Starting phenix.real_space_refine on Sun Aug 4 08:17:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xgr_38330/08_2024/8xgr_38330.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xgr_38330/08_2024/8xgr_38330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xgr_38330/08_2024/8xgr_38330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xgr_38330/08_2024/8xgr_38330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xgr_38330/08_2024/8xgr_38330.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xgr_38330/08_2024/8xgr_38330.cif" } resolution = 3.2 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= 1.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2378 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 5225 2.51 5 N 1394 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 36": "OD1" <-> "OD2" Residue "G GLU 287": "OE1" <-> "OE2" Residue "G PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 73": "OD1" <-> "OD2" Residue "R TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8206 Number of models: 1 Model: "" Number of chains: 5 Chain: "G" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2062 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 251} Chain breaks: 3 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2415 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 171 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Time building chain proxies: 4.88, per 1000 atoms: 0.59 Number of scatterers: 8206 At special positions: 0 Unit cell: (95.865, 100.707, 137.503, 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 67 16.00 O 1520 8.00 N 1394 7.00 C 5225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.03 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " distance=2.03 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 15 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 11 " 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: 3.09 Conformation dependent library (CDL) restraints added in 1.5 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 15 sheets defined 41.3% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'G' and resid 12 through 22 removed outlier: 3.594A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 6.131A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 88 through 112 removed outlier: 3.918A pdb=" N ARG G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 132 removed outlier: 3.701A pdb=" N ILE G 129 " --> pdb=" O GLY G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 296 Processing helix chain 'G' and resid 323 through 335 Processing helix chain 'G' and resid 350 through 359 Processing helix chain 'G' and resid 362 through 366 removed outlier: 3.678A pdb=" N ASP G 365 " --> pdb=" O PRO G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 372 removed outlier: 4.106A pdb=" N ALA G 371 " --> pdb=" O PRO G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 390 removed outlier: 3.591A pdb=" N GLN G 386 " --> pdb=" O TYR G 382 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE G 387 " --> pdb=" O ILE G 383 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU G 390 " --> pdb=" O GLN G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 410 through 432 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.017A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 129 removed outlier: 3.700A pdb=" N VAL R 106 " --> pdb=" O TYR R 102 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU R 122 " --> pdb=" O GLY R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 133 Processing helix chain 'R' and resid 134 through 153 removed outlier: 3.867A pdb=" N LEU R 139 " --> pdb=" O GLY R 135 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU R 149 " --> pdb=" O LEU R 145 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS R 150 " --> pdb=" O GLY R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 164 removed outlier: 3.530A pdb=" N LYS R 161 " --> pdb=" O ILE R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 175 Processing helix chain 'R' and resid 176 through 205 removed outlier: 3.732A pdb=" N LYS R 182 " --> pdb=" O PRO R 178 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL R 203 " --> pdb=" O ARG R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 210 removed outlier: 3.950A pdb=" N LYS R 210 " --> pdb=" O TRP R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 233 removed outlier: 3.784A pdb=" N VAL R 223 " --> pdb=" O ALA R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 239 removed outlier: 3.922A pdb=" N ALA R 237 " --> pdb=" O ALA R 233 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 271 removed outlier: 3.622A pdb=" N THR R 271 " --> pdb=" O GLN R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 281 removed outlier: 4.178A pdb=" N PHE R 278 " --> pdb=" O ASP R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 301 removed outlier: 3.573A pdb=" N ALA R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 350 removed outlier: 3.939A pdb=" N GLU R 320 " --> pdb=" O LYS R 316 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA R 322 " --> pdb=" O ARG R 318 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS R 323 " --> pdb=" O ARG R 319 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL R 325 " --> pdb=" O VAL R 321 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU R 328 " --> pdb=" O THR R 324 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU R 330 " --> pdb=" O PHE R 326 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS R 335 " --> pdb=" O VAL R 331 " (cutoff:3.500A) Proline residue: R 338 - end of helix Processing helix chain 'R' and resid 357 through 380 removed outlier: 3.548A pdb=" N VAL R 366 " --> pdb=" O SER R 362 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE R 372 " --> pdb=" O ASP R 368 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN R 373 " --> pdb=" O TYR R 369 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER R 379 " --> pdb=" O ALA R 375 " (cutoff:3.500A) Processing helix chain 'R' and resid 381 through 388 Processing helix chain 'R' and resid 390 through 402 Processing helix chain 'L' and resid 8 through 18 removed outlier: 3.690A pdb=" N VAL L 12 " --> pdb=" O ASP L 8 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 265 through 266 removed outlier: 3.613A pdb=" N ASP G 280 " --> pdb=" O ILE G 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 265 through 266 removed outlier: 3.613A pdb=" N ASP G 280 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL G 114 " --> pdb=" O ARG G 277 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N PHE G 279 " --> pdb=" O VAL G 114 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU G 116 " --> pdb=" O PHE G 279 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N ALA G 300 " --> pdb=" O THR G 113 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LYS G 115 " --> pdb=" O ALA G 300 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ILE G 302 " --> pdb=" O LYS G 115 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU G 117 " --> pdb=" O ILE G 302 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.506A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.715A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.734A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 4.125A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 152 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.690A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 233 through 234 removed outlier: 3.574A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 277 removed outlier: 4.031A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.537A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'N' and resid 36 through 39 removed outlier: 6.348A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 240 through 242 Processing sheet with id=AB6, first strand: chain 'R' and resid 245 through 247 357 hydrogen bonds defined for protein. 984 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: 2.17 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2343 1.33 - 1.45: 1460 1.45 - 1.58: 4472 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 8367 Sorted by residual: bond pdb=" N GLU B 260 " pdb=" CA GLU B 260 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.24e-02 6.50e+03 7.90e+00 bond pdb=" N MET B 262 " pdb=" CA MET B 262 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.27e+00 bond pdb=" N LYS B 301 " pdb=" CA LYS B 301 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.42e-02 4.96e+03 6.51e+00 bond pdb=" N LEU B 261 " pdb=" CA LEU B 261 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.32e+00 bond pdb=" N GLN R 181 " pdb=" CA GLN R 181 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.69e+00 ... (remaining 8362 not shown) Histogram of bond angle deviations from ideal: 100.12 - 106.90: 188 106.90 - 113.68: 4649 113.68 - 120.45: 3218 120.45 - 127.23: 3191 127.23 - 134.01: 81 Bond angle restraints: 11327 Sorted by residual: angle pdb=" CA GLN R 181 " pdb=" C GLN R 181 " pdb=" O GLN R 181 " ideal model delta sigma weight residual 120.55 116.43 4.12 1.06e+00 8.90e-01 1.51e+01 angle pdb=" CA MET G 38 " pdb=" C MET G 38 " pdb=" O MET G 38 " ideal model delta sigma weight residual 120.55 116.49 4.06 1.06e+00 8.90e-01 1.47e+01 angle pdb=" CA ASP N 106 " pdb=" C ASP N 106 " pdb=" O ASP N 106 " ideal model delta sigma weight residual 121.66 117.52 4.14 1.17e+00 7.31e-01 1.25e+01 angle pdb=" CA MET B 262 " pdb=" C MET B 262 " pdb=" O MET B 262 " ideal model delta sigma weight residual 121.45 117.72 3.73 1.07e+00 8.73e-01 1.22e+01 angle pdb=" N THR R 294 " pdb=" CA THR R 294 " pdb=" C THR R 294 " ideal model delta sigma weight residual 111.36 107.80 3.56 1.09e+00 8.42e-01 1.07e+01 ... (remaining 11322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 4544 17.36 - 34.71: 388 34.71 - 52.07: 63 52.07 - 69.42: 18 69.42 - 86.78: 10 Dihedral angle restraints: 5023 sinusoidal: 1974 harmonic: 3049 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 160.83 -67.83 1 1.00e+01 1.00e-02 5.98e+01 dihedral pdb=" CB CYS L 3 " pdb=" SG CYS L 3 " pdb=" SG CYS L 11 " pdb=" CB CYS L 11 " ideal model delta sinusoidal sigma weight residual -86.00 -140.45 54.45 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CA SER G 31 " pdb=" C SER