Starting phenix.real_space_refine on Mon Jun 16 00:27:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0f_39703/06_2025/8z0f_39703_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0f_39703/06_2025/8z0f_39703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z0f_39703/06_2025/8z0f_39703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0f_39703/06_2025/8z0f_39703.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0f_39703/06_2025/8z0f_39703_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0f_39703/06_2025/8z0f_39703_neut_trim.cif" } resolution = 3.27 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= 0.008 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 52 5.16 5 C 5796 2.51 5 N 1556 2.21 5 O 1594 1.98 5 H 9062 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18066 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 9002 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 15, 'TRANS': 533} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 9002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 9002 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 15, 'TRANS': 533} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.11, per 1000 atoms: 0.50 Number of scatterers: 18066 At special positions: 0 Unit cell: (69.55, 82.39, 132.68, 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 52 16.00 P 6 15.00 O 1594 8.00 N 1556 7.00 C 5796 6.00 H 9062 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.23 Conformation dependent library (CDL) restraints added in 1.4 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2044 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 57.6% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 60 through 72 removed outlier: 3.651A pdb=" N ILE A 70 " --> pdb=" O ARG A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 84 through 92 removed outlier: 3.852A pdb=" N ALA A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 115 removed outlier: 3.800A pdb=" N ASP A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 126 through 167 Proline residue: A 134 - end of helix removed outlier: 3.957A pdb=" N ASN A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 5.845A pdb=" N GLY A 176 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.739A pdb=" N LEU A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 184 through 189' Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.718A pdb=" N VAL A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 242 removed outlier: 3.618A pdb=" N LEU A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 275 removed outlier: 4.072A pdb=" N LYS A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 284 through 318 removed outlier: 3.850A pdb=" N VAL A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.622A pdb=" N VAL A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 395 removed outlier: 3.896A pdb=" N THR A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE A 387 " --> pdb=" O ARG A 383 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.608A pdb=" N LYS A 399 " --> pdb=" O GLN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 487 removed outlier: 4.422A pdb=" N PHE A 483 " --> pdb=" O LYS A 479 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 524 removed outlier: 3.569A pdb=" N VAL A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.991A pdb=" N LYS A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 549 removed outlier: 4.181A pdb=" N ASP A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 577 removed outlier: 3.678A pdb=" N LYS A 576 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN A 577 " --> pdb=" O GLY A 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 573 through 577' Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.683A pdb=" N HIS A 587 " --> pdb=" O ARG A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 616 Processing helix chain 'B' and resid 60 through 72 removed outlier: 3.917A pdb=" N ILE B 70 " --> pdb=" O ARG B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 89 removed outlier: 3.653A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 109 removed outlier: 4.085A pdb=" N VAL B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 167 removed outlier: 4.154A pdb=" N ASN B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE B 129 " --> pdb=" O TYR B 125 " (cutoff:3.500A) Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 170 through 175 removed outlier: 3.610A pdb=" N LYS B 174 " --> pdb=" O PHE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 removed outlier: 3.804A pdb=" N LEU B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 189' Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 213 through 221 removed outlier: 3.823A pdb=" N LYS B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 removed outlier: 3.619A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 275 removed outlier: 3.808A pdb=" N GLY B 252 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 257 " --> pdb=" O LYS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 284 through 318 removed outlier: 3.945A pdb=" N VAL B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 311 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 361 through 378 removed outlier: 3.775A pdb=" N VAL B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 395 removed outlier: 3.939A pdb=" N THR B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 387 " --> pdb=" O ARG B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.657A pdb=" N LYS B 399 " --> pdb=" O GLN B 396 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP B 400 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 401 " --> pdb=" O LEU B 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 401' Processing helix chain 'B' and resid 479 through 487 removed outlier: 4.224A pdb=" N PHE B 483 " --> pdb=" O LYS B 479 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 524 removed outlier: 3.547A pdb=" N VAL B 523 " --> pdb=" O LEU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.814A pdb=" N LYS B 533 " --> pdb=" O ARG B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 549 removed outlier: 3.951A pdb=" N ASP B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN B 548 " --> pdb=" O GLU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 577 removed outlier: 3.688A pdb=" N LYS B 576 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN B 577 " --> pdb=" O GLY B 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 577' Processing helix chain 'B' and resid 580 through 582 No H-bonds generated for 'chain 'B' and resid 580 through 582' Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 605 through 614 removed outlier: 3.614A pdb=" N TYR B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 432 through 435 Processing sheet with id=AA2, first strand: chain 'A' and resid 447 through 448 removed outlier: 7.498A pdb=" N LEU A 447 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 455 " --> pdb=" O LEU A 447 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 469 through 471 removed outlier: 6.444A pdb=" N VAL A 469 " --> pdb=" O THR A 622 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 623 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N PHE A 506 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASP A 595 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 508 " --> pdb=" O ASP A 595 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 434 through 436 removed outlier: 3.664A pdb=" N LYS B 499 " --> pdb=" O ILE B 434 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 496 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 443 " --> pdb=" O ARG B 496 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B 498 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 441 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 447 through 448 removed outlier: 7.445A pdb=" N LEU B 447 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 455 " --> pdb=" O LEU B 447 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 469 through 471 removed outlier: 6.499A pdb=" N VAL B 469 " --> pdb=" O THR B 622 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 638 through 639 377 hydrogen bonds defined for protein. 1107 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: 6.38 Time building geometry restraints manager: 6.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9046 1.03 - 1.23: 19 1.23 - 1.42: 3894 1.42 - 1.62: 5207 1.62 - 1.81: 88 Bond restraints: 18254 Sorted by residual: bond pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 1.592 1.455 0.137 1.10e-02 8.26e+03 1.55e+02 bond pdb=" C4 ATP A 701 " pdb=" N9 ATP A 701 " ideal model delta sigma weight residual 1.374 1.252 0.122 1.00e-02 1.00e+04 1.49e+02 bond pdb=" C4 ATP A 702 " pdb=" N9 ATP A 702 " ideal model delta sigma weight residual 1.374 1.254 0.120 1.00e-02 1.00e+04 1.44e+02 bond pdb=" O3A ATP A 702 " pdb=" PB ATP A 702 " ideal model delta sigma weight residual 1.592 1.464 0.128 1.10e-02 8.26e+03 1.36e+02 bond pdb=" C5 ATP A 702 " pdb=" N7 ATP A 702 " ideal model delta sigma weight residual 1.387 1.289 0.098 1.00e-02 1.00e+04 9.52e+01 ... (remaining 18249 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.10: 32876 8.10 - 16.20: 22 16.20 - 24.29: 1 24.29 - 32.39: 6 