Starting phenix.real_space_refine on Mon Mar 11 08:13:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kmf_0724/03_2024/6kmf_0724.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kmf_0724/03_2024/6kmf_0724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kmf_0724/03_2024/6kmf_0724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kmf_0724/03_2024/6kmf_0724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kmf_0724/03_2024/6kmf_0724.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kmf_0724/03_2024/6kmf_0724.pdb" } resolution = 3.6 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= 1.000 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 27 5.16 5 C 4860 2.51 5 N 1293 2.21 5 O 1524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 52": "OD1" <-> "OD2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B ASP 162": "OD1" <-> "OD2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 264": "OD1" <-> "OD2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 356": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7704 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2403 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain: "B" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2568 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 323} Chain: "C" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2568 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 323} Chain: "D" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Time building chain proxies: 4.61, per 1000 atoms: 0.60 Number of scatterers: 7704 At special positions: 0 Unit cell: (170.24, 73.92, 181.44, 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 27 16.00 O 1524 8.00 N 1293 7.00 C 4860 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: 2.80 Conformation dependent library (CDL) restraints added in 1.5 seconds 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 20 sheets defined 7.2% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.694A pdb=" N GLN A 125 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 126 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 127 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.525A pdb=" N TYR A 186 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 187 " --> pdb=" O ALA A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 183 through 187' Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 121 through 125 removed outlier: 3.716A pdb=" N ASN B 124 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 125 " --> pdb=" O ALA B 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 125' Processing helix chain 'B' and resid 294 through 301 removed outlier: 3.839A pdb=" N ALA B 300 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 114 removed outlier: 3.570A pdb=" N LYS C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.700A pdb=" N GLN C 125 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU C 126 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 removed outlier: 3.680A pdb=" N TYR C 186 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP C 187 " --> pdb=" O ALA C 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 187' Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.983A pdb=" N GLN C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 74 removed outlier: 5.895A pdb=" N LEU A 164 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 363 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS A 87 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL B 367 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU A 83 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N CYS B 369 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS A 81 " --> pdb=" O CYS B 369 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 74 removed outlier: 5.895A pdb=" N LEU A 164 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN B 366 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR A 147 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.767A pdb=" N THR A 118 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 206 " --> pdb=" O THR A 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 256 through 260 removed outlier: 3.669A pdb=" N GLN A 256 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG A 172 " --> pdb=" O TYR A 341 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE A 343 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA A 174 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU A 345 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR A 176 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN B 379 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASP A 342 " --> pdb=" O GLN B 379 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA B 381 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LYS A 344 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 196 removed outlier: 3.627A pdb=" N VAL A 193 " --> pdb=" O LYS A 282 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR A 280 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 279 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 77 removed outlier: 3.575A pdb=" N LYS B 74 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL B 62 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 98 " --> pdb=" O MET B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.699A pdb=" N VAL C 367 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU B 164 " --> pdb=" O THR C 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.649A pdb=" N GLY B 90 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.598A pdb=" N TYR B 147 " --> pdb=" O ASN B 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 257 through 260 removed outlier: 6.567A pdb=" N ARG B 172 " --> pdb=" O TYR B 341 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE B 343 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 174 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU B 345 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N THR B 176 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE B 347 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LYS B 340 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLN C 379 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASP B 342 " --> pdb=" O GLN C 379 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA C 381 " --> pdb=" O ASP B 342 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LYS B 344 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TRP C 383 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR B 346 " --> pdb=" O TRP C 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 190 through 192 Processing sheet with id=AB4, first strand: chain 'B' and resid 263 through 264 removed outlier: 3.669A pdb=" N ASN B 263 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 70 through 73 removed outlier: 4.398A pdb=" N ALA C 72 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 64 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU C 164 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE C 85 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL D 367 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLU C 83 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N CYS D 369 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS C 81 " --> pdb=" O CYS D 369 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 90 through 91 Processing sheet with id=AB7, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AB8, first strand: chain 'C' and resid 256 through 260 removed outlier: 3.955A pdb=" N GLN C 256 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG C 172 " --> pdb=" O TYR C 341 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE C 343 " --> pdb=" O ARG C 172 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA C 174 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU C 345 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR C 176 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 190 through 196 removed outlier: 5.585A pdb=" N PHE C 192 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLN C 284 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS C 282 " --> pdb=" O PRO C 194 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 221 through 222 removed outlier: 3.564A pdb=" N THR C 222 " --> pdb=" O ALA C 238 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 263 through 264 removed outlier: 3.502A pdb=" N ASN C 263 " --> pdb=" O ILE C 335 " (cutoff:3.500A) 125 hydrogen bonds defined for protein. 