Starting phenix.real_space_refine on Thu Mar 13 18:31:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hf5_34713/03_2025/8hf5_34713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hf5_34713/03_2025/8hf5_34713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hf5_34713/03_2025/8hf5_34713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hf5_34713/03_2025/8hf5_34713.map" model { file = "/net/cci-nas-00/data/ceres_data/8hf5_34713/03_2025/8hf5_34713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hf5_34713/03_2025/8hf5_34713.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 64 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 5732 2.51 5 N 1462 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "B" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.76, per 1000 atoms: 0.65 Number of scatterers: 8918 At special positions: 0 Unit cell: (81.51, 80.652, 143.286, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 6 15.00 Mg 2 11.99 O 1686 8.00 N 1462 7.00 C 5732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 4 sheets defined 66.7% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 157 through 164 removed outlier: 3.776A pdb=" N LEU A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 195 removed outlier: 3.561A pdb=" N LEU A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 250 removed outlier: 4.201A pdb=" N LEU A 205 " --> pdb=" O MET A 201 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 removed outlier: 4.085A pdb=" N ARG A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 289 removed outlier: 3.903A pdb=" N ILE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.876A pdb=" N ILE A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.773A pdb=" N ILE A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 320 " --> pdb=" O PRO A 316 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.522A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 362 through 417 removed outlier: 4.064A pdb=" N ARG A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 443 removed outlier: 3.870A pdb=" N VAL A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 444 through 464 removed outlier: 4.362A pdb=" N GLU A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.683A pdb=" N VAL A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 559 Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 588 through 598 Processing helix chain 'A' and resid 623 through 638 removed outlier: 4.004A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 removed outlier: 4.230A pdb=" N ALA A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.607A pdb=" N GLU A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 678 through 683' Processing helix chain 'A' and resid 700 through 706 removed outlier: 3.530A pdb=" N LEU A 704 " --> pdb=" O LYS A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 717 Processing helix chain 'B' and resid 157 through 162 Processing helix chain 'B' and resid 168 through 194 removed outlier: 3.628A pdb=" N TYR B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 196 No H-bonds generated for 'chain 'B' and resid 195 through 196' Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 200 through 250 removed outlier: 3.569A pdb=" N ALA B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 274 removed outlier: 3.820A pdb=" N ILE B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 278 through 304 removed outlier: 5.630A pdb=" N SER B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N THR B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 314 through 325 removed outlier: 4.096A pdb=" N VAL B 320 " --> pdb=" O PRO B 316 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 325 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 353 removed outlier: 4.159A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 removed outlier: 3.676A pdb=" N ILE B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 387 removed outlier: 3.970A pdb=" N TYR B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 416 Processing helix chain 'B' and resid 420 through 431 removed outlier: 3.572A pdb=" N LEU B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 444 through 463 removed outlier: 4.272A pdb=" N VAL B 453 " --> pdb=" O GLN B 449 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 529 removed outlier: 3.545A pdb=" N MET B 529 " --> pdb=" O THR B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 559 Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 587 through 598 removed outlier: 3.552A pdb=" N ILE B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 623 through 638 removed outlier: 3.683A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 666 removed outlier: 3.595A pdb=" N ILE B 665 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 683 removed outlier: 4.216A pdb=" N ALA B 681 " --> pdb=" O ARG B 677 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG B 683 " --> pdb=" O THR B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 708 removed outlier: 3.828A pdb=" N GLY B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 717 Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 503 removed outlier: 3.803A pdb=" N LEU A 500 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL A 489 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 489 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLN A 538 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 563 removed outlier: 6.608A pdb=" N ASN A 561 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASP A 646 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU A 563 " --> pdb=" O ASP A 646 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 643 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ILE A 674 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 645 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 513 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU A 697 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 500 through 506 removed outlier: 6.937A pdb=" N SER B 501 " --> pdb=" O HIS B 490 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N HIS B 490 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE B 503 " --> pdb=" O GLN B 488 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 505 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL B 489 " --> pdb=" O GLN B 538 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN B 538 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 560 through 562 removed outlier: 6.577A pdb=" N ASN B 561 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL B 513 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS B 512 " --> pdb=" O LYS B 686 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL B 688 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ALA B 514 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU B 690 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 516 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU B 697 " --> pdb=" O VAL B 689 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 1952 1.33 - 1.47: 2924 1.47 - 1.61: 4116 1.61 - 1.76: 0 1.76 - 1.90: 58 Bond restraints: 9050 Sorted by residual: bond pdb=" CA GLN A 226 " pdb=" C GLN A 226 " ideal model delta sigma weight residual 1.523 1.451 0.072 1.30e-02 5.92e+03 3.08e+01 bond pdb=" CA LEU B 645 " pdb=" C LEU B 645 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.23e-02 6.61e+03 2.61e+01 bond pdb=" CA GLN A 612 " pdb=" C GLN A 612 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.34e-02 5.57e+03 2.50e+01 bond pdb=" CA LEU A 222 " pdb=" C LEU A 222 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.30e-02 5.92e+03 2.43e+01 bond pdb=" CA GLN A 235 " pdb=" C GLN A 235 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.30e-02 5.92e+03 2.43e+01 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 11678 2.88 - 5.76: 496 5.76 - 8.64: 72 8.64 - 11.52: 23 11.52 - 14.40: 9 Bond angle restraints: 12278 Sorted by residual: angle pdb=" N ARG A 202 " pdb=" CA ARG A 202 " pdb=" C ARG A 202 " ideal model delta sigma weight residual 113.28 99.73 13.55 1.22e+00 6.72e-01 1.23e+02 angle pdb=" N ALA B 169 " pdb=" CA ALA B 169 " pdb=" C ALA B 169 " ideal model delta sigma weight residual 111.28 121.97 -10.69 1.09e+00 8.42e-01 9.61e+01 angle pdb=" N PRO A 608 " pdb=" CA PRO A 608 " pdb=" C PRO A 608 " ideal model delta sigma weight residual 114.18 100.76 13.42 1.39e+00 5.18e-01 9.32e+01 angle pdb=" N TYR A 196 " pdb=" CA TYR A 196 " pdb=" C TYR A 196 " ideal model delta sigma weight residual 112.58 124.06 -11.48 1.22e+00 6.72e-01 8.86e+01 angle pdb=" N LYS B 163 " pdb=" CA LYS B 163 " pdb=" C LYS B 163 " ideal model delta sigma weight residual 114.12 101.16 12.96 1.39e+00 5.18e-01 8.69e+01 ... (remaining 12273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.53: 5094 22.53 - 45.05: 343 45.05 - 67.58: 45 67.58 - 90.11: 6 90.11 - 112.63: 