Starting phenix.real_space_refine on Tue May 7 21:34:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoh_38529/05_2024/8xoh_38529.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoh_38529/05_2024/8xoh_38529.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/8xoh_38529/05_2024/8xoh_38529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoh_38529/05_2024/8xoh_38529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoh_38529/05_2024/8xoh_38529.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoh_38529/05_2024/8xoh_38529.pdb" } 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= -0.000 sd= 0.007 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 55 5.16 5 C 5600 2.51 5 N 1529 2.21 5 O 1625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "R ASP 111": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 8809 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1875 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2581 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1746 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2171 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 7, 'TRANS': 257} Chain breaks: 3 Time building chain proxies: 5.12, per 1000 atoms: 0.58 Number of scatterers: 8809 At special positions: 0 Unit cell: (111.384, 118.881, 108.171, 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 55 16.00 O 1625 8.00 N 1529 7.00 C 5600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.7 seconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 41.7% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.792A pdb=" N ALA A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.515A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.601A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.035A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.335A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.986A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 removed outlier: 4.008A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 25 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 52 through 87 removed outlier: 3.749A pdb=" N GLY R 58 " --> pdb=" O GLN R 54 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Proline residue: R 71 - end of helix removed outlier: 3.555A pdb=" N PHE R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 91 removed outlier: 3.524A pdb=" N MET R 91 " --> pdb=" O ARG R 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 88 through 91' Processing helix chain 'R' and resid 92 through 116 removed outlier: 3.705A pdb=" N LEU R 96 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 124 removed outlier: 3.590A pdb=" N TYR R 123 " --> pdb=" O LEU R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 160 Processing helix chain 'R' and resid 163 through 168 removed outlier: 3.615A pdb=" N SER R 166 " --> pdb=" O MET R 163 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU R 167 " --> pdb=" O ARG R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 200 Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 211 through 223 Processing helix chain 'R' and resid 223 through 248 Processing helix chain 'R' and resid 254 through 285 removed outlier: 3.545A pdb=" N LEU R 258 " --> pdb=" O ARG R 254 " (cutoff:3.500A) Proline residue: R 274 - end of helix Processing helix chain 'R' and resid 302 through 325 removed outlier: 3.931A pdb=" N SER R 317 " --> pdb=" O ALA R 313 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 328 through 342 removed outlier: 3.578A pdb=" N ARG R 332 " --> pdb=" O GLY R 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.891A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.660A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.502A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.790A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.599A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.714A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.477A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.751A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.784A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.463A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.012A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1326 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: 3.20 Time building geometry restraints manager: 3.61 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: 2012 