Starting phenix.real_space_refine on Wed Feb 14 11:47:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y35_33588/02_2024/7y35_33588_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y35_33588/02_2024/7y35_33588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y35_33588/02_2024/7y35_33588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y35_33588/02_2024/7y35_33588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y35_33588/02_2024/7y35_33588_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y35_33588/02_2024/7y35_33588_updated.pdb" } resolution = 2.9 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= 0.003 sd= 0.038 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 56 5.16 5 C 5841 2.51 5 N 1616 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9191 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3053 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 3 Chain: "P" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 274 Unusual residues: {'NH2': 1} Classifications: {'peptide': 33, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 32} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1858 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 3 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: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Time building chain proxies: 5.40, per 1000 atoms: 0.59 Number of scatterers: 9191 At special positions: 0 Unit cell: (127.764, 98.358, 151.086, 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 56 16.00 O 1678 8.00 N 1616 7.00 C 5841 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 117 " distance=2.05 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.02 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " 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: 3.52 Conformation dependent library (CDL) restraints added in 1.6 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 11 sheets defined 37.3% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'R' and resid 34 through 56 Processing helix chain 'R' and resid 168 through 171 No H-bonds generated for 'chain 'R' and resid 168 through 171' Processing helix chain 'R' and resid 180 through 211 Processing helix chain 'R' and resid 213 through 215 No H-bonds generated for 'chain 'R' and resid 213 through 215' Processing helix chain 'R' and resid 218 through 243 Processing helix chain 'R' and resid 279 through 311 Processing helix chain 'R' and resid 317 through 329 removed outlier: 3.507A pdb=" N TRP R 329 " --> pdb=" O THR R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 346 Processing helix chain 'R' and resid 361 through 390 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 401 through 416 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 421 through 423 No H-bonds generated for 'chain 'R' and resid 421 through 423' Processing helix chain 'R' and resid 435 through 460 removed outlier: 3.568A pdb=" N PHE R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 464 through 480 Processing helix chain 'P' and resid 3 through 31 removed outlier: 4.097A pdb=" N LYS P 30 " --> pdb=" O LYS P 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 37 removed outlier: 4.128A pdb=" N LYS A 17 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA A 18 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN A 31 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.658A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 53 through 57' Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 334 through 350 removed outlier: 3.980A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 390 removed outlier: 3.952A pdb=" N ILE A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 23 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' 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 126 through 130 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.041A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.894A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.956A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.160A 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: 6.640A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 207 through 212 removed outlier: 4.371A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.508A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.011A 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: 6.432A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.436A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.555A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.372A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1134 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: 2.51 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1492 1.31 - 1.44: 2659 1.44 - 1.57: 5161 1.57 - 1.70: 0 1.70 - 1.83: 78 Bond restraints: 9390 Sorted by residual: bond pdb=" CA PHE R 173 " pdb=" C PHE R 173 " ideal model delta sigma weight residual 1.524 1.463 0.060 1.32e-02 5.74e+03 2.10e+01 bond pdb=" C GLU R 180 " pdb=" O GLU R 180 " ideal model delta sigma weight residual 1.236 1.182 0.055 1.47e-02 4.63e+03 1.38e+01 bond pdb=" N GLU R 177 " pdb=" CA GLU R 177 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.29e-02 6.01e+03 1.30e+01 bond pdb=" CA GLU R 177 " pdb=" C GLU R 177 " ideal model delta sigma weight residual 1.523 1.566 -0.043 1.34e-02 5.57e+03 1.03e+01 bond pdb=" N THR R 175 " pdb=" CA THR R 175 " ideal model delta sigma weight residual 1.457 1.423 0.035 1.29e-02 6.01e+03 7.27e+00 ... (remaining 9385 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.55: 312 107.55 - 114.73: 5401 114.73 - 121.92: 5029 121.92 - 129.10: 1881 129.10 - 136.29: 87 Bond angle restraints: 12710 Sorted by residual: angle pdb=" CA LYS R 172 " pdb=" C LYS R 172 " pdb=" N PHE R 173 " ideal model delta sigma weight residual 117.63 100.39 17.24 1.25e+00 6.40e-01 1.90e+02 angle pdb=" C LYS R 172 " pdb=" N PHE R 173 " pdb=" CA PHE R 173 " ideal model delta sigma weight residual 120.54 136.29 -15.75 1.35e+00 5.49e-01 1.36e+02 angle pdb=" O LYS R 172 " pdb=" C LYS R 172 " pdb=" N PHE R 173 " ideal model delta sigma weight residual 122.22 133.17 -10.95 1.17e+00 7.31e-01 8.75e+01 angle pdb=" N ASN R 176 " pdb=" CA ASN R 176 " pdb=" C ASN R 176 " ideal model delta sigma weight residual 112.23 120.32 -8.09 1.26e+00 6.30e-01 4.12e+01 angle pdb=" C ASN R 176 " pdb=" N GLU R 177 " pdb=" CA GLU R 177 " ideal model delta sigma weight residual 121.54 130.38 -8.84 1.91e+00 2.74e-01 2.14e+01 ... (remaining 12705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 5084 16.82 - 33.64: 391 33.64 - 50.46: 77 50.46 - 67.28: 11 67.28 - 84.11: 11 Dihedral angle restraints: 5574 sinusoidal: 2231 harmonic: 3343 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -9.29 -76.71 1 1.00e+01 1.00e-02 7.39e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual -180.00 -152.07 -27.93 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 5571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 846 0.040 - 0.081: 380 0.081 - 0.121: 145 0.121 - 0.162: 30 0.162 - 0.202: 4 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA PHE R 335 " pdb=" N PHE R 335 " pdb=" C PHE R 335 " pdb=" CB PHE R 335 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA TYR R 191 " pdb=" N TYR R 191 " pdb=" C TYR R 191 " pdb=" CB TYR R 191 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA VAL R 157 " pdb=" N VAL R 157 " pdb=" C VAL R 157 " pdb=" CB VAL R 157 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.26e-01 ... (remaining 1402 not shown) Planarity restraints: 1618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS R 172 " 0.032 2.00e-02 2.50e+03 7.65e-02 5.85e+01 pdb=" C LYS R 172 " -0.132 2.00e-02 2.50e+03 pdb=" O LYS R 172 " 0.056 2.00e-02 2.50e+03 pdb=" N PHE R 173 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO B 236 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 175 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C THR R 175 " -0.042 2.00e-02 2.50e+03 pdb=" O THR R 175 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN R 176 " 0.014 2.00e-02 2.50e+03 ... (remaining 1615 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1447 2.75 - 3.29: 8490 3.29 - 3.83: 15193 3.83 - 4.36: 18286 4.36 - 4.90: 31860 Nonbonded interactions: 75276 Sorted by model distance: nonbonded pdb=" ND2 ASN R 448 " pdb=" OE2 GLU P 4 " model vdw 2.217 2.520 nonbonded pdb=" NH1 ARG B 49 " pdb=" O PHE G 61 " model vdw 2.226 2.520 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.264 2.440 nonbonded pdb=" OE2 GLU A 27 " pdb=" NZ LYS B 89 " model vdw 2.306 2.520 nonbonded pdb=" NE1 TRP R 437 " pdb=" OD2 ASP P 10 " model vdw 2.341 2.520 ... (remaining 75271 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.790 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.860 Find NCS groups from input model: 0.230 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:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 0.009 0.071 9390 Z= 0.591 Angle : 0.795 17.243 12710 Z= 0.478 Chirality : 0.052 0.202 1405 Planarity : 0.005 0.076 1618 Dihedral : 12.994 84.106 3394 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.95 % 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 (0.23), residues: 1123 helix: -0.13 (0.23), residues: 440 sheet: -1.02 (0.30), residues: 258 loop : -1.51 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 99 HIS 0.016 0.002 HIS A 357 PHE 0.022 0.002 PHE R 335 TYR 0.042 0.002 TYR B 59 ARG 0.005 0.001 ARG R 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 344 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8776 (mp0) cc_final: 0.8368 (mp0) REVERT: R 36 GLU cc_start: 0.8431 (tp30) cc_final: 0.7972 (tp30) REVERT: R 37 GLN cc_start: 0.8764 (tp40) cc_final: 0.8237 (tp-100) REVERT: R 45 GLN cc_start: 0.8892 (tt0) cc_final: 0.8514 (tt0) REVERT: R 47 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8624 (mm110) REVERT: R 137 ASP cc_start: 0.8025 (m-30) cc_final: 0.7727 (m-30) REVERT: R 149 ASP cc_start: 0.7503 (t70) cc_final: 0.7222 (t0) REVERT: R 156 LEU cc_start: 0.7207 (mt) cc_final: 0.6890 (tt) REVERT: R 160 HIS cc_start: 0.7424 (m90) cc_final: 0.6797 (m90) REVERT: R 407 LEU cc_start: 0.8372 (tp) cc_final: 0.8170 (tt) REVERT: P 18 LEU cc_start: 0.9086 (tp) cc_final: 0.8617 (tm) REVERT: P 19 ARG cc_start: 0.8945 (mtp180) cc_final: 0.8688 (mtm180) REVERT: P 22 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 17 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7857 (mmtm) REVERT: A 27 GLU cc_start: 0.7022 (mp0) cc_final: 0.6815 (mp0) REVERT: A 34 LYS cc_start: 0.8928 (tttt) cc_final: 0.8518 (ttpp) REVERT: A 38 ARG cc_start: 0.7705 (mtm110) cc_final: 0.7477 (mtm110) REVERT: A 311 TYR cc_start: 0.8140 (m-80) cc_final: 0.7845 (m-80) REVERT: A 344 GLU cc_start: 0.7881 (tp30) cc_final: 0.7530 (tp30) REVERT: A 378 ASP cc_start: 0.8003 (m-30) cc_final: 0.7755 (m-30) REVERT: B 22 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7199 (mtm180) REVERT: B 25 CYS cc_start: 0.8133 (m) cc_final: 0.7273 (p) REVERT: B 52 ARG cc_start: 0.8571 (mtt90) cc_final: 0.8293 (mtt-85) REVERT: B 215 GLU cc_start: 0.7835 (mp0) cc_final: 0.7546 (mp0) REVERT: B 254 ASP cc_start: 0.7917 (m-30) cc_final: 0.7693 (m-30) REVERT: B 258 ASP cc_start: 0.7908 (t0) cc_final: 0.6962 (t0) REVERT: B 267 ASP cc_start: 0.7648 (p0) cc_final: 0.7319 (p0) REVERT: B 312 ASP cc_start: 0.7262 (p0) cc_final: 0.6330 (p0) REVERT: N 35 ASN cc_start: 0.8318 (m-40) cc_final: 0.8084 (m-40) REVERT: N 69 THR cc_start: 0.8574 (m) cc_final: 0.7969 (p) REVERT: N 78 THR cc_start: 0.8495 (t) cc_final: 