2 Dihedral angle restraints: 5490 sinusoidal: 2196 harmonic: 3294 Sorted by residual: dihedral pdb=" CA GLU A 469 " pdb=" C GLU A 469 " pdb=" N GLU A 470 " pdb=" CA GLU A 470 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" C TYR A 216 " pdb=" N TYR A 216 " pdb=" CA TYR A 216 " pdb=" CB TYR A 216 " ideal model delta harmonic sigma weight residual -122.60 -135.72 13.12 0 2.50e+00 1.60e-01 2.76e+01 dihedral pdb=" C GLN A 200 " pdb=" N GLN A 200 " pdb=" CA GLN A 200 " pdb=" CB GLN A 200 " ideal model delta harmonic sigma weight residual -122.60 -135.31 12.71 0 2.50e+00 1.60e-01 2.58e+01 ... (remaining 5487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 1355 0.142 - 0.285: 108 0.285 - 0.427: 26 0.427 - 0.569: 9 0.569 - 0.711: 4 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CB ILE A 600 " pdb=" CA ILE A 600 " pdb=" CG1 ILE A 600 " pdb=" CG2 ILE A 600 " both_signs ideal model delta sigma weight residual False 2.64 1.93 0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CA TYR A 216 " pdb=" N TYR A 216 " pdb=" C TYR A 216 " pdb=" CB TYR A 216 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.26e+00 chirality pdb=" CA GLN A 200 " pdb=" N GLN A 200 " pdb=" C GLN A 200 " pdb=" CB GLN A 200 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.13e+00 ... (remaining 1499 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 239 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C ILE B 239 " -0.062 2.00e-02 2.50e+03 pdb=" O ILE B 239 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP B 240 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 610 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.87e+00 pdb=" C ASN B 610 " 0.049 2.00e-02 2.50e+03 pdb=" O ASN B 610 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR B 611 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 286 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C ILE B 286 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE B 286 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE B 287 " -0.014 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 158 2.63 - 3.20: 7833 3.20 - 3.77: 13204 3.77 - 4.33: 17427 4.33 - 4.90: 28304 Nonbonded interactions: 66926 Sorted by model distance: nonbonded pdb=" O2B AGS A 801 " pdb="MG MG A 802 " model vdw 2.063 2.170 nonbonded pdb=" O2B AGS B 801 " pdb="MG MG B 802 " model vdw 2.064 2.170 nonbonded pdb=" OG1 THR A 524 " pdb="MG MG A 802 " model vdw 2.145 2.170 nonbonded pdb=" O2G AGS B 801 " pdb="MG MG B 802 " model vdw 2.170 2.170 nonbonded pdb=" O2G AGS A 801 " pdb="MG MG A 802 " model vdw 2.171 2.170 ... (remaining 66921 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.480 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.079 9050 Z= 0.699 Angle : 1.384 14.404 12278 Z= 0.848 Chirality : 0.099 0.711 1502 Planarity : 0.007 0.057 1522 Dihedral : 14.892 112.635 3366 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.44 % Favored : 93.94 % Rotamer: Outliers : 3.74 % Allowed : 3.13 % Favored : 93.13 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.23), residues: 1122 helix: -0.60 (0.18), residues: 694 sheet: -0.01 (0.67), residues: 70 loop : -2.43 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 408 HIS 0.010 0.002 HIS A 399 PHE 0.034 0.003 PHE A 468 TYR 0.021 0.002 TYR B 228 ARG 0.008 0.001 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 1.032 Fit side-chains REVERT: A 173 LEU cc_start: 0.8835 (tp) cc_final: 0.8594 (tm) REVERT: A 201 MET cc_start: 0.7964 (mmm) cc_final: 0.7688 (mpp) REVERT: A 663 ASN cc_start: 0.9070 (m-40) cc_final: 0.8623 (m-40) REVERT: A 677 ARG cc_start: 0.8107 (mmp-170) cc_final: 0.7854 (mmp-170) REVERT: A 710 PHE cc_start: 0.8632 (t80) cc_final: 0.8177 (t80) REVERT: B 164 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8412 (mp10) REVERT: B 471 LYS cc_start: 0.8417 (mmpt) cc_final: 0.8193 (mmmt) REVERT: B 713 HIS cc_start: 0.8998 (t70) cc_final: 0.8788 (t70) outliers start: 37 outliers final: 14 residues processed: 152 average time/residue: 0.9354 time to fit residues: 155.3471 Evaluate side-chains 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 199 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.0070 chunk 101 optimal weight: 6.