327 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: 1.97 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2296 1.33 - 1.45: 1137 1.45 - 1.57: 4378 1.57 - 1.68: 0 1.68 - 1.80: 45 Bond restraints: 7856 Sorted by residual: bond pdb=" N THR B 138 " pdb=" CA THR B 138 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.42e-02 4.96e+03 3.64e+00 bond pdb=" N THR C 138 " pdb=" CA THR C 138 " ideal model delta sigma weight residual 1.457 1.478 -0.020 1.29e-02 6.01e+03 2.47e+00 bond pdb=" N THR A 138 " pdb=" CA THR A 138 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.37e+00 bond pdb=" CG LEU C 315 " pdb=" CD1 LEU C 315 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.06e+00 bond pdb=" N ASN B 286 " pdb=" CA ASN B 286 " ideal model delta sigma weight residual 1.460 1.479 -0.020 1.42e-02 4.96e+03 1.89e+00 ... (remaining 7851 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.52: 192 106.52 - 113.38: 4297 113.38 - 120.25: 2632 120.25 - 127.11: 3490 127.11 - 133.98: 93 Bond angle restraints: 10704 Sorted by residual: angle pdb=" C LEU C 225 " pdb=" N THR C 226 " pdb=" CA THR C 226 " ideal model delta sigma weight residual 122.08 128.86 -6.78 1.47e+00 4.63e-01 2.13e+01 angle pdb=" C LYS A 137 " pdb=" N THR A 138 " pdb=" CA THR A 138 " ideal model delta sigma weight residual 121.54 129.72 -8.18 1.91e+00 2.74e-01 1.84e+01 angle pdb=" C GLY A 149 " pdb=" N TYR A 150 " pdb=" CA TYR A 150 " ideal model delta sigma weight residual 122.46 128.36 -5.90 1.41e+00 5.03e-01 1.75e+01 angle pdb=" C LYS C 137 " pdb=" N THR C 138 " pdb=" CA THR C 138 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C LYS B 137 " pdb=" N THR B 138 " pdb=" CA THR B 138 " ideal model delta sigma weight residual 122.82 128.56 -5.74 1.42e+00 4.96e-01 1.63e+01 ... (remaining 10699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 4121 16.62 - 33.24: 442 33.24 - 49.86: 76 49.86 - 66.49: 21 66.49 - 83.11: 10 Dihedral angle restraints: 4670 sinusoidal: 1740 harmonic: 2930 Sorted by residual: dihedral pdb=" CA VAL A 248 " pdb=" C VAL A 248 " pdb=" N ALA A 249 " pdb=" CA ALA A 249 " ideal model delta harmonic sigma weight residual 180.00 155.91 24.09 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA GLY A 199 " pdb=" C GLY A 199 " pdb=" N LEU A 200 " pdb=" CA LEU A 200 " ideal model delta harmonic sigma weight residual 180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ASN A 246 " pdb=" C ASN A 246 " pdb=" N TYR A 247 " pdb=" CA TYR A 247 " ideal model delta harmonic sigma weight residual -180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 4667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 907 0.058 - 0.116: 242 0.116 - 0.174: 50 0.174 - 0.232: 15 0.232 - 0.290: 4 Chirality restraints: 1218 Sorted by residual: chirality pdb=" CB ILE B 197 " pdb=" CA ILE B 197 " pdb=" CG1 ILE B 197 " pdb=" CG2 ILE B 197 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB ILE C 148 " pdb=" CA ILE C 148 " pdb=" CG1 ILE C 148 " pdb=" CG2 ILE C 148 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB ILE A 178 " pdb=" CA ILE A 178 " pdb=" CG1 ILE A 178 " pdb=" CG2 ILE A 178 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 1215 not shown) Planarity restraints: 1397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 193 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.11e+00 pdb=" N PRO A 194 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 194 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 194 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 248 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C VAL A 248 " -0.046 2.00e-02 2.50e+03 pdb=" O VAL A 248 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA A 249 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 233 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.80e+00 pdb=" N PRO B 234 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " -0.027 5.00e-02 4.00e+02 ... (remaining 1394 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2397 2.82 - 3.34: 6458 3.34 - 3.86: 11953 3.86 - 4.38: 12372 4.38 - 4.90: 22342 Nonbonded interactions: 55522 Sorted by model distance: nonbonded pdb=" OH TYR C 147 " pdb=" O GLU C 155 " model vdw 2.298 2.440 nonbonded pdb=" O SER B 266 " pdb=" OG SER B 266 " model vdw 2.303 2.440 nonbonded pdb=" ND2 ASN A 146 " pdb=" OD1 ASN A 157 " model vdw 2.315 2.520 nonbonded pdb=" O LEU C 200 " pdb=" OG1 THR C 222 " model vdw 2.372 2.440 nonbonded pdb=" O THR B 80 " pdb=" OG1 THR B 80 " model vdw 2.373 2.440 ... (remaining 