0.8058 (p) REVERT: N 83 MET cc_start: 0.8287 (mtp) cc_final: 0.8013 (mtm) REVERT: N 123 GLN cc_start: 0.8670 (tp40) cc_final: 0.8384 (tm-30) REVERT: N 125 THR cc_start: 0.8250 (p) cc_final: 0.7520 (p) outliers start: 1 outliers final: 0 residues processed: 345 average time/residue: 1.5043 time to fit residues: 546.1519 Evaluate side-chains 286 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 101 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 358 ASN R 364 GLN ** R 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 420 HIS R 440 GLN R 463 ASN A 213 GLN A 236 GLN A 384 GLN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 32 GLN B 75 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9390 Z= 0.218 Angle : 0.609 8.291 12710 Z= 0.326 Chirality : 0.043 0.237 1405 Planarity : 0.005 0.059 1618 Dihedral : 4.794 25.176 1260 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.44 % Allowed : 16.72 % Favored : 79.84 % 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: -0.24 (0.25), residues: 1123 helix: 1.03 (0.25), residues: 436 sheet: -0.37 (0.33), residues: 237 loop : -1.16 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS R 114 PHE 0.020 0.002 PHE R 314 TYR 0.026 0.001 TYR R 191 ARG 0.008 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 289 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8863 (mp0) cc_final: 0.8502 (mp0) REVERT: R 36 GLU cc_start: 0.8444 (tp30) cc_final: 0.7847 (tp30) REVERT: R 37 GLN cc_start: 0.8957 (tp40) cc_final: 0.8316 (tp-100) REVERT: R 39 PHE cc_start: 0.8948 (t80) cc_final: 0.8578 (t80) REVERT: R 40 LEU cc_start: 0.9287 (mm) cc_final: 0.8888 (mm) REVERT: R 43 ARG cc_start: 0.8734 (mmm160) cc_final: 0.8221 (mmm160) REVERT: R 47 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8778 (mm110) REVERT: R 149 ASP cc_start: 0.7679 (t70) cc_final: 0.7358 (t0) REVERT: R 150 ARG cc_start: 0.6529 (mmm160) cc_final: 0.6309 (ttp80) REVERT: R 156 LEU cc_start: 0.7151 (mt) cc_final: 0.6650 (tt) REVERT: R 160 HIS cc_start: 0.7356 (m90) cc_final: 0.6678 (m90) REVERT: R 182 GLU cc_start: 0.7030 (tp30) cc_final: 0.6748 (tp30) REVERT: R 207 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8446 (mm) REVERT: R 346 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8566 (mt) REVERT: R 407 LEU cc_start: 0.8383 (tp) cc_final: 0.8065 (tt) REVERT: P 4 GLU cc_start: 0.7749 (mp0) cc_final: 0.7545 (mp0) REVERT: P 15 ILE cc_start: 0.8275 (mt) cc_final: 0.8045 (pp) REVERT: P 26 LYS cc_start: 0.9054 (ttpp) cc_final: 0.8849 (tmmt) REVERT: A 34 LYS cc_start: 0.8813 (tttt) cc_final: 0.8467 (ttpp) REVERT: A 46 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8059 (tt) REVERT: A 54 SER cc_start: 0.9206 (OUTLIER) cc_final: 0.8853 (t) REVERT: A 295 ASP cc_start: 0.7668 (p0) cc_final: 0.7439 (p0) REVERT: A 311 TYR cc_start: 0.8131 (m-80) cc_final: 0.7827 (m-80) REVERT: B 12 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7840 (pp20) REVERT: B 22 ARG cc_start: 0.7844 (mtt180) cc_final: 0.7087 (mtm-85) REVERT: B 25 CYS cc_start: 0.8199 (m) cc_final: 0.7464 (p) REVERT: B 32 GLN cc_start: 0.8070 (mt0) cc_final: 0.7699 (mt0) REVERT: B 46 ARG cc_start: 0.7431 (mtp180) cc_final: 0.7199 (ttm110) REVERT: B 52 ARG cc_start: 0.8641 (mtt90) cc_final: 0.8372 (mtt-85) REVERT: B 75 GLN cc_start: 0.8417 (mt0) cc_final: 0.8086 (mt0) REVERT: B 89 LYS cc_start: 0.8506 (mttp) cc_final: 0.8103 (mttp) REVERT: B 228 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7246 (m-30) REVERT: B 258 ASP cc_start: 0.7893 (t0) cc_final: 0.6531 (t0) REVERT: B 259 GLN cc_start: 0.8185 (mt0) cc_final: 0.6499 (mt0) REVERT: G 58 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7327 (mm-30) REVERT: N 25 SER cc_start: 0.7860 (t) cc_final: 0.7643 (m) REVERT: N 69 THR cc_start: 0.8676 (m) cc_final: 0.8175 (p) REVERT: N 78 THR cc_start: 0.8764 (t) cc_final: 0.8470 (p) REVERT: N 123 GLN cc_start: 0.8659 (tp40) cc_final: 0.8442 (tm-30) outliers start: 34 outliers final: 13 residues processed: 301 average time/residue: 1.4682 time to fit residues: 465.7617 Evaluate side-chains 296 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 278 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 404 ARG Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 5 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 358 ASN R 374 ASN R 402 GLN R 440 GLN P 5 HIS A 236 GLN A 357 HIS N 31 ASN N 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9390 Z= 0.253 Angle : 0.588 8.304 12710 Z= 0.312 Chirality : 0.043 0.198 1405 Planarity : 0.004 0.055 1618 Dihedral : 4.508 24.336 1260 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.76 % Allowed : 19.55 % Favored : 75.68 % 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: 0.17 (0.25), residues: 1123 helix: 1.30 (0.25), residues: 441 sheet: -0.27 (0.32), residues: 251 loop : -0.80 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.019 0.002 PHE R 314 TYR 0.025 0.001 TYR R 191 ARG 0.007 0.001 ARG R 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 285 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8896 (mp0) cc_final: 0.8502 (mp0) REVERT: R 36 GLU cc_start: 0.8397 (tp30) cc_final: 0.7725 (tp30) REVERT: R 37 GLN cc_start: 0.9039 (tp40) cc_final: 0.8429 (tp40) REVERT: R 39 PHE cc_start: 0.8958 (t80) cc_final: 0.8615 (t80) REVERT: R 40 LEU cc_start: 0.9351 (mm) cc_final: 0.8779 (mt) REVERT: R 43 ARG cc_start: 0.8807 (mmm160) cc_final: 0.8378 (mmm160) REVERT: R 137 ASP cc_start: 0.8179 (m-30) cc_final: 0.7902 (m-30) REVERT: R 156 LEU cc_start: 0.7004 (mt) cc_final: 0.6332 (tt) REVERT: R 182 GLU cc_start: 0.7202 (tp30) cc_final: 0.6880 (tp30) REVERT: R 207 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8443 (mm) REVERT: R 346 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8584 (mt) REVERT: R 407 LEU