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 226 GLN B 164 GLN B 423 GLN B 490 HIS B 610 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.100520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.075261 restraints weight = 17658.238| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.85 r_work: 0.3103 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9050 Z= 0.210 Angle : 0.669 8.169 12278 Z= 0.348 Chirality : 0.043 0.419 1502 Planarity : 0.004 0.044 1522 Dihedral : 9.749 131.450 1281 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 4.34 % Allowed : 11.82 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1122 helix: 0.63 (0.19), residues: 706 sheet: -0.24 (0.65), residues: 70 loop : -2.06 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 408 HIS 0.003 0.001 HIS B 399 PHE 0.013 0.001 PHE A 382 TYR 0.024 0.001 TYR A 196 ARG 0.006 0.001 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 100 time to evaluate : 1.086 Fit side-chains REVERT: A 201 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7586 (mpt) REVERT: A 203 SER cc_start: 0.7720 (OUTLIER) cc_final: 0.7491 (m) REVERT: A 239 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8690 (tt) REVERT: A 610 ASN cc_start: 0.7912 (m-40) cc_final: 0.7102 (t0) REVERT: A 663 ASN cc_start: 0.9138 (m-40) cc_final: 0.8746 (m-40) REVERT: A 677 ARG cc_start: 0.8326 (mmp-170) cc_final: 0.7931 (mmp-170) REVERT: A 710 PHE cc_start: 0.8566 (t80) cc_final: 0.8228 (t80) REVERT: B 207 ILE cc_start: 0.7391 (mm) cc_final: 0.7116 (mt) REVERT: B 337 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8576 (mtt) REVERT: B 409 MET cc_start: 0.8286 (tmm) cc_final: 0.7880 (tmm) REVERT: B 471 LYS cc_start: 0.8177 (mmpt) cc_final: 0.7976 (mmmt) REVERT: B 518 ILE cc_start: 0.8731 (tt) cc_final: 0.8422 (pp) outliers start: 43 outliers final: 13 residues processed: 132 average time/residue: 0.7338 time to fit residues: 107.6142 Evaluate side-chains 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 521 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.096372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.070575 restraints weight = 18176.138| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.87 r_work: 0.3016 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9050 Z= 0.358 Angle : 0.679 7.259 12278 Z= 0.359 Chirality : 0.045 0.366 1502 Planarity : 0.004 0.045 1522 Dihedral : 9.046 134.481 1268 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.97 % Favored : 93.94 % Rotamer: Outliers : 4.34 % Allowed : 16.06 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1122 helix: 1.16 (0.20), residues: 702 sheet: -0.45 (0.64), residues: 70 loop : -1.91 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 408 HIS 0.004 0.001 HIS B 713 PHE 0.017 0.002 PHE A 382 TYR 0.011 0.001 TYR A 433 ARG 0.007 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 85 time to evaluate : 1.157 Fit side-chains REVERT: A 201 MET cc_start: 0.7890 (mmm) cc_final: 0.7624 (mpm) REVERT: A 203 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.7643 (m) REVERT: A 239 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8746 (tt) REVERT: A 610 ASN cc_start: 0.8028 (m-40) cc_final: 0.7320 (t0) REVERT: A 663 ASN cc_start: 0.9179 (m-40) cc_final: 0.8822 (m-40) REVERT: A 677 ARG cc_start: 0.8418 (mmp-170) cc_final: 0.8190 (mmt180) REVERT: A 710 PHE cc_start: 0.8716 (t80) cc_final: 0.8414 (t80) REVERT: B 207 ILE cc_start: 0.7191 (mm) cc_final: 0.6955 (mp) REVERT: B 409 MET cc_start: 0.8319 (tmm) cc_final: 0.8014 (tmm) REVERT: B 471 LYS cc_start: 0.8216 (mmpt) cc_final: 0.7957 (mmmt) REVERT: B 518 ILE cc_start: 0.8930 (tt) cc_final: 0.8649 (pp) outliers start: 43 outliers final: 25 residues processed: 121 average time/residue: 0.8736 time to fit residues: 117.2970 Evaluate side-chains 107 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 521 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.100103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074547 restraints weight = 17818.209| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.87 r_work: 0.3088 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9050 Z= 0.168 Angle : 0.559 7.332 12278 Z= 0.290 Chirality : 0.040 0.306 1502 Planarity : 0.003 0.040 1522 Dihedral : 8.481 128.604 1266 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 3.64 % Allowed : 18.18 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1122 helix: 1.58 (0.20), residues: 702 sheet: -0.25 (0.66), residues: 70 loop : -1.83 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 408 HIS 0.004 0.001 HIS B 713 PHE 0.012 0.001 PHE A 308 TYR 0.007 0.001 TYR B 491 ARG 0.007 