32.39 - 40.49: 1 Bond angle restraints: 32906 Sorted by residual: angle pdb=" PB ATP A 702 " pdb=" O3B ATP A 702 " pdb=" PG ATP A 702 " ideal model delta sigma weight residual 139.87 99.38 40.49 1.00e+00 1.00e+00 1.64e+03 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 109.52 27.31 1.00e+00 1.00e+00 7.46e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 112.67 27.20 1.00e+00 1.00e+00 7.40e+02 angle pdb=" PA ATP A 702 " pdb=" O3A ATP A 702 " pdb=" PB ATP A 702 " ideal model delta sigma weight residual 136.83 112.08 24.75 1.00e+00 1.00e+00 6.12e+02 angle pdb=" O3A ATP A 702 " pdb=" PB ATP A 702 " pdb=" O3B ATP A 702 " ideal model delta sigma weight residual 101.57 129.12 -27.55 1.54e+00 4.24e-01 3.22e+02 ... (remaining 32901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 7243 17.91 - 35.82: 903 35.82 - 53.73: 313 53.73 - 71.63: 69 71.63 - 89.54: 14 Dihedral angle restraints: 8542 sinusoidal: 4686 harmonic: 3856 Sorted by residual: dihedral pdb=" CA MET B 74 " pdb=" C MET B 74 " pdb=" N VAL B 75 " pdb=" CA VAL B 75 " ideal model delta harmonic sigma weight residual -180.00 -153.80 -26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA THR A 245 " pdb=" C THR A 245 " pdb=" N ARG A 246 " pdb=" CA ARG A 246 " ideal model delta harmonic sigma weight residual -180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA MET B 395 " pdb=" C MET B 395 " pdb=" N GLN B 396 " pdb=" CA GLN B 396 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 8539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1003 0.037 - 0.074: 268 0.074 - 0.112: 75 0.112 - 0.149: 22 0.149 - 0.186: 2 Chirality restraints: 1370 Sorted by residual: chirality pdb=" C2' ATP A 701 " pdb=" C1' ATP A 701 " pdb=" C3' ATP A 701 " pdb=" O2' ATP A 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.49 -0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" C2' ATP A 702 " pdb=" C1' ATP A 702 " pdb=" C3' ATP A 702 " pdb=" O2' ATP A 702 " both_signs ideal model delta sigma weight residual False -2.68 -2.49 -0.19 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CA VAL B 616 " pdb=" N VAL B 616 " pdb=" C VAL B 616 " pdb=" CB VAL B 616 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 1367 not shown) Planarity restraints: 2606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 501 " 0.028 2.00e-02 2.50e+03 5.34e-02 2.85e+01 pdb=" N ARG B 502 " -0.092 2.00e-02 2.50e+03 pdb=" CA ARG B 502 " 0.024 2.00e-02 2.50e+03 pdb=" H ARG B 502 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 353 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C LEU B 353 " -0.027 2.00e-02 2.50e+03 pdb=" O LEU B 353 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU B 354 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 366 " -0.131 9.50e-02 1.11e+02 4.39e-02 2.38e+00 pdb=" NE ARG A 366 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 366 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 366 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 366 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 366 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 366 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 366 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 366 " -0.000 2.00e-02 2.50e+03 ... (remaining 2603 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 427 2.10 - 2.72: 31179 2.72 - 3.35: 52075 3.35 - 3.97: 64156 3.97 - 4.60: 101737 Nonbonded interactions: 249574 Sorted by model distance: nonbonded pdb=" OE1 GLU B 111 " pdb=" H GLU B 111 " model vdw 1.470 2.450 nonbonded pdb=" OE1 GLU A 111 " pdb=" H GLU A 111 " model vdw 1.475 2.450 nonbonded pdb=" OD1 ASP A 100 " pdb=" H VAL A 101 " model vdw 1.594 2.450 nonbonded pdb=" O ARG B 246 " pdb=" HE ARG B 246 " model vdw 1.597 2.450 nonbonded pdb=" O THR B 515 " pdb="HE22 GLN B 522 " model vdw 1.607 2.450 ... (remaining 249569 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' and resid 56 through 649) 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.300 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 40.670 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 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 : 0.010 0.714 9193 Z= 0.880 Angle : 1.067 40.488 12400 Z= 0.762 Chirality : 0.040 0.186 1370 Planarity : 0.003 0.057 1546 Dihedral : 19.328 89.542 3490 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 0.51 % Allowed : 36.76 % Favored : 62.73 % 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: -2.49 (0.26), residues: 1082 helix: -0.91 (0.22), residues: 590 sheet: -1.52 (0.85), residues: 44 loop : -2.65 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 