Starting phenix.real_space_refine on Fri Mar 15 09:44:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9f_12103/03_2024/7b9f_12103.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9f_12103/03_2024/7b9f_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_12103/03_2024/7b9f_12103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9f_12103/03_2024/7b9f_12103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9f_12103/03_2024/7b9f_12103.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9f_12103/03_2024/7b9f_12103.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.24, 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: 4.41 Conformation dependent library (CDL) restraints added in 2.1 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: 1.14 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: 3.37 Time building geometry restraints manager: 4.74 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: 3.670 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: 18.940 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.830 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:14.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.070 ------------------------------------------------------------------------------- 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 % Allowed : 0.08 % Favored : 99.92 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP C 149 HIS 0.019 0.002 HIS E 102 PHE 0.027 0.003 PHE X 358 TYR 0.024 0.003 TYR C 207 ARG 0.012 0.001 ARG E 229 *********************** 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 : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 204 MET cc_start: 0.8959 (ttp) cc_final: 0.8729 (ttp) REVERT: X 172 PHE cc_start: 0.8477 (m-80) cc_final: 0.7945 (m-80) REVERT: X 205 LEU cc_start: 0.8820 (tp) cc_final: 0.8606 (tm) REVERT: X 378 CYS cc_start: 0.9234 (m) cc_final: 0.8897 (m) REVERT: C 148 MET cc_start: 0.8429 (ptt) cc_final: 0.8177 (ptt) REVERT: C 291 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7958 (tpm170) REVERT: D 164 HIS cc_start: 0.8720 (m90) cc_final: 0.8352 (m90) REVERT: D 186 MET cc_start: 0.8746 (tpt) cc_final: 0.8492 (OUTLIER) REVERT: D 381 HIS cc_start: 0.5555 (p-80) cc_final: 0.4938 (t-90) REVERT: D 472 LYS cc_start: 0.8120 (tptt) cc_final: 0.7074 (mptt) REVERT: B 50 ARG cc_start: 0.6652 (tpt170) cc_final: 0.6125 (tpt170) REVERT: B 54 LEU cc_start: 0.9108 (mt) cc_final: 0.8644 (mt) outliers start: 0 outliers final: 2 residues processed: 232 average time/residue: 1.0902 time to fit residues: 274.7736 Evaluate side-chains 179 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 GLN 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: 0.9990 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: 0.8024 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11529 Z= 0.215 Angle : 0.688 8.122 15769 Z= 0.343 Chirality : 0.044 0.196 1891 Planarity : 0.005 0.055 1982 Dihedral : 4.995 29.763 1605 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.12 % Allowed : 10.33 % Favored : 87.55 % 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: 0.88 (0.22), residues: 1453 helix: 1.65 (0.18), residues: 788 sheet: -0.29 (0.42), residues: 134 loop : -0.77 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 73 HIS 0.008 0.001 HIS E 102 PHE 0.036 0.002 PHE X 396 TYR 0.016 0.001 TYR E 110 ARG 0.005 0.000 ARG B 39 *********************** 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 217 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 202 LEU cc_start: 0.9243 (mt) cc_final: 0.9000 (mp) REVERT: X 172 PHE cc_start: 0.8437 (m-80) cc_final: 0.7883 (m-80) REVERT: X 186 MET cc_start: 0.8940 (mtp) cc_final: 0.8636 (tpt) REVERT: X 378 CYS cc_start: 0.8881 (m) cc_final: 0.8607 (m) REVERT: C 19 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7374 (mm-30) REVERT: C 20 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8613 (m-40) REVERT: C 180 GLN cc_start: 0.7919 (pp30) cc_final: 0.7662 (pp30) REVERT: C 201 