Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 03:33:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9f_12103/04_2023/7b9f_12103.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9f_12103/04_2023/7b9f_12103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9f_12103/04_2023/7b9f_12103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9f_12103/04_2023/7b9f_12103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9f_12103/04_2023/7b9f_12103.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9f_12103/04_2023/7b9f_12103.pdb" } resolution = 3.0 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= 0.001 sd= 0.014 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 7264 2.51 5 N 1985 2.21 5 O 1968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 99": "NH1" <-> "NH2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "E GLU 195": "OE1" <-> "OE2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "E ARG 238": "NH1" <-> "NH2" Residue "E ARG 242": "NH1" <-> "NH2" Residue "X ARG 70": "NH1" <-> "NH2" Residue "X GLU 113": "OE1" <-> "OE2" Residue "X PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 322": "NH1" <-> "NH2" Residue "X TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 475": "OE1" <-> "OE2" Residue "D GLU 478": "OE1" <-> "OE2" Residue "D TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11270 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1305 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 3 Chain: "X" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3162 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 23, 'TRANS': 401} Chain breaks: 1 Chain: "C" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2679 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 28, 'TRANS': 308} Chain breaks: 2 Chain: "D" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3644 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 455} Chain: "B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Time building chain proxies: 6.15, per 1000 atoms: 0.55 Number of scatterers: 11270 At special positions: 0 Unit cell: (91.59, 143.19, 125.13, 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 1968 8.00 N 1985 7.00 C 7264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.74 Conformation dependent library (CDL) restraints added in 1.7 seconds 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2744 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 59.1% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'E' and resid 144 through 150 removed outlier: 4.331A pdb=" N ALA E 147 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 208 Processing helix chain 'E' and resid 209 through 215 removed outlier: 3.747A pdb=" N ALA E 215 " --> pdb=" O ALA E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 235 removed outlier: 3.785A pdb=" N LEU E 223 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 258 removed outlier: 3.639A pdb=" N ASP E 250 " --> pdb=" O SER E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 303 removed outlier: 4.331A pdb=" N ARG E 301 " --> pdb=" O GLU E 297 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 60 removed outlier: 4.540A pdb=" N ASP X 47 " --> pdb=" O SER X 43 " (cutoff:3.500A) Proline residue: X 48 - end of helix removed outlier: 3.575A pdb=" N LYS X 51 " --> pdb=" O ASP X 47 " (cutoff:3.500A) Processing helix chain 'X' and resid 117 through 130 Processing helix chain 'X' and resid 134 through 164 removed outlier: 3.697A pdb=" N GLN X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 168 through 191 removed outlier: 3.730A pdb=" N PHE X 172 " --> pdb=" O LEU X 168 " (cutoff:3.500A) Processing helix chain 'X' and resid 194 through 196 No H-bonds generated for 'chain 'X' and resid 194 through 196' Processing helix chain 'X' and resid 197 through 218 removed outlier: 4.340A pdb=" N VAL X 209 " --> pdb=" O LEU X 205 " (cutoff:3.500A) Proline residue: X 210 - end of helix Processing helix chain 'X' and resid 224 through 246 Processing helix chain 'X' and resid 249 through 272 Processing helix chain 'X' and resid 276 through 303 removed outlier: 3.720A pdb=" N HIS X 293 " --> pdb=" O VAL X 289 " (cutoff:3.500A) Proline residue: X 296 - end of helix removed outlier: 3.782A pdb=" N ARG X 300 " --> pdb=" O PRO X 296 " (cutoff:3.500A) Processing helix chain 'X' and resid 304 through 306 No H-bonds generated for 'chain 'X' and resid 304 through 306' Processing helix chain 'X' and resid 312 through 320 Processing helix chain 'X' and resid 341 through 378 removed outlier: 3.970A pdb=" N VAL X 345 " --> pdb=" O GLY X 341 " (cutoff:3.500A) Processing helix chain 'X' and resid 385 through 404 removed outlier: 3.947A pdb=" N LEU X 389 " --> pdb=" O ARG X 385 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG X 404 " --> pdb=" O ILE X 400 " (cutoff:3.500A) Processing helix chain 'X' and resid 408 through 434 removed outlier: 3.882A pdb=" N ILE X 423 " --> pdb=" O ALA X 419 " (cutoff:3.500A) Processing helix chain 'X' and resid 436 through 457 removed outlier: 3.798A pdb=" N VAL X 448 " --> pdb=" O VAL X 444 " (cutoff:3.500A) Proline residue: X 451 - end of helix Processing helix chain 'C' and resid 97 through 133 Processing helix chain 'C' and resid 136 through 141 removed outlier: 3.602A pdb=" N LEU C 139 