55517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 47 through 362) selection = (chain 'C' and resid 47 through 362) } 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 group one per residue 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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 12.840 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 23.650 Find NCS groups from input model: 0.470 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7856 Z= 0.380 Angle : 0.901 10.181 10704 Z= 0.492 Chirality : 0.058 0.290 1218 Planarity : 0.006 0.067 1397 Dihedral : 14.663 83.107 2804 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.36 % Favored : 86.64 % Rotamer: Outliers : 0.62 % Allowed : 14.80 % Favored : 84.58 % 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: -4.41 (0.21), residues: 1003 helix: -4.98 (0.23), residues: 54 sheet: -1.79 (0.44), residues: 144 loop : -3.32 (0.17), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 242 HIS 0.003 0.001 HIS B 364 PHE 0.011 0.002 PHE B 318 TYR 0.030 0.003 TYR C 150 ARG 0.003 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 221 time to evaluate : 0.942 Fit side-chains REVERT: A 56 LYS cc_start: 0.8511 (tttm) cc_final: 0.8212 (tppt) REVERT: A 97 MET cc_start: 0.8361 (mtp) cc_final: 0.8097 (mtt) REVERT: A 119 GLU cc_start: 0.8774 (mp0) cc_final: 0.8521 (mt-10) REVERT: A 124 ASN cc_start: 0.9007 (m110) cc_final: 0.8525 (m110) REVERT: A 182 MET cc_start: 0.8145 (mmt) cc_final: 0.7850 (mmt) REVERT: A 200 LEU cc_start: 0.8614 (mt) cc_final: 0.8380 (mt) REVERT: A 258 PHE cc_start: 0.8922 (m-80) cc_final: 0.8216 (m-80) REVERT: A 259 TYR cc_start: 0.8845 (m-80) cc_final: 0.8619 (m-80) REVERT: A 318 PHE cc_start: 0.8582 (t80) cc_final: 0.8088 (t80) REVERT: B 92 ARG cc_start: 0.8386 (mmt-90) cc_final: 0.8122 (mmt-90) REVERT: B 131 ILE cc_start: 0.8694 (mt) cc_final: 0.8492 (mp) REVERT: B 195 GLU cc_start: 0.8091 (tp30) cc_final: 0.7828 (tp30) REVERT: B 256 GLN cc_start: 0.8968 (mm110) cc_final: 0.8710 (mm-40) REVERT: B 317 ASN cc_start: 0.8224 (t0) cc_final: 0.7981 (t0) REVERT: B 329 TYR cc_start: 0.9064 (t80) cc_final: 0.8804 (t80) REVERT: B 354 ASN cc_start: 0.8154 (t0) cc_final: 0.7870 (t0) REVERT: C 53 ASP cc_start: 0.8274 (m-30) cc_final: 0.7866 (t0) REVERT: C 83 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6971 (mm-30) REVERT: C 236 ASN cc_start: 0.8181 (t0) cc_final: 0.7587 (t0) outliers start: 5 outliers final: 2 residues processed: 225 average time/residue: 0.1742 time to fit residues: 54.1357 Evaluate side-chains 183 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain B residue 316 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 0.0770 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 0.0170 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 99 ASN A 286 ASN A 333 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN B 157 ASN B 161 ASN B 219 ASN B 286 ASN B 317 ASN C 205 GLN C 236 ASN C 286 ASN C 321 ASN D 368 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7856 Z= 0.199 Angle : 0.599 9.396 10704 Z= 0.319 Chirality : 0.044 0.256 1218 Planarity : 0.004 0.076 1397 Dihedral : 5.906 45.307 1084 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 4.35 % Allowed : 20.52 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.23), residues: 1003 helix: -4.24 (0.40), residues: 54 sheet: -1.39 (0.44), residues: 148 loop : -3.01 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 242 HIS 0.003 0.001 HIS A 158 PHE 0.012 0.001 PHE C 48 TYR 0.020 0.002 TYR B 198 ARG 0.002 0.000 ARG C 245 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 197 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7077 (p0) REVERT: A 56 LYS cc_start: 0.8480 (tttm) cc_final: 0.8201 (tppt) REVERT: A 80 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8145 (m) REVERT: A 97 MET cc_start: 0.8267 (mtp) cc_final: 0.7960 (mtt) REVERT: A 124 ASN cc_start: 0.9007 (m110) cc_final: 0.8632 (m110) REVERT: A 258 PHE cc_start: 0.8787 (m-80) cc_final: 0.8074 (m-80) REVERT: A 318 PHE cc_start: 0.8514 (t80) cc_final: 0.7991 (t80) REVERT: B 195 GLU cc_start: 0.8208 (tp30) cc_final: 0.7935 (tp30) REVERT: B 256 GLN cc_start: 0.8986 (mm110) cc_final: 0.8688 (mm-40) REVERT: B 329 TYR cc_start: 0.9019 (t80) cc_final: 0.8663 (t80) REVERT: B 348 THR cc_start: 0.8658 (m) cc_final: 0.8335 (p) REVERT: B 354 ASN cc_start: 0.8211 (t0) cc_final: 0.7994 (t0) REVERT: C 53 ASP cc_start: 0.8303 (m-30) cc_final: 0.7919 (t0) REVERT: C 83 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6829 (mm-30) REVERT: D 368 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7017 (tm-30) outliers start: 35 outliers final: 24 residues processed: 215 average time/residue: 0.1433 time to fit residues: 45.3016 Evaluate side-chains 203 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 176 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 368 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 74 optimal weight: 0.0980 chunk 61 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 256 GLN A 333 ASN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7856 Z= 0.250 Angle : 0.615 10.027 10704 Z= 0.327 Chirality : 0.045 0.265 1218 Planarity : 0.004 0.078 1397 Dihedral : 5.796 41.792 1084 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 5.97 % Allowed : 19.90 % Favored : 74.13 % 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: -3.64 (0.24), residues: 1003 helix: -3.22 (0.61), residues: 42 sheet: -1.34 (0.44), residues: 148 loop : -2.86 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 242 HIS 0.004 0.001 HIS A 158 PHE 0.019 0.002 PHE C 192 TYR 0.022 0.002 TYR B 198 ARG 0.002 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 186 time to evaluate : 0.903 Fit side-chains REVERT: A 56 LYS cc_start: 0.8502 (tttm) cc_final: 0.8249 (tppt) REVERT: A 80 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8258 (m) REVERT: A 97 MET cc_start: 0.8218 (mtp) cc_final: 0.7921 (mtt) REVERT: A 124 ASN cc_start: 0.9085 (m110) cc_final: 0.8675 (m110) REVERT: A 213 LEU cc_start: 0.9254 (pt) cc_final: 0.8536 (pp) REVERT: A 258 PHE cc_start: 0.8729 (m-80) cc_final: 0.8094 (m-80) REVERT: A 318 PHE cc_start: 0.8617 (t80) cc_final: 0.8034 (t80) REVERT: A 329 TYR cc_start: 0.8389 (t80) cc_final: 0.7977 (t80) REVERT: B 195 GLU cc_start: 0.8244 (tp30) cc_final: 0.7963 (tp30) REVERT: B 256 GLN cc_start: 0.8989 (mm110) cc_final: 0.8693 (mm-40) REVERT: B 329 TYR cc_start: 0.9026 (t80) cc_final: 0.8655 (t80) REVERT: B 354 ASN cc_start: 0.8272 (t0) cc_final: 0.8055 (t0) REVERT: C 53 ASP cc_start: 0.8434 (m-30) cc_final: 0.7944 (t0) REVERT: C 83 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6963 (mm-30) REVERT: C 299 GLN cc_start: 0.8376 (mt0) cc_final: 0.8175 (mt0) outliers start: 48 outliers final: 39 residues processed: 207 average time/residue: 0.1423 time to fit residues: 43.8035 Evaluate side-chains 212 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 172 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 366 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 219 ASN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7856 Z= 0.215 Angle : 0.594 10.350 10704 Z= 0.314 Chirality : 0.044 0.278 1218 Planarity : 0.004 0.074 1397 Dihedral : 5.632 40.347 1084 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 6.09 % Allowed : 22.26 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.24), residues: 1003 helix: -3.16 (0.54), residues: 55 sheet: -1.26 (0.44), residues: 148 loop : -2.77 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 242 HIS 0.002 0.001 HIS C 170 PHE 0.018 0.001 PHE B 48 TYR 0.021 0.002 TYR B 198 ARG 0.002 0.000 ARG C 245 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 181 time to evaluate : 0.938 Fit side-chains REVERT: A 53 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7114 (p0) REVERT: A 56 LYS cc_start: 0.8532 (tttm) cc_final: 0.8251 (tppt) REVERT: A 80 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8266 (m) REVERT: A 97 MET cc_start: 0.8189 (mtp) cc_final: 0.7888 (mtt) REVERT: A 124 ASN cc_start: 0.9076 (m110) cc_final: 0.8661 (m110) REVERT: A 187 ASP cc_start: 0.8029 (m-30) cc_final: 0.7516 (m-30) REVERT: A 213 LEU cc_start: 0.9213 (pt) cc_final: 0.8560 (pp) REVERT: A 258 PHE cc_start: 0.8692 (m-80) cc_final: 0.8065 (m-80) REVERT: A 318 PHE cc_start: 0.8600 (t80) cc_final: 0.8052 (t80) REVERT: A 329 TYR cc_start: 0.8402 (t80) cc_final: 0.8043 (t80) REVERT: B 195 GLU cc_start: 0.8323 (tp30) cc_final: 0.8054 (tp30) REVERT: B 256 GLN cc_start: 0.9005 (mm110) cc_final: 0.8703 (mm-40) REVERT: B 329 TYR cc_start: 0.9033 (t80) cc_final: 0.8535 (t80) REVERT: B 354 ASN cc_start: 0.8292 (t0) cc_final: 0.8062 (t0) REVERT: C 53 