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8604 (ttt90) REVERT: C 291 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7865 (tpm170) REVERT: D 50 LEU cc_start: 0.8504 (pt) cc_final: 0.8181 (tp) REVERT: D 164 HIS cc_start: 0.8751 (m90) cc_final: 0.8437 (m90) REVERT: D 186 MET cc_start: 0.8735 (tpt) cc_final: 0.8450 (OUTLIER) REVERT: D 291 MET cc_start: 0.8854 (tpt) cc_final: 0.8540 (tpt) REVERT: D 381 HIS cc_start: 0.5739 (p-80) cc_final: 0.5030 (t-90) REVERT: D 399 LEU cc_start: 0.9523 (mt) cc_final: 0.9263 (mm) REVERT: D 472 LYS cc_start: 0.8102 (tptt) cc_final: 0.7050 (mptt) REVERT: B 47 GLU cc_start: 0.8639 (pm20) cc_final: 0.8404 (pm20) REVERT: B 50 ARG cc_start: 0.6502 (tpt170) cc_final: 0.5912 (tpt170) REVERT: B 54 LEU cc_start: 0.9130 (mt) cc_final: 0.8793 (mt) outliers start: 25 outliers final: 10 residues processed: 208 average time/residue: 1.0461 time to fit residues: 237.4611 Evaluate side-chains 186 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 399 LEU Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain D residue 271 MET 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: 9.9990 chunk 131 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 44 optimal weight: 0.0170 chunk 105 optimal weight: 8.9990 overall best weight: 1.5022 ------------------------------------------------------------------------------- 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 20 ASN C 249 HIS ** 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: 0.8062 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11529 Z= 0.357 Angle : 0.705 9.589 15769 Z= 0.351 Chirality : 0.046 0.313 1891 Planarity : 0.005 0.060 1982 Dihedral : 4.782 23.971 1602 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.64 % Allowed : 13.55 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.23), residues: 1453 helix: 1.86 (0.18), residues: 799 sheet: -0.73 (0.39), residues: 152 loop : -0.73 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 317 HIS 0.005 0.001 HIS C 249 PHE 0.027 0.002 PHE X 396 TYR 0.019 0.002 TYR D 466 ARG 0.005 0.000 ARG B 39 *********************** 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 219 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 176 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 195 GLU cc_start: 0.7443 (pm20) cc_final: 0.7229 (pm20) REVERT: X 134 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7700 (p0) REVERT: X 165 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7743 (mm-30) REVERT: X 172 PHE cc_start: 0.8446 (m-80) cc_final: 0.7888 (m-80) REVERT: X 186 MET cc_start: 0.8975 (mtp) cc_final: 0.8770 (tpt) REVERT: X 378 CYS cc_start: 0.8727 (m) cc_final: 0.8509 (m) REVERT: C 19 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7748 (mm-30) REVERT: C 20 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.8603 (m-40) REVERT: C 180 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7684 (OUTLIER) REVERT: C 291 ARG cc_start: 0.8332 (ttp80) cc_final: 0.7966 (tpm170) REVERT: D 164 HIS cc_start: 0.8743 (m90) cc_final: 0.8481 (m90) REVERT: D 186 MET cc_start: 0.8742 (tpt) cc_final: 0.8460 (OUTLIER) REVERT: D 291 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8556 (tpt) REVERT: D 381 HIS cc_start: 0.5810 (p-80) cc_final: 0.5187 (t-90) REVERT: B 54 LEU cc_start: 0.9192 (mt) cc_final: 0.8958 (mt) outliers start: 43 outliers final: 23 residues processed: 200 average time/residue: 0.9962 time to fit residues: 218.4554 Evaluate side-chains 189 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 315 SER Chi-restraints excluded: chain X residue 399 LEU Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 72 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 140 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** C 20 ASN ** 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: 0.8027 moved from start: 0.2052 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= 0.219 Angle : 0.650 8.060 15769 Z= 0.320 Chirality : 0.043 0.280 1891 Planarity : 0.005 0.050 1982 Dihedral : 4.559 