Starting phenix.real_space_refine on Mon Mar 11 12:42:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hix_33480/03_2024/8hix_33480.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hix_33480/03_2024/8hix_33480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hix_33480/03_2024/8hix_33480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hix_33480/03_2024/8hix_33480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hix_33480/03_2024/8hix_33480.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hix_33480/03_2024/8hix_33480.pdb" } resolution = 3.12 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= 0.006 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 53 5.16 5 C 5258 2.51 5 N 1433 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 331": "OD1" <-> "OD2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 227": "OE1" <-> "OE2" Residue "R PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 275": "OE1" <-> "OE2" Residue "R PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8274 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1980 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2297 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 4.85, per 1000 atoms: 0.59 Number of scatterers: 8274 At special positions: 0 Unit cell: (88.4, 98.8, 126.88, 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 53 16.00 O 1530 8.00 N 1433 7.00 C 5258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " 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: 3.34 Conformation dependent library (CDL) restraints added in 1.5 seconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 43.0% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.966A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.574A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.748A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 279 removed outlier: 4.223A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU A 268 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.546A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.531A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.510A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 removed outlier: 3.532A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.606A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.620A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.825A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 56 removed outlier: 4.154A pdb=" N LEU R 41 " --> pdb=" O PHE R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 91 removed outlier: 5.071A pdb=" N VAL R 84 " --> pdb=" O VAL R 80 " (cutoff:3.500A) Proline residue: R 85 - end of helix Processing helix chain 'R' and resid 99 through 133 removed outlier: 3.898A pdb=" N GLN R 103 " --> pdb=" O SER R 99 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE R 107 " --> pdb=" O GLN R 103 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER R 110 " --> pdb=" O GLY R 106 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER R 119 " --> pdb=" O VAL R 115 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR R 128 " --> pdb=" O SER R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 141 Processing helix chain 'R' and resid 142 through 161 removed outlier: 3.714A pdb=" N PHE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 167 removed outlier: 3.645A pdb=" N HIS R 167 " --> pdb=" O SER R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 185 removed outlier: 3.863A pdb=" N ALA R 182 " --> pdb=" O PHE R 178 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP R 185 " --> pdb=" O CYS R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 199 removed outlier: 3.541A pdb=" N MET R 197 " --> pdb=" O LEU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 232 removed outlier: 4.083A pdb=" N ALA R 203 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA R 204 " --> pdb=" O TYR R 200 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 278 Proline residue: R 267 - end of helix removed outlier: 3.567A pdb=" N THR R 278 " --> pdb=" O LEU R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 295 Processing helix chain 'R' and resid 295 through 308 Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 324 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 5.998A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.619A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.780A 