Starting phenix.real_space_refine on Thu Jul 2 23:13:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8k53_36896/07_2026/8k53_36896.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k53_36896/07_2026/8k53_36896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k53_36896/07_2026/8k53_36896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k53_36896/07_2026/8k53_36896.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8k53_36896/07_2026/8k53_36896.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8k53_36896/07_2026/8k53_36896.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k53_36896/07_2026/8k53_36896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k53_36896/07_2026/8k53_36896.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6663 2.51 5 N 1852 2.21 5 O 2043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 5998 Classifications: {'peptide': 777} Link IDs: {'PCIS': 8, 'PTRANS': 48, 'TRANS': 720} Chain: "B" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4439 Classifications: {'peptide': 573} Link IDs: {'PCIS': 6, 'PTRANS': 31, 'TRANS': 535} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.92, per 1000 atoms: 0.18 Number of scatterers: 10602 At special positions: 0 Unit cell: (106.72, 168.36, 207.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 2043 8.00 N 1852 7.00 C 6663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 348 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 440 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 348 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 440 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 587 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1101 " - " ASN A 76 " " NAG A1102 " - " ASN A 477 " " NAG B1101 " - " ASN B 76 " " NAG C 1 " - " ASN A 461 " " NAG D 1 " - " ASN A 498 " " NAG E 1 " - " ASN B 461 " " NAG F 1 " - " ASN B 498 " Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 392.0 milliseconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 44 sheets defined 3.0% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.684A pdb=" N LEU A 202 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.863A pdb=" N GLU A 301 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.739A pdb=" N ASP A 482 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 483 " --> pdb=" O ARG A 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 483' Processing helix chain 'B' and resid 101 through 106 removed outlier: 4.118A pdb=" N ALA B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.616A pdb=" N LEU B 202 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.845A pdb=" N GLU B 301 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 483 removed outlier: 3.596A pdb=" N GLU B 483 " --> pdb=" O ARG B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 582 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 41 removed outlier: 5.690A pdb=" N GLY A 36 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N SER A 66 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG A 62 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.297A pdb=" N VAL A 46 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLY A 130 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE A 48 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N LEU A 132 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 59 Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 145 removed outlier: 6.277A pdb=" N VAL A 143 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 203 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 143 through 145 removed outlier: 6.277A pdb=" N VAL A 143 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 203 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA8, first strand: chain 'A' and resid 237 through 243 removed outlier: 5.682A pdb=" N ALA A 238 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ASN A 266 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE A 262 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 248 through 252 removed outlier: 6.471A pdb=" N THR A 249 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLN A 324 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA A 251 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 257 through 260 Processing sheet with id=AB2, first strand: chain 'A' and resid 328 through 331 removed outlier: 6.457A pdb=" N ALA A 349 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 336 through 339 Processing sheet with id=AB4, first strand: chain 'A' and resid 343 through 347 Processing sheet with id=AB5, first strand: chain 'A' and resid 430 through 431 removed outlier: 6.863A pdb=" N ALA A 430 " --> pdb=" O ARG A 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 435 through 438 Processing sheet with id=AB7, first strand: chain 'A' and resid 457 through 458 Processing sheet with id=AB8, first strand: chain 'A' and resid 510 through 513 removed outlier: 6.311A pdb=" N HIS A 531 " --> pdb=" O THR A 512 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 518 through 520 removed outlier: 3.615A pdb=" N VAL A 602 " --> pdb=" O GLY A 583 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 583 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.687A pdb=" N LEU A 526 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 612 through 617 removed outlier: 3.621A pdb=" N GLY A 612 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A 614 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER A 627 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL A 616 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN A 625 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.311A