cc_start: 0.8430 (tp) cc_final: 0.8159 (tt) REVERT: A 27 GLU cc_start: 0.7328 (mp0) cc_final: 0.6927 (mp0) REVERT: A 34 LYS cc_start: 0.8795 (tttt) cc_final: 0.8355 (ttpp) REVERT: A 38 ARG cc_start: 0.7450 (mtm110) cc_final: 0.7200 (mtm110) REVERT: A 46 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8085 (tt) REVERT: A 54 SER cc_start: 0.9236 (m) cc_final: 0.8854 (t) REVERT: A 311 TYR cc_start: 0.8139 (m-80) cc_final: 0.7914 (m-80) REVERT: B 22 ARG cc_start: 0.7976 (mtt180) cc_final: 0.7132 (mtm-85) REVERT: B 25 CYS cc_start: 0.8204 (m) cc_final: 0.7459 (p) REVERT: B 32 GLN cc_start: 0.8060 (mt0) cc_final: 0.7713 (mt0) REVERT: B 61 MET cc_start: 0.8549 (ppp) cc_final: 0.8344 (ppp) REVERT: B 89 LYS cc_start: 0.8340 (mttp) cc_final: 0.7918 (mttp) REVERT: B 219 ARG cc_start: 0.8067 (tpp80) cc_final: 0.7832 (tpp80) REVERT: B 228 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: B 234 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: B 258 ASP cc_start: 0.7915 (t0) cc_final: 0.6558 (t0) REVERT: B 259 GLN cc_start: 0.8287 (mt0) cc_final: 0.6396 (mt0) REVERT: G 58 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7385 (mm-30) REVERT: N 5 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7211 (pt0) REVERT: N 69 THR cc_start: 0.8748 (m) cc_final: 0.8322 (p) REVERT: N 78 THR cc_start: 0.8875 (t) cc_final: 0.8548 (p) REVERT: N 123 GLN cc_start: 0.8767 (tp40) cc_final: 0.8498 (tm-30) outliers start: 47 outliers final: 23 residues processed: 302 average time/residue: 1.4450 time to fit residues: 459.4891 Evaluate side-chains 309 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 280 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 404 ARG Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 5 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 463 ASN A 236 GLN A 357 HIS A 384 GLN N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9390 Z= 0.226 Angle : 0.571 9.117 12710 Z= 0.300 Chirality : 0.042 0.191 1405 Planarity : 0.004 0.052 1618 Dihedral : 4.334 22.778 1260 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.07 % Allowed : 20.16 % Favored : 74.77 % 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: 0.47 (0.26), residues: 1123 helix: 1.55 (0.26), residues: 435 sheet: -0.13 (0.32), residues: 249 loop : -0.60 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 164 HIS 0.003 0.001 HIS B 91 PHE 0.015 0.001 PHE R 314 TYR 0.025 0.001 TYR R 191 ARG 0.007 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 280 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 GLU cc_start: 0.8869 (mp0) cc_final: 0.8460 (mp0) REVERT: R 36 GLU cc_start: 0.8347 (tp30) cc_final: 0.7570 (tp30) REVERT: R 37 GLN cc_start: 0.9077 (tp40) cc_final: 0.8490 (tp40) REVERT: R 39 PHE cc_start: 0.8970 (t80) cc_final: 0.8605 (t80) REVERT: R 40 LEU cc_start: 0.9373 (mm) cc_final: 0.8723 (mt) REVERT: R 156 LEU cc_start: 0.6999 (mt) cc_final: 0.6332 (tt) REVERT: R 182 GLU cc_start: 0.7223 (tp30) cc_final: 0.6874 (tp30) REVERT: R 207 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8413 (mm) REVERT: R 407 LEU cc_start: 0.8415 (tp) cc_final: 0.8176 (tt) REVERT: A 27 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: A 29 GLN cc_start: 0.8177 (tp-100) cc_final: 0.7732 (tm-30) REVERT: A 34 LYS cc_start: 0.8793 (tttt) cc_final: 0.8238 (ttpp) REVERT: A 38 ARG cc_start: 0.7446 (mtm110) cc_final: 0.7087 (mtm110) REVERT: A 46 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8012 (tt) REVERT: A 209 GLU cc_start: 0.7274 (tt0) cc_final: 0.7066 (tt0) REVERT: A 311 TYR cc_start: 0.8230 (m-80) cc_final: 0.7974 (m-80) REVERT: B 12 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7804 (pp20) REVERT: B 22 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7342 (mtm180) REVERT: B 25 CYS cc_start: 0.8217 (m) cc_final: 0.7518 (p) REVERT: B 32 GLN cc_start: 0.8010 (mt0) cc_final: 0.7646 (mt0) REVERT: B 89 LYS cc_start: 0.8362 (mttp) cc_final: 0.8038 (mttp) REVERT: B 127 LYS cc_start: 0.8828 (mmtp) cc_final: 0.8587 (mmtp) REVERT: B 215 GLU cc_start: 0.7757 (mp0) cc_final: 0.7191 (mp0) REVERT: B 228 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: B 234 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.7994 (m-80) REVERT: B 258 ASP cc_start: 0.7851 (t0) cc_final: 0.6840 (t0) REVERT: B 259 GLN cc_start: 0.8114 (mt0) cc_final: 0.6537 (mt0) REVERT: B 304 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7855 (ttp80) REVERT: G 18 GLN cc_start: 0.8598 (tp40) cc_final: 0.8014 (tp40) REVERT: N 5 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.7110 (pt0) REVERT: N 25 SER cc_start: 0.8097 (t) cc_final: 0.7766 (p) REVERT: N 69 THR cc_start: 0.8754 (m) cc_final: 0.8320 (p) REVERT: N 78 THR cc_start: 0.8932 (t) cc_final: 0.8627 (p) REVERT: N 123 GLN cc_start: 0.8781 (tp40) cc_final: 0.8545 (tm-30) outliers start: 50 outliers final: 27 residues processed: 301 average time/residue: 1.5062 time to fit residues: 477.1878 Evaluate side-chains 315 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 281 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 5 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 357 HIS A 384 GLN B 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9390 Z= 0.253 Angle : 0.590 8.918 12710 Z= 0.308 Chirality : 0.042 0.205 1405 Planarity : 0.005 0.052 1618 Dihedral : 4.322 21.970 1260 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.47 % Allowed : 21.68 % Favored : 72.85 % 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: 0.62 (0.26), residues: 1123 helix: 1.63 (0.26), residues: 435 sheet: -0.08 (0.32), residues: 249 loop : -0.44 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE R 314 TYR 0.024 0.001 TYR R 191 ARG 0.010 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 287 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.8065 (tpp) cc_final: 0.7844 (tpp) REVERT: R 35 GLU cc_start: 0.8866 (mp0) cc_final: 0.8455 (mp0) REVERT: R 36 GLU cc_start: 0.8369 (tp30) cc_final: 0.7514 (tp30) REVERT: R 37 GLN cc_start: 0.9130 (tp40) cc_final: 0.8551 (tp40) REVERT: R 39 PHE cc_start: 0.8986 (t80) cc_final: 0.8709 (t80) REVERT: R 40 LEU cc_start: 0.9371 (mm) cc_final: 0.8642 (mt) REVERT: R 154 TRP cc_start: 0.6681 (m100) cc_final: 0.6405 (m100) REVERT: R 156 LEU cc_start: 0.7167 (mt) cc_final: 0.6448 (tt) REVERT: R 182 GLU cc_start: 0.7275 (tp30) cc_final: 0.6877 (tp30) REVERT: R 207 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8414 (mm) REVERT: R 241 ASP cc_start: 0.8221 (t0) cc_final: 0.7990 (t0) REVERT: R 407 LEU cc_start: 0.8427 (tp) cc_final: 0.8177 (tt) REVERT: A 27 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: A 29 GLN cc_start: 0.8148 (tp-100) cc_final: 0.7706 (tm-30) REVERT: A 34 LYS cc_start: 0.8771 (tttt) cc_final: 0.8160 (ttpp) REVERT: A 38 ARG cc_start: 0.7394 (mtm110) cc_final: 0.7018 (mtm110) REVERT: A 46 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8031 (tt) REVERT: A 209 GLU cc_start: 0.7316 (tt0) cc_final: 0.7060 (tt0) REVERT: A 347 ARG cc_start: 0.7914 (ttm-80) cc_final: 0.7537 (ttm-80) REVERT: B 12 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7747 (pp20) REVERT: B 22 ARG cc_start: 0.8084 (mtt180) cc_final: 0.7374 (mtm180) REVERT: B 25 CYS cc_start: 0.8195 (m) cc_final: 0.7461 (p) REVERT: B 32 GLN cc_start: 0.8033 (mt0) cc_final: 0.7667 (mt0) REVERT: B 75 GLN cc_start: 0.8399 (mt0) cc_final: 0.8106 (mt0) REVERT: B 89 LYS cc_start: 0.8358 (mttp) cc_final: 0.8066 (mttp) REVERT: B 127 LYS cc_start: 0.8848 (mmtp) cc_final: 0.8622 (mmtp) REVERT: B 197 ARG cc_start: 0.7795 (tpp80) cc_final: 0.7030 (tpp80) REVERT: B 214 ARG cc_start: 0.7574 (ptp90) cc_final: 0.7097 (pmm-80) REVERT: B 215 GLU cc_start: 0.7881 (mp0) cc_final: 0.6906 (mp0) REVERT: B 219 ARG cc_start: 0.8005 (tpp80) cc_final: 0.7773 (tpp80) REVERT: B 228 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: B 234 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8103 (m-80) REVERT: B 258 ASP cc_start: 0.7872 (t0) cc_final: 0.6881 (t0) REVERT: B 259 GLN cc_start: 0.8242 (mt0) cc_final: 0.6642 (mt0) REVERT: B 304 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7945 (ttp80) REVERT: B 325 MET cc_start: 0.8426 (mmt) cc_final: 0.8165 (mmm) REVERT: G 18 GLN cc_start: 0.8659 (tp40) cc_final: 0.8055 (tp40) REVERT: G 20 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8703 (mtpt) REVERT: N 5 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7087 (pt0) REVERT: N 13 GLN cc_start: 0.8271 (pp30) cc_final: 0.8033 (mm-40) REVERT: N 34 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8672 (mmm) REVERT: N 69 THR cc_start: 0.8738 (m) cc_final: 0.8297 (p) REVERT: N 78 THR cc_start: 0.8867 (t) cc_final: 0.8560 (p) REVERT: N 123 GLN cc_start: 0.8779 (tp40) cc_final: 0.8554 (tm-30) outliers start: 54 outliers final: 28 residues processed: 312 average time/residue: 1.4828 time to fit residues: 486.6488 Evaluate side-chains 321 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 285 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 140 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 34 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 440 GLN R 463 ASN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 357 HIS A 384 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9390 Z= 0.210 Angle : 0.582 9.091 12710 Z= 0.303 Chirality : 0.042 0.203 1405 Planarity : 0.004 0.051 1618 Dihedral : 4.218 21.281 1260 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.26 % Allowed : 23.10 % Favored : 72.64 % 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: 0.77 (0.26), residues: 1123 helix: 1.71 (0.26), residues: 435 sheet: 0.02 (0.32), residues: 248 loop : -0.31 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 164 HIS 0.002 0.001 HIS B 91 PHE 0.012 0.001 PHE A 212 TYR 0.023 0.001 TYR R 191 ARG 0.010 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 278 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.8053 (tpp) cc_final: 0.7843 (tpp) REVERT: R 35 GLU cc_start: 0.8868 (mp0) cc_final: 0.8446 (mp0) REVERT: R 36 GLU cc_start: 0.8384 (tp30) cc_final: 0.7491 (tp30) REVERT: R 37 GLN cc_start: 0.9129 (tp40) cc_final: 0.8558 (tp40) REVERT: R 39 PHE cc_start: 0.8978 (t80) cc_final: 0.8705 (t80) REVERT: R 40 LEU cc_start: 0.9375 (mm) cc_final: 0.8645 (mt) REVERT: R 154 TRP cc_start: 0.6676 (m100) cc_final: 0.6429 (m100) REVERT: R 156 LEU cc_start: 0.7083 (mt) cc_final: 0.6399 (tt) REVERT: R 182 GLU cc_start: 0.7229 (tp30) cc_final: 0.6829 (tp30) REVERT: R 207 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8385 (mm) REVERT: R 241 ASP cc_start: 0.8178 (t0) cc_final: 0.7932 (t0) REVERT: R 407 LEU cc_start: 0.8413 (tp) cc_final: 0.8167 (tt) REVERT: P 21 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8099 (tpp80) REVERT: A 27 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: A 34 LYS cc_start: 0.8758 (tttt) cc_final: 0.8070 (ttpp) REVERT: A 35 GLN cc_start: 0.8074 (pt0) cc_final: 0.7821 (pt0) REVERT: A 38 ARG cc_start: 0.7429 (mtm110) cc_final: 0.7138 (mtm110) REVERT: A 46 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7912 (tt) REVERT: A 209 GLU cc_start: 0.7364 (tt0) cc_final: 0.7099 (tt0) REVERT: A 295 ASP cc_start: 0.7619 (p0) cc_final: 0.7279 (p0) REVERT: A 311 TYR cc_start: 0.8260 (m-80) cc_final: 0.7998 (m-80) REVERT: A 347 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7653 (ttm-80) REVERT: B 12 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7852 (pp20) REVERT: B 22 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7559 (mtt180) REVERT: B 32 GLN cc_start: 0.8049 (mt0) cc_final: 0.7679 (mt0) REVERT: B 89 LYS cc_start: 0.8366 (mttp) cc_final: 