567 HIS 0.003 0.001 HIS A 293 PHE 0.006 0.001 PHE A 591 TYR 0.012 0.001 TYR A 166 ARG 0.009 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.20855 ( 377) hydrogen bonds : angle 7.77060 ( 1107) covalent geometry : bond 0.00712 ( 9192) covalent geometry : angle 1.06669 (12400) Misc. bond : bond 0.71423 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 608 TYR cc_start: 0.6948 (t80) cc_final: 0.6739 (t80) outliers start: 5 outliers final: 5 residues processed: 167 average time/residue: 0.4632 time to fit residues: 108.6491 Evaluate side-chains 165 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 465 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 444 HIS A 460 ASN A 577 GLN B 577 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.157786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124625 restraints weight = 34756.187| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.51 r_work: 0.3574 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9193 Z= 0.156 Angle : 0.616 6.669 12400 Z= 0.337 Chirality : 0.040 0.145 1370 Planarity : 0.004 0.034 1546 Dihedral : 10.896 86.734 1305 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 3.90 % Allowed : 33.78 % Favored : 62.32 % 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: -2.60 (0.25), residues: 1082 helix: -0.89 (0.21), residues: 610 sheet: -2.01 (0.69), residues: 60 loop : -2.89 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 102 HIS 0.003 0.001 HIS A 444 PHE 0.011 0.001 PHE B 306 TYR 0.012 0.001 TYR A 166 ARG 0.004 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.05993 ( 377) hydrogen bonds : angle 5.68745 ( 1107) covalent geometry : bond 0.00341 ( 9192) covalent geometry : angle 0.61563 (12400) Misc. bond : bond 0.00183 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.8352 (pm20) cc_final: 0.7930 (pm20) REVERT: A 144 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7632 (ttmm) REVERT: A 165 GLU cc_start: 0.8474 (tp30) cc_final: 0.8251 (tp30) REVERT: A 172 TYR cc_start: 0.8464 (p90) cc_final: 0.7995 (p90) REVERT: B 293 HIS cc_start: 0.7613 (OUTLIER) cc_final: 0.7139 (t-90) outliers start: 38 outliers final: 25 residues processed: 187 average time/residue: 0.4556 time to fit residues: 119.2787 Evaluate side-chains 191 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 623 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 GLN B 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.157685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124376 restraints weight = 34718.635| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.53 r_work: 0.3571 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9193 Z= 0.155 Angle : 0.587 7.500 12400 Z= 0.320 Chirality : 0.039 0.143 1370 Planarity : 0.004 0.037 1546 Dihedral : 10.168 80.484 1302 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 4.52 % Allowed : 33.37 % Favored : 62.11 % 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: -2.57 (0.25), residues: 1082 helix: -0.84 (0.21), residues: 610 sheet: -1.87 (0.71), residues: 58 loop : -2.96 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 567 HIS 0.003 0.001 HIS A 632 PHE 0.010 0.001 PHE A 647 TYR 0.011 0.001 TYR B 166 ARG 0.002 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04980 ( 377) hydrogen bonds : angle 5.27273 ( 1107) covalent geometry : bond 0.00340 ( 9192) covalent geometry : angle 0.58741 (12400) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.8197 (pm20) cc_final: 0.7910 (pm20) REVERT: A 172 TYR cc_start: 0.8481 (p90) cc_final: 0.8042 (p90) REVERT: B 293 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.7115 (t-90) REVERT: B 334 SER cc_start: 0.8060 (m) cc_final: 0.7523 (p) outliers start: 44 outliers final: 32 residues processed: 191 average time/residue: 0.4559 time to fit residues: 122.2436 Evaluate side-chains 190 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 632 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.159572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126274 restraints weight = 34443.651| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.53 r_work: 0.3587 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9193 Z= 0.124 Angle : 0.559 4.708 12400 Z= 0.305 Chirality : 0.039 0.145 1370 Planarity : 0.003 0.044 1546 Dihedral : 9.334 82.304 1302 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 4.62 % Allowed : 33.98 % Favored : 61.40 % 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: -2.46 (0.25), residues: 1082 helix: -0.76 (0.21), residues: 612 sheet: -1.77 (0.72), residues: 58 loop : -2.91 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 567 HIS 