1.33 - 1.45: 1970 1.45 - 1.57: 4927 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 8989 Sorted by residual: bond pdb=" C THR A 325 " pdb=" N PRO A 326 " ideal model delta sigma weight residual 1.329 1.365 -0.036 1.25e-02 6.40e+03 8.13e+00 bond pdb=" C LEU R 304 " pdb=" O LEU R 304 " ideal model delta sigma weight residual 1.236 1.210 0.026 1.15e-02 7.56e+03 5.22e+00 bond pdb=" CB ASP A 272 " pdb=" CG ASP A 272 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.16e+00 bond pdb=" C ASP R 111 " pdb=" O ASP R 111 " ideal model delta sigma weight residual 1.236 1.210 0.026 1.29e-02 6.01e+03 4.04e+00 bond pdb=" N THR G 6 " pdb=" CA THR G 6 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 ... (remaining 8984 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.31: 254 107.31 - 114.27: 5180 114.27 - 121.22: 4443 121.22 - 128.17: 2208 128.17 - 135.12: 84 Bond angle restraints: 12169 Sorted by residual: angle pdb=" C THR A 325 " pdb=" N PRO A 326 " pdb=" CA PRO A 326 " ideal model delta sigma weight residual 120.14 114.67 5.47 1.06e+00 8.90e-01 2.66e+01 angle pdb=" C SER R 325 " pdb=" N PHE R 326 " pdb=" CA PHE R 326 " ideal model delta sigma weight residual 122.65 116.64 6.01 1.60e+00 3.91e-01 1.41e+01 angle pdb=" CB LYS G 32 " pdb=" CG LYS G 32 " pdb=" CD LYS G 32 " ideal model delta sigma weight residual 111.30 118.75 -7.45 2.30e+00 1.89e-01 1.05e+01 angle pdb=" N VAL A 241 " pdb=" CA VAL A 241 " pdb=" C VAL A 241 " ideal model delta sigma weight residual 110.05 106.84 3.21 1.09e+00 8.42e-01 8.69e+00 angle pdb=" CA PRO A 326 " pdb=" C PRO A 326 " pdb=" O PRO A 326 " ideal model delta sigma weight residual 121.86 118.38 3.48 1.22e+00 6.72e-01 8.13e+00 ... (remaining 12164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4753 17.96 - 35.92: 459 35.92 - 53.88: 89 53.88 - 71.84: 22 71.84 - 89.81: 9 Dihedral angle restraints: 5332 sinusoidal: 2092 harmonic: 3240 Sorted by residual: dihedral pdb=" CA THR A 364 " pdb=" C THR A 364 " pdb=" N CYS A 365 " pdb=" CA CYS A 365 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA PHE R 326 " pdb=" C PHE R 326 " pdb=" N LEU R 327 " pdb=" CA LEU R 327 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASP R 111 " pdb=" CB ASP R 111 " pdb=" CG ASP R 111 " pdb=" OD1 ASP R 111 " ideal model delta sinusoidal sigma weight residual -30.00 -90.52 60.52 1 2.00e+01 2.50e-03 1.22e+01 ... (remaining 5329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1103 0.044 - 0.088: 182 0.088 - 0.132: 88 0.132 - 0.176: 4 0.176 - 0.220: 1 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA ASP E 73 " pdb=" N ASP E 73 " pdb=" C ASP E 73 " pdb=" CB ASP E 73 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ASN R 100 " pdb=" N ASN R 100 " pdb=" C ASN R 100 " pdb=" CB ASN R 100 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CA ASP R 111 " pdb=" N ASP R 111 " pdb=" C ASP R 111 " pdb=" CB ASP R 111 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 1375 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 180 " 0.037 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO E 181 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 181 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 181 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 13 " 0.171 9.50e-02 1.11e+02 7.67e-02 3.88e+00 pdb=" NE ARG G 13 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG G 13 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG G 13 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG G 13 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 325 " 0.007 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" C SER R 325 " -0.022 2.00e-02 2.50e+03 pdb=" O SER R 325 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE R 326 " 0.008 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1237 2.75 - 3.29: 8899 3.29 - 3.83: 14753 3.83 - 4.36: 18021 4.36 - 4.90: 31192 Nonbonded interactions: 74102 Sorted by model distance: nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.215 2.440 nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.237 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.267 2.440 nonbonded pdb=" OD1 ASP A 249 " pdb=" OG SER A 251 " model vdw 2.287 2.440 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.293 2.440 ... (remaining 74097 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.280 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.880 Find NCS