pdb=" N VAL A 685 " --> pdb=" O PRO A 696 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ALA A 687 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 663 through 664 removed outlier: 4.671A pdb=" N ILE A 663 " --> pdb=" O TYR A 641 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 703 " --> pdb=" O TYR A 681 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 718 through 719 Processing sheet with id=AC6, first strand: chain 'A' and resid 759 through 764 removed outlier: 6.437A pdb=" N ILE A 788 " --> pdb=" O GLU A 799 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU A 799 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N SER A 790 " --> pdb=" O GLY A 797 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 759 through 764 Processing sheet with id=AC8, first strand: chain 'B' and resid 35 through 41 removed outlier: 5.948A pdb=" N GLY B 36 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER B 66 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG B 62 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.275A pdb=" N VAL B 46 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLY B 130 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N PHE B 48 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N LEU B 132 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 78 through 79 removed outlier: 3.504A pdb=" N THR B 78 " --> pdb=" O MET B 75 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.664A pdb=" N VAL B 96 " --> pdb=" O GLN B 89 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 143 through 144 removed outlier: 6.063A pdb=" N VAL B 143 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 203 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 143 through 144 removed outlier: 6.063A pdb=" N VAL B 143 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 203 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 151 through 153 Processing sheet with id=AD6, first strand: chain 'B' and resid 237 through 243 removed outlier: 5.571A pdb=" N ALA B 238 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ASN B 266 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE B 262 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 248 through 252 removed outlier: 3.689A pdb=" N ILE B 322 " --> pdb=" O THR B 249 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 248 through 252 removed outlier: 3.689A pdb=" N ILE B 322 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLN B 326 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LYS B 353 " --> pdb=" O GLN B 326 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA B 349 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 257 through 260 Processing sheet with id=AE1, first strand: chain 'B' and resid 336 through 339 removed outlier: 6.491A pdb=" N THR B 336 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLN B 413 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA B 338 " --> pdb=" O GLN B 413 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 343 through 347 Processing sheet with id=AE3, first strand: chain 'B' and resid 415 through 418 removed outlier: 5.513A pdb=" N ALA B 416 " --> pdb=" O ALA B 445 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ALA B 445 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 427 through 431 removed outlier: 7.016A pdb=" N ILE B 428 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ARG B 506 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA B 430 " --> pdb=" O ARG B 506 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 436 through 438 Processing sheet with id=AE6, first strand: chain 'B' and resid 510 through 513 removed outlier: 6.196A pdb=" N HIS B 531 " --> pdb=" O THR B 512 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 518 through 521 Processing sheet with id=AE8, first strand: chain 'B' and resid 526 through 528 391 hydrogen bonds defined for protein. 906 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: 1.97 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3525 1.34 - 1.46: 2407 1.46 - 1.58: 4858 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 10854 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.31e+00 bond pdb=" C1 NAG A1102 " pdb=" O5 NAG A1102 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.78e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.557 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" CB PRO B 469 " pdb=" CG PRO B 469 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.56e+00 bond pdb=" C1 NAG B1101 " pdb=" O5 NAG B1101 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 10849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 14382 1.67 - 3.35: 338 3.35 - 5.02: 33 5.02 - 6.69: 16 6.69 - 8.36: 6 Bond angle restraints: 14775 Sorted by residual: angle pdb=" CA PRO B 469 " pdb=" N PRO B 469 " pdb=" CD PRO B 469 " ideal model delta sigma weight residual 112.00 104.14 7.86 1.40e+00 5.10e-01 3.15e+01 angle pdb=" C ASN A 498 " pdb=" CA ASN A 498 " pdb=" CB ASN A 498 " ideal model delta sigma weight residual 109.72 115.30 -5.58 1.61e+00 3.86e-01 1.20e+01 angle pdb=" CA GLN B 318 " pdb=" CB GLN B 318 " pdb=" CG GLN B 318 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CB GLN B 318 " pdb=" CG GLN B 318 " pdb=" CD GLN B 318 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.70e+00 3.46e-01 1.08e+01 angle pdb=" C SER B 86 " pdb=" N ARG B 87 " pdb=" CA ARG B 87 " ideal model delta sigma weight residual 120.99 127.11 -6.12 1.86e+00 2.89e-01 1.08e+01 ... (remaining 14770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5990 17.59 - 35.18: 539 35.18 - 52.78: 120 52.78 - 