Starting phenix.real_space_refine on Fri Aug 22 20:06:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nou_49617/08_2025/9nou_49617.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nou_49617/08_2025/9nou_49617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nou_49617/08_2025/9nou_49617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nou_49617/08_2025/9nou_49617.map" model { file = "/net/cci-nas-00/data/ceres_data/9nou_49617/08_2025/9nou_49617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nou_49617/08_2025/9nou_49617.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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 49 5.16 5 C 4799 2.51 5 N 1266 2.21 5 O 1405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7519 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3611 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 24, 'TRANS': 440} Chain breaks: 4 Chain: "A" Number of atoms: 3698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3698 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 21, 'TRANS': 436} Chain breaks: 3 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 1.79, per 1000 atoms: 0.24 Number of scatterers: 7519 At special positions: 0 Unit cell: (92.999, 88.061, 92.176, 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 49 16.00 O 1405 8.00 N 1266 7.00 C 4799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 517 " distance=2.02 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 513 " distance=2.03 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 366 " distance=2.03 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 514 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 487 " " NAG A 602 " - " ASN A 84 " " NAG A 603 " - " ASN A 428 " " NAG A 604 " - " ASN A 312 " " NAG A 605 " - " ASN A 248 " " NAG A 606 " - " ASN A 292 " " NAG A 607 " - " ASN A 368 " " NAG B 601 " - " ASN B 475 " " NAG B 602 " - " ASN B 285 " " NAG B 603 " - " ASN B 264 " " NAG B 604 " - " ASN B 411 " " NAG B 605 " - " ASN B 85 " " NAG B 606 " - " ASN B 130 " " NAG B 607 " - " ASN B 380 " " NAG B 608 " - " ASN B 432 " Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 416.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1746 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 9 sheets defined 42.5% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 66 through 86 removed outlier: 3.541A pdb=" N LEU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 removed outlier: 3.760A pdb=" N ALA B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 130 through 134 removed outlier: 3.777A pdb=" N GLN B 133 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 161 removed outlier: 4.090A pdb=" N PHE B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.941A pdb=" N GLN B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 234 removed outlier: 3.614A pdb=" N ALA B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 266 removed outlier: 3.557A pdb=" N SER B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 290 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 333 through 345 Processing helix chain 'B' and resid 347 through 354 Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.517A pdb=" N ASP B 374 " --> pdb=" O PRO B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 385 removed outlier: 3.788A pdb=" N SER B 382 " --> pdb=" O GLN B 379 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ALA B 383 " --> pdb=" O ASN B 380 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 384 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 385 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 408 removed outlier: 3.645A pdb=" N SER B 392 " --> pdb=" O HIS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 425 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 482 through 485 Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 65 through 85 removed outlier: 3.888A pdb=" N TYR A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 143 through 155 removed outlier: 3.664A pdb=" N PHE A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 213 through 228 Processing helix chain 'A' and resid 250 through 267 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.515A pdb=" N GLU A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 314 No H-bonds generated for 'chain 'A' and resid 313 through 314' Processing helix chain 'A' and resid 315 through 318 removed outlier: 3.987A pdb=" N HIS A 318 " --> pdb=" O GLU A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 318' Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.072A pdb=" N SER A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 384 through 404 Processing helix chain 'A' and resid 416 through 425 removed outlier: 3.662A pdb=" N TRP A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.541A pdb=" N MET B 31 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR B 35 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ASP B 98 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU B 37 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE B 100 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLY B 39 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL B 36 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ILE B 142 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY B 38 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLN B 164 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA3, first strand: chain 'B' and resid 124 through 126 Processing sheet with id=AA4, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.901A pdb=" N VAL B 209 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ALA B 211 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU B 242 