G 31 " pdb=" N LYS G 32 " pdb=" CA LYS G 32 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 5020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 833 0.030 - 0.061: 306 0.061 - 0.091: 86 0.091 - 0.122: 53 0.122 - 0.152: 15 Chirality restraints: 1293 Sorted by residual: chirality pdb=" CA ARG N 98 " pdb=" N ARG N 98 " pdb=" C ARG N 98 " pdb=" CB ARG N 98 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA ILE G 399 " pdb=" N ILE G 399 " pdb=" C ILE G 399 " pdb=" CB ILE G 399 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA LEU B 261 " pdb=" N LEU B 261 " pdb=" C LEU B 261 " pdb=" CB LEU B 261 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1290 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 337 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO R 338 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 338 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 338 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 98 " -0.192 9.50e-02 1.11e+02 8.59e-02 4.56e+00 pdb=" NE ARG N 98 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG N 98 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG N 98 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG N 98 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO B 236 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.024 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 183 2.68 - 3.24: 8478 3.24 - 3.79: 12195 3.79 - 4.35: 17377 4.35 - 4.90: 28156 Nonbonded interactions: 66389 Sorted by model distance: nonbonded pdb=" O ASP B 66 " pdb=" OG SER B 67 " model vdw 2.126 3.040 nonbonded pdb=" NZ LYS R 161 " pdb=" O ASP L 18 " model vdw 2.209 3.120 nonbonded pdb=" ND1 HIS B 311 " pdb=" OG SER B 331 " model vdw 2.223 3.120 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.276 3.040 nonbonded pdb=" O MET G 323 " pdb=" OG SER G 326 " model vdw 2.299 3.040 ... (remaining 66384 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.000 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 : 0.003 0.039 8367 Z= 0.202 Angle : 0.562 5.995 11327 Z= 0.333 Chirality : 0.040 0.152 1293 Planarity : 0.004 0.086 1431 Dihedral : 13.833 86.778 3028 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.22 % Allowed : 0.33 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.26), residues: 1031 helix: -0.52 (0.27), residues: 371 sheet: -2.41 (0.34), residues: 200 loop : -1.57 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 291 HIS 0.007 0.001 HIS B 142 PHE 0.013 0.001 PHE B 234 TYR 0.007 0.001 TYR R 387 ARG 0.004 0.000 ARG G 288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 311 time to evaluate : 0.930 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 265 PHE cc_start: 0.5559 (t80) cc_final: 0.5220 (t80) outliers start: 2 outliers final: 0 residues processed: 312 average time/residue: 0.2210 time to fit residues: 90.5908 Evaluate side-chains 186 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN N 3 GLN ** R 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8367 Z= 0.303 Angle : 0.728 8.009 11327 Z= 0.375 Chirality : 0.045 0.197 1293 Planarity : 0.005 0.056 1431 Dihedral : 4.769 23.026 1128 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.23 % Allowed : 14.14 % Favored : 82.63 % 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: -1.49 (0.26), residues: 1031 helix: 0.30 (0.26), residues: 384 sheet: -2.22 (0.35), residues: 203 loop : -1.43 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 339 HIS 0.009 0.002 HIS G 402 PHE 0.028 0.002 PHE G 271 TYR 0.018 0.002 TYR B 145 ARG 0.007 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: G 24 ASN cc_start: 0.7040 (p0) cc_final: 0.6728 (p0) REVERT: G 388 LEU cc_start: 0.7699 (mt) cc_final: 0.7319 (pp) REVERT: B 23 LYS cc_start: 0.7858 (ptpp) cc_final: 0.7585 (ptpp) outliers start: 29 outliers final: 17 residues processed: 225 average time/residue: 0.2198 time to fit residues: 65.9615 Evaluate side-chains 189 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 82 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 328 ASN ** G 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8367 Z= 0.303 Angle : 0.689 8.749 11327 Z= 0.354 Chirality : 0.045 0.184 1293 Planarity : 0.005 0.058 1431 Dihedral : 4.727 18.526 1128 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.12 % Allowed : 16.82 % Favored : 79.06 % 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: -1.13 (0.26), residues: 1031 helix: 0.64 (0.26), residues: 391 sheet: -2.13 (0.36), residues: 195 loop : -1.26 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.008 0.002 HIS G 402 PHE 0.025 0.002 PHE G 271 TYR 0.018 0.002 TYR B 145 ARG 0.006 0.001 ARG G 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 195 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 24 ASN cc_start: 0.7010 (p0) cc_final: 0.6772 (p0) REVERT: G 273 ASP cc_start: 0.7140 (t0) cc_final: 0.6924 (t0) REVERT: G 347 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: G 388 LEU cc_start: 0.7691 (mt) cc_final: 0.7351 (mt) REVERT: B 336 LEU cc_start: 0.8106 (mt) cc_final: 0.7734 (mt) outliers start: 37 outliers final: 25 residues processed: 216 