Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 03:13:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvr_22511/04_2023/7jvr_22511_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvr_22511/04_2023/7jvr_22511.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvr_22511/04_2023/7jvr_22511_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvr_22511/04_2023/7jvr_22511_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvr_22511/04_2023/7jvr_22511_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvr_22511/04_2023/7jvr_22511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvr_22511/04_2023/7jvr_22511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvr_22511/04_2023/7jvr_22511_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvr_22511/04_2023/7jvr_22511_updated.pdb" } resolution = 2.8 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= 0.002 sd= 0.029 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 64 5.16 5 C 5648 2.51 5 N 1496 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 61": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8872 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2164 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 1 Chain: "A" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1807 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'08Y': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.11, per 1000 atoms: 0.58 Number of scatterers: 8872 At special positions: 0 Unit cell: (103.455, 123.31, 118.085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 64 16.00 O 1663 8.00 N 1496 7.00 C 5648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS R 399 " - pdb=" SG CYS R 401 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.9 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 34.7% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'R' and resid 35 through 61 removed outlier: 3.718A pdb=" N LEU R 40 " --> pdb=" O TYR R 36 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU R 41 " --> pdb=" O TYR R 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU R 44 " --> pdb=" O LEU R 40 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU R 54 " --> pdb=" O PHE R 50 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER R 60 " --> pdb=" O CYS R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 86 removed outlier: 4.001A pdb=" N LEU R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 97 Processing helix chain 'R' and resid 104 through 137 Processing helix chain 'R' and resid 139 through 143 Processing helix chain 'R' and resid 145 through 172 Proline residue: R 169 - end of helix removed outlier: 3.705A pdb=" N PHE R 172 " --> pdb=" O CYS R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 197 removed outlier: 3.670A pdb=" N TYR R 192 " --> pdb=" O ALA R 188 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL R 196 " --> pdb=" O TYR R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 224 Processing helix chain 'R' and resid 366 through 385 Processing helix chain 'R' and resid 387 through 399 removed outlier: 3.642A pdb=" N HIS R 393 " --> pdb=" O PHE R 389 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE R 394 " --> pdb=" O PHE R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 426 removed outlier: 3.716A pdb=" N ASN R 418 " --> pdb=" O LEU R 414 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 431 through 440 removed outlier: 3.949A pdb=" N LYS R 435 " --> pdb=" O ILE R 431 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA R 436 " --> pdb=" O GLU R 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 46 through 54 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 216 removed outlier: 3.638A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) 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: 3.785A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.674A 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: 3.840A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.540A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.749A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 7.050A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 4.510A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.004A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.619A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 202 removed outlier: 3.557A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.693A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.463A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 45 through 52 removed outlier: 6.625A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 115 through 117 removed outlier: 6.129A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.743A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.608A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 