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL B 270 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TRP B 297 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE B 324 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA B 299 " --> pdb=" O PHE B 324 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N GLN B 326 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL B 321 " --> pdb=" O TRP B 459 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU B 458 " --> pdb=" O ASP B 470 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP B 470 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 460 " --> pdb=" O LEU B 468 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU B 468 " --> pdb=" O VAL B 460 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 434 through 437 Processing sheet with id=AA6, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AA7, first strand: chain 'A' and resid 28 through 29 removed outlier: 6.122A pdb=" N LEU A 35 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL A 99 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLY A 37 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL A 101 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE A 39 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU A 34 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ILE A 139 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLY A 36 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N ILE A 162 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 138 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLN A 161 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 233 through 240 removed outlier: 7.195A pdb=" N ILE A 206 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLU A 238 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 208 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU A 240 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A 210 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TRP A 205 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N VAL A 273 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 207 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE A 275 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 209 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 272 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A 296 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU A 323 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TRP A 298 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE A 325 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA A 300 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N ILE A 327 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N PHE A 322 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 448 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N SER A 467 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 450 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 474 " --> pdb=" O TYR A 469 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 428 through 431 280 hydrogen bonds defined for protein. 771 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: 0.92 Time building geometry restraints manager: 0.83 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: 2394 1.34 - 1.46: 1885 1.46 - 1.59: 3349 1.59 - 1.71: 0 1.71 - 1.83: 71 Bond restraints: 7699 Sorted by residual: bond pdb=" N VAL B 511 " pdb=" CA VAL B 511 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.23e+00 bond pdb=" N VAL A 108 " pdb=" CA VAL A 108 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.68e+00 bond pdb=" N VAL A 385 " pdb=" CA VAL A 385 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.64e+00 bond pdb=" N VAL A 384 " pdb=" CA VAL A 384 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.28e-02 6.10e+03 7.59e+00 bond pdb=" N PHE A 285 " pdb=" CA PHE A 285 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.33e-02 5.65e+03 7.55e+00 ... (remaining 7694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 10211 1.90 - 3.80: 232 3.80 - 5.71: 23 5.71 - 7.61: 2 7.61 - 9.51: 3 Bond angle restraints: 10471 Sorted by residual: angle pdb=" N VAL A 384 " pdb=" CA VAL A 384 " pdb=" C VAL A 384 " ideal model delta sigma weight residual 113.16 107.55 5.61 1.49e+00 4.50e-01 1.42e+01 angle pdb=" N VAL A 288 " pdb=" CA VAL A 288 " pdb=" C VAL A 288 " ideal model delta sigma weight residual 110.62 106.35 4.27 1.14e+00 7.69e-01 1.40e+01 angle pdb=" O PHE A 284 " pdb=" C PHE A 284 " pdb=" N PHE A 285 " ideal model delta sigma weight residual 122.12 118.20 3.92 1.06e+00 8.90e-01 1.36e+01 angle pdb=" N TYR B 128 " pdb=" CA TYR B 128 " pdb=" C TYR B 128 " ideal model delta sigma weight residual 110.59 105.28 5.31 1.45e+00 4.76e-01 1.34e+01 angle pdb=" CA PHE A 284 " pdb=" C PHE A 284 " pdb=" N PHE A 285 " ideal model delta sigma weight residual 117.30 121.38 -4.08 1.16e+00 7.43e-01 1.24e+01 ... (remaining 10466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4094 17.94 - 35.89: 486 35.89 - 53.83: 158 53.83 - 71.78: 36 71.78 - 89.72: 10 Dihedral angle restraints: 4784 sinusoidal: 2092 harmonic: 2692 Sorted by residual: dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS A 102 " pdb=" CB CYS A 102 " ideal model delta sinusoidal sigma weight residual -86.00 -155.30 69.30 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CB CYS A 363 " pdb=" SG CYS A 363 " pdb=" SG CYS A 366 " pdb=" CB CYS A 366 " ideal model delta sinusoidal sigma weight residual -86.00 -147.08 61.08 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" CB CYS A 495 " pdb=" SG CYS A 495 " pdb=" SG CYS A 514 " pdb=" CB CYS A 514 " ideal model delta sinusoidal sigma weight residual -86.00 -136.73 