groups from input model: 0.430 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 0.051 8989 Z= 0.193 Angle : 0.557 10.123 12169 Z= 0.325 Chirality : 0.041 0.220 1378 Planarity : 0.004 0.077 1546 Dihedral : 15.157 89.805 3234 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.21 % Allowed : 13.66 % Favored : 86.13 % 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: 0.74 (0.26), residues: 1092 helix: 1.45 (0.25), residues: 408 sheet: -0.34 (0.31), residues: 258 loop : 0.28 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS R 197 PHE 0.016 0.001 PHE E 68 TYR 0.019 0.001 TYR A 311 ARG 0.009 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 211 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 391 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: B 101 MET cc_start: 0.8881 (mtp) cc_final: 0.8641 (mtp) REVERT: E 34 MET cc_start: 0.8982 (mmt) cc_final: 0.8772 (mmt) REVERT: E 142 GLN cc_start: 0.6582 (mt0) cc_final: 0.6316 (mt0) REVERT: E 229 CYS cc_start: 0.8419 (p) cc_final: 0.8110 (p) REVERT: R 135 LEU cc_start: 0.8393 (mt) cc_final: 0.8019 (mp) outliers start: 2 outliers final: 1 residues processed: 212 average time/residue: 0.2622 time to fit residues: 72.3609 Evaluate side-chains 176 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain R residue 304 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN E 194 ASN E 232 HIS ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 282 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8989 Z= 0.271 Angle : 0.573 7.177 12169 Z= 0.309 Chirality : 0.043 0.192 1378 Planarity : 0.004 0.030 1546 Dihedral : 5.445 57.188 1217 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.92 % Allowed : 14.70 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1092 helix: 1.60 (0.25), residues: 401 sheet: -0.51 (0.30), residues: 249 loop : 0.15 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.004 0.001 HIS E 232 PHE 0.014 0.002 PHE R 326 TYR 0.014 0.001 TYR R 324 ARG 0.006 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 193 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 390 GLU cc_start: 0.8234 (tt0) cc_final: 0.8030 (tt0) REVERT: A 391 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: E 34 MET cc_start: 0.9010 (mmt) cc_final: 0.8720 (mmt) REVERT: E 68 PHE cc_start: 0.6083 (m-80) cc_final: 0.5246 (m-10) REVERT: E 80 PHE cc_start: 0.7857 (m-80) cc_final: 0.7415 (m-80) REVERT: E 83 MET cc_start: 0.7825 (mmt) cc_final: 0.7157 (mmt) REVERT: G 21 MET cc_start: 0.7225 (mtp) cc_final: 0.6556 (tpp) REVERT: G 48 ASP cc_start: 0.8420 (t0) cc_final: 0.8117 (t0) REVERT: R 91 MET cc_start: 0.6601 (mtm) cc_final: 0.6043 (mtt) REVERT: R 135 LEU cc_start: 0.8383 (mt) cc_final: 0.7964 (mp) REVERT: R 154 ASP cc_start: 0.8701 (t0) cc_final: 0.7897 (t0) REVERT: R 248 ARG cc_start: 0.6085 (ptp-170) cc_final: 0.5881 (ptp-170) outliers start: 28 outliers final: 17 residues processed: 205 average time/residue: 0.2214 time to fit residues: 62.2007 Evaluate side-chains 188 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 323 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 392 ASN E 77 ASN E 179 GLN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8989 Z= 0.249 Angle : 0.546 6.735 12169 Z= 0.293 Chirality : 0.043 0.205 1378 Planarity : 0.003 0.037 1546 Dihedral : 5.019 59.782 1215 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.02 % Allowed : 16.48 % Favored : 80.50 % 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: 0.63 (0.25), residues: 1092 helix: 1.71 (0.25), residues: 401 sheet: -0.66 (0.30), residues: 255 loop : 0.02 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.014 0.002 PHE E 68 TYR 0.011 0.001 TYR R 338 ARG 0.008 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 179 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7304 (t0) cc_final: 0.7042 (t0) REVERT: A 390 GLU cc_start: 0.8217 (tt0) cc_final: 0.8008 (tt0) REVERT: A 391 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7959 (m-80) REVERT: E 34 MET cc_start: 0.9013 (mmt) cc_final: 0.8706 (mmt) REVERT: E 80 PHE cc_start: 0.7884 (m-80) cc_final: 0.7605 (m-80) REVERT: E 83 MET cc_start: 0.7891 (mmt) cc_final: 0.7553 (mmt) REVERT: R 91 MET cc_start: 0.6629 (mtm) cc_final: 0.6112 (mtt) REVERT: R 154 ASP cc_start: 0.8777 (t0) cc_final: 0.7746 (t0) outliers start: 29 outliers final: 19 residues processed: 196 average time/residue: 0.2410 time to fit residues: 63.6793 