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C 140 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA C 141 " --> pdb=" O THR C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 136 through 141' Processing helix chain 'C' and resid 156 through 161 removed outlier: 4.704A pdb=" N GLY C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 226 through 245 Processing helix chain 'C' and resid 258 through 267 removed outlier: 3.971A pdb=" N ASP C 263 " --> pdb=" O ASP C 260 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TRP C 264 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 265 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 266 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP C 267 " --> pdb=" O TRP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 295 through 300 removed outlier: 3.952A pdb=" N LEU C 300 " --> pdb=" O GLN C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 338 removed outlier: 4.132A pdb=" N VAL C 337 " --> pdb=" O GLN C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'C' and resid 401 through 413 Processing helix chain 'D' and resid 41 through 61 removed outlier: 4.647A pdb=" N ASP D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Proline residue: D 48 - end of helix removed outlier: 3.977A pdb=" N LYS D 51 " --> pdb=" O ASP D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.811A pdb=" N SER D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 164 Processing helix chain 'D' and resid 168 through 189 removed outlier: 4.089A pdb=" N PHE D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 219 removed outlier: 4.456A pdb=" N GLY D 200 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Proline residue: D 210 - end of helix removed outlier: 3.852A pdb=" N ALA D 219 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 246 removed outlier: 3.797A pdb=" N PHE D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 274 Processing helix chain 'D' and resid 276 through 303 removed outlier: 4.030A pdb=" N HIS D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) Proline residue: D 296 - end of helix Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 346 through 374 removed outlier: 3.738A pdb=" N LEU D 350 " --> pdb=" O ARG D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 385 through 403 removed outlier: 3.694A pdb=" N LEU D 389 " --> pdb=" O ARG D 385 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 406 No H-bonds generated for 'chain 'D' and resid 404 through 406' Processing helix chain 'D' and resid 408 through 434 removed outlier: 3.652A pdb=" N ILE D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 467 through 483 removed outlier: 4.147A pdb=" N GLU D 478 " --> pdb=" O VAL D 474 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR D 479 " --> pdb=" O GLU D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'B' and resid 19 through 40 Processing helix chain 'B' and resid 47 through 70 removed outlier: 3.867A pdb=" N ARG B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 96 through 97 Processing sheet with id=AA2, first strand: chain 'E' and resid 108 through 109 Processing sheet with id=AA3, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.538A pdb=" N MET E 204 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR E 198 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E 159 " --> pdb=" O ARG E 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 71 through 77 removed outlier: 8.536A pdb=" N LEU X 100 " --> pdb=" O VAL X 22 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA X 24 " --> pdb=" O LEU X 100 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU X 102 " --> pdb=" O ALA X 24 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N MET X 26 " --> pdb=" O LEU X 102 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N PHE X 104 " --> pdb=" O MET X 26 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 22 removed outlier: 7.091A pdb=" N GLU C 19 " --> pdb=" O THR C 175 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLY C 177 " --> pdb=" O GLU C 19 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE C 21 " --> pdb=" O GLY C 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 206 through 214 removed outlier: 5.694A pdb=" N GLY C 168 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY C 166 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N MET C 212 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG C 164 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER C 214 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL C 162 " --> pdb=" O SER C 214 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N MET C 169 " --> pdb=" O PHE C 394 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE C 394 " --> pdb=" O MET C 169 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N PHE C 393 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N THR C 376 " --> pdb=" O PHE C 393 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 395 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LEU C 365 " --> pdb=" O TRP C 220 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER C 222 " --> pdb=" O LEU C 365 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N PHE C 367 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C 224 " --> pdb=" O PHE C 367 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN C 251 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE C 326 " --> pdb=" O GLN C 251 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE C 253 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ASP C 328 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL C 255 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N TYR C 287 " --> pdb=" O MET C 252 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL C 254 " --> pdb=" O TYR C 287 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 272 through 277 removed outlier: 3.523A pdb=" N ALA C 283 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 30 through 37 Processing sheet with id=AA9, first strand: chain 'D' and resid 327 through 328 690 hydrogen bonds defined for protein. 