0.002 0.001 HIS A 293 PHE 0.008 0.001 PHE A 306 TYR 0.012 0.001 TYR B 166 ARG 0.003 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04449 ( 377) hydrogen bonds : angle 5.01704 ( 1107) covalent geometry : bond 0.00269 ( 9192) covalent geometry : angle 0.55858 (12400) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7496 (ttmm) REVERT: A 462 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7381 (pm20) REVERT: B 186 ASP cc_start: 0.8579 (p0) cc_final: 0.8372 (p0) REVERT: B 234 MET cc_start: 0.7964 (ppp) cc_final: 0.7686 (ptt) REVERT: B 246 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6771 (tpm170) REVERT: B 293 HIS cc_start: 0.7611 (OUTLIER) cc_final: 0.7133 (t-90) REVERT: B 334 SER cc_start: 0.8016 (m) cc_final: 0.7507 (p) outliers start: 45 outliers final: 31 residues processed: 195 average time/residue: 0.4711 time to fit residues: 130.5268 Evaluate side-chains 186 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 632 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 chunk 100 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.159262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.125826 restraints weight = 34644.737| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.54 r_work: 0.3580 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9193 Z= 0.137 Angle : 0.564 5.259 12400 Z= 0.307 Chirality : 0.039 0.141 1370 Planarity : 0.004 0.067 1546 Dihedral : 8.909 84.939 1300 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 5.34 % Allowed : 33.06 % Favored : 61.60 % 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: -2.39 (0.25), residues: 1082 helix: -0.70 (0.21), residues: 616 sheet: -1.76 (0.72), residues: 58 loop : -2.91 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 567 HIS 0.003 0.000 HIS A 632 PHE 0.007 0.001 PHE B 306 TYR 0.013 0.001 TYR A 166 ARG 0.003 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 377) hydrogen bonds : angle 4.92823 ( 1107) covalent geometry : bond 0.00303 ( 9192) covalent geometry : angle 0.56382 (12400) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.8077 (pm20) cc_final: 0.7863 (pm20) REVERT: A 144 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7424 (ttmm) REVERT: A 462 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: B 234 MET cc_start: 0.8043 (ppp) cc_final: 0.7719 (ptt) REVERT: B 293 HIS cc_start: 0.7604 (OUTLIER) cc_final: 0.7128 (t-90) REVERT: B 307 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8032 (tt) REVERT: B 334 SER cc_start: 0.7925 (m) cc_final: 0.7438 (p) outliers start: 52 outliers final: 38 residues processed: 197 average time/residue: 0.4486 time to fit residues: 123.0932 Evaluate side-chains 193 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 632 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.159869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.126822 restraints weight = 34571.159| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.53 r_work: 0.3597 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9193 Z= 0.126 Angle : 0.550 4.829 12400 Z= 0.300 Chirality : 0.039 0.141 1370 Planarity : 0.004 0.060 1546 Dihedral : 8.388 84.156 1300 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 5.75 % Allowed : 32.75 % Favored : 61.50 % 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: -2.28 (0.26), residues: 1082 helix: -0.61 (0.21), residues: 618 sheet: -1.71 (0.72), residues: 58 loop : -2.88 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 567 HIS 0.002 0.001 HIS A 632 PHE 0.007 0.001 PHE A 647 TYR 0.012 0.001 TYR A 166 ARG 0.006 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 377) hydrogen bonds : angle 4.80645 ( 1107) covalent geometry : bond 0.00275 ( 9192) covalent geometry : angle 0.54966 (12400) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 157 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7420 (ttmm) REVERT: A 462 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7350 (pm20) REVERT: B 142 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7516 (t80) REVERT: B 234 MET cc_start: 0.8035 (ppp) cc_final: 0.7705 (ptt) REVERT: B 246 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6690 (tpm170) REVERT: B 293 HIS cc_start: 0.7595 (OUTLIER) cc_final: 0.7130 (t-90) REVERT: B 307 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7998 (tt) REVERT: B 334 SER cc_start: 0.7925 (m) cc_final: 0.7492 (p) outliers start: 56 outliers final: 41 residues processed: 199 average time/residue: 0.4683 time to fit residues: 130.6054 Evaluate side-chains 195 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 632 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 