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 1.241 Fit side-chains REVERT: A 201 MET cc_start: 0.7791 (mmm) cc_final: 0.7318 (mpp) REVERT: A 227 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8142 (tt0) REVERT: A 239 ILE cc_start: 0.8687 (tt) cc_final: 0.8486 (tt) REVERT: A 309 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: A 663 ASN cc_start: 0.9144 (m-40) cc_final: 0.8751 (m-40) REVERT: A 677 ARG cc_start: 0.8461 (mmp-170) cc_final: 0.8232 (mmt180) REVERT: A 710 PHE cc_start: 0.8733 (t80) cc_final: 0.8399 (t80) REVERT: B 157 PHE cc_start: 0.4952 (m-10) cc_final: 0.4637 (m-10) REVERT: B 227 GLU cc_start: 0.8299 (tt0) cc_final: 0.7997 (tt0) REVERT: B 240 ASP cc_start: 0.8209 (t0) cc_final: 0.7932 (t0) REVERT: B 409 MET cc_start: 0.8264 (tmm) cc_final: 0.7996 (tmm) REVERT: B 471 LYS cc_start: 0.8315 (mmpt) cc_final: 0.8053 (mmmt) REVERT: B 479 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.6029 (pt) REVERT: B 518 ILE cc_start: 0.8821 (tt) cc_final: 0.8482 (pp) outliers start: 36 outliers final: 18 residues processed: 119 average time/residue: 1.0664 time to fit residues: 139.0039 Evaluate side-chains 105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 479 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.098986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.073391 restraints weight = 17857.008| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.84 r_work: 0.3064 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9050 Z= 0.214 Angle : 0.586 8.086 12278 Z= 0.300 Chirality : 0.041 0.249 1502 Planarity : 0.003 0.045 1522 Dihedral : 8.143 129.227 1260 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 4.65 % Allowed : 19.49 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1122 helix: 1.79 (0.20), residues: 698 sheet: -0.18 (0.66), residues: 70 loop : -1.71 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 408 HIS 0.002 0.001 HIS B 399 PHE 0.016 0.001 PHE A 308 TYR 0.007 0.001 TYR B 491 ARG 0.011 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 85 time to evaluate : 1.006 Fit side-chains REVERT: A 227 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8194 (tt0) REVERT: A 239 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8500 (tt) REVERT: A 309 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: A 663 ASN cc_start: 0.9167 (m-40) cc_final: 0.8797 (m-40) REVERT: A 677 ARG cc_start: 0.8450 (mmp-170) cc_final: 0.8206 (mmt180) REVERT: A 710 PHE cc_start: 0.8754 (t80) cc_final: 0.8408 (t80) REVERT: B 205 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5522 (tt) REVERT: B 227 GLU cc_start: 0.8404 (tt0) cc_final: 0.8050 (tt0) REVERT: B 409 MET cc_start: 0.8335 (tmm) cc_final: 0.8082 (tmm) REVERT: B 471 LYS cc_start: 0.8280 (mmpt) cc_final: 0.8015 (mmmt) REVERT: B 518 ILE cc_start: 0.8867 (tt) cc_final: 0.8549 (pp) outliers start: 46 outliers final: 24 residues processed: 119 average time/residue: 0.8328 time to fit residues: 109.1560 Evaluate side-chains 108 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 479 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 32 optimal weight: 0.0070 chunk 40 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 0.0030 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.3208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN B 538 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.102471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.076659 restraints weight = 17766.002| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.89 r_work: 0.3127 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9050 Z= 0.147 Angle : 0.557 8.593 12278 Z= 0.280 Chirality : 0.039 0.250 1502 Planarity : 0.003 0.038 1522 Dihedral : 8.003 125.296 1260 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 2.73 % Allowed : 21.62 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1122 helix: 1.98 (0.21), residues: 702 sheet: -0.01 (0.67), residues: 70 loop : -1.68 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 408 HIS 0.004 0.001 HIS B 713 PHE 0.011 0.001 PHE A 308 TYR 0.006 0.001 TYR A 711 ARG 0.008 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 1.019 Fit side-chains REVERT: A 227 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8082 (tt0) REVERT: A 239 ILE cc_start: 0.8556 (tt) cc_final: 0.8346 (tt) REVERT: A 309 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: A 663 ASN cc_start: 0.9156 (m-40) cc_final: 0.8779 (m-40) REVERT: A 677 ARG cc_start: 