70.37: 33 70.37 - 87.96: 8 Dihedral angle restraints: 6690 sinusoidal: 2817 harmonic: 3873 Sorted by residual: dihedral pdb=" CA ALA A 497 " pdb=" C ALA A 497 " pdb=" N ASN A 498 " pdb=" CA ASN A 498 " ideal model delta harmonic sigma weight residual -180.00 -159.08 -20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA TRP A 678 " pdb=" C TRP A 678 " pdb=" N MET A 679 " pdb=" CA MET A 679 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA LEU A 376 " pdb=" C LEU A 376 " pdb=" N ALA A 377 " pdb=" CA ALA A 377 " ideal model delta harmonic sigma weight residual 180.00 162.46 17.54 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1657 0.151 - 0.301: 7 0.301 - 0.452: 1 0.452 - 0.603: 0 0.603 - 0.753: 1 Chirality restraints: 1666 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 461 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 498 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.81 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1663 not shown) Planarity restraints: 1937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 468 " -0.071 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 469 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 469 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 469 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 498 " 0.038 2.00e-02 2.50e+03 3.51e-02 1.54e+01 pdb=" CG ASN A 498 " -0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 498 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 498 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 498 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" CG ASN A 498 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 498 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 498 " 0.012 2.00e-02 2.50e+03 ... (remaining 1934 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 313 2.70 - 3.25: 9310 3.25 - 3.80: 15472 3.80 - 4.35: 19189 4.35 - 4.90: 33322 Nonbonded interactions: 77606 Sorted by model distance: nonbonded pdb=" NZ LYS B 218 " pdb=" O SER B 219 " model vdw 2.149 3.120 nonbonded pdb=" N GLU B 55 " pdb=" OE1 GLU B 55 " model vdw 2.251 3.120 nonbonded pdb=" OG SER A 165 " pdb=" OG1 THR A 210 " model vdw 2.256 3.040 nonbonded pdb=" NH2 ARG A 464 " pdb=" OD2 ASP A 482 " model vdw 2.294 3.120 nonbonded pdb=" NH2 ARG A 355 " pdb=" O MET B 538 " model vdw 2.295 3.120 ... (remaining 77601 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 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue 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: 4.070 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.630 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 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 : 0.003 0.080 10878 Z= 0.148 Angle : 0.693 18.534 14835 Z= 0.334 Chirality : 0.049 0.753 1666 Planarity : 0.005 0.103 1930 Dihedral : 14.587 87.959 4164 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 0.18 % Allowed : 17.13 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.23), residues: 1346 helix: None (None), residues: 0 sheet: 0.86 (0.20), residues: 657 loop : -0.82 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 506 TYR 0.014 0.001 TYR B 166 PHE 0.022 0.001 PHE A 173 TRP 0.007 0.001 TRP A 73 HIS 0.008 0.001 HIS B 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (10854) covalent geometry : angle 0.62542 / 0.32 (14775) SS BOND : bond 0.00189 / 0.12 ( 12) SS BOND : angle 0.44012 / 0.28 ( 24) hydrogen bonds : bond 0.10743 / 6.93 ( 352) hydrogen bonds : angle 5.67333 / 3.72 ( 906) link_BETA1-4 : bond 0.00578 / 0.28 ( 5) link_BETA1-4 : angle 3.09671 / 1.76 ( 15) link_NAG-ASN : bond 0.01058 / 0.43 ( 7) link_NAG-ASN : angle 7.51686 / 5.58 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.322 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 0.0872 time to fit residues: 7.6100 Evaluate side-chains 54 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain B residue 306 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0770 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 HIS B 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.193417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.174696 restraints weight = 17708.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.170026 restraints weight = 26577.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.166861 restraints weight = 31737.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.165748 restraints weight = 36777.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.164099 restraints weight = 27521.319| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.0566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10878 Z= 0.115 Angle : 0.611 17.316 14835 Z= 0.296 Chirality : 0.045 0.618 1666 Planarity : 0.004 0.065 1930 Dihedral : 6.210 52.904 1702 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.20 % Favored : 94.65 % Rotamer: Outliers : 2.48 % Allowed : 15.79 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.23), residues: 1346 helix: -5.40 (0.25), residues: 6 sheet: 0.88 (0.20), residues: 656 loop : -0.84 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.009 0.001 TYR B 405 PHE 0.026 0.002 PHE B 184 TRP 0.007 0.001 TRP A 73 HIS 0.006 0.001 HIS B 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (10854) covalent geometry : angle 0.55675 / 0.28 (14775) SS BOND : bond 0.00177 / 0.11 ( 12) SS BOND : angle 0.43530 / 0.29 ( 24) hydrogen bonds : bond 0.02737 / 1.80 ( 352) hydrogen bonds : angle 5.05827 / 3.33 ( 906) link_BETA1-4 : bond 0.00591 / 0.28 ( 5) link_BETA1-4 : angle 2.29905 / 1.31 ( 15) link_NAG-ASN : bond 0.01139 / 0.46 ( 7) link_NAG-ASN : angle 6.47459 / 4.97 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7536 (ppp) cc_final: 0.6997 (ppp) REVERT: A 468 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8259 (m) REVERT: B 152 MET cc_start: 0.6983 (tmm) cc_final: 0.5939 (ttt) outliers start: 28 outliers final: 15 residues processed: 81 average time/residue: 0.0826 time to fit residues: 10.0809 Evaluate side-chains 72 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 106 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.188924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.171074 restraints weight = 17794.