24.587 1602 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.06 % Allowed : 14.56 % Favored : 81.37 % 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: 1.31 (0.23), residues: 1453 helix: 2.15 (0.19), residues: 794 sheet: -0.43 (0.40), residues: 142 loop : -0.77 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 317 HIS 0.004 0.001 HIS E 102 PHE 0.023 0.001 PHE X 396 TYR 0.009 0.001 TYR E 110 ARG 0.010 0.000 ARG X 129 *********************** 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 228 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 180 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 195 GLU cc_start: 0.7492 (pm20) cc_final: 0.7154 (pm20) REVERT: X 134 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7817 (p0) REVERT: X 145 MET cc_start: 0.6769 (mmt) cc_final: 0.6281 (tpt) REVERT: X 165 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7711 (mm-30) REVERT: X 172 PHE cc_start: 0.8447 (m-80) cc_final: 0.7911 (m-80) REVERT: X 291 MET cc_start: 0.9318 (mmm) cc_final: 0.9099 (mmm) REVERT: X 378 CYS cc_start: 0.8669 (m) cc_final: 0.8436 (m) REVERT: C 20 ASN cc_start: 0.8947 (t0) cc_final: 0.8646 (m-40) REVERT: C 180 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7612 (OUTLIER) REVERT: C 291 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7914 (tpm170) REVERT: D 50 LEU cc_start: 0.8524 (pt) cc_final: 0.8147 (tm) REVERT: D 74 MET cc_start: 0.8110 (ptp) cc_final: 0.7803 (ptt) REVERT: D 164 HIS cc_start: 0.8731 (m90) cc_final: 0.8511 (m90) REVERT: D 186 MET cc_start: 0.8733 (tpt) cc_final: 0.8444 (OUTLIER) REVERT: D 291 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8471 (tpt) REVERT: D 381 HIS cc_start: 0.5797 (p-80) cc_final: 0.5189 (t-90) REVERT: D 472 LYS cc_start: 0.8064 (tptt) cc_final: 0.7085 (mptt) REVERT: B 47 GLU cc_start: 0.8520 (pm20) cc_final: 0.8245 (pm20) REVERT: B 50 ARG cc_start: 0.6573 (tpt170) cc_final: 0.6099 (tpt170) outliers start: 48 outliers final: 22 residues processed: 204 average time/residue: 1.0492 time to fit residues: 234.5200 Evaluate side-chains 193 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 165 GLU Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 315 SER Chi-restraints excluded: chain X residue 399 LEU Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 72 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 2 optimal weight: 0.0570 chunk 104 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.2504 ------------------------------------------------------------------------------- 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: 0.8058 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11529 Z= 0.310 Angle : 0.679 8.786 15769 Z= 0.335 Chirality : 0.044 0.237 1891 Planarity : 0.005 0.075 1982 Dihedral : 4.487 23.663 1602 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.90 % Allowed : 16.34 % Favored : 79.76 % 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: 1.27 (0.23), residues: 1453 helix: 2.14 (0.18), residues: 803 sheet: -0.51 (0.40), residues: 142 loop : -0.88 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 317 HIS 0.004 0.001 HIS C 414 PHE 0.020 0.001 PHE X 396 TYR 0.011 0.001 TYR E 110 ARG 0.008 0.000 ARG C 151 *********************** 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 218 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 158 ASP cc_start: 0.8560 (t0) cc_final: 0.8219 (m-30) REVERT: E 195 GLU cc_start: 0.7596 (pm20) cc_final: 0.7217 (pm20) REVERT: X 134 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7618 (p0) REVERT: X 145 MET cc_start: 0.6824 (mmt) cc_final: 0.6304 (tpt) REVERT: X 172 PHE cc_start: 0.8467 (m-80) cc_final: 0.7915 (m-80) REVERT: C 20 ASN cc_start: 0.8941 (t0) cc_final: 0.8614 (m-40) REVERT: C 180 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7647 (OUTLIER) REVERT: C 291 ARG cc_start: 0.8263 (ttp80) cc_final: 0.7950 (tpm170) REVERT: D 128 LYS cc_start: 0.8988 (pptt) cc_final: 0.8673 (pmtt) REVERT: D 164 HIS cc_start: 0.8707 (m90) cc_final: 0.8490 (m90) REVERT: D 186 MET cc_start: 0.8754 (tpt) cc_final: 0.8466 (OUTLIER) REVERT: D 291 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8500 (tpt) REVERT: D 381 HIS cc_start: 0.5801 (p-80) cc_final: 0.5118 (t-90) REVERT: B 47 GLU cc_start: 0.8624 (pm20) cc_final: 0.8357 (pm20) outliers start: 46 outliers final: 24 residues processed: 200 average time/residue: 0.9643 time to fit residues: 212.0495 Evaluate side-chains 190 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 315 SER Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 72 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** D 411 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11529 Z= 0.242 Angle : 0.673 8.307 15769 Z= 0.326 Chirality : 0.044 0.227 1891 Planarity : 0.005 0.048 1982 Dihedral : 4.395 23.356 1602 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.30 % Allowed : 17.53 % Favored : 79.17 % 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: 1.36 (0.23), residues: 1453 helix: 2.23 (0.18), residues: 802 sheet: -0.47 (0.40), residues: 142 loop : -0.86 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP X 317 HIS 0.004 0.001 HIS X 227 PHE 0.016 0.001 PHE X 396 TYR 0.009 0.001 TYR C 207 ARG 0.007 0.000 ARG C 151 *********************** 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 216 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 177 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 158 ASP cc_start: 0.8523 (t0) cc_final: 0.8152 (m-30) REVERT: E 195 GLU cc_start: 0.7590 (pm20) cc_final: 0.7181 (pm20) REVERT: E 199 TRP cc_start: 0.8692 (m-90) cc_final: 0.8357 (m100) REVERT: X 91 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8790 (mp0) REVERT: X 128 LYS cc_start: 0.9357 (ttpp) cc_final: 0.9080 (tmmm) REVERT: X 134 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7835 (p0) REVERT: X 172 PHE cc_start: 0.8447 (m-80) cc_final: 0.7880 (m-80) REVERT: X 421 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8859 (mp) REVERT: C 20 ASN cc_start: 0.8957 (t0) cc_final: 0.8633 (m-40) REVERT: C 180 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7590 (OUTLIER) REVERT: C 291 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7938 (tpm170) REVERT: D 50 LEU cc_start: 0.8575 (pt) cc_final: 0.8337 (tp) REVERT: D 74 MET cc_start: 0.8108 (ptp) cc_final: 0.7730 (ptt) REVERT: D 128 LYS cc_start: 0.8968 (pptt) cc_final: 0.8583 (pmtt) REVERT: D 164 HIS cc_start: 0.8759 (m90) cc_final: 0.8545 (m90) REVERT: D 186 MET cc_start: 0.8748 (tpt) cc_final: 0.8460 (OUTLIER) REVERT: D 291 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8428 (tpt) REVERT: D 298 LEU cc_start: 0.9456 (tp) cc_final: 0.9195 (tp) REVERT: D 381 HIS cc_start: 0.5810 (p-80) cc_final: 0.5132 (t-90) REVERT: B 47 GLU cc_start: 0.8597 (pm20) cc_final: 0.8329 (pm20) outliers start: 39 outliers final: 24 residues processed: 202 average time/residue: 1.0525 time to fit residues: 232.2797 Evaluate side-chains 197 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain X residue 91 GLU Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 315 SER Chi-restraints excluded: chain X residue 399 LEU Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 72 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 chunk 118 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 139 optimal weight: 0.0970 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2605 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= 0.187 Angle : 0.666 9.317 15769 Z= 0.320 Chirality : 0.044 0.301 1891 Planarity : 0.004 0.049 1982 Dihedral : 4.187 23.014 1602 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.96 % Allowed : 19.05 % Favored : 77.98 % 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: 1.56 (0.23), residues: 1453 helix: 2.38 (0.19), residues: 796 sheet: -0.22 (0.40), residues: 142 loop : -0.76 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP X 317 HIS 0.003 0.000 HIS X 227 PHE 0.017 0.001 PHE X 396 TYR 0.010 0.001 TYR C 207 ARG 0.008 0.000 ARG B 39 *********************** 