50.73 1 1.00e+01 1.00e-02 3.52e+01 ... (remaining 4781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1011 0.061 - 0.123: 181 0.123 - 0.184: 18 0.184 - 0.245: 5 0.245 - 0.307: 2 Chirality restraints: 1217 Sorted by residual: chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 84 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2 NAG A 604 " pdb=" C1 NAG A 604 " pdb=" C3 NAG A 604 " pdb=" N2 NAG A 604 " both_signs ideal model delta sigma weight residual False -2.49 -2.19 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C1 NAG B 608 " pdb=" ND2 ASN B 432 " pdb=" C2 NAG B 608 " pdb=" O5 NAG B 608 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1214 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 130 " 0.038 2.00e-02 2.50e+03 4.12e-02 2.12e+01 pdb=" CG ASN B 130 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN B 130 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 130 " -0.065 2.00e-02 2.50e+03 pdb=" C1 NAG B 606 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 510 " 0.212 9.50e-02 1.11e+02 9.50e-02 5.54e+00 pdb=" NE ARG B 510 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 510 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 510 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 510 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 127 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C ALA B 127 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA B 127 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR B 128 " -0.013 2.00e-02 2.50e+03 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2938 2.89 - 3.40: 6954 3.40 - 3.90: 12905 3.90 - 4.40: 14840 4.40 - 4.90: 24651 Nonbonded interactions: 62288 Sorted by model distance: nonbonded pdb=" O PRO B 416 " pdb=" OE1 GLN B 418 " model vdw 2.394 3.040 nonbonded pdb=" N TYR B 128 " pdb=" O TYR B 128 " model vdw 2.523 2.496 nonbonded pdb=" N GLN B 418 " pdb=" OE1 GLN B 418 " model vdw 2.531 3.120 nonbonded pdb=" O ARG B 510 " pdb=" N ASP B 520 " model vdw 2.559 3.120 nonbonded pdb=" CB ARG A 226 " pdb=" NE ARG A 226 " model vdw 2.560 2.816 ... (remaining 62283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 6.580 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.500 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:8.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.004 0.038 7727 Z= 0.217 Angle : 0.691 9.907 10542 Z= 0.384 Chirality : 0.049 0.307 1217 Planarity : 0.005 0.095 1320 Dihedral : 17.487 89.720 2999 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.24 % Allowed : 29.54 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.28), residues: 905 helix: 0.81 (0.28), residues: 330 sheet: -0.98 (0.41), residues: 143 loop : 0.10 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 256 TYR 0.025 0.002 TYR B 394 PHE 0.024 0.002 PHE B 65 TRP 0.021 0.002 TRP A 455 HIS 0.004 0.001 HIS B 341 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 7699) covalent geometry : angle 0.66332 (10471) SS BOND : bond 0.00319 ( 13) SS BOND : angle 1.29377 ( 26) hydrogen bonds : bond 0.18255 ( 280) hydrogen bonds : angle 6.25606 ( 771) link_NAG-ASN : bond 0.00672 ( 15) link_NAG-ASN : angle 2.89910 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 32 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7761 (pptt) REVERT: B 45 GLU cc_start: 0.6897 (mt-10) cc_final: 0.5820 (tp30) REVERT: B 81 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7205 (mm-30) REVERT: B 86 LYS cc_start: 0.7683 (mtpp) cc_final: 0.7444 (ttmm) REVERT: B 87 SER cc_start: 0.8398 (m) cc_final: 0.8125 (p) REVERT: B 111 LYS cc_start: 0.7680 (ttmm) cc_final: 0.6992 (ttpp) REVERT: B 122 SER cc_start: 0.7765 (t) cc_final: 0.7486 (t) REVERT: B 123 ARG cc_start: 0.7214 (ttm170) cc_final: 0.7001 (ttm170) REVERT: B 146 SER cc_start: 0.8349 (m) cc_final: 0.8017 (t) REVERT: B 151 MET cc_start: 0.8090 (tpp) cc_final: 0.7848 (mmt) REVERT: B 155 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7777 (ttpt) REVERT: B 178 GLU cc_start: 0.8151 (tt0) cc_final: 0.7804 (mp0) REVERT: B 191 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7512 (ttt180) REVERT: B 220 ARG cc_start: 0.7634 (mtp85) cc_final: 0.6789 (mtm-85) REVERT: B 258 ASP cc_start: 0.6631 (t0) cc_final: 0.6404 (m-30) REVERT: B 428 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7128 (tt0) REVERT: B 469 HIS cc_start: 0.7260 (m90) cc_final: 0.6963 (m170) REVERT: A 58 MET cc_start: 0.5038 (ttm) cc_final: 0.4579 (ttt) REVERT: A 93 LEU cc_start: 0.7686 (mt) cc_final: 0.7235 (mm) REVERT: A 126 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7571 (tp30) REVERT: A 202 ARG cc_start: 0.8381 (mtm180) cc_final: 0.8093 (mtm110) REVERT: A 221 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7273 (tp40) outliers start: 10 outliers final: 3 residues processed: 111 average time/residue: 0.6438 time to fit residues: 75.1114 Evaluate side-chains 102 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain A residue 359 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.166940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.128757 restraints weight = 7705.496| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.18 r_work: 0.3190 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7727 Z= 0.185 Angle : 0.611 10.798 10542 Z= 0.300 Chirality : 0.048 0.319 1217 Planarity : 0.004 0.032 1320 Dihedral : 7.428 59.302 1316 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 5.81 % Allowed : 24.23 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.28), residues: 905 helix: 1.20 (0.28), residues: 326 sheet: -0.92 (0.41), residues: 143 loop : 0.14 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 510 TYR 0.028 0.002 TYR B 394 PHE 0.016 0.002 PHE B 65 