Starting phenix.real_space_refine on Fri Nov 15 15:24:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf5_34713/11_2024/8hf5_34713.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf5_34713/11_2024/8hf5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf5_34713/11_2024/8hf5_34713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf5_34713/11_2024/8hf5_34713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf5_34713/11_2024/8hf5_34713.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf5_34713/11_2024/8hf5_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-5513/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: 5.47, per 1000 atoms: 0.61 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: 2.33 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: 0.86 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: 2.52 Time building geometry restraints manager: 2.65 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: 0.00 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.870 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.940 ------------------------------------------------------------------------------- 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 : 1.037 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: 0.9439 time to fit residues: 156.4871 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 : 1.020 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9050 Z= 0.212 Angle : 0.670 8.184 12278 Z= 0.349 Chirality : 0.043 0.420 1502 Planarity : 0.004 0.044 1522 Dihedral : 9.745 131.394 1281 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 4.44 % Allowed : 11.72 % 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 144 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 100 time to evaluate : 1.046 Fit side-chains REVERT: A 203 SER cc_start: 0.7647 (OUTLIER) cc_final: 0.7437 (m) REVERT: A 239 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8654 (tt) REVERT: A 283 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8901 (pt) REVERT: A 610 ASN cc_start: 0.7752 (m-40) cc_final: 0.6984 (t0) REVERT: A 663 ASN cc_start: 0.9082 (m-40) cc_final: 0.8685 (m-40) REVERT: A 677 ARG cc_start: 0.8030 (mmp-170) cc_final: 0.7687 (mmp-170) REVERT: A 710 PHE cc_start: 0.8517 (t80) cc_final: 0.8202 (t80) REVERT: B 207 ILE cc_start: 0.7381 (mm) cc_final: 0.7110 (mt) REVERT: B 409 MET cc_start: 0.8137 (tmm) cc_final: 0.7728 (tmm) REVERT: B 518 ILE cc_start: 0.8640 (tt) cc_final: 0.8366 (pp) outliers start: 44 outliers final: 13 residues processed: 133 average time/residue: 0.8067 time to fit residues: 118.8086 Evaluate side-chains 99 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 203 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 ILE 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 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 56 optimal weight: 10.0000 chunk 31 optimal weight: 0.0170 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 90 optimal weight: 0.3980 chunk 34 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2311 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 : 0.576 7.829 12278 Z= 0.298 Chirality : 0.041 0.349 1502 Planarity : 0.003 0.034 1522 Dihedral : 8.963 132.067 1268 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 3.43 % Allowed : 14.55 % Favored : 82.02 % 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: 0.40 (0.25), residues: 1122 helix: 1.32 (0.20), residues: 704 sheet: -0.14 (0.65), residues: 70 loop : -1.86 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 408 HIS 0.004 0.001 HIS B 713 PHE 0.012 0.001 PHE A 382 TYR 0.007 0.001 TYR A 559 ARG 0.004 0.000 ARG B 386 *********************** 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 126 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.984 Fit side-chains REVERT: A 203 SER cc_start: 0.7735 (OUTLIER) cc_final: 0.7485 (m) REVERT: A 239 ILE cc_start: 0.8633 (tt) cc_final: 0.8393 (tt) REVERT: A 309 PHE cc_start: 0.7728 (t80) cc_final: 0.7507 (m-80) REVERT: A 663 ASN cc_start: 0.9105 (m-40) cc_final: 0.8695 (m-40) REVERT: A 710 PHE cc_start: 0.8574 (t80) cc_final: 0.8275 (t80) REVERT: B 207 ILE cc_start: 0.7063 (mm) cc_final: 0.6856 (mp) REVERT: B 409 MET cc_start: 0.8104 (tmm) cc_final: 0.7810 (tmm) REVERT: B 479 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5656 (pt) REVERT: B 518 ILE cc_start: 0.8565 (tt) cc_final: 0.8243 (pp) outliers start: 34 outliers final: 13 residues processed: 118 average time/residue: 0.8541 time to fit residues: 110.8327 Evaluate side-chains 99 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 283 ILE Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 559 TYR 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 