522 GLN B 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.160057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.126982 restraints weight = 34286.779| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.52 r_work: 0.3599 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9193 Z= 0.124 Angle : 0.553 5.919 12400 Z= 0.301 Chirality : 0.039 0.139 1370 Planarity : 0.004 0.055 1546 Dihedral : 8.135 86.931 1300 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 6.16 % Allowed : 32.24 % Favored : 61.60 % 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: -2.26 (0.26), residues: 1082 helix: -0.57 (0.21), residues: 620 sheet: -1.71 (0.72), residues: 58 loop : -2.92 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 567 HIS 0.003 0.000 HIS A 632 PHE 0.006 0.001 PHE B 621 TYR 0.013 0.001 TYR B 166 ARG 0.007 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 377) hydrogen bonds : angle 4.71883 ( 1107) covalent geometry : bond 0.00272 ( 9192) covalent geometry : angle 0.55321 (12400) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 151 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.7492 (mtp) cc_final: 0.7219 (ttp) REVERT: A 144 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7473 (ttmm) REVERT: B 142 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7489 (t80) REVERT: B 234 MET cc_start: 0.8042 (ppp) cc_final: 0.7716 (ptt) REVERT: B 246 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6769 (tpm170) REVERT: B 293 HIS cc_start: 0.7578 (OUTLIER) cc_final: 0.7126 (t-90) REVERT: B 307 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7976 (tt) REVERT: B 334 SER cc_start: 0.8090 (m) cc_final: 0.7707 (p) REVERT: B 569 ASP cc_start: 0.8305 (p0) cc_final: 0.8100 (p0) outliers start: 60 outliers final: 46 residues processed: 197 average time/residue: 0.6592 time to fit residues: 188.5951 Evaluate side-chains 201 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 632 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.0770 chunk 38 optimal weight: 3.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN B 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.162087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.129024 restraints weight = 34218.686| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.53 r_work: 0.3621 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9193 Z= 0.110 Angle : 0.543 5.479 12400 Z= 0.295 Chirality : 0.038 0.140 1370 Planarity : 0.003 0.052 1546 Dihedral : 7.832 88.196 1300 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 5.65 % Allowed : 32.96 % Favored : 61.40 % 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: -2.12 (0.26), residues: 1082 helix: -0.48 (0.21), residues: 622 sheet: -1.33 (0.63), residues: 80 loop : -2.95 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 567 HIS 0.002 0.000 HIS A 632 PHE 0.006 0.001 PHE B 315 TYR 0.010 0.001 TYR B 166 ARG 0.007 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 377) hydrogen bonds : angle 4.61859 ( 1107) covalent geometry : bond 0.00238 ( 9192) covalent geometry : angle 0.54278 (12400) Misc. bond : bond 0.00343 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 162 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.7487 (mtp) cc_final: 0.7236 (ttp) REVERT: B 142 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7462 (t80) REVERT: B 234 MET cc_start: 0.8034 (ppp) cc_final: 0.7710 (ptt) REVERT: B 246 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6834 (tpm170) REVERT: B 293 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.7123 (t-90) REVERT: B 307 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7836 (tt) REVERT: B 334 SER cc_start: 0.8003 (m) cc_final: 0.7669 (p) outliers start: 55 outliers final: 43 residues processed: 202 average time/residue: 0.6064 time to fit residues: 181.5200 Evaluate side-chains 203 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 632 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 4.9990 chunk 104 optimal weight: 0.0980 chunk 105 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN B 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.157596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124332 restraints weight = 34718.583| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.53 r_work: 0.3568 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9193 Z= 0.183 Angle : 0.589 5.830 12400 Z= 0.323 Chirality : 0.040 0.143 1370 Planarity : 0.004 0.054 1546 Dihedral : 7.906 88.132 1300 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 5.44 % Allowed : 33.16 % Favored : 61.40 % 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: -2.32 (0.25), residues: 1082 helix: -0.62 (0.21), residues: 620 sheet: -1.67 (0.72), residues: 58 loop : -2.95 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 567 HIS 0.004 0.001 HIS A 632 PHE 0.009 0.001 PHE A 621 TYR 0.014 0.001 TYR B 166 ARG 0.009 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 377) hydrogen bonds : angle 4.77391 ( 1107) covalent geometry : bond 0.00407 ( 9192) covalent geometry : angle 0.58897 (12400) Misc. bond : bond 0.00250 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 156 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.8459 (tp30) cc_final: 0.8245 (tp30) REVERT: A 462 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7323 (pm20) REVERT: B 142 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7579 (t80) REVERT: B 211 PHE cc_start: 0.8260 (t80) cc_final: 0.8007 (t80) REVERT: B 234 MET cc_start: 0.8064 (ppp) cc_final: 0.7754 (ptt) REVERT: B 293 HIS cc_start: 0.7614 (OUTLIER) cc_final: 0.7167 (t-90) REVERT: B 307 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7997 (tt) REVERT: B 334 SER cc_start: 0.8159 (m) cc_final: 0.7722 (p) outliers start: 53 outliers final: 42 residues processed: 196 average time/residue: 0.4762 time to fit residues: 133.9517 Evaluate side-chains 199 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 632 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN B 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.159129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.126063 restraints weight = 34223.748| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.52 r_work: 0.3587 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9193 Z= 0.132 Angle : 0.566 5.278 12400 Z= 0.309 Chirality : 0.039 0.137 1370 Planarity : 0.004 0.053 1546 Dihedral : 7.871 89.495 1300 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 5.03 % Allowed : 33.68 % Favored : 61.29 % 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: -2.17 (0.26), residues: 1082 helix: -0.53 (0.21), residues: 620 sheet: -1.31 (0.63), residues: 80 loop : -2.94 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 567 HIS 0.003 0.001 HIS A 632 PHE 0.007 0.001 PHE B 621 TYR 0.012 0.001 TYR B 166 ARG 0.008 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 377) hydrogen bonds : angle 4.68410 ( 1107) covalent geometry : bond 0.00291 ( 9192) covalent geometry : angle 0.56586 (12400) Misc. bond : bond 0.00115 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue THR 349 is missing expected H atoms. Skipping. Residue LYS 615 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7189 (ttp) REVERT: B 133 MET cc_start: 0.7480 (mtp) cc_final: 0.7264 (ttp) REVERT: B 142 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7521 (t80) REVERT: B 186 ASP cc_start: 0.8523 (p0) cc_final: 0.8235 (p0) REVERT: B 234 MET cc_start: 0.8005 (ppp) cc_final: 0.7719 (ptt) REVERT: B 293 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.7165 (t-90) REVERT: B 307 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7948 (tt) REVERT: B 334 SER cc_start: 0.8096 (m) cc_final: 0.7692 (p) outliers start: 49 outliers final: 41 residues processed: 198 average time/residue: 0.4333 time to fit residues: 122.5439 Evaluate side-chains 200 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 597 CYS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 632 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 90 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN B 180 ASN B 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.160819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.127710 restraints weight = 34219.435| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.54 r_work: 0.3613 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9193 Z= 0.115 Angle : 0.558 5.218 12400 Z= 0.303 Chirality : 0.038 0.139 1370 Planarity : 0.004 0.082 1546 Dihedral : 7.637 84.922 1300 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 4.72 % Allowed : 34.29 % Favored : 60.99 % 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: -2.03 (0.26), residues: 1082 helix: -0.42 (0.21), residues: 624 sheet: -1.21 (0.64), residues: 80 loop : -2.90 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 567 HIS 0.002 0.000 HIS B 638 PHE 0.005 0.001 PHE B 315 TYR 0.011 0.001 TYR B 166 ARG 0.008 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 377) hydrogen bonds : angle 4.58646 ( 1107) covalent geometry : bond 0.00252 ( 9192) covalent geometry : angle 0.55798 (12400) Misc. bond : bond 0.00073 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9829.46 seconds wall clock time: 173 minutes 4.36 seconds (10384.36 seconds total)