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 228 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 193 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 158 ASP cc_start: 0.8522 (t0) cc_final: 0.8145 (m-30) REVERT: E 195 GLU cc_start: 0.7645 (pm20) cc_final: 0.7270 (pm20) REVERT: E 199 TRP cc_start: 0.8603 (m-90) cc_final: 0.8296 (m100) REVERT: E 235 ASN cc_start: 0.8920 (t0) cc_final: 0.8712 (t0) REVERT: X 134 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7796 (p0) REVERT: X 145 MET cc_start: 0.6391 (mmt) cc_final: 0.5992 (tpt) REVERT: X 172 PHE cc_start: 0.8423 (m-80) cc_final: 0.7861 (m-80) REVERT: X 291 MET cc_start: 0.8842 (mmm) cc_final: 0.8417 (mmm) REVERT: X 421 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8856 (mp) REVERT: C 20 ASN cc_start: 0.8912 (t0) cc_final: 0.8662 (m-40) REVERT: C 180 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7609 (OUTLIER) REVERT: D 50 LEU cc_start: 0.8513 (pt) cc_final: 0.8264 (tp) REVERT: D 74 MET cc_start: 0.8050 (ptp) cc_final: 0.7669 (ptt) REVERT: D 186 MET cc_start: 0.8771 (tpt) cc_final: 0.8486 (OUTLIER) REVERT: D 253 TYR cc_start: 0.8631 (m-80) cc_final: 0.8293 (m-80) REVERT: D 291 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8369 (tpt) REVERT: D 298 LEU cc_start: 0.9427 (tp) cc_final: 0.9200 (tp) REVERT: D 320 GLU cc_start: 0.6612 (mp0) cc_final: 0.6402 (mp0) REVERT: D 381 HIS cc_start: 0.5775 (p-80) cc_final: 0.5029 (t-90) outliers start: 35 outliers final: 20 residues processed: 214 average time/residue: 0.9478 time to fit residues: 223.1315 Evaluate side-chains 196 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 315 SER Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 72 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 88 optimal weight: 0.0270 chunk 95 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 13 optimal weight: 4.9990 chunk 109 optimal weight: 0.0020 chunk 127 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 overall best weight: 0.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 HIS C 208 ASN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11529 Z= 0.185 Angle : 0.656 10.041 15769 Z= 0.316 Chirality : 0.043 0.320 1891 Planarity : 0.004 0.049 1982 Dihedral : 4.082 20.751 1602 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.71 % Allowed : 20.91 % Favored : 76.38 % 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: 1.63 (0.23), residues: 1453 helix: 2.42 (0.19), residues: 796 sheet: -0.11 (0.41), residues: 142 loop : -0.74 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP X 317 HIS 0.003 0.000 HIS X 227 PHE 0.013 0.001 PHE X 396 TYR 0.009 0.001 TYR C 207 ARG 0.008 0.000 ARG B 39 *********************** 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 227 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 158 ASP cc_start: 0.8510 (t0) cc_final: 0.8126 (m-30) REVERT: E 195 GLU cc_start: 0.7653 (pm20) cc_final: 0.7248 (pm20) REVERT: E 199 TRP cc_start: 0.8635 (m-90) cc_final: 0.8323 (m100) REVERT: E 235 ASN cc_start: 0.8845 (t0) cc_final: 0.8618 (t0) REVERT: X 29 ASP cc_start: 0.8568 (p0) cc_final: 0.8356 (p0) REVERT: X 98 ASP cc_start: 0.8428 (m-30) cc_final: 0.8166 (m-30) REVERT: X 128 LYS cc_start: 0.9338 (ttpp) cc_final: 0.9086 (tmmm) REVERT: X 134 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7742 (p0) REVERT: X 145 MET cc_start: 0.6479 (mmt) cc_final: 0.6061 (tpt) REVERT: X 172 PHE cc_start: 0.8457 (m-80) cc_final: 0.7896 (m-80) REVERT: X 186 MET cc_start: 0.8950 (mtp) cc_final: 0.8743 (tpt) REVERT: X 291 MET cc_start: 0.8827 (mmm) cc_final: 0.8392 (mmm) REVERT: X 421 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8926 (mp) REVERT: C 20 ASN cc_start: 0.8871 (t0) cc_final: 0.8621 (m-40) REVERT: C 180 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7619 (OUTLIER) REVERT: C 185 ASP cc_start: 0.8454 (m-30) cc_final: 0.7947 (t0) REVERT: D 50 LEU cc_start: 0.8482 (pt) cc_final: 0.8233 (tp) REVERT: D 74 MET cc_start: 0.8044 (ptp) cc_final: 0.7678 (ptt) REVERT: D 186 MET cc_start: 0.8774 (tpt) cc_final: 0.8486 (OUTLIER) REVERT: D 253 TYR cc_start: 0.8689 (m-80) cc_final: 0.8457 (m-80) REVERT: D 291 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8382 (tpt) REVERT: D 298 LEU cc_start: 0.9424 (tp) cc_final: 0.9179 (tp) REVERT: D 320 GLU cc_start: 0.6664 (mp0) cc_final: 0.6447 (mp0) REVERT: D 381 HIS cc_start: 0.5645 (p-80) cc_final: 0.5035 (t-90) REVERT: D 415 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.8994 (mt) REVERT: D 418 THR cc_start: 0.9110 (m) cc_final: 0.8823 (p) REVERT: B 47 GLU cc_start: 0.8475 (pm20) cc_final: 0.8265 (pm20) outliers start: 32 outliers final: 21 residues processed: 214 average time/residue: 0.8698 time to fit residues: 206.1426 Evaluate side-chains 205 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 181 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain X residue 134 ASP Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 315 SER Chi-restraints excluded: chain X residue 399 LEU Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 72 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 123 optimal weight: 0.4980 chunk 129 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2903 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= 0.221 Angle : 0.715 14.701 15769 Z= 0.342 Chirality : 0.045 0.365 1891 Planarity : 0.005 0.053 1982 Dihedral : 4.083 19.171 1602 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.37 % Allowed : 22.44 % Favored : 75.19 % 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: 1.61 (0.23), residues: 1453 helix: 2.39 (0.18), residues: 795 sheet: -0.07 (0.42), residues: 137 loop : -0.74 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP X 317 HIS 0.003 0.000 HIS X 227 PHE 0.014 0.001 PHE D 394 TYR 0.010 0.001 TYR C 207 ARG 0.009 0.000 ARG B 39 *********************** 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 219 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 158 ASP cc_start: 0.8506 (t0) cc_final: 0.8108 (m-30) REVERT: E 195 GLU cc_start: 0.7662 (pm20) cc_final: 0.7217 (pm20) REVERT: E 199 TRP cc_start: 0.8640 (m-90) cc_final: 0.8338 (m100) REVERT: E 235 ASN cc_start: 0.8854 (t0) cc_final: 0.8615 (t0) REVERT: X 128 LYS cc_start: 0.9345 (ttpp) cc_final: 0.9101 (tmmm) REVERT: X 145 MET cc_start: 0.6512 (mmt) cc_final: 0.6085 (tpt) REVERT: X 172 PHE cc_start: 0.8389 (m-80) cc_final: 0.7943 (m-80) REVERT: X 186 MET cc_start: 0.8997 (mtp) cc_final: 0.8742 (tpt) REVERT: X 291 MET cc_start: 0.8827 (mmm) cc_final: 0.8394 (mmm) REVERT: X 421 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8953 (mp) REVERT: C 20 ASN cc_start: 0.8910 (t0) cc_final: 0.8633 (m-40) REVERT: C 180 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7613 (OUTLIER) REVERT: C 185 ASP cc_start: 0.8453 (m-30) cc_final: 0.7966 (t0) REVERT: D 50 LEU cc_start: 0.8491 (pt) cc_final: 0.8251 (tp) REVERT: D 74 MET cc_start: 0.8063 (ptp) cc_final: 0.7720 (ptt) REVERT: D 186 MET cc_start: 0.8776 (tpt) cc_final: 0.8486 (OUTLIER) REVERT: D 253 TYR cc_start: 0.8669 (m-80) cc_final: 0.8453 (m-80) REVERT: D 291 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8368 (tpt) REVERT: D 298 LEU cc_start: 0.9431 (tp) cc_final: 0.9175 (tp) REVERT: D 320 GLU cc_start: 0.6809 (mp0) cc_final: 0.6590 (mp0) REVERT: D 381 HIS cc_start: 0.5663 (p-80) cc_final: 0.4488 (t-90) REVERT: D 415 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9021 (mt) REVERT: D 418 THR cc_start: 0.9124 (m) cc_final: 0.8815 (p) REVERT: D 430 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7513 (t80) REVERT: B 47 GLU cc_start: 0.8501 (pm20) cc_final: 0.8300 (pm20) outliers start: 28 outliers final: 20 residues processed: 207 average time/residue: 0.9505 time to fit residues: 217.7429 Evaluate side-chains 204 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 315 SER Chi-restraints excluded: chain X residue 399 LEU Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 72 LEU 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: 0.8980 chunk 65 optimal