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 62 removed outlier: 3.955A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.891A 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: 6.991A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.859A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.116A 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: 3.652A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.313A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 5.987A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.335A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1188 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: 2.32 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2628 1.34 - 1.46: 1594 1.46 - 1.57: 4164 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8458 Sorted by residual: bond pdb=" CB PHE A 222 " pdb=" CG PHE A 222 " ideal model delta sigma weight residual 1.502 1.465 0.037 2.30e-02 1.89e+03 2.62e+00 bond pdb=" CG1 ILE A 276 " pdb=" CD1 ILE A 276 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.47e+00 bond pdb=" CG1 ILE B 58 " pdb=" CD1 ILE B 58 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.44e+00 bond pdb=" CG1 ILE R 150 " pdb=" CD1 ILE R 150 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.17e+00 bond pdb=" C THR A 325 " pdb=" N PRO A 326 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.07e+00 ... (remaining 8453 not shown) Histogram of bond angle deviations from ideal: 97.57 - 104.89: 100 104.89 - 112.20: 4080 112.20 - 119.52: 2943 119.52 - 126.84: 4226 126.84 - 134.15: 118 Bond angle restraints: 11467 Sorted by residual: angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C TRP R 265 " pdb=" N LEU R 266 " pdb=" CA LEU R 266 " ideal model delta sigma weight residual 120.09 125.86 -5.77 1.25e+00 6.40e-01 2.13e+01 angle pdb=" C GLN A 59 " pdb=" N MET A 60 " pdb=" CA MET A 60 " ideal model delta sigma weight residual 121.58 113.32 8.26 1.95e+00 2.63e-01 1.79e+01 angle pdb=" N GLN A 59 " pdb=" CA GLN A 59 " pdb=" CB GLN A 59 " ideal model delta sigma weight residual 110.16 115.89 -5.73 1.48e+00 4.57e-01 1.50e+01 angle pdb=" N GLY R 279 " pdb=" CA GLY R 279 " pdb=" C GLY R 279 " ideal model delta sigma weight residual 113.18 121.67 -8.49 2.37e+00 1.78e-01 1.28e+01 ... (remaining 11462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4434 17.90 - 35.81: 475 35.81 - 53.71: 71 53.71 - 71.61: 23 71.61 - 89.51: 7 Dihedral angle restraints: 5010 sinusoidal: 1971 harmonic: 3039 Sorted by residual: dihedral pdb=" CA THR R 278 " pdb=" C THR R 278 " pdb=" N GLY R 279 " pdb=" CA GLY R 279 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 53.86 39.14 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CA VAL N 110 " pdb=" C VAL N 110 " pdb=" N THR N 111 " pdb=" CA THR N 111 " ideal model delta harmonic sigma weight residual -180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 5007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1094 0.076 - 0.152: 178 0.152 - 0.228: 10 0.228 - 0.304: 2 0.304 - 0.380: 2 Chirality restraints: 1286 Sorted by residual: chirality pdb=" CB THR N 114 " pdb=" CA THR N 114 " pdb=" OG1 THR N 114 " pdb=" CG2 THR N 114 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CG LEU B 286 " pdb=" CB LEU B 286 " pdb=" CD1 LEU B 286 " pdb=" CD2 LEU B 286 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1283 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " -0.061 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO B 39 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 142 " 0.052 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO R 143 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 143 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 143 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 52 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C ARG B 52 " 0.049 2.00e-02 2.50e+03 pdb=" O ARG B 52 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY B 53 " -0.016 2.00e-02 2.50e+03 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 418 2.72 - 3.27: 8249 3.27 - 3.81: 14269 3.81 - 4.36: 17546 4.36 - 4.90: 29638 Nonbonded interactions: 70120 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.178 2.440 nonbonded pdb=" OH TYR R 156 " pdb=" O MET R 198 " model vdw 2.232 2.440 nonbonded pdb=" O SER R 116 " pdb=" OG SER R 119 " model vdw 2.239 2.440 nonbonded pdb=" O