226 through 231 removed outlier: 3.652A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1128 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: 2.56 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1441 1.32 - 1.45: 2608 1.45 - 1.59: 4912 1.59 - 1.73: 0 1.73 - 1.87: 94 Bond restraints: 9055 Sorted by residual: bond pdb=" C16 08Y R 500 " pdb=" C22 08Y R 500 " ideal model delta sigma weight residual 0.960 1.526 -0.566 2.00e-02 2.50e+03 8.01e+02 bond pdb=" C16 08Y R 500 " pdb=" C18 08Y R 500 " ideal model delta sigma weight residual 2.019 1.522 0.497 2.00e-02 2.50e+03 6.17e+02 bond pdb=" C21 08Y R 500 " pdb=" C22 08Y R 500 " ideal model delta sigma weight residual 1.794 1.347 0.447 2.00e-02 2.50e+03 4.99e+02 bond pdb=" C17 08Y R 500 " pdb=" C21 08Y R 500 " ideal model delta sigma weight residual 1.139 1.554 -0.415 2.00e-02 2.50e+03 4.30e+02 bond pdb=" C17 08Y R 500 " pdb=" N4 08Y R 500 " ideal model delta sigma weight residual 1.814 1.485 0.329 2.00e-02 2.50e+03 2.70e+02 ... (remaining 9050 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.15: 180 106.15 - 113.13: 4925 113.13 - 120.11: 3068 120.11 - 127.10: 4012 127.10 - 134.08: 98 Bond angle restraints: 12283 Sorted by residual: angle pdb=" C1 08Y R 500 " pdb=" N2 08Y R 500 " pdb=" C9 08Y R 500 " ideal model delta sigma weight residual 110.69 129.35 -18.66 3.00e+00 1.11e-01 3.87e+01 angle pdb=" C6 08Y R 500 " pdb=" N2 08Y R 500 " pdb=" C9 08Y R 500 " ideal model delta sigma weight residual 137.12 121.37 15.75 3.00e+00 1.11e-01 2.76e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 130.95 -9.41 1.91e+00 2.74e-01 2.43e+01 angle pdb=" C16 08Y R 500 " pdb=" C22 08Y R 500 " pdb=" C21 08Y R 500 " ideal model delta sigma weight residual 108.42 123.01 -14.59 3.00e+00 1.11e-01 2.36e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 123.47 130.29 -6.82 1.53e+00 4.27e-01 1.99e+01 ... (remaining 12278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.08: 5116 14.08 - 28.17: 200 28.17 - 42.25: 52 42.25 - 56.34: 9 56.34 - 70.42: 3 Dihedral angle restraints: 5380 sinusoidal: 2098 harmonic: 3282 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 161.30 -68.30 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 5377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1147 0.061 - 0.121: 211 0.121 - 0.182: 36 0.182 - 0.242: 10 0.242 - 0.303: 3 Chirality restraints: 1407 Sorted by residual: chirality pdb=" CB ILE E 70 " pdb=" CA ILE E 70 " pdb=" CG1 ILE E 70 " pdb=" CG2 ILE E 70 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C5 08Y R 500 " pdb=" C11 08Y R 500 " pdb=" C8 08Y R 500 " pdb=" O1 08Y R 500 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1404 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 08Y R 500 " -0.018 2.00e-02 2.50e+03 3.06e-02 1.17e+01 pdb=" C16 08Y R 500 " 0.030 2.00e-02 2.50e+03 pdb=" C5 08Y R 500 " 0.037 2.00e-02 2.50e+03 pdb=" N3 08Y R 500 " -0.045 2.00e-02 2.50e+03 pdb=" O5 08Y R 500 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 08Y R 500 " 0.027 2.00e-02 2.50e+03 3.02e-02 1.14e+01 pdb=" C17 08Y R 500 " -0.018 2.00e-02 2.50e+03 pdb=" C21 08Y R 500 " 0.031 2.00e-02 2.50e+03 pdb=" C22 08Y R 500 " -0.050 2.00e-02 2.50e+03 pdb=" C24 08Y R 500 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 403 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO R 404 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO R 404 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 404 " 0.033 5.00e-02 4.00e+02 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1139 2.77 - 3.30: 8502 3.30 - 3.83: 14703 3.83 - 4.37: 17177 4.37 - 4.90: 30172 Nonbonded interactions: 71693 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.235 2.440 nonbonded pdb=" OG SER A 263 " pdb=" O GLU A 318 " model vdw 2.332 2.440 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.347 2.440 nonbonded pdb=" OG1 THR R 69 " pdb=" OH TYR R 142 " model vdw 2.356 2.440 nonbonded pdb=" O CYS B 218 " pdb=" NE2 GLN C 18 " model vdw 2.364 2.520 ... (remaining 71688 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.490 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 26.160 Find NCS groups from input model: 0.270 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:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 : 0.012 0.566 9055 Z= 0.884 Angle : 0.926 18.658 12283 Z= 0.487 Chirality : 0.052 0.303 1407 Planarity : 0.006 0.060 1543 Dihedral : 8.659 70.421 3245 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.85 (0.22), residues: 1110 helix: 1.15 (0.22), residues: 384 sheet: -0.83 (0.32), residues: 251 loop : -1.86 (0.23), residues: 475 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.8361 time to fit residues: 261.8684 Evaluate