235 GLN Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 414 VAL 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 76 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2458 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= 0.200 Angle : 0.584 8.250 12278 Z= 0.300 Chirality : 0.041 0.258 1502 Planarity : 0.003 0.032 1522 Dihedral : 8.388 128.355 1261 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.08 % Favored : 94.83 % Rotamer: Outliers : 3.54 % Allowed : 17.17 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1122 helix: 1.66 (0.20), residues: 700 sheet: -0.06 (0.66), residues: 70 loop : -1.76 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 408 HIS 0.004 0.001 HIS B 713 PHE 0.014 0.001 PHE A 308 TYR 0.007 0.001 TYR B 491 ARG 0.003 0.000 ARG A 457 *********************** 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 124 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 1.046 Fit side-chains REVERT: A 227 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7489 (tt0) REVERT: A 239 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8357 (tt) REVERT: A 663 ASN cc_start: 0.9120 (m-40) cc_final: 0.8707 (m-40) REVERT: A 677 ARG cc_start: 0.8059 (mmp-170) cc_final: 0.7705 (mmt180) REVERT: A 710 PHE cc_start: 0.8664 (t80) cc_final: 0.8322 (t80) REVERT: B 227 GLU cc_start: 0.7831 (tt0) cc_final: 0.7560 (tt0) REVERT: B 409 MET cc_start: 0.8111 (tmm) cc_final: 0.7748 (tmm) REVERT: B 479 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5916 (pt) REVERT: B 518 ILE cc_start: 0.8689 (tt) cc_final: 0.8363 (pp) outliers start: 35 outliers final: 22 residues processed: 111 average time/residue: 0.8150 time to fit residues: 100.0778 Evaluate side-chains 105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 192 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 ILE 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 212 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2574 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= 0.292 Angle : 0.617 7.804 12278 Z= 0.319 Chirality : 0.042 0.266 1502 Planarity : 0.003 0.036 1522 Dihedral : 8.202 129.905 1260 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.70 % Favored : 94.21 % Rotamer: Outliers : 5.05 % Allowed : 18.69 % Favored : 76.26 % 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: 0.87 (0.26), residues: 1122 helix: 1.73 (0.20), residues: 702 sheet: -0.13 (0.66), residues: 70 loop : -1.73 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 408 HIS 0.005 0.001 HIS B 713 PHE 0.016 0.001 PHE A 308 TYR 0.009 0.001 TYR B 491 ARG 0.006 0.000 ARG A 457 *********************** 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 133 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 83 time to evaluate : 1.043 Fit side-chains REVERT: A 227 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7515 (tt0) REVERT: A 239 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8531 (tt) REVERT: A 480 MET cc_start: 0.7846 (mmm) cc_final: 0.7582 (pmm) REVERT: A 663 ASN cc_start: 0.9116 (m-40) cc_final: 0.8725 (m-40) REVERT: A 677 ARG cc_start: 0.8034 (mmp-170) cc_final: 0.7779 (mmt180) REVERT: A 710 PHE cc_start: 0.8685 (t80) cc_final: 0.8359 (t80) REVERT: B 205 LEU cc_start: 0.5948 (OUTLIER) cc_final: 0.5575 (tt) REVERT: B 227 GLU cc_start: 0.7884 (tt0) cc_final: 0.7665 (tt0) REVERT: B 240 ASP cc_start: 0.7957 (t0) cc_final: 0.7702 (t0) REVERT: B 409 MET cc_start: 0.8173 (tmm) cc_final: 0.7797 (tmm) REVERT: B 518 ILE cc_start: 0.8806 (tt) cc_final: 0.8527 (pp) outliers start: 50 outliers final: 28 residues processed: 122 average time/residue: 0.8524 time to fit residues: 114.3699 Evaluate side-chains 110 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 186 SER 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 204 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE 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 165 ARG Chi-restraints excluded: chain B residue 180 VAL 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 249 VAL 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 459 ASN Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 521 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 108 optimal weight: 0.4980 chunk 89 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.0070 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 B 713 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9050 Z= 0.160 Angle : 0.575 9.924 12278 Z= 0.289 Chirality : 0.040 0.231 1502 Planarity : 0.003 0.032 1522 Dihedral : 8.037 126.120 1260 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 3.64 % Allowed : 19.49 % Favored : 76.87 % 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: 1.20 (0.26), residues: 1122 helix: 2.01 (0.20), residues: 700 sheet: -0.01 (0.67), residues: 70 loop : -1.63 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 408 HIS 0.006 0.001 HIS B 713 PHE 0.012 0.001 PHE A 308 TYR 0.007 0.001 TYR A 711 ARG 0.002 0.000 ARG A 202 *********************** 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 127 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 1.079 Fit side-chains REVERT: A 227 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7470 (tt0) REVERT: A 239 ILE cc_start: 0.8560 (tt) cc_final: 0.8332 (tt) REVERT: A 480 MET cc_start: 0.7885 (mmm) cc_final: 0.7592 (pmm) REVERT: A 663 ASN cc_start: 0.9095 (m-40) cc_final: 0.8699 (m-40) REVERT: A 710 PHE cc_start: 0.8731 (t80) cc_final: 0.8367 (t80) REVERT: B 205 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5613 (tt) REVERT: B 402 LEU cc_start: 0.8650 (tm) cc_final: 0.8328 (mt) REVERT: B 518 ILE cc_start: 0.8721 (tt) cc_final: 0.8392 (pp) outliers start: 36 outliers final: 19 residues processed: 120 average time/residue: 0.9273 time to fit residues: 122.1876 Evaluate side-chains 106 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 406 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9050 Z= 0.214 Angle : 0.596 9.571 12278 Z= 0.304 Chirality : 0.041 0.224 1502 Planarity : 0.003 0.040 1522 Dihedral : 7.865 128.182 1256 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.53 % Favored : 94.39 % Rotamer: Outliers : 3.13 % Allowed : 21.31 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1122 helix: 2.04 (0.21), residues: 700 sheet: -0.03 (0.67), residues: 70 loop : -1.60 (0.31), residues: 352 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 0.017 0.001 PHE A 308 TYR 0.022 0.001 TYR A 196 ARG 0.010 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 115 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 1.023 Fit side-chains REVERT: A 227 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7489 (tt0) REVERT: A 239 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8403 (tt) REVERT: A 415 MET cc_start: 0.6647 (ttt) cc_final: 0.6380 (ttt) REVERT: A 663 ASN cc_start: 0.9124 (m-40) cc_final: 0.8737 (m-40) REVERT: A 710 PHE cc_start: 0.8775 (t80) cc_final: 0.8402 (t80) REVERT: B 205 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5491 (tt) REVERT: B 227 GLU cc_start: 0.7934 (tt0) cc_final: 0.7583 (tt0) REVERT: B 518 ILE cc_start: 0.8773 (tt) cc_final: 0.8469 (pp) outliers start: 31 outliers final: 22 residues processed: 106 average time/residue: 0.9338 time to fit residues: 108.9627 Evaluate side-chains 104 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE 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 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 406 ILE 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 285 SER 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 0.0020 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 0.0370 chunk 10 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 98 optimal weight: 0.0270 chunk 103 optimal weight: 3.9990 overall best weight: 0.2524 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9050 Z= 0.151 Angle : 0.586 9.547 12278 Z= 0.293 Chirality : 0.040 0.238 1502 Planarity : 0.003 0.040 1522 Dihedral : 7.743 123.891 1256 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 2.83 % Allowed : 22.02 % Favored : 75.15 % 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: 1.39 (0.27), residues: 1122 helix: 2.17 (0.21), residues: 702 sheet: 0.08 (0.67), residues: 70 loop : -1.58 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 408 HIS 0.006 0.001 HIS B 713 PHE 0.014 0.001 PHE A 308 TYR 0.021 0.001 TYR A 196 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 117 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 1.124 Fit side-chains REVERT: A 227 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7439 (tt0) REVERT: A 239 ILE cc_start: 0.8429 (tt) cc_final: 0.8197 (tt) REVERT: A 663 ASN cc_start: 0.9103 (m-40) cc_final: 0.8721 (m-40) REVERT: A 710 PHE cc_start: 0.8697 (t80) cc_final: 0.8262 (t80) REVERT: B 205 LEU cc_start: 0.5753 (OUTLIER) cc_final: 0.5367 (tt) REVERT: B 227 GLU cc_start: 0.7795 (tt0) cc_final: 0.7522 (tt0) REVERT: B 402 LEU cc_start: 0.8582 (tm) cc_final: 0.8327 (mt) REVERT: B 518 ILE cc_start: 0.8692 (tt) cc_final: 0.8333 (pp) REVERT: B 605 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7348 (mp0) outliers start: 28 outliers final: 13 residues processed: 110 average time/residue: 0.8342 time to fit residues: 101.5708 Evaluate side-chains 98 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 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 285 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 