0.8467 (mmp-170) cc_final: 0.8094 (mmp-170) REVERT: A 710 PHE cc_start: 0.8793 (t80) cc_final: 0.8413 (t80) REVERT: B 205 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5590 (tt) REVERT: B 402 LEU cc_start: 0.8672 (tm) cc_final: 0.8369 (mt) REVERT: B 471 LYS cc_start: 0.8251 (mmpt) cc_final: 0.7978 (mmmt) REVERT: B 518 ILE cc_start: 0.8818 (tt) cc_final: 0.8457 (pp) outliers start: 27 outliers final: 15 residues processed: 111 average time/residue: 0.9615 time to fit residues: 117.5887 Evaluate side-chains 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.098165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.072101 restraints weight = 18390.847| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.91 r_work: 0.3040 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9050 Z= 0.296 Angle : 0.622 9.878 12278 Z= 0.318 Chirality : 0.042 0.218 1502 Planarity : 0.003 0.041 1522 Dihedral : 7.930 129.928 1256 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 3.84 % Allowed : 21.62 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1122 helix: 1.95 (0.20), residues: 696 sheet: -0.12 (0.66), residues: 70 loop : -1.71 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 408 HIS 0.005 0.001 HIS B 713 PHE 0.016 0.001 PHE A 382 TYR 0.020 0.001 TYR A 196 ARG 0.009 0.001 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 82 time to evaluate : 1.284 Fit side-chains REVERT: A 227 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8195 (tt0) REVERT: A 239 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8591 (tt) REVERT: A 309 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8023 (m-80) REVERT: A 663 ASN cc_start: 0.9190 (m-40) cc_final: 0.8852 (m-40) REVERT: A 677 ARG cc_start: 0.8468 (mmp-170) cc_final: 0.8082 (mmp-170) REVERT: A 710 PHE cc_start: 0.8869 (t80) cc_final: 0.8511 (t80) REVERT: B 205 LEU cc_start: 0.6021 (OUTLIER) cc_final: 0.5578 (tt) REVERT: B 227 GLU cc_start: 0.8439 (tt0) cc_final: 0.8158 (tt0) REVERT: B 518 ILE cc_start: 0.8888 (tt) cc_final: 0.8580 (pp) outliers start: 38 outliers final: 17 residues processed: 111 average time/residue: 1.2922 time to fit residues: 157.0120 Evaluate side-chains 102 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 705 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.100395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.074446 restraints weight = 18174.304| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.92 r_work: 0.3084 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9050 Z= 0.173 Angle : 0.592 10.434 12278 Z= 0.295 Chirality : 0.040 0.228 1502 Planarity : 0.003 0.045 1522 Dihedral : 7.856 127.069 1256 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 2.93 % Allowed : 22.32 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1122 helix: 2.03 (0.20), residues: 698 sheet: -0.01 (0.67), residues: 70 loop : -1.61 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 408 HIS 0.005 0.001 HIS B 713 PHE 0.013 0.001 PHE A 308 TYR 0.007 0.001 TYR B 491 ARG 0.009 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 1.119 Fit side-chains REVERT: A 227 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8104 (tt0) REVERT: A 309 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: A 663 ASN cc_start: 0.9175 (m-40) cc_final: 0.8802 (m-40) REVERT: A 677 ARG cc_start: 0.8482 (mmp-170) cc_final: 0.8183 (mmp-170) REVERT: A 710 PHE cc_start: 0.8844 (t80) cc_final: 0.8420 (t80) REVERT: B 205 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5467 (tt) REVERT: B 227 GLU cc_start: 0.8365 (tt0) cc_final: 0.8107 (tt0) REVERT: B 402 LEU cc_start: 0.8637 (tm) cc_final: 0.8363 (mt) REVERT: B 471 LYS cc_start: 0.8257 (mmpt) cc_final: 0.7988 (mmmt) REVERT: B 518 ILE cc_start: 0.8868 (tt) cc_final: 0.8513 (pp) REVERT: B 605 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7369 (mp0) outliers start: 29 outliers final: 19 residues processed: 106 average time/residue: 0.8721 time to fit residues: 101.5464 Evaluate side-chains 107 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 605 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 4 optimal weight: 5.9990 chunk 71 optimal weight: 0.0770 chunk 8 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.102237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076589 restraints weight = 17931.192| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.91 r_work: 0.3126 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9050 