B 205 ASP cc_start: 0.8124 (p0) cc_final: 0.7216 (t0) REVERT: B 214 ARG cc_start: 0.9229 (tpp80) cc_final: 0.8706 (mmt180) REVERT: B 217 MET cc_start: 0.8839 (ptt) cc_final: 0.8582 (ppp) REVERT: B 239 ASN cc_start: 0.8346 (m-40) cc_final: 0.7992 (t0) REVERT: B 339 TRP cc_start: 0.8809 (m100) cc_final: 0.8357 (m-10) REVERT: G 21 MET cc_start: 0.7690 (mtt) cc_final: 0.7049 (tmm) REVERT: N 38 ARG cc_start: 0.8978 (ptt180) cc_final: 0.8509 (ptm-80) REVERT: N 90 ASP cc_start: 0.7876 (p0) cc_final: 0.7581 (p0) outliers start: 16 outliers final: 12 residues processed: 109 average time/residue: 1.2188 time to fit residues: 141.7550 Evaluate side-chains 116 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 185 ASN Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 82 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 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 160 GLN ** 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 = 0.4247 r_free = 0.4247 target = 0.176782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.130316 restraints weight = 9605.718| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.21 r_work: 0.3632 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8712 Z= 0.157 Angle : 0.505 9.369 11796 Z= 0.259 Chirality : 0.040 0.144 1334 Planarity : 0.003 0.047 1453 Dihedral : 5.805 58.589 1625 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.56 % Allowed : 17.28 % Favored : 81.16 % 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: 1.33 (0.27), residues: 1024 helix: 2.94 (0.25), residues: 421 sheet: 0.02 (0.33), residues: 227 loop : -1.01 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 123 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE B 199 TYR 0.015 0.001 TYR N 60 ARG 0.004 0.000 ARG R 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3270.97 seconds wall clock time: 58 minutes 58.61 seconds (3538.61 seconds total)