ASP cc_start: 0.8489 (m-30) cc_final: 0.7921 (t0) REVERT: C 83 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6898 (mm-30) outliers start: 49 outliers final: 39 residues processed: 202 average time/residue: 0.1563 time to fit residues: 45.4496 Evaluate side-chains 208 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 167 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN B 219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7856 Z= 0.210 Angle : 0.592 10.380 10704 Z= 0.311 Chirality : 0.044 0.263 1218 Planarity : 0.004 0.073 1397 Dihedral : 5.516 39.806 1084 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 6.09 % Allowed : 22.14 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.24), residues: 1003 helix: -2.86 (0.55), residues: 61 sheet: -1.20 (0.45), residues: 148 loop : -2.72 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 242 HIS 0.002 0.001 HIS A 158 PHE 0.023 0.002 PHE C 192 TYR 0.022 0.002 TYR C 280 ARG 0.002 0.000 ARG C 245 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 174 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7119 (p0) REVERT: A 56 LYS cc_start: 0.8535 (tttm) cc_final: 0.8252 (tppt) REVERT: A 80 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8343 (m) REVERT: A 97 MET cc_start: 0.8180 (mtp) cc_final: 0.7865 (mtt) REVERT: A 124 ASN cc_start: 0.9081 (m110) cc_final: 0.8663 (m110) REVERT: A 187 ASP cc_start: 0.8030 (m-30) cc_final: 0.7514 (m-30) REVERT: A 213 LEU cc_start: 0.9214 (pt) cc_final: 0.8507 (pp) REVERT: A 258 PHE cc_start: 0.8676 (m-80) cc_final: 0.8021 (m-80) REVERT: A 318 PHE cc_start: 0.8610 (t80) cc_final: 0.8041 (t80) REVERT: A 329 TYR cc_start: 0.8445 (t80) cc_final: 0.8118 (t80) REVERT: B 195 GLU cc_start: 0.8308 (tp30) cc_final: 0.8028 (tp30) REVERT: B 329 TYR cc_start: 0.9042 (t80) cc_final: 0.8648 (t80) REVERT: B 354 ASN cc_start: 0.8281 (t0) cc_final: 0.8050 (t0) REVERT: C 83 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6945 (mm-30) REVERT: C 131 ILE cc_start: 0.9240 (mt) cc_final: 0.8980 (mm) outliers start: 49 outliers final: 37 residues processed: 197 average time/residue: 0.1402 time to fit residues: 40.3505 Evaluate side-chains 203 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 164 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.0670 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 0.0570 chunk 23 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7856 Z= 0.149 Angle : 0.561 9.575 10704 Z= 0.293 Chirality : 0.043 0.231 1218 Planarity : 0.004 0.069 1397 Dihedral : 5.210 40.000 1084 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 4.60 % Allowed : 24.88 % Favored : 70.52 % 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: -3.31 (0.24), residues: 1003 helix: -2.51 (0.60), residues: 61 sheet: -1.09 (0.45), residues: 148 loop : -2.64 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 242 HIS 0.001 0.000 HIS A 158 PHE 0.024 0.001 PHE C 192 TYR 0.018 0.001 TYR B 198 ARG 0.001 0.000 ARG C 245 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7204 (p0) REVERT: A 56 LYS cc_start: 0.8501 (tttm) cc_final: 0.8231 (tppt) REVERT: A 80 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8177 (m) REVERT: A 97 MET cc_start: 0.8147 (mtp) cc_final: 0.7804 (mtt) REVERT: A 124 ASN cc_start: 0.9077 (m110) cc_final: 0.8627 (m110) REVERT: A 187 ASP cc_start: 0.8003 (m-30) cc_final: 0.7489 (m-30) REVERT: A 213 LEU cc_start: 0.9104 (pt) cc_final: 0.8449 (pp) REVERT: A 318 PHE cc_start: 0.8555 (t80) cc_final: 0.7928 (t80) REVERT: A 329 TYR cc_start: 0.8469 (t80) cc_final: 0.8206 (t80) REVERT: B 195 GLU cc_start: 0.8283 (tp30) cc_final: 0.8001 (tp30) REVERT: B 256 GLN cc_start: 0.8994 (mm110) cc_final: 0.8676 (mm-40) REVERT: B 262 GLU cc_start: 0.8096 (tp30) cc_final: 0.7787 (mm-30) REVERT: B 329 TYR cc_start: 0.9047 (t80) cc_final: 0.8706 (t80) REVERT: B 354 ASN cc_start: 0.8246 (t0) cc_final: 0.8027 (t0) REVERT: C 53 ASP cc_start: 0.8929 (m-30) cc_final: 0.8006 (t0) REVERT: C 83 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6757 (mm-30) outliers start: 37 outliers final: 30 residues processed: 198 average time/residue: 0.1507 time to fit residues: 43.5775 Evaluate side-chains 205 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain D residue 366 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7856 Z= 0.196 Angle : 0.583 10.602 