average time/residue: 0.2105 time to fit residues: 61.3174 Evaluate side-chains 189 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 399 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 386 LEU Chi-restraints excluded: chain L residue 12 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 328 ASN B 75 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 ASN R 158 ASN ** R 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8367 Z= 0.262 Angle : 0.679 8.621 11327 Z= 0.346 Chirality : 0.044 0.220 1293 Planarity : 0.005 0.056 1431 Dihedral : 4.681 20.218 1128 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.79 % Allowed : 16.93 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.26), residues: 1031 helix: 0.70 (0.26), residues: 391 sheet: -2.04 (0.35), residues: 203 loop : -1.21 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.011 0.002 HIS G 402 PHE 0.011 0.001 PHE B 241 TYR 0.018 0.002 TYR B 145 ARG 0.009 0.001 ARG G 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 183 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 ASN cc_start: 0.7034 (p0) cc_final: 0.6798 (p0) REVERT: G 388 LEU cc_start: 0.7753 (mt) cc_final: 0.7467 (mt) REVERT: B 336 LEU cc_start: 0.8158 (mt) cc_final: 0.7865 (mt) REVERT: N 91 THR cc_start: 0.7596 (OUTLIER) cc_final: 0.7335 (p) outliers start: 43 outliers final: 25 residues processed: 209 average time/residue: 0.2189 time to fit residues: 61.0704 Evaluate side-chains 178 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 399 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 0.0070 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 328 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8367 Z= 0.206 Angle : 0.665 9.019 11327 Z= 0.341 Chirality : 0.043 0.244 1293 Planarity : 0.005 0.054 1431 Dihedral : 4.645 22.674 1128 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.79 % Allowed : 19.04 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.26), residues: 1031 helix: 0.70 (0.26), residues: 392 sheet: -1.71 (0.35), residues: 208 loop : -1.15 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.011 0.001 HIS G 402 PHE 0.010 0.001 PHE B 241 TYR 0.024 0.001 TYR B 145 ARG 0.010 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 180 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 ASN cc_start: 0.7058 (p0) cc_final: 0.6827 (p0) REVERT: G 388 LEU cc_start: 0.7779 (mt) cc_final: 0.7501 (mt) REVERT: B 336 LEU cc_start: 0.8067 (mt) cc_final: 0.7773 (mt) REVERT: N 91 THR cc_start: 0.7512 (OUTLIER) cc_final: 0.7269 (p) outliers start: 43 outliers final: 33 residues processed: 205 average time/residue: 0.1872 time to fit residues: 53.4033 Evaluate side-chains 195 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain G residue 434 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 214 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8367 Z= 0.229 Angle : 0.658 8.485 11327 Z= 0.336 Chirality : 0.043 0.204 1293 Planarity : 0.005 0.054 1431 Dihedral : 4.588 22.887 1128 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.01 % Allowed : 19.15 % Favored : 75.84 % 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: -0.91 (0.26), residues: 1031 helix: 0.68 (0.26), residues: 399 sheet: -1.76 (0.35), residues: 207 loop : -1.13 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.011 0.001 HIS G 402 PHE 0.014 0.001 PHE L 14 TYR 0.023 0.002 TYR B 145 ARG 0.009 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 171 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 24 ASN cc_start: 0.7070 (p0) cc_final: 0.6735 (p0) REVERT: G 392 MET cc_start: 0.2851 (mmp) cc_final: 0.2499 (mmp) REVERT: N 91 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7369 (p) REVERT: R 380 CYS cc_start: 0.5490 (t) cc_final: 0.5253 (t) outliers start: 45 outliers final: 35 residues processed: 199 average time/residue: 0.1754 time to fit residues: 49.3306 Evaluate side-chains 194 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain G residue 434 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 0.1980 chunk 39 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8367 Z= 0.271 Angle : 0.688 9.132 11327 Z= 0.355 Chirality : 0.044 0.284 1293 Planarity : 0.005 0.054 1431 Dihedral : 4.642 24.323 1128 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.90 % Allowed : 20.49 % Favored : 74.61 % 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: 1031 helix: 0.68 (0.26), residues: 399 sheet: -1.69 (0.35), residues: 207 loop : -1.11 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.011 0.002 HIS G 402 PHE 0.010 0.001 PHE B 241 TYR 0.031 0.002 TYR R 281 ARG 0.006 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 165 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: G 338 TRP cc_start: 0.7771 (m-10) cc_final: 0.7563 (m-10) REVERT: G 382 TYR cc_start: 0.7842 (t80) cc_final: 0.7620 (t80) REVERT: N 91 THR cc_start: 0.7760 (OUTLIER) cc_final: 0.7432 (p) REVERT: R 380 CYS cc_start: 0.5840 (t) cc_final: 0.5483 (t) outliers start: 44 outliers final: 40 residues processed: 193 average time/residue: 0.1835 time to fit residues: 49.6258 Evaluate side-chains 195 