2004 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: 3.55 Time building geometry restraints manager: 5.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3589 1.34 - 1.46: 2171 1.46 - 1.58: 5678 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 11529 Sorted by residual: bond pdb=" CB TRP C 149 " pdb=" CG TRP C 149 " ideal model delta sigma weight residual 1.498 1.415 0.083 3.10e-02 1.04e+03 7.24e+00 bond pdb=" CG1 ILE D 473 " pdb=" CD1 ILE D 473 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.89e+00 bond pdb=" CG1 ILE D 477 " pdb=" CD1 ILE D 477 " ideal model delta sigma weight residual 1.513 1.427 0.086 3.90e-02 6.57e+02 4.84e+00 bond pdb=" CA GLN C 203 " pdb=" C GLN C 203 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.80e-02 3.09e+03 4.49e+00 bond pdb=" CG ARG C 304 " pdb=" CD ARG C 304 " ideal model delta sigma weight residual 1.520 1.457 0.063 3.00e-02 1.11e+03 4.38e+00 ... (remaining 11524 not shown) Histogram of bond angle deviations from ideal: 96.13 - 103.73: 220 103.73 - 111.33: 5068 111.33 - 118.93: 4403 118.93 - 126.52: 5803 126.52 - 134.12: 275 Bond angle restraints: 15769 Sorted by residual: angle pdb=" N VAL X 309 " pdb=" CA VAL X 309 " pdb=" C VAL X 309 " ideal model delta sigma weight residual 106.55 114.16 -7.61 1.45e+00 4.76e-01 2.76e+01 angle pdb=" CA TRP C 149 " pdb=" CB TRP C 149 " pdb=" CG TRP C 149 " ideal model delta sigma weight residual 113.60 104.93 8.67 1.90e+00 2.77e-01 2.08e+01 angle pdb=" CA THR C 320 " pdb=" C THR C 320 " pdb=" N PRO C 321 " ideal model delta sigma weight residual 118.44 125.62 -7.18 1.59e+00 3.96e-01 2.04e+01 angle pdb=" C ALA X 28 " pdb=" N ASP X 29 " pdb=" CA ASP X 29 " ideal model delta sigma weight residual 121.54 130.07 -8.53 1.91e+00 2.74e-01 1.99e+01 angle pdb=" N GLU D 353 " pdb=" CA GLU D 353 " pdb=" CB GLU D 353 " ideal model delta sigma weight residual 110.28 116.83 -6.55 1.55e+00 4.16e-01 1.78e+01 ... (remaining 15764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6359 17.86 - 35.72: 414 35.72 - 53.58: 41 53.58 - 71.44: 9 71.44 - 89.30: 9 Dihedral angle restraints: 6832 sinusoidal: 2600 harmonic: 4232 Sorted by residual: dihedral pdb=" CA GLY D 224 " pdb=" C GLY D 224 " pdb=" N ALA D 225 " pdb=" CA ALA D 225 " ideal model delta harmonic sigma weight residual 180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" C THR C 320 " pdb=" N THR C 320 " pdb=" CA THR C 320 " pdb=" CB THR C 320 " ideal model delta harmonic sigma weight residual -122.00 -133.62 11.62 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" CA GLY C 161 " pdb=" C GLY C 161 " pdb=" N VAL C 162 " pdb=" CA VAL C 162 " ideal model delta harmonic sigma weight residual 180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 6829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1525 0.072 - 0.145: 321 0.145 - 0.217: 38 0.217 - 0.290: 6 0.290 - 0.362: 1 Chirality restraints: 1891 Sorted by residual: chirality pdb=" CA THR C 320 " pdb=" N THR C 320 " pdb=" C THR C 320 " pdb=" CB THR C 320 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CB ILE D 133 " pdb=" CA ILE D 133 " pdb=" CG1 ILE D 133 " pdb=" CG2 ILE D 133 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CG LEU C 241 " pdb=" CB LEU C 241 " pdb=" CD1 LEU C 241 " pdb=" CD2 LEU C 241 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1888 not shown) Planarity restraints: 1982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 149 " 0.044 2.00e-02 2.50e+03 2.76e-02 1.91e+01 pdb=" CG TRP C 149 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP C 149 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 149 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 149 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 149 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 149 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 149 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 149 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 149 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP X 317 " -0.030 2.00e-02 2.50e+03 2.43e-02 1.47e+01 pdb=" CG TRP X 317 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP X 317 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP X 317 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP X 317 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP X 317 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP X 317 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 317 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 317 