10704 Z= 0.304 Chirality : 0.044 0.276 1218 Planarity : 0.004 0.072 1397 Dihedral : 5.152 39.305 1083 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 5.60 % Allowed : 26.00 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.24), residues: 1003 helix: -2.19 (0.63), residues: 61 sheet: -1.02 (0.45), residues: 148 loop : -2.62 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 242 HIS 0.002 0.001 HIS C 170 PHE 0.008 0.001 PHE B 318 TYR 0.020 0.001 TYR B 198 ARG 0.002 0.000 ARG C 245 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 179 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7222 (p0) REVERT: A 56 LYS cc_start: 0.8507 (tttm) cc_final: 0.8273 (tppt) REVERT: A 80 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8199 (m) REVERT: A 97 MET cc_start: 0.8148 (mtp) cc_final: 0.7819 (mtt) REVERT: A 124 ASN cc_start: 0.9047 (m110) cc_final: 0.8653 (m110) REVERT: A 187 ASP cc_start: 0.8031 (m-30) cc_final: 0.7535 (m-30) REVERT: A 213 LEU cc_start: 0.9170 (pt) cc_final: 0.8489 (pp) REVERT: A 228 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8107 (p90) REVERT: A 318 PHE cc_start: 0.8581 (t80) cc_final: 0.7969 (t80) REVERT: A 329 TYR cc_start: 0.8525 (t80) cc_final: 0.8289 (t80) REVERT: B 205 GLN cc_start: 0.8295 (pt0) cc_final: 0.8008 (pt0) REVERT: B 256 GLN cc_start: 0.8976 (mm110) cc_final: 0.8697 (mm-40) REVERT: B 262 GLU cc_start: 0.8117 (tp30) cc_final: 0.7801 (mm-30) REVERT: B 329 TYR cc_start: 0.9061 (t80) cc_final: 0.8735 (t80) REVERT: B 333 ASN cc_start: 0.7776 (t0) cc_final: 0.7469 (t0) REVERT: B 354 ASN cc_start: 0.8252 (t0) cc_final: 0.8010 (t0) REVERT: C 53 ASP cc_start: 0.9008 (m-30) cc_final: 0.8210 (t0) REVERT: C 83 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6761 (mm-30) outliers start: 45 outliers final: 38 residues processed: 201 average time/residue: 0.1495 time to fit residues: 43.7854 Evaluate side-chains 204 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain D residue 366 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 229 ASN ** B 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7856 Z= 0.351 Angle : 0.664 11.600 10704 Z= 0.351 Chirality : 0.046 0.279 1218 Planarity : 0.004 0.077 1397 Dihedral : 5.733 38.993 1083 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 6.09 % Allowed : 25.25 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.24), residues: 1003 helix: -1.49 (0.75), residues: 49 sheet: -1.17 (0.45), residues: 148 loop : -2.69 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 242 HIS 0.003 0.001 HIS A 158 PHE 0.017 0.002 PHE C 192 TYR 0.023 0.002 TYR B 198 ARG 0.003 0.001 ARG C 245 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 166 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8557 (tttm) cc_final: 0.8260 (tppt) REVERT: A 80 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8402 (m) REVERT: A 97 MET cc_start: 0.8337 (mtp) cc_final: 0.8029 (mtt) REVERT: A 124 ASN cc_start: 0.9034 (m110) cc_final: 0.8629 (m110) REVERT: A 187 ASP cc_start: 0.8126 (m-30) cc_final: 0.7692 (m-30) REVERT: A 213 LEU cc_start: 0.9313 (pt) cc_final: 0.8553 (pp) REVERT: A 228 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8171 (p90) REVERT: A 318 PHE cc_start: 0.8786 (t80) cc_final: 0.8265 (t80) REVERT: A 329 TYR cc_start: 0.8517 (t80) cc_final: 0.8287 (t80) REVERT: B 329 TYR cc_start: 0.9030 (t80) cc_final: 0.8682 (t80) REVERT: B 354 ASN cc_start: 0.8398 (t0) cc_final: 0.8125 (t0) REVERT: C 53 ASP cc_start: 0.9095 (m-30) cc_final: 0.8289 (t0) REVERT: C 83 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6907 (mm-30) REVERT: C 131 ILE cc_start: 0.9251 (mt) cc_final: 0.9017 (mm) outliers start: 49 outliers final: 42 residues processed: 191 average time/residue: 0.1466 time to fit residues: 41.1845 Evaluate side-chains 205 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 161 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain D residue 366 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7856 Z= 0.159 Angle : 0.584 10.705 10704 Z= 0.306 Chirality : 0.044 0.282 1218 Planarity : 0.004 0.074 1397 Dihedral : 5.255 40.327 1083 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 5.22 % Allowed : 26.74 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.25), residues: 1003 helix: -1.34 (0.75), residues: 49 sheet: -0.98 (0.45), residues: 148 loop : -2.56 