Evaluate side-chains 184 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 282 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 0.0010 chunk 104 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN E 77 ASN R 84 ASN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8989 Z= 0.143 Angle : 0.496 6.568 12169 Z= 0.263 Chirality : 0.041 0.196 1378 Planarity : 0.003 0.029 1546 Dihedral : 4.633 58.785 1215 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.29 % Allowed : 18.04 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1092 helix: 1.93 (0.25), residues: 401 sheet: -0.48 (0.30), residues: 250 loop : 0.00 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.002 0.001 HIS B 54 PHE 0.010 0.001 PHE R 326 TYR 0.010 0.001 TYR R 338 ARG 0.006 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7229 (t0) cc_final: 0.6978 (t0) REVERT: A 391 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: B 59 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.8242 (m-80) REVERT: B 215 GLU cc_start: 0.8311 (tp30) cc_final: 0.7881 (tp30) REVERT: B 254 ASP cc_start: 0.8084 (t70) cc_final: 0.7776 (t0) REVERT: E 80 PHE cc_start: 0.7850 (m-80) cc_final: 0.7510 (m-80) REVERT: G 62 ARG cc_start: 0.6963 (mmp80) cc_final: 0.6636 (mmp80) REVERT: R 57 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7501 (pt) REVERT: R 82 VAL cc_start: 0.8039 (m) cc_final: 0.7744 (p) REVERT: R 154 ASP cc_start: 0.8715 (t70) cc_final: 0.7599 (t0) REVERT: R 342 LYS cc_start: 0.5344 (mmtm) cc_final: 0.4582 (mmtt) outliers start: 22 outliers final: 12 residues processed: 197 average time/residue: 0.2397 time to fit residues: 63.1397 Evaluate side-chains 184 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 282 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN E 39 GLN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8989 Z= 0.204 Angle : 0.521 6.919 12169 Z= 0.275 Chirality : 0.041 0.170 1378 Planarity : 0.003 0.029 1546 Dihedral : 4.651 58.242 1215 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.23 % Allowed : 18.77 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1092 helix: 2.04 (0.25), residues: 401 sheet: -0.47 (0.30), residues: 252 loop : 0.01 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.014 0.001 PHE R 326 TYR 0.016 0.001 TYR R 65 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7217 (t0) cc_final: 0.6984 (t0) REVERT: A 220 HIS cc_start: 0.8355 (m170) cc_final: 0.8097 (m-70) REVERT: A 391 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.7922 (m-80) REVERT: B 59 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: B 215 GLU cc_start: 0.8269 (tp30) cc_final: 0.7926 (tp30) REVERT: B 234 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.7654 (m-80) REVERT: E 34 MET cc_start: 0.8931 (mmt) cc_final: 0.8577 (mmm) REVERT: E 80 PHE cc_start: 0.7838 (m-80) cc_final: 0.7435 (m-80) REVERT: E 83 MET cc_start: 0.7833 (mmt) cc_final: 0.7469 (mmt) REVERT: G 62 ARG cc_start: 0.6905 (mmp80) cc_final: 0.6488 (mmp80) REVERT: R 57 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7585 (pt) REVERT: R 154 ASP cc_start: 0.8860 (t70) cc_final: 0.7471 (t0) outliers start: 31 outliers final: 22 residues processed: 194 average time/residue: 0.2370 time to fit residues: 61.8125 Evaluate side-chains 192 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 225 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 86 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN E 77 ASN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8989 Z= 0.165 Angle : 0.493 6.742 12169 Z= 0.262 Chirality : 0.041 0.165 1378 Planarity : 0.003 0.029 1546 Dihedral : 4.543 57.945 1215 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.13 % Allowed : 20.02 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.25), residues: 1092 helix: 2.12 (0.25), residues: 401 sheet: -0.44 (0.30), residues: 250 loop : -0.01 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.012 0.001 PHE R 326 TYR 0.015 0.001 TYR R 65 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 177 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7222 (t0) cc_final: 0.6987 (t0) REVERT: A 220 HIS cc_start: 0.8209 (m170) cc_final: 0.7979 (m-70) REVERT: A 391 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: B 59 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: B 215 GLU cc_start: 0.8180 (tp30) cc_final: 0.7908 (tp30) REVERT: B 234 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: E 18 ARG cc_start: 0.6564 (tpp-160) cc_final: 0.6281 (tpp80) REVERT: E 34 MET cc_start: 0.8924 (mmt) cc_final: 0.8596 (mmm) REVERT: E 80 PHE cc_start: 0.7856 (m-80) cc_final: 0.7425 (m-80) REVERT: E 83 MET cc_start: 0.7728 (mmt) cc_final: 0.7410 (mmt) REVERT: G 62 ARG cc_start: 0.6886 (mmp80) cc_final: 0.6675 (mmp80) REVERT: R 57 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7587 (pt) REVERT: R 154 ASP cc_start: 0.8836 (t70) cc_final: 0.7447 (t0) REVERT: R 342 LYS cc_start: 0.5083 (mmtm) cc_final: 0.4260 (mmtt) outliers start: 30 outliers final: 21 residues processed: 199 average time/residue: 0.2494 time to fit residues: 65.7089 Evaluate side-chains 190 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 225 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN E 77 ASN E 179 GLN R 84 ASN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8989 Z= 0.288 Angle : 0.555 8.096 12169 Z= 0.294 Chirality : 0.043 0.170 1378 Planarity : 0.003 0.028 1546 Dihedral : 4.758 57.634 1215 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.28 % Allowed : 18.77 % Favored : 76.96 % 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: 0.84 (0.25), residues: 1092 helix: 2.00 (0.25), residues: 407 sheet: -0.41 (0.30), residues: 248 loop : -0.14 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.015 0.002 PHE R 326 TYR 0.010 0.001 TYR R 65 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 167 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7233 (t0) cc_final: 0.7012 (t0) REVERT: A 29 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8373 (tp-100) REVERT: A 220 HIS cc_start: 0.8290 (m170) cc_final: 0.7973 (m-70) REVERT: A 391 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.7959 (m-80) REVERT: B 215 GLU cc_start: 0.8249 (tp30) cc_final: 0.7998 (tp30) REVERT: B 234 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.7873 (m-80) REVERT: B 249 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8083 (t) REVERT: B 254 ASP cc_start: 0.8161 (t70) cc_final: 0.7880 (t0) REVERT: E 34 MET cc_start: 0.9023 (mmt) cc_final: 0.8566 (mmt) REVERT: E 80 PHE cc_start: 0.7843 (m-80) cc_final: 0.7439 (m-80) REVERT: E 83 MET cc_start: 0.7651 (mmt) cc_final: 0.7363 (mmt) REVERT: E 166 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8829 (tt) REVERT: G 62 ARG cc_start: 0.7217 (mmp80) cc_final: 0.6956 (mmp80) REVERT: R 57 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7565 (pt) REVERT: R 91 MET cc_start: 0.6468 (mtm) cc_final: 0.6074 (mtt) REVERT: R 154 ASP cc_start: 0.8936 (t70) cc_final: 0.7715 (t0) outliers start: 41 outliers final: 30 residues processed: 196 average time/residue: 0.2164 time to fit residues: 58.4649 Evaluate side-chains 195 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 240 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.0970 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8989 Z= 0.168 Angle : 0.505 7.027 12169 Z= 0.267 Chirality : 0.041 0.161 1378 Planarity : 0.003 0.029 1546 Dihedral : 4.544 57.675 1215 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.34 % Allowed : 19.71 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1092 helix: 2.20 (0.25), residues: 401 sheet: -0.30 (0.30), residues: 246 loop : -0.08 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.013 0.001 PHE E 212 TYR 0.018 0.001 TYR R 65 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7225 (t0) cc_final: 0.6993 (t0) REVERT: A 220 HIS cc_start: 0.8255 (m170) cc_final: 0.8049 (m90) REVERT: A 391 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: B 59 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: B 234 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: B 254 ASP cc_start: 0.8110 (t70) cc_final: 0.7802 (t0) REVERT: E 80 PHE cc_start: 0.7804 (m-80) cc_final: 0.7291 (m-80) REVERT: E 166 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8885 (tt) REVERT: E 191 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8260 (mtt90) REVERT: R 57 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7554 (pt) REVERT: R 154 ASP cc_start: 0.8823 (t70) cc_final: 0.7468 (t0) REVERT: R 342 LYS cc_start: 0.5386 (mmtm) cc_final: 0.4543 (mmtt) outliers start: 32 outliers final: 23 residues processed: 191 average time/residue: 0.2367 time to fit residues: 61.0224 Evaluate side-chains 191 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 323 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8989 