Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 17:55:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kmf_0724/10_2023/6kmf_0724.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kmf_0724/10_2023/6kmf_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_0724/10_2023/6kmf_0724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kmf_0724/10_2023/6kmf_0724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kmf_0724/10_2023/6kmf_0724.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kmf_0724/10_2023/6kmf_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-1.21rc1-5097/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: 4.45, per 1000 atoms: 0.58 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: 3.03 Conformation dependent library (CDL) restraints added in 1.2 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: 0.88 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: 2.04 Time building geometry restraints manager: 3.30 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: 3.620 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: 12.630 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.630 Find NCS groups from input model: 0.500 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.270 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.869 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 225 average time/residue: 0.1692 time to fit residues: 52.6272 Evaluate side-chains 176 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0653 time to fit residues: 1.3442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 78 ASN C 205 GLN C 236 ASN C 286 ASN C 321 ASN D 368 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7856 Z= 0.306 Angle : 0.656 9.954 10704 Z= 0.350 Chirality : 0.045 0.257 1218 Planarity : 0.005 0.078 1397 Dihedral : 6.179 45.356 1082 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.96 % Favored : 88.04 % Rotamer: Outliers : 5.10 % Allowed : 21.02 % Favored : 73.88 % 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: -3.96 (0.23), residues: 1003 helix: -4.02 (0.49), residues: 42 sheet: -1.51 (0.43), residues: 155 loop : -3.08 (0.18), residues: 806 *********************** 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 221 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 180 time to evaluate : 0.899 Fit side-chains outliers start: 41 outliers final: 29 residues processed: 200 average time/residue: 0.1405 time to fit residues: 41.8795 Evaluate side-chains 190 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 0.826 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.0720 time to fit residues: 5.2158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.0030 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 333 ASN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7856 Z= 0.180 Angle : 0.592 9.146 10704 Z= 0.313 Chirality : 0.044 0.251 1218 Planarity : 0.004 0.070 1397 Dihedral : 5.605 42.437 1082 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 2.11 % Allowed : 23.01 % Favored : 74.88 % 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: -3.77 (0.23), residues: 1003 helix: -3.62 (0.45), residues: 61 sheet: -1.31 (0.45), residues: 148 loop : -2.92 (0.19), residues: 794 *********************** 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 203 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 0.922 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 197 average time/residue: 0.1470 time to fit residues: 42.1825 Evaluate side-chains 173 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 0.845 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0762 time to fit residues: 2.5520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.4980 chunk 67 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN B 78 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 317 ASN C 299 GLN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 : 0.007 0.049 7856 Z= 0.478 Angle : 0.753 12.794 10704 Z= 0.399 Chirality : 0.048 0.271 1218 Planarity : 0.005 0.077 1397 Dihedral : 6.366 41.777 1082 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.96 % Favored : 85.04 % Rotamer: Outliers : 5.35 % Allowed : 24.50 % Favored : 70.15 % 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: -3.73 (0.23), residues: 1003 helix: -2.58 (0.70), residues: 42 sheet: -1.45 (0.42), residues: 160 loop : -2.97 (0.19), residues: 801 *********************** 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 203 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 160 time to evaluate : 1.062 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 36 residues processed: 184 average time/residue: 0.1493 time to fit residues: 40.6379 Evaluate side-chains 187 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 151 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.0803 time to fit residues: 6.6182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 205 GLN A 333 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN C 236 ASN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2128 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= 0.233 Angle : 0.631 11.540 10704 Z= 0.332 Chirality : 0.045 0.234 1218 Planarity : 0.004 0.071 1397 Dihedral : 5.874 42.704 1082 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 2.24 % Allowed : 26.12 % 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: -3.54 (0.24), residues: 1003 helix: -2.06 (0.75), residues: 42 sheet: -1.61 (0.43), residues: 158 loop : -2.78 (0.20), residues: 803 *********************** 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 194 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 0.915 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 185 average time/residue: 0.1444 time to fit residues: 39.4443 Evaluate side-chains 172 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0717 time to fit residues: 2.2609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.0370 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN B 236 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7895 