Z= 0.156 Angle : 0.587 10.221 12278 Z= 0.293 Chirality : 0.040 0.268 1502 Planarity : 0.003 0.041 1522 Dihedral : 7.764 124.947 1256 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 2.12 % Allowed : 23.74 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 1122 helix: 2.12 (0.21), residues: 702 sheet: 0.07 (0.67), residues: 70 loop : -1.54 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 408 HIS 0.005 0.001 HIS B 713 PHE 0.013 0.001 PHE A 308 TYR 0.010 0.001 TYR A 196 ARG 0.009 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.996 Fit side-chains REVERT: A 227 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8162 (tt0) REVERT: A 309 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: A 663 ASN cc_start: 0.9183 (m-40) cc_final: 0.8797 (m-40) REVERT: A 677 ARG cc_start: 0.8500 (mmp-170) cc_final: 0.8194 (mmp-170) REVERT: A 710 PHE cc_start: 0.8757 (t80) cc_final: 0.8353 (t80) REVERT: B 205 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.5367 (tt) REVERT: B 227 GLU cc_start: 0.8341 (tt0) cc_final: 0.8100 (tt0) REVERT: B 402 LEU cc_start: 0.8599 (tm) cc_final: 0.8352 (mt) REVERT: B 471 LYS cc_start: 0.8311 (mmpt) cc_final: 0.8069 (mmmt) REVERT: B 518 ILE cc_start: 0.8803 (tt) cc_final: 0.8436 (pp) REVERT: B 605 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7349 (mp0) outliers start: 21 outliers final: 14 residues processed: 101 average time/residue: 0.9500 time to fit residues: 105.3543 Evaluate side-chains 98 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 605 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 713 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.100716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074858 restraints weight = 17991.186| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.89 r_work: 0.3093 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9050 Z= 0.199 Angle : 0.596 11.283 12278 Z= 0.299 Chirality : 0.041 0.239 1502 Planarity : 0.003 0.044 1522 Dihedral : 7.806 126.859 1256 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 2.32 % Allowed : 23.64 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.27), residues: 1122 helix: 2.18 (0.21), residues: 700 sheet: -0.01 (0.67), residues: 70 loop : -1.55 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 408 HIS 0.006 0.001 HIS B 713 PHE 0.020 0.001 PHE A 308 TYR 0.008 0.001 TYR A 196 ARG 0.010 0.000 ARG B 386 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 1.115 Fit side-chains REVERT: A 227 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8084 (tt0) REVERT: A 309 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.8015 (m-10) REVERT: A 663 ASN cc_start: 0.9189 (m-40) cc_final: 0.8824 (m-40) REVERT: A 677 ARG cc_start: 0.8529 (mmp-170) cc_final: 0.8057 (mmp-170) REVERT: A 710 PHE cc_start: 0.8813 (t80) cc_final: 0.8412 (t80) REVERT: B 205 LEU cc_start: 0.5791 (OUTLIER) cc_final: 0.5332 (tt) REVERT: B 227 GLU cc_start: 0.8403 (tt0) cc_final: 0.8146 (tt0) REVERT: B 402 LEU cc_start: 0.8603 (tm) cc_final: 0.8355 (mt) REVERT: B 471 LYS cc_start: 0.8299 (mmpt) cc_final: 0.8072 (mmmt) REVERT: B 518 ILE cc_start: 0.8846 (tt) cc_final: 0.8522 (pp) REVERT: B 605 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7366 (mp0) outliers start: 23 outliers final: 16 residues processed: 98 average time/residue: 0.8532 time to fit residues: 92.1891 Evaluate side-chains 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 705 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN B 713 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.101730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.075811 restraints weight = 17971.013| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.89 r_work: 0.3111 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9050 Z= 0.171 Angle : 0.593 11.331 12278 Z= 0.294 Chirality : 0.040 0.236 1502 Planarity : 0.003 0.044 1522 Dihedral : 7.773 125.318 1256 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 2.12 % Allowed : 23.94 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.27), residues: 1122 helix: 2.22 (0.21), residues: 700 sheet: 0.04 (0.67), residues: 70 loop : -1.53 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 408 HIS 0.006 0.001 HIS B 713 PHE 0.020 0.001 PHE A 308 TYR 0.007 0.001 TYR A 196 ARG 0.010 0.000 ARG B 386 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5252.88 seconds wall clock time: 93 minutes 52.87 seconds (5632.87 seconds total)