TRP 0.014 0.002 TRP A 455 HIS 0.005 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 7699) covalent geometry : angle 0.58415 (10471) SS BOND : bond 0.00305 ( 13) SS BOND : angle 0.96997 ( 26) hydrogen bonds : bond 0.04613 ( 280) hydrogen bonds : angle 4.76789 ( 771) link_NAG-ASN : bond 0.00712 ( 15) link_NAG-ASN : angle 2.72658 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 108 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8111 (ttm170) REVERT: B 81 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7589 (mm-30) REVERT: B 86 LYS cc_start: 0.7805 (mtpp) cc_final: 0.7590 (ttmm) REVERT: B 111 LYS cc_start: 0.7927 (ttmm) cc_final: 0.7300 (ttpp) REVERT: B 115 MET cc_start: 0.8657 (tpt) cc_final: 0.8412 (tpt) REVERT: B 122 SER cc_start: 0.8039 (t) cc_final: 0.7750 (t) REVERT: B 146 SER cc_start: 0.8414 (m) cc_final: 0.8117 (t) REVERT: B 151 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7954 (mmt) REVERT: B 178 GLU cc_start: 0.8192 (tt0) cc_final: 0.7838 (mp0) REVERT: B 191 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7571 (ttt180) REVERT: B 220 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7200 (mtm-85) REVERT: B 221 GLN cc_start: 0.8426 (mm-40) cc_final: 0.6938 (pp30) REVERT: B 318 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7845 (mmm) REVERT: B 409 GLN cc_start: 0.8253 (mt0) cc_final: 0.7878 (mp10) REVERT: B 469 HIS cc_start: 0.7412 (m90) cc_final: 0.7201 (m170) REVERT: A 58 MET cc_start: 0.4714 (ttm) cc_final: 0.3987 (ttt) REVERT: A 93 LEU cc_start: 0.8092 (mt) cc_final: 0.7685 (mm) REVERT: A 121 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7990 (mp) REVERT: A 126 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8026 (tp30) REVERT: A 202 ARG cc_start: 0.8329 (mtm180) cc_final: 0.8080 (mtm180) REVERT: A 221 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7649 (tp40) REVERT: A 477 ASN cc_start: 0.7694 (t0) cc_final: 0.7352 (t0) outliers start: 47 outliers final: 16 residues processed: 137 average time/residue: 0.5254 time to fit residues: 75.9479 Evaluate side-chains 108 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 318 MET Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 87 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 HIS ** B 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 255 GLN A 460 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.162593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.123927 restraints weight = 7738.523| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.25 r_work: 0.3145 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 7727 Z= 0.241 Angle : 0.690 14.833 10542 Z= 0.334 Chirality : 0.052 0.369 1217 Planarity : 0.005 0.034 1320 Dihedral : 7.530 59.865 1310 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 5.93 % Allowed : 23.11 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.28), residues: 905 helix: 0.95 (0.28), residues: 333 sheet: -1.12 (0.40), residues: 147 loop : -0.04 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 226 TYR 0.030 0.002 TYR B 394 PHE 0.017 0.002 PHE A 338 TRP 0.017 0.002 TRP A 455 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 7699) covalent geometry : angle 0.64870 (10471) SS BOND : bond 0.00318 ( 13) SS BOND : angle 1.06792 ( 26) hydrogen bonds : bond 0.05041 ( 280) hydrogen bonds : angle 4.82139 ( 771) link_NAG-ASN : bond 0.00837 ( 15) link_NAG-ASN : angle 3.61880 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7989 (ttm110) REVERT: B 81 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7439 (mm-30) REVERT: B 111 LYS cc_start: 0.7848 (ttmm) cc_final: 0.7144 (ttpp) REVERT: B 115 MET cc_start: 0.8525 (tpt) cc_final: 0.8227 (tpt) REVERT: B 122 SER cc_start: 0.8228 (t) cc_final: 0.7950 (t) REVERT: B 135 GLN cc_start: 0.7847 (tp40) cc_final: 0.7560 (mm-40) REVERT: B 146 SER cc_start: 0.8454 (m) cc_final: 0.8126 (t) REVERT: B 151 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7901 (mmt) REVERT: B 155 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.7916 (ttpt) REVERT: B 178 GLU cc_start: 0.7953 (tt0) cc_final: 0.7685 (mp0) REVERT: B 191 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7708 (ttt180) REVERT: B 220 ARG cc_start: 0.7964 (mtp85) cc_final: 0.7207 (mtm-85) REVERT: B 221 GLN cc_start: 0.8300 (mm-40) cc_final: 0.6851 (pp30) REVERT: B 409 GLN cc_start: 0.8066 (mt0) cc_final: 0.7803 (mm110) REVERT: B 457 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7096 (mmpt) REVERT: B 469 HIS cc_start: 0.7545 (m90) cc_final: 0.7173 (m170) REVERT: B 514 PHE cc_start: 0.8707 (t80) cc_final: 0.8448 (t80) REVERT: A 58 MET cc_start: 0.5126 (ttm) cc_final: 0.4392 (ttt) REVERT: A 93 LEU cc_start: 0.8462 (mt) cc_final: 0.8216 (mt) REVERT: A 126 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7844 (tp30) REVERT: A 202 ARG cc_start: 0.8172 (mtm180) cc_final: 0.7922 (mtm110) REVERT: A 221 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7519 (tp40) REVERT: A 477 ASN cc_start: 0.7625 (t0) cc_final: 0.7287 (t0) REVERT: A 506 LYS cc_start: 0.5579 (pttp) cc_final: 0.5029 (pmtt) outliers start: 48 outliers final: 26 residues processed: 133 average time/residue: 0.5617 time to fit residues: 78.8321 Evaluate side-chains 121 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 HIS ** B 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN A 460 ASN A 488 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.164586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.126424 restraints weight = 7754.542| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.25 r_work: 0.3182 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7727 Z= 0.160 Angle : 0.600 12.124 10542 Z= 0.289 Chirality : 0.048 0.426 1217 Planarity : 0.004 0.030 1320 Dihedral : 6.930 59.499 1307 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 5.32 % Allowed : 23.24 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.28), residues: 905 helix: 1.24 (0.29), residues: 333 sheet: -1.01 (0.41), residues: 143 loop : 0.02 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 254 TYR 0.026 0.002 TYR B 394 PHE 0.021 0.002 PHE B 65 TRP 0.013 0.002 TRP A 455 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 7699) covalent geometry : angle 0.55200 (10471) SS BOND : bond 0.00210 ( 13) SS BOND : angle 1.16443 ( 26) hydrogen bonds : bond 0.04132 ( 280) hydrogen bonds : angle 4.48341 ( 771) link_NAG-ASN : bond 0.00726 ( 15) link_NAG-ASN : angle 3.54606 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 99 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7446 (mm-30) REVERT: B 111 LYS cc_start: 0.7734 (ttmm) cc_final: 0.7094 (ttpp) REVERT: B 115 MET cc_start: 0.8535 (tpt) cc_final: 0.8242 (tpt) REVERT: B 122 SER cc_start: 0.8289 (t) cc_final: 0.8014 (t) REVERT: B 135 GLN cc_start: 0.7835 (tp40) cc_final: 0.7550 (mm-40) REVERT: B 146 SER cc_start: 0.8307 (m) cc_final: 0.7999 (t) REVERT: B 151 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7816 (mmt) REVERT: B 155 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.7881 (ttpt) REVERT: B 178 GLU cc_start: 0.7944 (tt0) cc_final: 0.7685 (mp0) REVERT: B 191 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7544 (ttt180) REVERT: B 220 ARG cc_start: 0.7934 (mtp85) cc_final: 0.7150 (mtt90) REVERT: B 221 GLN cc_start: 0.8280 (mm-40) cc_final: 0.6848 (pp30) REVERT: B 409 GLN cc_start: 0.8029 (mt0) cc_final: 0.7777 (mm110) REVERT: B 452 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8127 (mtt) REVERT: B 469 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.7101 (m170) REVERT: B 486 ARG cc_start: 0.7629 (tpt90) cc_final: 0.7316 (tpt170) REVERT: A 58 MET cc_start: 0.5277 (ttm) cc_final: 0.4548 (ttt) REVERT: A 93 LEU cc_start: 0.8437 (mt) cc_final: 0.8223 (mt) REVERT: A 121 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8038 (mt) REVERT: A 126 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7837 (tp30) REVERT: A 221 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7496 (tp40) REVERT: A 254 ARG cc_start: 0.7404 (ttm-80) cc_final: 0.7186 (ttm-80) REVERT: A 477 ASN cc_start: 0.7504 (t0) cc_final: 0.7165 (t0) REVERT: A 493 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8346 (t) REVERT: A 506 LYS cc_start: 0.5456 (pttp) cc_final: 0.5163 (ptpt) outliers start: 43 outliers final: 25 residues processed: 130 average time/residue: 0.5534 time to fit residues: 76.1194 Evaluate side-chains 124 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 88 optimal weight: 0.0770 chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 488 HIS A 117 HIS A 255 GLN A 460 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.166234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.128393 restraints weight = 7687.004| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.23 r_work: 0.3212 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7727 Z= 0.136 Angle : 0.564 12.220 10542 Z= 0.272 Chirality : 0.046 0.357 1217 Planarity : 0.004 0.029 1320 Dihedral : 6.587 58.553 1307 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 5.19 % Allowed : 23.98 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.28), residues: 905 helix: 1.45 (0.29), residues: 334 sheet: -1.05 (0.40), residues: 149 loop : 0.11 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 254 TYR 0.024 0.002 TYR B 394 PHE 0.014 0.001 PHE A 338 TRP 0.011 0.001 TRP A 455 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7699) covalent geometry : angle 0.52107 (10471) SS BOND : bond 0.00199 ( 13) SS BOND : angle 1.18677 ( 26) hydrogen bonds : bond 0.03822 ( 280) hydrogen bonds : angle 4.28177 ( 771) link_NAG-ASN : bond 0.00753 ( 15) link_NAG-ASN : angle 3.24070 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7452 (mm-30) REVERT: B 111 LYS cc_start: 0.7691 (ttmm) cc_final: 0.7053 (ttpp) REVERT: B 122 SER cc_start: 0.8335 (t) cc_final: 0.8033 (t) REVERT: B 135 GLN cc_start: 0.7821 (tp40) cc_final: 0.7493 (mm-40) REVERT: B 146 SER cc_start: 0.8162 (m) cc_final: 0.7887 (t) REVERT: B 151 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7161 (mpp) REVERT: B 155 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7875 (ttpt) REVERT: B 178 GLU cc_start: 0.7949 (tt0) cc_final: 0.7710 (mp0) REVERT: B 191 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7563 (ttt180) REVERT: B 220 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7130 (mtt90) REVERT: B 221 GLN cc_start: 0.8247 (mm-40) cc_final: 0.6819 (pp30) REVERT: B 409 GLN cc_start: 0.8014 (mt0) cc_final: 0.7762 (mm110) REVERT: B 469 HIS cc_start: 0.7365 (OUTLIER) cc_final: 0.7065 (m170) REVERT: B 486 ARG cc_start: 0.7648 (tpt90) cc_final: 0.7330 (tpt170) REVERT: A 58 MET cc_start: 0.5191 (ttm) cc_final: 0.4555 (ttt) REVERT: A 126 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7859 (tp30) REVERT: A 221 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7492 (tp40) REVERT: A 365 ASN cc_start: 0.4649 (OUTLIER) cc_final: 0.4427 (m-40) REVERT: A 422 GLU cc_start: 0.8274 (tt0) cc_final: 0.7979 (tt0) REVERT: A 476 LYS cc_start: 0.8128 (ptmm) cc_final: 0.7791 (ptmt) REVERT: A 477 ASN cc_start: 0.7349 (t0) cc_final: 0.7095 (t0) REVERT: A 493 SER cc_start: 0.8554 (OUTLIER) cc_final: 0.8331 (t) REVERT: A 506 LYS cc_start: 0.5523 (pttp) cc_final: 0.5226 (ptpt) outliers start: 42 outliers final: 27 residues processed: 130 average time/residue: 0.5782 time to fit residues: 79.5556 Evaluate side-chains 123 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 