side-chains 240 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 52 ASN R 106 HIS R 398 HIS A 188 HIS A 244 HIS A 322 HIS B 88 ASN B 110 ASN B 237 ASN B 239 ASN B 259 GLN B 340 ASN C 18 GLN C 44 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 9055 Z= 0.238 Angle : 0.685 15.421 12283 Z= 0.332 Chirality : 0.044 0.211 1407 Planarity : 0.004 0.055 1543 Dihedral : 4.675 48.203 1226 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.24), residues: 1110 helix: 2.11 (0.24), residues: 388 sheet: -0.74 (0.31), residues: 263 loop : -1.48 (0.25), residues: 459 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 250 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 12 residues processed: 265 average time/residue: 0.9126 time to fit residues: 263.0839 Evaluate side-chains 232 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 220 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.1242 time to fit residues: 2.4747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.1980 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 0.0570 chunk 80 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN C 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9055 Z= 0.210 Angle : 0.650 15.408 12283 Z= 0.312 Chirality : 0.043 0.232 1407 Planarity : 0.004 0.049 1543 Dihedral : 4.616 49.248 1226 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 4.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.20 (0.24), residues: 1110 helix: 2.19 (0.25), residues: 383 sheet: -0.62 (0.31), residues: 267 loop : -1.17 (0.26), residues: 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 238 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 19 residues processed: 258 average time/residue: 0.8409 time to fit residues: 237.3744 Evaluate side-chains 246 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 227 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 11 residues processed: 9 average time/residue: 0.2754 time to fit residues: 4.6779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 422 ASN A 331 ASN B 62 HIS B 239 ASN C 18 GLN E 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 9055 Z= 0.250 Angle : 0.659 15.341 12283 Z= 0.315 Chirality : 0.043 0.263 1407 Planarity : 0.004 0.046 1543 Dihedral : 4.622 49.059 1226 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 4.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.31 (0.24), residues: 1110 helix: 2.07 (0.25), residues: 397 sheet: -0.58 (0.30), residues: 273 loop : -0.98 (0.27), residues: 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 253 time to evaluate : 1.242 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 20 residues processed: 269 average time/residue: 0.9229 time to fit residues: 270.5402 Evaluate side-chains 237 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 217 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 11 residues processed: 10 average time/residue: 0.1951 time to fit residues: 4.1209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 125 ASN B 230 ASN B 239 ASN B 259 GLN C 18 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 9055 Z= 0.259 Angle : 0.675 15.308 12283 Z= 0.323 Chirality : 0.044 0.290 1407 Planarity : 0.004 0.041 1543 Dihedral : 4.643 48.905 1226 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 4.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.28 (0.25), residues: 1110 helix: 2.03 (0.25), residues: 397 sheet: -0.70 (0.31), residues: 269 loop : -0.89 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 222 time to evaluate : 1.016 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 25 residues processed: 242 average time/residue: 0.8446 time to fit residues: 224.3054 Evaluate side-chains 240 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 215 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 15 residues processed: 12 average time/residue: 0.2677 time to fit residues: 5.6508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 0.1980 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 9055 Z= 0.245 Angle : 0.663 15.292 12283 Z= 0.317 Chirality : 0.044 0.303 1407 Planarity : 0.003 0.041 1543 Dihedral : 4.586 48.661 1226 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 5.