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 154 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain G residue 434 PHE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 117 ILE Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** G 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8367 Z= 0.197 Angle : 0.700 10.825 11327 Z= 0.353 Chirality : 0.044 0.286 1293 Planarity : 0.004 0.053 1431 Dihedral : 4.556 24.348 1128 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.90 % Allowed : 21.83 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.26), residues: 1031 helix: 0.77 (0.26), residues: 399 sheet: -1.61 (0.36), residues: 199 loop : -1.15 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.013 0.001 HIS G 402 PHE 0.020 0.001 PHE R 265 TYR 0.027 0.001 TYR R 281 ARG 0.009 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 348 LEU cc_start: 0.8386 (mt) cc_final: 0.8175 (mp) REVERT: G 403 MET cc_start: 0.5080 (pmm) cc_final: 0.4384 (ptp) REVERT: N 91 THR cc_start: 0.7587 (OUTLIER) cc_final: 0.7280 (p) REVERT: R 167 TRP cc_start: 0.6386 (t-100) cc_final: 0.6012 (t-100) REVERT: R 380 CYS cc_start: 0.5866 (t) cc_final: 0.5522 (t) outliers start: 35 outliers final: 27 residues processed: 209 average time/residue: 0.1916 time to fit residues: 55.3552 Evaluate side-chains 192 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 303 PHE Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain G residue 434 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 82 optimal weight: 30.0000 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN G 328 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8367 Z= 0.273 Angle : 0.760 15.009 11327 Z= 0.376 Chirality : 0.047 0.344 1293 Planarity : 0.005 0.069 1431 Dihedral : 4.654 22.329 1128 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.90 % Allowed : 23.94 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.26), residues: 1031 helix: 0.69 (0.26), residues: 401 sheet: -1.67 (0.35), residues: 205 loop : -1.04 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.013 0.002 HIS G 402 PHE 0.018 0.001 PHE R 265 TYR 0.022 0.002 TYR B 145 ARG 0.005 0.001 ARG R 318 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 348 LEU cc_start: 0.8440 (mt) cc_final: 0.8221 (mp) REVERT: G 403 MET cc_start: 0.5045 (pmm) cc_final: 0.4394 (ptp) REVERT: N 91 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7343 (p) outliers start: 35 outliers final: 30 residues processed: 189 average time/residue: 0.1679 time to fit residues: 45.4515 Evaluate side-chains 186 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 155 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 303 PHE Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain G residue 434 PHE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 356 ASN Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 0.0370 chunk 11 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN G 324 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8367 Z= 0.209 Angle : 0.762 12.193 11327 Z= 0.378 Chirality : 0.046 0.328 1293 Planarity : 0.005 0.062 1431 Dihedral : 4.592 20.350 1128 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.34 % Allowed : 24.16 % Favored : 72.49 % 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: -0.75 (0.26), residues: 1031 helix: 0.82 (0.26), residues: 393 sheet: -1.59 (0.35), residues: 203 loop : -1.08 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 291 HIS 0.014 0.001 HIS G 402 PHE 0.016 0.001 PHE R 265 TYR 0.022 0.002 TYR B 145 ARG 0.007 0.001 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 348 LEU cc_start: 0.8308 (mt) cc_final: 0.8099 (mp) REVERT: G 403 MET cc_start: 0.4934 (pmm) cc_final: 0.4376 (ptp) REVERT: N 91 THR cc_start: 0.7439 (OUTLIER) cc_final: 0.7186 (p) REVERT: R 147 ASP cc_start: 0.7350 (t70) cc_final: 0.7146 (t0) REVERT: R 380 CYS cc_start: 0.5815 (t) cc_final: 0.5589 (t) outliers start: 30 outliers final: 26 residues processed: 201 average time/residue: 0.1872 time to fit residues: 52.3793 Evaluate side-chains 192 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 303 PHE Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 415 VAL Chi-restraints excluded: chain G residue 434 PHE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.117194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.091357 restraints weight = 18274.421| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 4.17 r_work: 0.3444 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8367 Z= 0.216 Angle : 0.748 11.710 11327 Z= 0.373 Chirality : 0.047 0.358 1293 Planarity : 0.005 0.052 1431 Dihedral : 4.588 23.057 1128 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.45 % Allowed : 24.50 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.26), residues: 1031 helix: 0.75 (0.26), residues: 395 sheet: -1.65 (0.34), residues: 207 loop : -1.00 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 167 HIS 0.014 0.001 HIS G 402 PHE 0.023 0.001 PHE R 280 TYR 0.022 0.002 TYR B 145 ARG 0.009 0.001 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2200.94 seconds wall clock time: 39 minutes 46.15 seconds (2386.15 seconds total)