Z= 0.208 Angle : 0.540 9.189 12169 Z= 0.281 Chirality : 0.042 0.210 1378 Planarity : 0.003 0.028 1546 Dihedral : 4.573 57.498 1215 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.44 % Allowed : 20.23 % Favored : 76.33 % 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: 1.04 (0.25), residues: 1092 helix: 2.31 (0.25), residues: 395 sheet: -0.40 (0.30), residues: 260 loop : -0.03 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.023 0.001 PHE E 212 TYR 0.010 0.001 TYR R 65 ARG 0.005 0.000 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7220 (t0) cc_final: 0.7010 (t0) REVERT: A 220 HIS cc_start: 0.8300 (m170) cc_final: 0.8083 (m90) REVERT: A 336 ARG cc_start: 0.7661 (ttp80) cc_final: 0.7389 (mtp-110) REVERT: A 391 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: B 59 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8287 (m-80) REVERT: B 234 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: B 254 ASP cc_start: 0.8116 (t70) cc_final: 0.7835 (t0) REVERT: E 80 PHE cc_start: 0.7831 (m-80) cc_final: 0.7295 (m-80) REVERT: E 90 ASP cc_start: 0.8034 (m-30) cc_final: 0.7726 (m-30) REVERT: E 166 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8878 (tt) REVERT: E 191 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8330 (mtt90) REVERT: R 57 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7517 (pt) REVERT: R 154 ASP cc_start: 0.8849 (t70) cc_final: 0.7432 (t0) REVERT: R 342 LYS cc_start: 0.5320 (mmtm) cc_final: 0.4476 (mmtt) outliers start: 33 outliers final: 24 residues processed: 191 average time/residue: 0.2348 time to fit residues: 60.5198 Evaluate side-chains 194 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 323 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8989 Z= 0.211 Angle : 0.533 7.363 12169 Z= 0.280 Chirality : 0.042 0.265 1378 Planarity : 0.003 0.029 1546 Dihedral : 4.590 57.256 1215 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.65 % Allowed : 20.13 % Favored : 76.23 % 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: 0.95 (0.25), residues: 1092 helix: 2.20 (0.25), residues: 401 sheet: -0.37 (0.30), residues: 260 loop : -0.14 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 272 HIS 0.004 0.001 HIS G 44 PHE 0.021 0.001 PHE E 212 TYR 0.018 0.001 TYR R 65 ARG 0.006 0.000 ARG E 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7220 (t0) cc_final: 0.7001 (t0) REVERT: A 220 HIS cc_start: 0.8304 (m170) cc_final: 0.8086 (m90) REVERT: A 336 ARG cc_start: 0.7657 (ttp80) cc_final: 0.7384 (mtp-110) REVERT: A 391 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8006 (m-80) REVERT: B 59 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: B 234 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: B 246 ASP cc_start: 0.8208 (m-30) cc_final: 0.7920 (t0) REVERT: E 80 PHE cc_start: 0.7861 (m-80) cc_final: 0.7227 (m-80) REVERT: E 166 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8882 (tt) REVERT: R 68 PHE cc_start: 0.6968 (m-80) cc_final: 0.6752 (m-80) REVERT: R 154 ASP cc_start: 0.8852 (t70) cc_final: 0.7465 (t0) REVERT: R 342 LYS cc_start: 0.5284 (mmtm) cc_final: 0.4472 (mmtt) outliers start: 35 outliers final: 23 residues processed: 195 average time/residue: 0.2504 time to fit residues: 64.9747 Evaluate side-chains 193 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 323 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 26 optimal weight: 0.0470 chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 75 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.165828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128848 restraints weight = 10778.652| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.47 r_work: 0.3272 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8989 Z= 0.153 Angle : 0.524 11.276 12169 Z= 0.273 Chirality : 0.041 0.251 1378 Planarity : 0.003 0.029 1546 Dihedral : 4.420 57.462 1215 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.61 % Allowed : 21.06 % Favored : 76.33 % 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 (0.25), residues: 1092 helix: 2.41 (0.25), residues: 395 sheet: -0.27 (0.30), residues: 259 loop : -0.05 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.017 0.001 PHE E 212 TYR 0.017 0.001 TYR R 65 ARG 0.006 0.000 ARG E 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2374.97 seconds wall clock time: 43 minutes 52.39 seconds (2632.39 seconds total)