0.8076 (mttp) REVERT: B 127 LYS cc_start: 0.8850 (mmtp) cc_final: 0.8623 (mmtp) REVERT: B 197 ARG cc_start: 0.7808 (tpp80) cc_final: 0.7044 (tpp80) REVERT: B 214 ARG cc_start: 0.7607 (ptp90) cc_final: 0.7108 (pmm-80) REVERT: B 215 GLU cc_start: 0.7806 (mp0) cc_final: 0.6749 (mp0) REVERT: B 228 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: B 234 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: B 258 ASP cc_start: 0.7835 (t0) cc_final: 0.6790 (t0) REVERT: B 259 GLN cc_start: 0.8190 (mt0) cc_final: 0.7803 (mt0) REVERT: B 304 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.7987 (ttp80) REVERT: G 18 GLN cc_start: 0.8625 (tp40) cc_final: 0.7996 (tp40) REVERT: G 54 VAL cc_start: 0.8967 (t) cc_final: 0.8753 (p) REVERT: N 5 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.7032 (pt0) REVERT: N 90 ASP cc_start: 0.8859 (m-30) cc_final: 0.8639 (m-30) REVERT: N 123 GLN cc_start: 0.8744 (tp40) cc_final: 0.8515 (tm-30) outliers start: 42 outliers final: 23 residues processed: 298 average time/residue: 1.5843 time to fit residues: 495.6995 Evaluate side-chains 299 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 269 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 440 GLN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9390 Z= 0.177 Angle : 0.584 9.334 12710 Z= 0.301 Chirality : 0.042 0.203 1405 Planarity : 0.004 0.049 1618 Dihedral : 4.112 20.130 1260 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.15 % Allowed : 24.62 % Favored : 71.23 % 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: 0.88 (0.26), residues: 1123 helix: 1.78 (0.26), residues: 435 sheet: 0.28 (0.33), residues: 226 loop : -0.36 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 164 HIS 0.002 0.001 HIS R 140 PHE 0.011 0.001 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.009 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 280 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.8106 (tpp) cc_final: 0.7882 (tpp) REVERT: R 35 GLU cc_start: 0.8883 (mp0) cc_final: 0.8493 (mp0) REVERT: R 36 GLU cc_start: 0.8370 (tp30) cc_final: 0.7484 (tp30) REVERT: R 37 GLN cc_start: 0.9091 (tp40) cc_final: 0.8389 (tp40) REVERT: R 39 PHE cc_start: 0.8972 (t80) cc_final: 0.8669 (t80) REVERT: R 40 LEU cc_start: 0.9400 (mm) cc_final: 0.8697 (mt) REVERT: R 154 TRP cc_start: 0.6623 (m100) cc_final: 0.6373 (m100) REVERT: R 156 LEU cc_start: 0.7006 (mt) cc_final: 0.6307 (tt) REVERT: R 182 GLU cc_start: 0.7123 (tp30) cc_final: 0.6687 (tp30) REVERT: R 241 ASP cc_start: 0.8130 (t0) cc_final: 0.7904 (t0) REVERT: R 407 LEU cc_start: 0.8431 (tp) cc_final: 0.8192 (tt) REVERT: P 21 ARG cc_start: 0.8582 (ttm-80) cc_final: 0.8075 (tpp80) REVERT: A 27 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: A 34 LYS cc_start: 0.8731 (tttt) cc_final: 0.8112 (tttt) REVERT: A 35 GLN cc_start: 0.8004 (pt0) cc_final: 0.7777 (pt0) REVERT: A 38 ARG cc_start: 0.7369 (mtm110) cc_final: 0.7156 (mtm110) REVERT: A 311 TYR cc_start: 0.8193 (m-80) cc_final: 0.7976 (m-80) REVERT: A 347 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7656 (ttm-80) REVERT: B 22 ARG cc_start: 0.8078 (mtt180) cc_final: 0.7232 (mtt180) REVERT: B 25 CYS cc_start: 0.8215 (m) cc_final: 0.7464 (p) REVERT: B 32 GLN cc_start: 0.8040 (mt0) cc_final: 0.7664 (mt0) REVERT: B 75 GLN cc_start: 0.8312 (mt0) cc_final: 0.8068 (mt0) REVERT: B 89 LYS cc_start: 0.8373 (mttp) cc_final: 0.8074 (mttp) REVERT: B 127 LYS cc_start: 0.8841 (mmtp) cc_final: 0.8609 (mmtp) REVERT: B 175 GLN cc_start: 0.8523 (tp40) cc_final: 0.7951 (mp10) REVERT: B 197 ARG cc_start: 0.7804 (tpp80) cc_final: 0.7071 (tpp80) REVERT: B 214 ARG cc_start: 0.7584 (ptp90) cc_final: 0.7332 (pmm-80) REVERT: B 215 GLU cc_start: 0.7844 (mp0) cc_final: 0.6745 (mp0) REVERT: B 219 ARG cc_start: 0.7985 (tpp80) cc_final: 0.7507 (mmt90) REVERT: B 228 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7194 (m-30) REVERT: B 234 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: B 258 ASP cc_start: 0.7815 (t0) cc_final: 0.6735 (t0) REVERT: B 259 GLN cc_start: 0.8179 (mt0) cc_final: 0.6602 (mt0) REVERT: B 304 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8011 (ttp80) REVERT: G 18 GLN cc_start: 0.8617 (tp40) cc_final: 0.7972 (tp40) REVERT: N 5 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6981 (pt0) REVERT: N 13 GLN cc_start: 0.8241 (pp30) cc_final: 0.7958 (mm-40) REVERT: N 25 SER cc_start: 0.8181 (t) cc_final: 0.7923 (p) REVERT: N 29 PHE cc_start: 0.8653 (t80) cc_final: 0.8247 (t80) REVERT: N 35 ASN cc_start: 0.8723 (m-40) cc_final: 0.8422 (m-40) REVERT: N 90 ASP cc_start: 0.8847 (m-30) cc_final: 0.8637 (m-30) REVERT: N 123 GLN cc_start: 0.8727 (tp40) cc_final: 0.8504 (tm-30) outliers start: 41 outliers final: 21 residues processed: 299 average time/residue: 1.5334 time to fit residues: 481.6473 Evaluate side-chains 301 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 275 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 440 GLN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 357 HIS A 384 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9390 Z= 0.188 Angle : 0.602 9.300 12710 Z= 0.310 Chirality : 0.042 0.204 1405 Planarity : 0.004 0.047 1618 Dihedral : 4.083 19.923 1260 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.85 % Allowed : 25.33 % Favored : 70.82 % 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: 0.88 (0.26), residues: 1123 helix: 1.75 (0.25), residues: 435 sheet: 0.31 (0.33), residues: 226 loop : -0.34 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS R 140 PHE 0.010 0.001 PHE B 151 TYR 0.023 0.001 TYR R 191 ARG 0.009 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 281 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.8115 (tpp) cc_final: 0.7874 (tpp) REVERT: R 35 GLU cc_start: 0.8895 (mp0) cc_final: 