51 optimal weight: 0.0000 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 255 GLN A 460 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.166423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128827 restraints weight = 7674.223| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.21 r_work: 0.3217 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7727 Z= 0.123 Angle : 0.550 11.553 10542 Z= 0.264 Chirality : 0.046 0.376 1217 Planarity : 0.003 0.028 1320 Dihedral : 6.514 58.601 1307 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 5.19 % Allowed : 23.98 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.29), residues: 905 helix: 1.62 (0.29), residues: 330 sheet: -1.03 (0.39), residues: 159 loop : 0.34 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 254 TYR 0.022 0.001 TYR B 394 PHE 0.013 0.001 PHE A 338 TRP 0.010 0.001 TRP A 455 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7699) covalent geometry : angle 0.50897 (10471) SS BOND : bond 0.00162 ( 13) SS BOND : angle 0.86857 ( 26) hydrogen bonds : bond 0.03622 ( 280) hydrogen bonds : angle 4.20046 ( 771) link_NAG-ASN : bond 0.00696 ( 15) link_NAG-ASN : angle 3.17809 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 95 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7387 (mm-30) REVERT: B 111 LYS cc_start: 0.7649 (ttmm) cc_final: 0.6955 (ttpp) REVERT: B 122 SER cc_start: 0.8402 (t) cc_final: 0.8105 (t) REVERT: B 135 GLN cc_start: 0.7829 (tp40) cc_final: 0.7509 (mm-40) REVERT: B 146 SER cc_start: 0.7954 (m) cc_final: 0.7709 (t) REVERT: B 155 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7875 (ttpt) REVERT: B 178 GLU cc_start: 0.7925 (tt0) cc_final: 0.7707 (mp0) REVERT: B 191 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7522 (ttt180) REVERT: B 220 ARG cc_start: 0.7824 (mtp85) cc_final: 0.7216 (mtt90) REVERT: B 221 GLN cc_start: 0.8236 (mm-40) cc_final: 0.6817 (pp30) REVERT: B 315 MET cc_start: 0.8177 (tpt) cc_final: 0.7764 (tpt) REVERT: B 409 GLN cc_start: 0.8019 (mt0) cc_final: 0.7763 (mm110) REVERT: B 452 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8028 (mtt) REVERT: B 455 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7865 (t0) REVERT: B 457 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7100 (mtpt) REVERT: B 469 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.7044 (m170) REVERT: B 486 ARG cc_start: 0.7637 (tpt90) cc_final: 0.7321 (tpt170) REVERT: A 58 MET cc_start: 0.5151 (ttm) cc_final: 0.4560 (ttt) REVERT: A 126 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7835 (tp30) REVERT: A 221 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7492 (tp40) REVERT: A 422 GLU cc_start: 0.8261 (tt0) cc_final: 0.7971 (tt0) REVERT: A 476 LYS cc_start: 0.8059 (ptmm) cc_final: 0.7767 (ptmt) REVERT: A 477 ASN cc_start: 0.7223 (t0) cc_final: 0.6975 (t0) REVERT: A 479 GLN cc_start: 0.7193 (mt0) cc_final: 0.6788 (mm-40) REVERT: A 493 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8312 (t) REVERT: A 506 LYS cc_start: 0.5542 (pttp) cc_final: 0.5244 (ptpt) outliers start: 42 outliers final: 25 residues processed: 123 average time/residue: 0.5085 time to fit residues: 66.4809 Evaluate side-chains 124 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 67 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.0170 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.163966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.126011 restraints weight = 7722.935| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.22 r_work: 0.3179 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7727 Z= 0.174 Angle : 0.597 11.193 10542 Z= 0.289 Chirality : 0.048 0.376 1217 Planarity : 0.004 0.031 1320 Dihedral : 6.679 59.706 1307 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 5.32 % Allowed : 24.35 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.28), residues: 905 helix: 1.41 (0.29), residues: 333 sheet: -1.00 (0.40), residues: 152 loop : 0.21 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 254 TYR 0.027 0.002 TYR B 394 PHE 0.016 0.002 PHE A 338 TRP 0.013 0.002 TRP A 455 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 7699) covalent geometry : angle 0.55910 (10471) SS BOND : bond 0.00237 ( 13) SS BOND : angle 1.27705 ( 26) hydrogen bonds : bond 0.04149 ( 280) hydrogen bonds : angle 4.35934 ( 771) link_NAG-ASN : bond 0.00712 ( 15) link_NAG-ASN : angle 3.12091 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7407 (mm-30) REVERT: B 111 LYS cc_start: 0.7740 (ttmm) cc_final: 0.7089 (ttpp) REVERT: B 122 SER cc_start: 0.8392 (t) cc_final: 0.8111 (t) REVERT: B 135 GLN cc_start: 0.7824 (tp40) cc_final: 0.7540 (mm-40) REVERT: B 146 SER cc_start: 0.8024 (m) cc_final: 0.7802 (t) REVERT: B 151 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7146 (mpp) REVERT: B 155 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7866 (ttpt) REVERT: B 178 GLU cc_start: 0.7965 (tt0) cc_final: 0.7734 (mp0) REVERT: B 191 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7551 (ttt180) REVERT: B 220 ARG cc_start: 0.7891 (mtp85) cc_final: 0.7202 (mtm-85) REVERT: B 221 GLN cc_start: 0.8245 (mm-40) cc_final: 0.6845 (pp30) REVERT: B 315 MET cc_start: 0.8213 (tpt) cc_final: 0.7915 (tpt) REVERT: B 409 GLN cc_start: 0.8072 (mt0) cc_final: 0.7791 (mm110) REVERT: B 452 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8103 (mtt) REVERT: B 455 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7925 (t0) REVERT: B 457 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7115 (mtpt) REVERT: B 469 HIS cc_start: 0.7451 (OUTLIER) cc_final: 0.7123 (m170) REVERT: B 486 ARG cc_start: 0.7670 (tpt90) cc_final: 0.7341 (tpt170) REVERT: A 58 MET cc_start: 0.5247 (OUTLIER) cc_final: 0.4616 (ttt) REVERT: A 126 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7873 (tp30) REVERT: A 221 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7500 (tp40) REVERT: A 422 GLU cc_start: 0.8297 (tt0) cc_final: 0.7995 (tt0) REVERT: A 476 LYS cc_start: 0.8144 (ptmm) cc_final: 0.7811 (ptmt) REVERT: A 477 ASN cc_start: 0.7263 (t0) cc_final: 0.7019 (t0) REVERT: A 493 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.7919 (m) REVERT: A 506 LYS cc_start: 0.5500 (pttp) cc_final: 0.5157 (ptpt) outliers start: 43 outliers final: 28 residues processed: 129 average time/residue: 0.5375 time to fit residues: 73.8008 Evaluate side-chains 130 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.165465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.127768 restraints weight = 7738.567| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.22 r_work: 0.3203 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7727 Z= 0.136 Angle : 0.559 11.000 10542 Z= 0.270 Chirality : 0.046 0.371 1217 Planarity : 0.004 0.030 1320 Dihedral : 6.524 58.626 1307 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 5.32 % Allowed : 24.60 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.29), residues: 905 helix: 1.63 (0.29), residues: 330 sheet: -0.98 (0.40), residues: 152 loop : 0.34 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.023 0.002 TYR B 394 PHE 0.014 0.001 PHE A 338 TRP 0.010 0.001 TRP A 455 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7699) covalent geometry : angle 0.52427 (10471) SS BOND : bond 0.00185 ( 13) SS BOND : angle 1.01309 ( 26) hydrogen bonds : bond 0.03734 ( 280) hydrogen bonds : angle 4.24394 ( 771) link_NAG-ASN : bond 0.00668 ( 15) link_NAG-ASN : angle 2.93489 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 100 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7419 (mm-30) REVERT: B 111 LYS cc_start: 0.7671 (ttmm) cc_final: 0.7023 (ttpp) REVERT: B 122 SER cc_start: 0.8414 (t) cc_final: 0.8138 (t) REVERT: B 135 GLN cc_start: 0.7801 (tp40) cc_final: 0.7486 (mm-40) REVERT: B 146 SER cc_start: 0.7936 (m) cc_final: 0.7710 (t) REVERT: B 151 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7095 (mpp) REVERT: B 155 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7852 (ttpt) REVERT: B 178 GLU cc_start: 0.7968 (tt0) cc_final: 0.7692 (mp0) REVERT: B 220 ARG cc_start: 0.7856 (mtp85) cc_final: 0.7255 (mtt90) REVERT: B 221 GLN cc_start: 0.8218 (mm-40) cc_final: 0.6810 (pp30) REVERT: B 315 MET cc_start: 0.8214 (tpt) cc_final: 0.7932 (tpt) REVERT: B 409 GLN cc_start: 0.8044 (mt0) cc_final: 0.7777 (mm110) REVERT: B 452 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8035 (mtt) REVERT: B 455 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7920 (t0) REVERT: B 457 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7093 (mtpt) REVERT: B 469 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.7069 (m170) REVERT: B 483 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6835 (tp) REVERT: B 486 ARG cc_start: 0.7654 (tpt90) cc_final: 0.7328 (tpt170) REVERT: A 58 MET cc_start: 0.5210 (OUTLIER) cc_final: 0.4598 (ttt) REVERT: A 126 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7822 (tp30) REVERT: A 221 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7492 (tp40) REVERT: A 422 GLU cc_start: 0.8278 (tt0) cc_final: 0.7994 (tt0) REVERT: A 476 LYS cc_start: 0.8117 (ptmm) cc_final: 0.7815 (ptmt) REVERT: A 477 ASN cc_start: 0.7237 (t0) cc_final: 0.6927 (m-40) REVERT: A 479 GLN cc_start: 0.7207 (mt0) cc_final: 0.6759 (mm-40) REVERT: A 493 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8310 (t) REVERT: A 506 LYS cc_start: 0.5440 (OUTLIER) cc_final: 0.5084 (ptpt) outliers start: 43 outliers final: 26 residues processed: 130 average time/residue: 0.5237 time to fit residues: 72.5294 Evaluate side-chains 130 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 64 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 0.0980 chunk 87 optimal weight: 0.7980 chunk 43 optimal weight: 0.0570 chunk 72 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.168022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.130999 restraints weight = 7652.438| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.20 r_work: 0.3245 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7727 Z= 0.106 Angle : 0.527 11.132 10542 Z= 0.254 Chirality : 0.045 0.363 1217 Planarity : 0.003 0.028 1320 Dihedral : 6.319 56.481 1306 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 4.45 % Allowed : 25.71 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.29), residues: 905 helix: 1.86 (0.29), residues: 330 sheet: -0.95 (0.40), residues: 159 loop : 0.47 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.020 0.001 TYR B 394 PHE 0.012 0.001 PHE A 338 TRP 0.011 0.001 TRP A 205 HIS 0.003 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7699) covalent geometry : angle 0.49577 (10471) SS BOND : bond 0.00190 ( 13) SS BOND : angle 0.77825 ( 26) hydrogen bonds : bond 0.03323 ( 280) hydrogen bonds : angle 4.09311 ( 771) link_NAG-ASN : bond 0.00637 ( 15) link_NAG-ASN : angle 2.72303 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7382 (mm-30) REVERT: B 111 LYS cc_start: 0.7609 (ttmm) cc_final: 0.6913 (ttpp) REVERT: B 122 SER cc_start: 0.8414 (t) cc_final: 0.8161 (t) REVERT: B 135 GLN cc_start: 0.7780 (tp40) cc_final: 0.7455 (mm-40) REVERT: B 146 SER cc_start: 0.7744 (m) cc_final: 0.7541 (t) REVERT: B 155 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7884 (ttpt) REVERT: B 220 ARG cc_start: 0.7775 (mtp85) cc_final: 0.7188 (mtt90) REVERT: B 221 GLN cc_start: 0.8182 (mm-40) cc_final: 0.6812 (pp30) REVERT: B 409 GLN cc_start: 0.8012 (mt0) cc_final: 0.7759 (mm110) REVERT: B 452 