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.36 (0.25), residues: 1110 helix: 2.05 (0.25), residues: 398 sheet: -0.60 (0.31), residues: 269 loop : -0.86 (0.27), residues: 443 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 244 time to evaluate : 1.032 Fit side-chains revert: symmetry clash outliers start: 52 outliers final: 27 residues processed: 267 average time/residue: 0.8800 time to fit residues: 257.4141 Evaluate side-chains 265 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 238 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 12 residues processed: 16 average time/residue: 0.2904 time to fit residues: 7.4580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 220 GLN B 239 ASN B 259 GLN C 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 9055 Z= 0.254 Angle : 0.680 15.240 12283 Z= 0.326 Chirality : 0.044 0.354 1407 Planarity : 0.004 0.076 1543 Dihedral : 4.614 48.323 1226 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.46 (0.25), residues: 1110 helix: 2.04 (0.25), residues: 398 sheet: -0.58 (0.30), residues: 280 loop : -0.67 (0.29), residues: 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 235 time to evaluate : 1.044 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 24 residues processed: 252 average time/residue: 0.8584 time to fit residues: 237.5313 Evaluate side-chains 256 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 232 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 14 residues processed: 11 average time/residue: 0.4174 time to fit residues: 7.1017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.0570 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 176 GLN B 220 GLN C 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 9055 Z= 0.221 Angle : 0.667 15.311 12283 Z= 0.319 Chirality : 0.044 0.343 1407 Planarity : 0.004 0.043 1543 Dihedral : 4.526 48.126 1226 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.43 (0.25), residues: 1110 helix: 2.04 (0.25), residues: 398 sheet: -0.60 (0.30), residues: 280 loop : -0.70 (0.28), residues: 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 231 time to evaluate : 1.092 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 25 residues processed: 248 average time/residue: 0.8777 time to fit residues: 238.3716 Evaluate side-chains 256 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 231 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 15 residues processed: 10 average time/residue: 0.1684 time to fit residues: 3.9940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 176 GLN B 220 GLN C 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 9055 Z= 0.243 Angle : 0.688 15.205 12283 Z= 0.328 Chirality : 0.045 0.362 1407 Planarity : 0.004 0.090 1543 Dihedral : 4.592 48.228 1226 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.50 (0.25), residues: 1110 helix: 2.07 (0.25), residues: 398 sheet: -0.48 (0.31), residues: 277 loop : -0.70 (0.29), residues: 435 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 222 time to evaluate : 1.024 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 25 residues processed: 240 average time/residue: 0.8525 time to fit residues: 223.9431 Evaluate side-chains 253 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 228 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 17 residues processed: 9 average time/residue: 0.2514 time to fit residues: 4.3715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 109 optimal weight: 0.4980 chunk 100 optimal weight: 0.0470 chunk 87 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 176 GLN B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 9055 Z= 0.197 Angle : 0.669 15.342 12283 Z= 0.322 Chirality : 0.045 0.323 1407 Planarity : 0.003 0.037 1543 Dihedral : 4.518 47.410 1226 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.55 (0.25), residues: 1110 helix: 2.10 (0.25), residues: 398 sheet: -0.41 (0.32), residues: 269 loop : -0.68 (0.28), residues: 443 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 215 time to evaluate : 1.057 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 23 residues processed: 233 average time/residue: 0.8783 time to fit residues: 223.9312 Evaluate side-chains 237 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 6 average time/residue: 0.1572 time to fit residues: 2.5976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 0.0570 chunk 24 optimal weight: 0.3980 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 0.0470 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 422 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.156865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.134530 restraints weight = 11442.455| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.04 r_work: 0.3664 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 9055 Z= 0.199 Angle : 0.680 15.301 12283 Z= 0.325 Chirality : 0.045 0.302 1407 Planarity : 0.004 0.042 1543 Dihedral : 4.501 47.193 1226 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.58 (0.25), residues: 1110 helix: 2.11 (0.25), residues: 398 sheet: -0.40 (0.32), residues: 269 loop : -0.67 (0.29), residues: 443 =============================================================================== Job complete usr+sys time: 4199.15 seconds wall clock time: 75 minutes 19.65 seconds (4519.65 seconds total)