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP X 317 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 152 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO C 153 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 153 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 153 " -0.039 5.00e-02 4.00e+02 ... (remaining 1979 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2321 2.78 - 3.31: 11255 3.31 - 3.84: 18435 3.84 - 4.37: 20643 4.37 - 4.90: 35988 Nonbonded interactions: 88642 Sorted by model distance: nonbonded pdb=" O PHE C 160 " pdb=" NE2 HIS C 245 " model vdw 2.247 2.520 nonbonded pdb=" OG SER X 88 " pdb=" OE1 GLU X 91 " model vdw 2.247 2.440 nonbonded pdb=" NE ARG D 190 " pdb=" O THR D 193 " model vdw 2.257 2.520 nonbonded pdb=" OG1 THR E 307 " pdb=" O ALA E 309 " model vdw 2.270 2.440 nonbonded pdb=" O ILE D 187 " pdb=" OG1 THR D 193 " model vdw 2.284 2.440 ... (remaining 88637 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 18 through 323 or resid 339 through 457)) selection = chain 'X' } 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: 8.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 19.850 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.670 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:13.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 74.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.008 0.095 11529 Z= 0.521 Angle : 1.006 10.009 15769 Z= 0.530 Chirality : 0.060 0.362 1891 Planarity : 0.007 0.072 1982 Dihedral : 12.028 89.296 4088 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.07 % 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: -0.11 (0.21), residues: 1453 helix: 0.70 (0.18), residues: 781 sheet: -0.53 (0.41), residues: 140 loop : -1.01 (0.27), residues: 532 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 232 average time/residue: 1.1018 time to fit residues: 278.2384 Evaluate side-chains 180 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 1.371 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 1.4456 time to fit residues: 5.0924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 113 optimal weight: 0.0870 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 131 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS E 102 HIS E 332 HIS C 20 ASN C 181 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 11529 Z= 0.215 Angle : 0.698 8.170 15769 Z= 0.348 Chirality : 0.044 0.190 1891 Planarity : 0.005 0.062 1982 Dihedral : 4.943 23.451 1602 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 2.29 % 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: 0.86 (0.22), residues: 1453 helix: 1.62 (0.18), residues: 788 sheet: -0.28 (0.42), residues: 134 loop : -0.77 (0.28), residues: 531 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 10 residues processed: 207 average time/residue: 1.0723 time to fit residues: 242.3368 Evaluate side-chains 176 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 1.215 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.6084 time to fit residues: 3.0653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS E 102 HIS C 249 HIS D 54 ASN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 11529 Z= 0.323 Angle : 0.700 9.385 15769 Z= 0.348 Chirality : 0.045 0.259 1891 Planarity : 0.005 0.056 1982 Dihedral : 4.761 23.541 1602 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.22), residues: 1453 helix: 1.88 (0.18), residues: 799 sheet: -0.47 (0.41), residues: 142 loop : -0.85 (0.28), residues: 512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 175 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 23 residues processed: 199 average time/residue: 1.0153 time to fit residues: 222.3809 Evaluate side-chains 187 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 1.500 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 7 average time/residue: 0.6232 time to fit residues: 6.9179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 68 optimal weight: 0.0970 chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS E 102 HIS ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 11529 Z= 0.203 Angle : 0.647 8.099 15769 Z= 0.318 Chirality : 0.043 0.278 1891 Planarity : 0.005 0.072 1982 Dihedral : 4.503 24.340 1602 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.23), residues: 1453 helix: 2.17 (0.19), residues: 794 sheet: -0.38 (0.41), residues: 142 loop : -0.77 (0.28), residues: 517 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 20 residues processed: 200 average time/residue: 0.9890 time to fit residues: 219.0001 Evaluate side-chains 185 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 1.319 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 5 average time/residue: 0.7148 time to fit residues: 5.9256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 2 optimal weight: 0.0170 chunk 104 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS E 102 HIS D 31 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 11529 Z= 0.313 Angle : 0.681 8.651 15769 Z= 0.337 Chirality : 0.044 0.261 1891 Planarity : 0.005 0.056 1982 Dihedral : 4.466 22.566 1602 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.23), residues: 1453 helix: 2.18 (0.18), residues: 802 sheet: -0.53 (0.40), residues: 144 loop : -0.86 (0.28), residues: 507 