weight: 0.2980 chunk 95 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 132 optimal weight: 0.0970 chunk 115 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2937 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= 0.248 Angle : 0.733 14.482 15769 Z= 0.350 Chirality : 0.045 0.352 1891 Planarity : 0.005 0.056 1982 Dihedral : 4.124 18.226 1602 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.29 % Allowed : 22.78 % Favored : 74.94 % 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: 1.51 (0.23), residues: 1453 helix: 2.30 (0.19), residues: 795 sheet: -0.08 (0.42), residues: 137 loop : -0.77 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP X 317 HIS 0.003 0.001 HIS X 227 PHE 0.011 0.001 PHE X 396 TYR 0.010 0.001 TYR C 207 ARG 0.010 0.000 ARG C 151 ********************** 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 210 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 183 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 158 ASP cc_start: 0.8462 (t0) cc_final: 0.8014 (m-30) REVERT: E 195 GLU cc_start: 0.7675 (pm20) cc_final: 0.7228 (pm20) REVERT: E 199 TRP cc_start: 0.8655 (m-90) cc_final: 0.8350 (m100) REVERT: X 128 LYS cc_start: 0.9347 (ttpp) cc_final: 0.9098 (tmmm) REVERT: X 145 MET cc_start: 0.6533 (mmt) cc_final: 0.6097 (tpt) REVERT: X 172 PHE cc_start: 0.8313 (m-80) cc_final: 0.7960 (m-80) REVERT: X 186 MET cc_start: 0.9005 (mtp) cc_final: 0.8745 (tpt) REVERT: X 291 MET cc_start: 0.8827 (mmm) cc_final: 0.8396 (mmm) REVERT: X 421 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8962 (mp) REVERT: C 20 ASN cc_start: 0.8937 (t0) cc_final: 0.8634 (m-40) REVERT: C 180 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7626 (OUTLIER) REVERT: C 185 ASP cc_start: 0.8443 (m-30) cc_final: 0.7971 (t0) REVERT: D 74 MET cc_start: 0.8048 (ptp) cc_final: 0.7634 (ptt) REVERT: D 128 LYS cc_start: 0.8906 (pptt) cc_final: 0.8594 (pmtt) REVERT: D 186 MET cc_start: 0.8752 (tpt) cc_final: 0.8456 (OUTLIER) REVERT: D 282 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8851 (t) REVERT: D 291 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8381 (tpt) REVERT: D 298 LEU cc_start: 0.9438 (tp) cc_final: 0.9189 (tp) REVERT: D 320 GLU cc_start: 0.6826 (mp0) cc_final: 0.6604 (mp0) REVERT: D 381 HIS cc_start: 0.5760 (p-80) cc_final: 0.4682 (t-90) REVERT: D 430 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.7153 (t80) REVERT: B 47 GLU cc_start: 0.8530 (pm20) cc_final: 0.8313 (pm20) outliers start: 27 outliers final: 20 residues processed: 196 average time/residue: 0.9616 time to fit residues: 207.7589 Evaluate side-chains 202 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain X residue 307 LEU Chi-restraints excluded: chain X residue 315 SER Chi-restraints excluded: chain X residue 399 LEU Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain X residue 447 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 72 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.0670 chunk 115 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.7718 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.099000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.075135 restraints weight = 26927.124| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.29 r_work: 0.3073 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11529 Z= 0.247 Angle : 0.734 14.491 15769 Z= 0.352 Chirality : 0.045 0.345 1891 Planarity : 0.004 0.057 1982 Dihedral : 4.122 18.721 1602 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.20 % Allowed : 22.95 % Favored : 74.85 % 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: 1.51 (0.23), residues: 1453 helix: 2.30 (0.19), residues: 796 sheet: -0.08 (0.42), residues: 137 loop : -0.77 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP X 317 HIS 0.003 0.001 HIS X 227 PHE 0.011 0.001 PHE X 396 TYR 0.015 0.001 TYR D 253 ARG 0.010 0.000 ARG B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4298.12 seconds wall clock time: 76 minutes 19.76 seconds (4579.76 seconds total)