PHE R 161 " pdb=" OG SER R 164 " model vdw 2.249 2.440 nonbonded pdb=" OG1 THR N 104 " pdb=" OD2 ASP N 106 " model vdw 2.258 2.440 ... (remaining 70115 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: 0.300 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: 1.920 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 25.450 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 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 : 0.006 0.061 8458 Z= 0.393 Angle : 0.944 10.115 11467 Z= 0.512 Chirality : 0.056 0.380 1286 Planarity : 0.007 0.091 1460 Dihedral : 15.235 89.512 3035 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: -1.52 (0.24), residues: 1029 helix: -0.27 (0.23), residues: 399 sheet: -1.17 (0.34), residues: 201 loop : -1.52 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP N 47 HIS 0.026 0.003 HIS A 220 PHE 0.040 0.003 PHE R 287 TYR 0.029 0.003 TYR B 111 ARG 0.013 0.001 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.991 Fit side-chains REVERT: B 275 SER cc_start: 0.8082 (m) cc_final: 0.7874 (m) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2455 time to fit residues: 53.2712 Evaluate side-chains 132 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.0060 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 213 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN B 155 ASN N 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8458 Z= 0.177 Angle : 0.560 7.200 11467 Z= 0.294 Chirality : 0.042 0.147 1286 Planarity : 0.005 0.068 1460 Dihedral : 5.030 24.209 1138 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.44 % Allowed : 9.18 % Favored : 89.38 % 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: -0.52 (0.25), residues: 1029 helix: 0.95 (0.25), residues: 396 sheet: -1.13 (0.33), residues: 214 loop : -1.09 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.001 PHE R 287 TYR 0.014 0.001 TYR R 200 ARG 0.005 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 0.868 Fit side-chains REVERT: A 60 MET cc_start: 0.5200 (ptp) cc_final: 0.4897 (ptp) REVERT: A 220 HIS cc_start: 0.7376 (t70) cc_final: 0.7172 (t-90) REVERT: B 275 SER cc_start: 0.8195 (m) cc_final: 0.7972 (m) REVERT: G 21 MET cc_start: 0.4797 (mmt) cc_final: 0.4042 (mmm) outliers start: 13 outliers final: 9 residues processed: 170 average time/residue: 0.2262 time to fit residues: 51.3974 Evaluate side-chains 159 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN A 271 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8458 Z= 0.211 Angle : 0.566 6.921 11467 Z= 0.296 Chirality : 0.043 0.150 1286 Planarity : 0.005 0.066 1460 Dihedral : 4.842 24.029 1138 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.88 % Allowed : 14.60 % Favored : 83.52 % 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: -0.23 (0.26), residues: 1029 helix: 1.31 (0.25), residues: 405 sheet: -0.94 (0.35), residues: 206 loop : -1.14 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.016 0.002 PHE A 212 TYR 0.013 0.001 TYR B 105 ARG 0.005 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 0.889 Fit side-chains REVERT: A 220 HIS cc_start: 0.7377 (t70) cc_final: 0.7162 (t-90) REVERT: B 275 SER cc_start: 0.8205 (m) cc_final: 0.7974 (m) REVERT: G 21 MET cc_start: 0.4623 (mmt) cc_final: 0.4114 (mmm) REVERT: R 173 TYR cc_start: 0.7321 (m-80) cc_final: 0.6841 (m-80) REVERT: R 266 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7962 (tt) outliers start: 17 outliers final: 12 residues processed: 161 average time/residue: 0.2406 time to fit residues: 51.1348 Evaluate side-chains 157 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.0270 chunk 26 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS N 123 GLN R 221 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8458 Z= 0.148 Angle : 0.511 7.033 11467 Z= 0.268 Chirality : 0.041 0.147 1286 Planarity : 0.004 0.065 1460 Dihedral : 4.466 22.481 1138 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.77 % Allowed : 17.92 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1029 helix: 1.75 (0.25), residues: 400 sheet: -0.88 (0.34), residues: 212 loop : -0.93 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.022 0.001 PHE R 255 TYR 0.008 0.001 TYR B 145 ARG 0.007 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 160 time to evaluate : 0.954 Fit side-chains REVERT: G 21 MET cc_start: 0.4575 (mmt) cc_final: 0.4020 (mmm) REVERT: R 173 TYR cc_start: 0.7152 (m-80) cc_final: 0.6855 (m-80) outliers start: 16 outliers final: 11 residues processed: 167 average time/residue: 0.2509 time to fit residues: 54.9695 Evaluate side-chains 159 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 0.1980 chunk 87 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 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 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8458 Z= 0.189 Angle : 0.538 6.784 11467 Z= 0.283 Chirality : 0.042 0.137 1286 Planarity : 0.004 0.065 1460 Dihedral : 4.511 22.720 1138 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.54 % Allowed : 19.03 % Favored : 78.43 % 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: 0.21 (0.26), residues: 1029 helix: 1.80 (0.26), residues: 400 sheet: -0.79 (0.35), residues: 206 loop : -0.96 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.031 0.002 PHE R 255 TYR 0.011 0.001 TYR B 105 ARG 0.006 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 0.966 Fit side-chains REVERT: G 21 MET cc_start: 0.4751 (mmt) cc_final: 0.4107 (mmm) REVERT: N 21 SER cc_start: 0.7313 (t) cc_final: 0.6962 (t) REVERT: R 173 TYR cc_start: 0.7302 (m-80) cc_final: 0.6911 (m-80) REVERT: R 266 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7971 (tt) outliers start: 23 outliers final: 17 residues processed: 162 average time/residue: 0.2471 time to fit residues: 53.7212 Evaluate side-chains 159 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8458 Z= 0.207 Angle : 0.552 6.820 11467 Z= 0.290 Chirality : 0.042 0.140 1286 Planarity : 0.005 0.064 1460 Dihedral : 4.552 22.683 1138 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.99 % Allowed : 19.58 % Favored : 77.43 % 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: 0.29 (0.26), residues: 1029 helix: 1.95 (0.26), residues: 394 sheet: -0.66 (0.35), residues: 198 loop : -1.04 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.024 0.002 PHE R 255 TYR 0.016 0.001 TYR B 105 ARG 0.008 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 0.977 Fit side-chains REVERT: A 220 HIS cc_start: 0.7294 (t-90) cc_final: 0.7027 (t-90) REVERT: A 358 TYR cc_start: 0.7264 (m-80) cc_final: 0.6588 (m-80) REVERT: B 169 TRP cc_start: 0.8235 (OUTLIER) cc_final: 0.6459 (m100) REVERT: G 21 MET cc_start: 0.4836 (mmt) cc_final: 0.4211 (mmm) REVERT: N 21 SER cc_start: 0.7346 (t) cc_final: 0.6975 (t) REVERT: R 173 TYR cc_start: 0.7415 (m-80) cc_final: 0.6887 (m-80) REVERT: R 266 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7919 (tt) outliers start: 27 outliers final: 22 residues processed: 160 average time/residue: 0.2384 time to fit residues: 50.4015 Evaluate side-chains 167 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8458 Z= 0.211 Angle : 0.553 6.821 11467 Z= 0.289 Chirality : 0.042 0.138 1286 Planarity : 0.005 0.064 1460 Dihedral : 4.564 22.727 1138 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.54 % Allowed : 20.02 % Favored : 76.44 % 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: 0.37 (0.26), residues: 1029 helix: 2.00 (0.26), residues: 393 sheet: -0.70 (0.35), residues: 204 loop : -0.90 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.002 PHE R 255 TYR 0.014 0.001 TYR B 105 ARG 0.009 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 358 TYR cc_start: 0.7266 (m-80) cc_final: 0.6587 (m-80) REVERT: B 169 TRP cc_start: 0.8233 (OUTLIER) cc_final: 0.6490 (m100) REVERT: G 21 MET cc_start: 0.4648 (mmt) cc_final: 0.4043 (mmm) REVERT: N 21 SER cc_start: 0.7360 (t) cc_final: 0.6991 (t) REVERT: R 173 TYR cc_start: 0.7454 (m-80) cc_final: 0.6896 (m-80) REVERT: R 254 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5578 (tt) REVERT: R 266 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7992 (tt) outliers start: 32 outliers final: 25 residues processed: 164 average time/residue: 0.2299 time to fit residues: 50.0366 Evaluate side-chains 169 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 0.0570 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8458 Z= 0.159 Angle : 0.523 6.848 11467 Z= 0.274 Chirality : 0.041 0.141 1286 Planarity : 0.004 0.064 1460 Dihedral : 4.368 21.797 1138 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.21 % Allowed : 21.79 % Favored : 76.00 % 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: 0.54 (0.27), residues: 1029 helix: 2.17 (0.26), residues: 394 sheet: -0.65 (0.34), residues: 210 loop : -0.81 