0.8507 (mp0) REVERT: R 36 GLU cc_start: 0.8384 (tp30) cc_final: 0.7497 (tp30) REVERT: R 37 GLN cc_start: 0.9103 (tp40) cc_final: 0.8375 (tp-100) REVERT: R 39 PHE cc_start: 0.8990 (t80) cc_final: 0.8670 (t80) REVERT: R 40 LEU cc_start: 0.9408 (mm) cc_final: 0.8699 (mt) REVERT: R 154 TRP cc_start: 0.6635 (m100) cc_final: 0.6303 (m100) REVERT: R 156 LEU cc_start: 0.6871 (mt) cc_final: 0.6239 (tt) REVERT: R 182 GLU cc_start: 0.7176 (tp30) cc_final: 0.6742 (tp30) REVERT: R 241 ASP cc_start: 0.8127 (t0) cc_final: 0.7908 (t0) REVERT: R 407 LEU cc_start: 0.8431 (tp) cc_final: 0.8193 (tt) REVERT: P 21 ARG cc_start: 0.8596 (ttm-80) cc_final: 0.8070 (tpp80) REVERT: A 27 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: A 34 LYS cc_start: 0.8699 (tttt) cc_final: 0.8022 (tttt) REVERT: A 35 GLN cc_start: 0.8000 (pt0) cc_final: 0.7777 (pt0) REVERT: A 38 ARG cc_start: 0.7379 (mtm110) cc_final: 0.7149 (mtm110) REVERT: A 311 TYR cc_start: 0.8169 (m-80) cc_final: 0.7948 (m-80) REVERT: A 347 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7718 (ttm-80) REVERT: B 13 GLN cc_start: 0.8692 (mm110) cc_final: 0.8400 (mm-40) REVERT: B 17 GLN cc_start: 0.8141 (mp10) cc_final: 0.7935 (mp-120) REVERT: B 19 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7879 (ttp80) REVERT: B 22 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7267 (mtt180) REVERT: B 25 CYS cc_start: 0.8252 (m) cc_final: 0.7534 (p) REVERT: B 32 GLN cc_start: 0.8051 (mt0) cc_final: 0.7678 (mt0) REVERT: B 75 GLN cc_start: 0.8316 (mt0) cc_final: 0.8087 (mt0) REVERT: B 89 LYS cc_start: 0.8377 (mttp) cc_final: 0.8081 (mttp) REVERT: B 127 LYS cc_start: 0.8820 (mmtp) cc_final: 0.8582 (mmtp) REVERT: B 175 GLN cc_start: 0.8520 (tp40) cc_final: 0.7941 (mp10) REVERT: B 197 ARG cc_start: 0.7797 (tpp80) cc_final: 0.7030 (tpp80) REVERT: B 214 ARG cc_start: 0.7584 (ptp90) cc_final: 0.7302 (pmm-80) REVERT: B 215 GLU cc_start: 0.7806 (mp0) cc_final: 0.6725 (mp0) REVERT: B 228 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7290 (m-30) REVERT: B 234 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: B 258 ASP cc_start: 0.7842 (t0) cc_final: 0.6766 (t0) REVERT: B 259 GLN cc_start: 0.8127 (mt0) cc_final: 0.6580 (mt0) REVERT: B 304 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8027 (ttp80) REVERT: G 18 GLN cc_start: 0.8641 (tp40) cc_final: 0.8302 (tp40) REVERT: N 5 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6963 (pt0) REVERT: N 25 SER cc_start: 0.8203 (t) cc_final: 0.7930 (p) REVERT: N 29 PHE cc_start: 0.8642 (t80) cc_final: 0.8247 (t80) REVERT: N 35 ASN cc_start: 0.8724 (m-40) cc_final: 0.8433 (m-40) REVERT: N 90 ASP cc_start: 0.8847 (m-30) cc_final: 0.8638 (m-30) REVERT: N 123 GLN cc_start: 0.8737 (tp40) cc_final: 0.8455 (tm-30) outliers start: 38 outliers final: 22 residues processed: 300 average time/residue: 1.5400 time to fit residues: 485.8773 Evaluate side-chains 299 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 272 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 114 HIS ** R 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 440 GLN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9390 Z= 0.217 Angle : 0.634 9.880 12710 Z= 0.324 Chirality : 0.043 0.209 1405 Planarity : 0.004 0.047 1618 Dihedral : 4.127 20.202 1260 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.24 % Allowed : 27.05 % Favored : 69.71 % 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: 0.88 (0.26), residues: 1123 helix: 1.73 (0.25), residues: 435 sheet: 0.18 (0.33), residues: 237 loop : -0.25 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 164 HIS 0.005 0.001 HIS R 42 PHE 0.011 0.001 PHE B 151 TYR 0.024 0.001 TYR R 191 ARG 0.009 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 270 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.8116 (tpp) cc_final: 0.7835 (tpp) REVERT: R 35 GLU cc_start: 0.8908 (mp0) cc_final: 0.8529 (mp0) REVERT: R 36 GLU cc_start: 0.8391 (tp30) cc_final: 0.7493 (tp30) REVERT: R 37 GLN cc_start: 0.9113 (tp40) cc_final: 0.8387 (tp-100) REVERT: R 39 PHE cc_start: 0.8995 (t80) cc_final: 0.8705 (t80) REVERT: R 40 LEU cc_start: 0.9410 (mm) cc_final: 0.8693 (mt) REVERT: R 154 TRP cc_start: 0.6719 (m100) cc_final: 0.6405 (m100) REVERT: R 156 LEU cc_start: 0.6820 (mt) cc_final: 0.6186 (tt) REVERT: R 182 GLU cc_start: 0.7228 (tp30) cc_final: 0.6778 (tp30) REVERT: R 241 ASP cc_start: 0.8133 (t0) cc_final: 0.7920 (t0) REVERT: R 407 LEU cc_start: 0.8438 (tp) cc_final: 0.8199 (tt) REVERT: P 21 ARG cc_start: 0.8552 (ttm-80) cc_final: 0.8032 (tpp80) REVERT: A 27 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: A 34 LYS cc_start: 0.8658 (tttt) cc_final: 0.7976 (tttt) REVERT: A 35 GLN cc_start: 0.7993 (pt0) cc_final: 0.7773 (pp30) REVERT: A 38 ARG cc_start: 0.7371 (mtm110) cc_final: 0.7144 (mtm110) REVERT: A 311 TYR cc_start: 0.8130 (m-80) cc_final: 0.7886 (m-80) REVERT: A 347 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7740 (ttm-80) REVERT: B 12 GLU cc_start: 0.7818 (pp20) cc_final: 0.7055 (pp20) REVERT: B 13 GLN cc_start: 0.8695 (mm110) cc_final: 0.8397 (mm110) REVERT: B 22 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7596 (mtt180) REVERT: B 32 GLN cc_start: 0.8068 (mt0) cc_final: 0.7699 (mt0) REVERT: B 75 GLN cc_start: 0.8368 (mt0) cc_final: 0.8062 (mt0) REVERT: B 89 LYS cc_start: 0.8355 (mttp) cc_final: 0.8059 (mttp) REVERT: B 127 LYS cc_start: 0.8824 (mmtp) cc_final: 0.8586 (mmtp) REVERT: B 172 GLU cc_start: 0.7991 (tp30) cc_final: 0.7709 (tp30) REVERT: B 175 GLN cc_start: 0.8502 (tp40) cc_final: 0.7925 (mp10) REVERT: B 197 ARG cc_start: 0.7808 (tpp80) cc_final: 0.7027 (tpp80) REVERT: B 228 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: B 234 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: B 258 ASP cc_start: 0.7864 (t0) cc_final: 0.6808 (t0) REVERT: B 259 GLN cc_start: 0.8073 (mt0) cc_final: 0.7694 (mt0) REVERT: B 304 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8054 (ttp80) REVERT: G 18 GLN cc_start: 0.8773 (tp40) cc_final: 0.8400 (tp40) REVERT: N 5 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6940 (pt0) REVERT: N 29 PHE cc_start: 0.8647 (t80) cc_final: 0.8283 (t80) REVERT: N 90 ASP cc_start: 0.8846 (m-30) cc_final: 0.8642 (m-30) REVERT: N 123 GLN cc_start: 0.8747 (tp40) cc_final: 0.8448 (tm-30) outliers start: 32 outliers final: 24 residues processed: 284 average time/residue: 1.5530 time to fit residues: 463.1118 Evaluate side-chains 299 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 270 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 102 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 0.2980 chunk 94 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 114 HIS R 440 GLN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 384 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9390 Z= 0.192 Angle : 0.648 10.089 12710 Z= 0.332 Chirality : 0.043 0.209 1405 Planarity : 0.004 0.048 1618 Dihedral : 4.112 19.460 1260 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.14 % Allowed : 26.75 % Favored : 70.11 % 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: 0.90 (0.26), residues: 1123 helix: 1.70 (0.25), residues: 436 sheet: 0.46 (0.34), residues: 222 loop : -0.33 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP N 47 HIS 0.006 0.001 HIS R 42 PHE 0.011 0.001 PHE A 212 TYR 0.023 0.001 TYR R 191 ARG 0.010 0.001 ARG G 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 273 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.8106 (tpp) cc_final: 0.7869 (tpp) REVERT: R 35 GLU cc_start: 0.8898 (mp0) cc_final: 0.8544 (mp0) REVERT: R 36 GLU cc_start: 0.8388 (tp30) cc_final: 0.7483 (tp30) REVERT: R 37 GLN cc_start: 0.9125 (tp40) cc_final: 0.8408 (tp-100) REVERT: R 39 PHE cc_start: 0.8996 (t80) cc_final: 0.8708 (t80) REVERT: R 40 LEU cc_start: 0.9386 (mm) cc_final: 0.8668 (mt) REVERT: R 154 TRP cc_start: 0.6669 (m100) cc_final: 0.6373 (m100) REVERT: R 156 LEU cc_start: 0.6784 (mt) cc_final: 0.6147 (tt) REVERT: R 182 GLU cc_start: 0.7128 (tp30) cc_final: 0.6649 (tp30) REVERT: R 241 ASP cc_start: 0.8104 (t0) cc_final: 0.7888 (t0) REVERT: R 407 LEU cc_start: 0.8426 (tp) cc_final: 0.8191 (tt) REVERT: P 21 ARG cc_start: 0.8559 (ttm-80) cc_final: 0.8018 (tpp80) REVERT: A 27 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: A 34 LYS cc_start: 0.8645 (tttt) cc_final: 0.7980 (tttt) REVERT: A 38 ARG cc_start: 0.7364 (mtm110) cc_final: 0.7141 (mtm110) REVERT: A 311 TYR cc_start: 0.8110 (m-80) cc_final: 0.7888 (m-10) REVERT: A 347 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7731 (ttm-80) REVERT: A 373 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7259 (tpp-160) REVERT: B 12 GLU cc_start: 0.7815 (pp20) cc_final: 0.7052 (pp20) REVERT: B 13 GLN cc_start: 0.8674 (mm110) cc_final: 0.8408 (mm110) REVERT: B 22 ARG cc_start: 0.8130 (mtt180) cc_final: 0.7729 (mtm180) REVERT: B 75 GLN cc_start: 0.8335 (mt0) cc_final: 0.8027 (mt0) REVERT: B 89 LYS cc_start: 0.8365 (mttp) cc_final: 0.8078 (mttp) REVERT: B 127 LYS cc_start: 0.8820 (mmtp) cc_final: 0.8580 (mmtp) REVERT: B 172 GLU cc_start: 0.7977 (tp30) cc_final: 0.7688 (tp30) REVERT: B 175 GLN cc_start: 0.8507 (tp40) cc_final: 0.7949 (mp10) REVERT: B 197 ARG cc_start: 0.7746 (tpp80) cc_final: 0.7314 (tpp80) REVERT: B 214 ARG cc_start: 0.7632 (pmm-80) cc_final: 0.7102 (pmm-80) REVERT: B 217 MET cc_start: 0.8034 (ppp) cc_final: 0.7573 (ppp) REVERT: B 228 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7447 (m-30) REVERT: B 234 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: B 258 ASP cc_start: 0.7855 (t0) cc_final: 0.6875 (t0) REVERT: B 259 GLN cc_start: 0.8067 (mt0) cc_final: 0.7705 (mt0) REVERT: B 304 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8045 (ttp80) REVERT: N 5 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6919 (pt0) REVERT: N 25 SER cc_start: 0.8182 (t) cc_final: 0.7929 (p) REVERT: N 29 PHE cc_start: 0.8617 (t80) cc_final: 0.8238 (t80) REVERT: N 35 ASN cc_start: 0.8696 (m-40) cc_final: 0.8425 (m-40) REVERT: N 90 ASP cc_start: 0.8827 (m-30) cc_final: 0.8625 (m-30) REVERT: N 123 GLN cc_start: 0.8731 (tp40) cc_final: 0.8436 (tm-30) outliers start: 31 outliers final: 20 residues processed: 288 average time/residue: 1.5197 time to fit residues: 460.2006 Evaluate side-chains 290 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 264 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 HIS Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 472 LYS Chi-restraints excluded: chain R residue 475 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 11 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 114 HIS ** R 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 440 GLN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.102617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.086919 restraints weight = 18040.828| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.68 r_work: 0.3150 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9390 Z= 0.221 Angle : 0.657 11.060 12710 Z= 0.338 Chirality : 0.043 0.209 1405 Planarity : 0.005 0.057 1618 Dihedral : 4.160 20.134 1260 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.74 % Allowed : 27.46 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1123 helix: 1.63 (0.25), residues: 438 sheet: 0.36 (0.33), residues: 226 loop : -0.42 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 164 HIS 0.006 0.001 HIS R 42 PHE 0.012 0.001 PHE R 447 TYR 0.023 0.001 TYR R 191 ARG 0.012 0.001 ARG B 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6513.18 seconds wall clock time: 114 minutes 38.60 seconds (6878.60 seconds total)