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8036 (mtt) REVERT: B 455 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7942 (t0) REVERT: B 457 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7115 (mtpt) REVERT: B 469 HIS cc_start: 0.7161 (OUTLIER) cc_final: 0.6929 (m170) REVERT: B 483 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6833 (tp) REVERT: B 486 ARG cc_start: 0.7643 (tpt90) cc_final: 0.7323 (tpt170) REVERT: A 58 MET cc_start: 0.5102 (OUTLIER) cc_final: 0.4563 (ttt) REVERT: A 126 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7807 (tp30) REVERT: A 221 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7445 (tp40) REVERT: A 422 GLU cc_start: 0.8139 (tt0) cc_final: 0.7894 (tt0) REVERT: A 477 ASN cc_start: 0.7090 (t0) cc_final: 0.6830 (m-40) REVERT: A 479 GLN cc_start: 0.7185 (mt0) cc_final: 0.6746 (mm-40) REVERT: A 493 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.7757 (t) REVERT: A 506 LYS cc_start: 0.5460 (OUTLIER) cc_final: 0.5091 (ptpt) outliers start: 36 outliers final: 20 residues processed: 126 average time/residue: 0.5307 time to fit residues: 70.9963 Evaluate side-chains 126 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 506 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 11 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.165165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.127746 restraints weight = 7663.965| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.19 r_work: 0.3198 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7727 Z= 0.146 Angle : 0.572 11.459 10542 Z= 0.278 Chirality : 0.047 0.382 1217 Planarity : 0.004 0.056 1320 Dihedral : 6.457 59.200 1306 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 4.45 % Allowed : 25.96 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.29), residues: 905 helix: 1.77 (0.29), residues: 329 sheet: -1.01 (0.39), residues: 162 loop : 0.48 (0.33), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 317 TYR 0.024 0.002 TYR B 394 PHE 0.014 0.001 PHE A 338 TRP 0.010 0.001 TRP A 455 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7699) covalent geometry : angle 0.54219 (10471) SS BOND : bond 0.00171 ( 13) SS BOND : angle 1.21036 ( 26) hydrogen bonds : bond 0.03786 ( 280) hydrogen bonds : angle 4.22012 ( 771) link_NAG-ASN : bond 0.00658 ( 15) link_NAG-ASN : angle 2.73070 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7517 (mm-30) REVERT: B 111 LYS cc_start: 0.7779 (ttmm) cc_final: 0.7058 (ttpp) REVERT: B 122 SER cc_start: 0.8357 (t) cc_final: 0.8063 (t) REVERT: B 135 GLN cc_start: 0.7928 (tp40) cc_final: 0.7645 (mm-40) REVERT: B 146 SER cc_start: 0.7933 (m) cc_final: 0.7699 (t) REVERT: B 151 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7213 (mpp) REVERT: B 155 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.7916 (ttpt) REVERT: B 220 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7249 (mtt90) REVERT: B 221 GLN cc_start: 0.8313 (mm-40) cc_final: 0.6858 (pp30) REVERT: B 409 GLN cc_start: 0.8135 (mt0) cc_final: 0.7812 (mm110) REVERT: B 452 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8127 (mtt) REVERT: B 455 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8195 (t0) REVERT: B 457 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7186 (mtpt) REVERT: B 469 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.7230 (m170) REVERT: B 486 ARG cc_start: 0.7803 (tpt90) cc_final: 0.7440 (tpt170) REVERT: A 58 MET cc_start: 0.4966 (OUTLIER) cc_final: 0.4375 (ttt) REVERT: A 126 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7925 (tp30) REVERT: A 221 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7553 (tp40) REVERT: A 256 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6831 (tpt-90) REVERT: A 422 GLU cc_start: 0.8391 (tt0) cc_final: 0.8114 (tt0) REVERT: A 476 LYS cc_start: 0.8171 (ptmm) cc_final: 0.7858 (ptmt) REVERT: A 477 ASN cc_start: 0.7301 (t0) cc_final: 0.7010 (m-40) REVERT: A 479 GLN cc_start: 0.7412 (mt0) cc_final: 0.6825 (mm-40) REVERT: A 493 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8348 (t) REVERT: A 506 LYS cc_start: 0.5578 (OUTLIER) cc_final: 0.5125 (ptpt) outliers start: 36 outliers final: 23 residues processed: 123 average time/residue: 0.5450 time to fit residues: 70.9948 Evaluate side-chains 130 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 457 LYS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 506 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 14 optimal weight: 0.1980 chunk 81 optimal weight: 0.0570 chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.166596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129262 restraints weight = 7670.253| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.21 r_work: 0.3231 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7727 Z= 0.123 Angle : 0.544 11.308 10542 Z= 0.264 Chirality : 0.046 0.380 1217 Planarity : 0.004 0.032 1320 Dihedral : 6.350 57.534 1306 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 4.33 % Allowed : 25.83 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.29), residues: 905 helix: 1.89 (0.29), residues: 327 sheet: -0.99 (0.39), residues: 159 loop : 0.50 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.023 0.002 TYR B 394 PHE 0.020 0.001 PHE B 65 TRP 0.009 0.001 TRP A 455 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7699) covalent geometry : angle 0.51569 (10471) SS BOND : bond 0.00170 ( 13) SS BOND : angle 0.98296 ( 26) hydrogen bonds : bond 0.03539 ( 280) hydrogen bonds : angle 4.16972 ( 771) link_NAG-ASN : bond 0.00629 ( 15) link_NAG-ASN : angle 2.63378 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2559.67 seconds wall clock time: 44 minutes 24.68 seconds (2664.68 seconds total)