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 242 HIS 0.002 0.000 HIS A 158 PHE 0.017 0.001 PHE A 258 TYR 0.021 0.001 TYR B 198 ARG 0.004 0.000 ARG C 245 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7165 (p0) REVERT: A 56 LYS cc_start: 0.8525 (tttm) cc_final: 0.8246 (tppt) REVERT: A 80 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8226 (m) REVERT: A 97 MET cc_start: 0.8232 (mtp) cc_final: 0.7903 (mtt) REVERT: A 124 ASN cc_start: 0.9052 (m110) cc_final: 0.8651 (m110) REVERT: A 213 LEU cc_start: 0.9120 (pt) cc_final: 0.8509 (pp) REVERT: A 228 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8066 (p90) REVERT: A 318 PHE cc_start: 0.8628 (t80) cc_final: 0.8042 (t80) REVERT: A 329 TYR cc_start: 0.8560 (t80) cc_final: 0.8329 (t80) REVERT: B 195 GLU cc_start: 0.8297 (tp30) cc_final: 0.8023 (tp30) REVERT: B 262 GLU cc_start: 0.8229 (tp30) cc_final: 0.7916 (mm-30) REVERT: B 329 TYR cc_start: 0.9072 (t80) cc_final: 0.8751 (t80) REVERT: B 354 ASN cc_start: 0.8249 (t0) cc_final: 0.8031 (t0) REVERT: C 53 ASP cc_start: 0.8993 (m-30) cc_final: 0.8226 (t0) REVERT: C 83 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6925 (mm-30) outliers start: 42 outliers final: 35 residues processed: 199 average time/residue: 0.1431 time to fit residues: 41.9711 Evaluate side-chains 204 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain D residue 366 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.0470 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 chunk 78 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 83 optimal weight: 0.0070 chunk 24 optimal weight: 9.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7856 Z= 0.147 Angle : 0.573 10.306 10704 Z= 0.298 Chirality : 0.043 0.275 1218 Planarity : 0.003 0.070 1397 Dihedral : 4.860 41.533 1083 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.48 % Allowed : 28.98 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.25), residues: 1003 helix: -1.81 (0.67), residues: 61 sheet: -1.23 (0.43), residues: 158 loop : -2.45 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 374 HIS 0.001 0.000 HIS B 339 PHE 0.011 0.001 PHE C 48 TYR 0.019 0.001 TYR B 198 ARG 0.003 0.000 ARG B 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8497 (tttm) cc_final: 0.8240 (tppt) REVERT: A 80 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7807 (m) REVERT: A 97 MET cc_start: 0.8098 (mtp) cc_final: 0.7719 (mtt) REVERT: A 124 ASN cc_start: 0.9004 (m110) cc_final: 0.8607 (m110) REVERT: A 187 ASP cc_start: 0.7956 (m-30) cc_final: 0.7681 (m-30) REVERT: A 213 LEU cc_start: 0.9035 (pt) cc_final: 0.8451 (pp) REVERT: A 228 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7924 (p90) REVERT: B 195 GLU cc_start: 0.8290 (tp30) cc_final: 0.8014 (tp30) REVERT: B 262 GLU cc_start: 0.8204 (tp30) cc_final: 0.7930 (mm-30) REVERT: B 329 TYR cc_start: 0.9134 (t80) cc_final: 0.8862 (t80) REVERT: B 354 ASN cc_start: 0.8121 (t0) cc_final: 0.7872 (t0) REVERT: C 53 ASP cc_start: 0.8875 (m-30) cc_final: 0.8144 (t0) REVERT: C 83 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6726 (mm-30) outliers start: 28 outliers final: 22 residues processed: 202 average time/residue: 0.1449 time to fit residues: 42.7838 Evaluate side-chains 197 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 335 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 9.9990 chunk 11 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110963 restraints weight = 13827.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114782 restraints weight = 6859.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117384 restraints weight = 4180.749| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7856 Z= 0.153 Angle : 0.576 11.369 10704 Z= 0.303 Chirality : 0.043 0.283 1218 Planarity : 0.004 0.068 1397 Dihedral : 4.772 41.267 1082 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.48 % Allowed : 28.86 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.25), residues: 1003 helix: -1.62 (0.71), residues: 55 sheet: -1.14 (0.43), residues: 158 loop : -2.41 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 242 HIS 0.001 0.000 HIS B 339 PHE 0.023 0.001 PHE C 192 TYR 0.020 0.001 TYR C 247 ARG 0.003 0.000 ARG B 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1991.62 seconds wall clock time: 36 minutes 52.62 seconds (2212.62 seconds total)