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 265 HIS 0.005 0.001 HIS A 357 PHE 0.024 0.001 PHE R 287 TYR 0.030 0.001 TYR R 200 ARG 0.008 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.7344 (t-90) cc_final: 0.7111 (t-90) REVERT: A 358 TYR cc_start: 0.7241 (m-80) cc_final: 0.6587 (m-80) REVERT: B 169 TRP cc_start: 0.8184 (OUTLIER) cc_final: 0.6444 (m100) REVERT: G 21 MET cc_start: 0.4418 (mmt) cc_final: 0.4018 (mmm) REVERT: N 21 SER cc_start: 0.7166 (t) cc_final: 0.6741 (t) REVERT: N 80 TYR cc_start: 0.7418 (m-80) cc_final: 0.7178 (m-80) REVERT: R 173 TYR cc_start: 0.7263 (m-80) cc_final: 0.6837 (m-80) REVERT: R 254 LEU cc_start: 0.5718 (OUTLIER) cc_final: 0.5428 (tt) REVERT: R 266 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8027 (tt) outliers start: 20 outliers final: 17 residues processed: 162 average time/residue: 0.2402 time to fit residues: 51.1943 Evaluate side-chains 160 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8458 Z= 0.164 Angle : 0.527 6.756 11467 Z= 0.276 Chirality : 0.041 0.138 1286 Planarity : 0.004 0.064 1460 Dihedral : 4.345 21.664 1138 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.77 % Allowed : 21.68 % Favored : 75.55 % 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: 0.60 (0.27), residues: 1029 helix: 2.20 (0.26), residues: 393 sheet: -0.60 (0.34), residues: 210 loop : -0.78 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.023 0.001 PHE R 215 TYR 0.014 0.001 TYR R 200 ARG 0.008 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8194 (OUTLIER) cc_final: 0.6444 (m100) REVERT: G 21 MET cc_start: 0.4676 (mmt) cc_final: 0.4147 (mmm) REVERT: N 21 SER cc_start: 0.7166 (t) cc_final: 0.6736 (t) REVERT: N 65 LYS cc_start: 0.6666 (tppt) cc_final: 0.6456 (tptt) REVERT: N 80 TYR cc_start: 0.7416 (m-80) cc_final: 0.7174 (m-80) REVERT: R 173 TYR cc_start: 0.7269 (m-80) cc_final: 0.6826 (m-80) REVERT: R 254 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5433 (tt) REVERT: R 266 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8039 (tt) outliers start: 25 outliers final: 21 residues processed: 159 average time/residue: 0.2349 time to fit residues: 49.4918 Evaluate side-chains 162 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 80 optimal weight: 0.0040 chunk 8 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8458 Z= 0.145 Angle : 0.515 6.867 11467 Z= 0.269 Chirality : 0.041 0.147 1286 Planarity : 0.004 0.064 1460 Dihedral : 4.298 21.053 1138 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.32 % Allowed : 22.35 % Favored : 75.33 % 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: 0.71 (0.27), residues: 1029 helix: 2.28 (0.26), residues: 394 sheet: -0.52 (0.35), residues: 210 loop : -0.71 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.026 0.001 PHE R 287 TYR 0.018 0.001 TYR R 200 ARG 0.008 0.000 ARG R 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8172 (OUTLIER) cc_final: 0.6433 (m100) REVERT: G 21 MET cc_start: 0.4525 (mmt) cc_final: 0.3982 (mmm) REVERT: N 21 SER cc_start: 0.7185 (t) cc_final: 0.6777 (t) REVERT: N 65 LYS cc_start: 0.6480 (tppt) cc_final: 0.6248 (tptt) REVERT: N 80 TYR cc_start: 0.7367 (m-80) cc_final: 0.7136 (m-80) REVERT: R 173 TYR cc_start: 0.7139 (m-80) cc_final: 0.6757 (m-80) REVERT: R 254 LEU cc_start: 0.5533 (OUTLIER) cc_final: 0.5254 (tt) outliers start: 21 outliers final: 18 residues processed: 156 average time/residue: 0.2424 time to fit residues: 50.0285 Evaluate side-chains 156 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.0870 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.228970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.189759 restraints weight = 8270.245| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 1.72 r_work: 0.3945 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8458 Z= 0.152 Angle : 0.519 6.868 11467 Z= 0.270 Chirality : 0.041 0.144 1286 Planarity : 0.004 0.064 1460 Dihedral : 4.248 21.051 1138 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.43 % Allowed : 22.68 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 1029 helix: 2.33 (0.26), residues: 394 sheet: -0.51 (0.35), residues: 209 loop : -0.65 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.024 0.001 PHE R 215 TYR 0.019 0.001 TYR R 200 ARG 0.008 0.000 ARG R 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.08 seconds wall clock time: 39 minutes 19.54 seconds (2359.54 seconds total)