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 173 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 23 residues processed: 198 average time/residue: 1.0326 time to fit residues: 225.7207 Evaluate side-chains 184 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.500 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 16 residues processed: 7 average time/residue: 0.7031 time to fit residues: 7.4340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS E 102 HIS E 196 HIS D 31 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 11529 Z= 0.227 Angle : 0.673 8.500 15769 Z= 0.328 Chirality : 0.044 0.249 1891 Planarity : 0.004 0.057 1982 Dihedral : 4.365 22.700 1602 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.23), residues: 1453 helix: 2.25 (0.18), residues: 802 sheet: -0.39 (0.41), residues: 142 loop : -0.84 (0.28), residues: 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 22 residues processed: 200 average time/residue: 0.9980 time to fit residues: 219.5465 Evaluate side-chains 189 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 1.271 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 3 average time/residue: 0.4859 time to fit residues: 3.4576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS E 102 HIS D 31 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 11529 Z= 0.274 Angle : 0.690 9.004 15769 Z= 0.338 Chirality : 0.045 0.290 1891 Planarity : 0.004 0.058 1982 Dihedral : 4.343 21.131 1602 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.23), residues: 1453 helix: 2.23 (0.18), residues: 796 sheet: -0.41 (0.41), residues: 141 loop : -0.78 (0.28), residues: 516 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 176 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 22 residues processed: 203 average time/residue: 1.0032 time to fit residues: 224.5299 Evaluate side-chains 189 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 0.6603 time to fit residues: 4.7850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 127 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 11529 Z= 0.217 Angle : 0.685 10.618 15769 Z= 0.332 Chirality : 0.045 0.330 1891 Planarity : 0.004 0.058 1982 Dihedral : 4.256 19.020 1602 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.23), residues: 1453 helix: 2.28 (0.18), residues: 796 sheet: -0.40 (0.40), residues: 142 loop : -0.77 (0.28), residues: 515 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 172 time to evaluate : 1.359 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 21 residues processed: 197 average time/residue: 0.9968 time to fit residues: 217.8880 Evaluate side-chains 188 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.5771 time to fit residues: 3.7943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 123 optimal weight: 0.3980 chunk 129 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 11529 Z= 0.226 Angle : 0.701 11.101 15769 Z= 0.341 Chirality : 0.044 0.379 1891 Planarity : 0.004 0.058 1982 Dihedral : 4.205 17.986 1602 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.23), residues: 1453 helix: 2.27 (0.19), residues: 797 sheet: -0.40 (0.40), residues: 142 loop : -0.73 (0.28), residues: 514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 1.373 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 23 residues processed: 202 average time/residue: 0.9806 time to fit residues: 219.4454 Evaluate side-chains 192 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 1.405 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.1512 time to fit residues: 2.6348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 0.5980 chunk 84 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 11529 Z= 0.272 Angle : 0.745 15.004 15769 Z= 0.357 Chirality : 0.046 0.371 1891 Planarity : 0.005 0.064 1982 Dihedral : 4.242 17.559 1602 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.23), residues: 1453 helix: 2.25 (0.19), residues: 797 sheet: -0.46 (0.40), residues: 141 loop : -0.77 (0.28), residues: 515 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2906 Ramachandran restraints generated. 1453 Oldfield, 0 Emsley, 1453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 1.349 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 197 average time/residue: 0.9620 time to fit residues: 209.5078 Evaluate side-chains 187 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 1.241 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.6090 time to fit residues: 3.0330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 ASN D 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.099418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.075427 restraints weight = 26763.521| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.31 r_work: 0.3057 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 11529 Z= 0.255 Angle : 0.762 14.643 15769 Z= 0.366 Chirality : 0.047 0.414 1891 Planarity : 0.005 0.063 1982 Dihedral : 4.232 16.902 1602 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.23), residues: 1453 helix: 2.22 (0.19), residues: 797 sheet: -0.43 (0.40), residues: 141 loop : -0.77 (0.28), residues: 515 =============================================================================== Job complete usr+sys time: 4220.14 seconds wall clock time: 75 minutes 56.28 seconds (4556.28 seconds total)