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7856 Z= 0.270 Angle : 0.651 12.312 10704 Z= 0.339 Chirality : 0.046 0.266 1218 Planarity : 0.004 0.071 1397 Dihedral : 5.801 42.729 1082 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.86 % Favored : 87.14 % Rotamer: Outliers : 2.99 % Allowed : 27.36 % Favored : 69.65 % 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: -3.52 (0.24), residues: 1003 helix: -1.63 (0.77), residues: 43 sheet: -1.58 (0.42), residues: 165 loop : -2.81 (0.20), residues: 795 *********************** 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 191 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 0.887 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 20 residues processed: 179 average time/residue: 0.1574 time to fit residues: 41.0588 Evaluate side-chains 180 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0780 time to fit residues: 3.8922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7858 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7856 Z= 0.189 Angle : 0.618 10.597 10704 Z= 0.322 Chirality : 0.045 0.217 1218 Planarity : 0.004 0.072 1397 Dihedral : 5.512 42.846 1082 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 1.49 % Allowed : 28.86 % Favored : 69.65 % 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: -3.35 (0.24), residues: 1003 helix: -1.26 (0.81), residues: 43 sheet: -1.47 (0.43), residues: 158 loop : -2.70 (0.20), residues: 802 *********************** 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 183 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 0.900 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 177 average time/residue: 0.1472 time to fit residues: 38.3878 Evaluate side-chains 170 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 165 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0755 time to fit residues: 1.7054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 7.9990 chunk 28 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.0370 chunk 83 optimal weight: 6.9990 overall best weight: 2.0262 ------------------------------------------------------------------------------- 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 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7872 moved from start: 0.2384 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= 0.225 Angle : 0.617 10.843 10704 Z= 0.324 Chirality : 0.045 0.213 1218 Planarity : 0.004 0.073 1397 Dihedral : 5.502 42.250 1082 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 1.12 % Allowed : 29.60 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.24), residues: 1003 helix: -1.05 (0.83), residues: 43 sheet: -1.48 (0.43), residues: 158 loop : -2.68 (0.20), residues: 802 *********************** 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 168 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 159 time to evaluate : 0.931 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 163 average time/residue: 0.1495 time to fit residues: 35.9654 Evaluate side-chains 165 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 161 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0708 time to fit residues: 1.7069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 80 optimal weight: 0.0770 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 94 optimal weight: 0.0570 chunk 57 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7811 moved from start: 0.2616 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= 0.153 Angle : 0.585 8.433 10704 Z= 0.306 Chirality : 0.044 0.189 1218 Planarity : 0.004 0.071 1397 Dihedral : 5.087 42.413 1082 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 0.87 % Allowed : 31.09 % 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: -3.23 (0.24), residues: 1003 helix: -1.65 (0.72), residues: 55 sheet: -1.31 (0.43), residues: 158 loop : -2.60 (0.20), residues: 790 *********************** 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 188 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 181 time to evaluate : 0.925 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 183 average time/residue: 0.1590 time to fit residues: 42.7146 Evaluate side-chains 166 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0643 time to fit residues: 1.7719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.0060 chunk 65 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7856 Z= 0.174 Angle : 0.606 11.627 10704 Z= 0.316 Chirality : 0.045 0.287 1218 Planarity : 0.004 0.072 1397 Dihedral : 5.077 42.067 1082 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 0.37 % Allowed : 32.84 % Favored : 66.79 % 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: -3.16 (0.25), residues: 1003 helix: -1.55 (0.72), residues: 55 sheet: -1.26 (0.43), residues: 158 loop : -2.55 (0.20), residues: 790 ********************** 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 168 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 0.888 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 167 average time/residue: 0.1433 time to fit residues: 35.7099 Evaluate side-chains 168 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 4 optimal weight: 8.9990 chunk 56 optimal weight: 0.0370 overall best weight: 1.6864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.107515 restraints weight = 14002.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111158 restraints weight = 7171.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113653 restraints weight = 4459.806| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7856 Z= 0.209 Angle : 0.620 11.721 10704 Z= 0.325 Chirality : 0.045 0.284 1218 Planarity : 0.004 0.073 1397 Dihedral : 5.168 41.626 1082 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 0.25 % Allowed : 33.83 % Favored : 65.92 % 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: -3.04 (0.25), residues: 1003 helix: -0.54 (0.88), residues: 43 sheet: -1.20 (0.42), residues: 158 loop : -2.51 (0.20), residues: 802 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.73 seconds wall clock time: 34 minutes 38.14 seconds (2078.14 seconds total)