Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 12:09:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6t_25727/04_2023/7t6t_25727_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6t_25727/04_2023/7t6t_25727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6t_25727/04_2023/7t6t_25727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6t_25727/04_2023/7t6t_25727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6t_25727/04_2023/7t6t_25727_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6t_25727/04_2023/7t6t_25727_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 4593 2.51 5 N 1216 2.21 5 O 1302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "L PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7164 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2363 Unusual residues: {'PLM': 2} Classifications: {'peptide': 296, 'undetermined': 2} Link IDs: {'PTRANS': 12, 'TRANS': 283, None: 2} Not linked: pdbres="LEU R 316 " pdbres="PLM R 401 " Not linked: pdbres="PLM R 401 " pdbres="PLM R 402 " Time building chain proxies: 4.52, per 1000 atoms: 0.63 Number of scatterers: 7164 At special positions: 0 Unit cell: (87.78, 104.5, 123.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1302 8.00 N 1216 7.00 C 4593 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 9 sheets defined 42.7% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 10 through 32 Processing helix chain 'A' and resid 43 through 51 removed outlier: 5.818A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.728A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.761A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'R' and resid 24 through 52 removed outlier: 3.637A pdb=" N ILE R 28 " --> pdb=" O PHE R 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR R 29 " --> pdb=" O LEU R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 86 removed outlier: 3.717A pdb=" N PHE R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR R 75 " --> pdb=" O ASP R 71 " (cutoff:3.500A) Proline residue: R 79 - end of helix Processing helix chain 'R' and resid 96 through 128 removed outlier: 4.291A pdb=" N ILE R 116 " --> pdb=" O SER R 112 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 139 through 155 removed outlier: 3.958A pdb=" N ILE R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY R 148 " --> pdb=" O LYS R 144 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 158 through 163 Processing helix chain 'R' and resid 187 through 207 Processing helix chain 'R' and resid 211 through 230 Processing helix chain 'R' and resid 238 through 265 removed outlier: 3.838A pdb=" N ALA R 249 " --> pdb=" O PHE R 245 " (cutoff:3.500A) Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 268 through 271 No H-bonds generated for 'chain 'R' and resid 268 through 271' Processing helix chain 'R' and resid 277 through 301 removed outlier: 3.628A pdb=" N ILE R 281 " --> pdb=" O LYS R 277 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 306 through 315 Processing sheet with id= A, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 223 through 226 Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.808A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.767A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.944A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.792A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.336A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.528A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.585A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 990 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: 1.96 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1375 1.32 - 1.45: 1754 1.45 - 1.57: 4101 1.57 - 1.69: 0 1.69 - 1.82: 77 Bond restraints: 7307 Sorted by residual: bond pdb=" C LYS C 20 " pdb=" O LYS C 20 " ideal model delta sigma weight residual 1.236 1.291 -0.055 1.19e-02 7.06e+03 2.11e+01 bond pdb=" CA SER R 255 " pdb=" CB SER R 255 " ideal model delta sigma weight residual 1.531 1.474 0.057 1.33e-02 5.65e+03 1.85e+01 bond pdb=" N SER R 181 " pdb=" CA SER R 181 " ideal model delta sigma weight residual 1.458 1.486 -0.028 7.40e-03 1.83e+04 1.47e+01 bond pdb=" N VAL R 127 " pdb=" CA VAL R 127 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.28e+01 bond pdb=" N VAL R 174 " pdb=" CA VAL R 174 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.15e-02 7.56e+03 1.27e+01 ... (remaining 7302 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.97: 157 105.97 - 113.09: 3847 113.09 - 120.21: 3660 120.21 - 127.33: 2154 127.33 - 134.45: 65 Bond angle restraints: 9883 Sorted by residual: angle pdb=" N PRO R 182 " pdb=" CA PRO R 182 " pdb=" C PRO R 182 " ideal model delta sigma weight residual 113.84 104.41 9.43 1.30e+00 5.92e-01 5.26e+01 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 112.93 106.05 6.88 1.12e+00 7.97e-01 3.78e+01 angle pdb=" N LEU R 300 " pdb=" CA LEU R 300 " pdb=" CB LEU R 300 " ideal model delta sigma weight residual 110.88 102.71 8.17 1.38e+00 5.25e-01 3.51e+01 angle pdb=" N VAL R 266 " pdb=" CA VAL R 266 " pdb=" C VAL R 266 " ideal model delta sigma weight residual 112.83 107.05 5.78 9.90e-01 1.02e+00 3.41e+01 angle pdb=" N MET R 304 " pdb=" CA MET R 304 " pdb=" C MET R 304 " ideal model delta sigma weight residual 112.92 105.86 7.06 1.23e+00 6.61e-01 3.29e+01 ... (remaining 9878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 3909 16.92 - 33.85: 333 33.85 - 50.77: 80 50.77 - 67.69: 13 67.69 - 84.62: 3 Dihedral angle restraints: 4338 sinusoidal: 1709 harmonic: 2629 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual 93.00 177.62 -84.62 1 1.00e+01 1.00e-02 8.70e+01 dihedral pdb=" C PHE R 178 " pdb=" N PHE R 178 " pdb=" CA PHE R 178 " pdb=" CB PHE R 178 " ideal model delta harmonic sigma weight residual -122.60 -112.55 -10.05 0 2.50e+00 1.60e-01 1.62e+01 dihedral pdb=" C GLU R 189 " pdb=" N GLU R 189 " pdb=" CA GLU R 189 " pdb=" CB GLU R 189 " ideal model delta harmonic sigma weight residual -122.60 -132.08 9.48 0 2.50e+00 1.60e-01 1.44e+01 ... (remaining 4335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 532 0.070 - 0.140: 398 0.140 - 0.211: 169 0.211 - 0.281: 34 0.281 - 0.351: 4 Chirality restraints: 1137 Sorted by residual: chirality pdb=" CA PHE B 235 " pdb=" N PHE B 235 " pdb=" C PHE B 235 " pdb=" CB PHE B 235 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA PHE R 178 " pdb=" N PHE R 178 " pdb=" C PHE R 178 " pdb=" CB PHE R 178 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1134 not shown) Planarity restraints: 1241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N FME L 1 " 0.057 2.00e-02 2.50e+03 7.27e-02 5.28e+01 pdb=" CA FME L 1 " -0.064 2.00e-02 2.50e+03 pdb=" CN FME L 1 " 0.086 2.00e-02 2.50e+03 pdb=" O1 FME L 1 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 24 " -0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C ASN C 24 " 0.079 2.00e-02 2.50e+03 pdb=" O ASN C 24 " -0.029 2.00e-02 2.50e+03 pdb=" N ILE C 25 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 19 " 0.022 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C LEU C 19 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU C 19 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS C 20 " 0.025 2.00e-02 2.50e+03 ... (remaining 1238 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 973 2.76 - 3.29: 7537 3.29 - 3.83: 11826 3.83 - 4.36: 15397 4.36 - 4.90: 25456 Nonbonded interactions: 61189 Sorted by model distance: nonbonded pdb=" OD1 ASN B 313 " pdb=" N ARG B 314 " model vdw 2.223 2.520 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.232 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.279 2.440 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.339 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.350 2.440 ... (remaining 61184 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.360 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.180 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 0.011 0.075 7307 Z= 0.745 Angle : 1.550 9.431 9883 Z= 1.170 Chirality : 0.105 0.351 1137 Planarity : 0.008 0.073 1241 Dihedral : 13.221 78.320 2629 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.27), residues: 893 helix: 1.10 (0.25), residues: 395 sheet: -0.77 (0.38), residues: 178 loop : -0.42 (0.34), residues: 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 293 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 295 average time/residue: 0.2335 time to fit residues: 86.9980 Evaluate side-chains 253 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 252 time to evaluate : 0.872 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0655 time to fit residues: 1.3188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS C 18 GLN R 57 HIS R 231 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 : 0.003 0.041 7307 Z= 0.241 Angle : 0.603 6.908 9883 Z= 0.324 Chirality : 0.045 0.207 1137 Planarity : 0.004 0.049 1241 Dihedral : 5.564 49.237 1002 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.27), residues: 893 helix: 0.93 (0.25), residues: 399 sheet: -0.44 (0.38), residues: 170 loop : -0.75 (0.34), residues: 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 264 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 270 average time/residue: 0.2486 time to fit residues: 85.3698 Evaluate side-chains 257 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 247 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0725 time to fit residues: 2.5700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.0980 chunk 24 optimal weight: 0.0270 chunk 66 optimal weight: 0.0020 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 27 optimal weight: 0.0970 chunk 64 optimal weight: 0.6980 overall best weight: 0.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN R 57 HIS R 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 7307 Z= 0.180 Angle : 0.553 6.719 9883 Z= 0.291 Chirality : 0.043 0.178 1137 Planarity : 0.004 0.046 1241 Dihedral : 5.308 47.413 1002 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.28), residues: 893 helix: 0.90 (0.25), residues: 399 sheet: -0.31 (0.39), residues: 170 loop : -0.86 (0.33), residues: 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 256 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 262 average time/residue: 0.2189 time to fit residues: 74.0200 Evaluate side-chains 250 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 242 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0700 time to fit residues: 2.0967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN R 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 7307 Z= 0.221 Angle : 0.556 8.042 9883 Z= 0.294 Chirality : 0.043 0.160 1137 Planarity : 0.004 0.044 1241 Dihedral : 5.228 44.814 1002 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.28), residues: 893 helix: 0.83 (0.26), residues: 401 sheet: -0.20 (0.39), residues: 169 loop : -0.88 (0.34), residues: 323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 267 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 272 average time/residue: 0.2534 time to fit residues: 86.6855 Evaluate side-chains 264 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 254 