414 VAL 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 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 0.0970 chunk 43 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN B 713 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9050 Z= 0.160 Angle : 0.582 10.224 12278 Z= 0.291 Chirality : 0.040 0.242 1502 Planarity : 0.003 0.044 1522 Dihedral : 7.706 124.271 1256 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 2.22 % Allowed : 22.83 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.27), residues: 1122 helix: 2.26 (0.21), residues: 700 sheet: 0.13 (0.68), residues: 70 loop : -1.53 (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 0.021 0.001 PHE A 308 TYR 0.020 0.001 TYR A 196 ARG 0.010 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: 22 poor density : 84 time to evaluate : 0.991 Fit side-chains REVERT: A 207 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.6960 (pp) REVERT: A 227 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7476 (tt0) REVERT: A 239 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8178 (tt) REVERT: A 663 ASN cc_start: 0.9126 (m-40) cc_final: 0.8739 (m-40) REVERT: A 710 PHE cc_start: 0.8666 (t80) cc_final: 0.8293 (t80) REVERT: B 205 LEU cc_start: 0.5731 (OUTLIER) cc_final: 0.5326 (tt) REVERT: B 227 GLU cc_start: 0.7881 (tt0) cc_final: 0.7622 (tt0) REVERT: B 402 LEU cc_start: 0.8585 (tm) cc_final: 0.8347 (mt) REVERT: B 518 ILE cc_start: 0.8693 (tt) cc_final: 0.8337 (pp) REVERT: B 605 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7362 (mp0) outliers start: 22 outliers final: 12 residues processed: 99 average time/residue: 0.8469 time to fit residues: 92.7356 Evaluate side-chains 97 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 207 ILE 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 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 285 SER Chi-restraints excluded: chain B residue 406 ILE 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 64 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9050 Z= 0.224 Angle : 0.608 11.294 12278 Z= 0.308 Chirality : 0.041 0.229 1502 Planarity : 0.003 0.044 1522 Dihedral : 7.817 127.941 1256 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 2.32 % Allowed : 22.63 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.27), residues: 1122 helix: 2.22 (0.21), residues: 694 sheet: -0.02 (0.67), residues: 70 loop : -1.57 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 408 HIS 0.006 0.001 HIS B 713 PHE 0.019 0.001 PHE A 308 TYR 0.024 0.001 TYR A 196 ARG 0.010 0.001 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 106 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 1.088 Fit side-chains REVERT: A 207 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.6954 (pp) REVERT: A 227 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7510 (tt0) REVERT: A 663 ASN cc_start: 0.9142 (m-40) cc_final: 0.8757 (m-40) REVERT: A 710 PHE cc_start: 0.8754 (t80) cc_final: 0.8376 (t80) REVERT: B 205 LEU cc_start: 0.5722 (OUTLIER) cc_final: 0.5277 (tt) REVERT: B 227 GLU cc_start: 0.7941 (tt0) cc_final: 0.7664 (tt0) REVERT: B 402 LEU cc_start: 0.8595 (tm) cc_final: 0.8345 (mt) REVERT: B 518 ILE cc_start: 0.8755 (tt) cc_final: 0.8432 (pp) REVERT: B 605 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7359 (mp0) outliers start: 23 outliers final: 16 residues processed: 99 average time/residue: 0.8573 time to fit residues: 94.6132 Evaluate side-chains 100 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 207 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 350 ASP 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 285 SER Chi-restraints excluded: chain B residue 406 ILE 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 605 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.102830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076824 restraints weight = 17744.840| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.89 r_work: 0.3130 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9050 Z= 0.159 Angle : 0.592 10.672 12278 Z= 0.295 Chirality : 0.040 0.214 1502 Planarity : 0.003 0.041 1522 Dihedral : 7.721 124.476 1256 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 1.92 % Allowed : 23.23 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.27), residues: 1122 helix: 2.26 (0.21), residues: 700 sheet: 0.11 (0.67), residues: 70 loop : -1.50 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 408 HIS 0.006 0.001 HIS B 713 PHE 0.019 0.001 PHE A 308 TYR 0.022 0.001 TYR A 196 ARG 0.009 0.000 ARG B 386 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2773.80 seconds wall clock time: 51 minutes 10.00 seconds (3070.00 seconds total)