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0977 time to fit residues: 2.6550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 0.0270 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 57 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7307 Z= 0.226 Angle : 0.559 8.073 9883 Z= 0.295 Chirality : 0.043 0.169 1137 Planarity : 0.004 0.042 1241 Dihedral : 5.215 43.415 1002 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 893 helix: 0.84 (0.26), residues: 401 sheet: -0.22 (0.40), residues: 164 loop : -0.94 (0.33), residues: 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 263 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 268 average time/residue: 0.2494 time to fit residues: 83.8557 Evaluate side-chains 267 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 256 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0667 time to fit residues: 2.4980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 7307 Z= 0.212 Angle : 0.578 11.001 9883 Z= 0.298 Chirality : 0.043 0.172 1137 Planarity : 0.004 0.050 1241 Dihedral : 5.123 41.998 1002 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.28), residues: 893 helix: 0.88 (0.26), residues: 399 sheet: -0.17 (0.39), residues: 174 loop : -0.83 (0.34), residues: 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 260 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 268 average time/residue: 0.2503 time to fit residues: 84.2949 Evaluate side-chains 248 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 241 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0747 time to fit residues: 2.1438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 71 optimal weight: 0.0370 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 chunk 53 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN R 129 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7307 Z= 0.219 Angle : 0.594 13.309 9883 Z= 0.304 Chirality : 0.043 0.199 1137 Planarity : 0.004 0.040 1241 Dihedral : 5.122 41.920 1002 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 893 helix: 0.79 (0.26), residues: 399 sheet: -0.18 (0.39), residues: 174 loop : -0.90 (0.33), residues: 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 247 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 253 average time/residue: 0.2311 time to fit residues: 74.5090 Evaluate side-chains 249 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 240 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0673 time to fit residues: 2.3424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 0.0870 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 77 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 HIS ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7307 Z= 0.194 Angle : 0.608 13.742 9883 Z= 0.310 Chirality : 0.042 0.182 1137 Planarity : 0.004 0.039 1241 Dihedral : 5.002 39.700 1002 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.28), residues: 893 helix: 0.86 (0.26), residues: 399 sheet: -0.16 (0.39), residues: 174 loop : -0.90 (0.34), residues: 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 236 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 240 average time/residue: 0.2410 time to fit residues: 73.1045 Evaluate side-chains 238 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0671 time to fit residues: 1.5670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 0.0670 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 7307 Z= 0.214 Angle : 0.645 17.303 9883 Z= 0.324 Chirality : 0.042 0.181 1137 Planarity : 0.004 0.039 1241 Dihedral : 5.003 41.596 1002 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 0.65 % 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: -0.01 (0.28), residues: 893 helix: 0.94 (0.27), residues: 398 sheet: -0.25 (0.38), residues: 181 loop : -0.98 (0.34), residues: 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 242 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 243 average time/residue: 0.2334 time to fit residues: 72.4538 Evaluate side-chains 237 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 234 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0700 time to fit residues: 1.5085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 58 optimal weight: 0.0670 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7307 Z= 0.224 Angle : 0.662 17.007 9883 Z= 0.330 Chirality : 0.042 0.179 1137 Planarity : 0.004 0.040 1241 Dihedral : 5.067 44.303 1002 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.28), residues: 893 helix: 0.94 (0.27), residues: 399 sheet: -0.41 (0.37), residues: 185 loop : -1.02 (0.33), residues: 309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 236 average time/residue: 0.2435 time to fit residues: 73.0490 Evaluate side-chains 235 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0722 time to fit residues: 1.3263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.108461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095286 restraints weight = 12717.345| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.62 r_work: 0.3241 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7307 Z= 0.227 Angle : 0.673 15.513 9883 Z= 0.338 Chirality : 0.043 0.175 1137 Planarity : 0.004 0.041 1241 Dihedral : 5.129 46.703 1002 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.28), residues: 893 helix: 0.90 (0.26), residues: 398 sheet: -0.27 (0.38), residues: 179 loop : -1.04 (0.33), residues: 316 =============================================================================== Job complete usr+sys time: 2142.11 seconds wall clock time: 39 minutes 12.17 seconds (2352.17 seconds total)