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.165627 restraints weight = 26008.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.161438 restraints weight = 31099.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.161169 restraints weight = 39954.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.159710 restraints weight = 30065.698| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10878 Z= 0.153 Angle : 0.623 16.209 14835 Z= 0.306 Chirality : 0.046 0.605 1666 Planarity : 0.005 0.069 1930 Dihedral : 5.874 52.583 1701 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.20 % Favored : 94.73 % Rotamer: Outliers : 3.11 % Allowed : 15.53 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.23), residues: 1346 helix: -5.40 (0.25), residues: 6 sheet: 0.86 (0.20), residues: 630 loop : -0.89 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 123 TYR 0.012 0.001 TYR A 109 PHE 0.026 0.002 PHE A 493 TRP 0.008 0.001 TRP A 73 HIS 0.005 0.001 HIS B 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (10854) covalent geometry : angle 0.57994 / 0.30 (14775) SS BOND : bond 0.00255 / 0.15 ( 12) SS BOND : angle 0.62226 / 0.43 ( 24) hydrogen bonds : bond 0.03077 / 2.04 ( 352) hydrogen bonds : angle 5.01447 / 3.30 ( 906) link_BETA1-4 : bond 0.00374 / 0.19 ( 5) link_BETA1-4 : angle 2.15490 / 1.21 ( 15) link_NAG-ASN : bond 0.00936 / 0.35 ( 7) link_NAG-ASN : angle 5.80531 / 4.58 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 65 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7568 (ppp) cc_final: 0.7117 (ppp) REVERT: A 346 TRP cc_start: 0.9182 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: A 355 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7953 (mpt-90) REVERT: A 468 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8323 (m) outliers start: 35 outliers final: 20 residues processed: 92 average time/residue: 0.0850 time to fit residues: 11.6926 Evaluate side-chains 78 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 94 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 127 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.189594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.169560 restraints weight = 17683.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.165143 restraints weight = 30775.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.163861 restraints weight = 34298.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.162997 restraints weight = 35401.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.160908 restraints weight = 29325.699| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10878 Z= 0.127 Angle : 0.603 15.800 14835 Z= 0.295 Chirality : 0.045 0.606 1666 Planarity : 0.004 0.071 1930 Dihedral : 5.591 51.596 1701 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.32 % Rotamer: Outliers : 3.19 % Allowed : 16.06 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1346 helix: -5.37 (0.26), residues: 6 sheet: 0.90 (0.20), residues: 630 loop : -0.85 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 244 TYR 0.011 0.001 TYR B 405 PHE 0.027 0.001 PHE A 493 TRP 0.020 0.001 TRP A 273 HIS 0.005 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (10854) covalent geometry : angle 0.56428 / 0.29 (14775) SS BOND : bond 0.00241 / 0.14 ( 12) SS BOND : angle 0.48573 / 0.35 ( 24) hydrogen bonds : bond 0.02775 / 1.83 ( 352) hydrogen bonds : angle 4.86246 / 3.21 ( 906) link_BETA1-4 : bond 0.00354 / 0.18 ( 5) link_BETA1-4 : angle 2.15618 / 1.21 ( 15) link_NAG-ASN : bond 0.00899 / 0.33 ( 7) link_NAG-ASN : angle 5.40615 / 4.34 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 55 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7595 (ppp) cc_final: 0.7263 (ppp) REVERT: A 355 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8003 (mpt-90) REVERT: A 468 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8344 (m) REVERT: A 679 MET cc_start: 0.1856 (mpp) cc_final: 0.1621 (tpt) REVERT: A 789 ARG cc_start: -0.1471 (OUTLIER) cc_final: -0.2371 (tmt170) REVERT: B 233 ASP cc_start: 0.5930 (OUTLIER) cc_final: 0.5025 (p0) outliers start: 36 outliers final: 26 residues processed: 83 average time/residue: 0.0835 time to fit residues: 10.3170 Evaluate side-chains 85 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 109 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.188585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.167514 restraints weight = 17611.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.162764 restraints weight = 33327.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.160764 restraints weight = 37515.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.160809 restraints weight = 37129.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.159930 restraints weight = 25075.032| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10878 Z= 0.152 Angle : 0.613 15.547 14835 Z= 0.301 Chirality : 0.046 0.613 1666 Planarity : 0.005 0.076 1930 Dihedral : 5.473 51.572 1701 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.35 % Favored : 94.58 % Rotamer: Outliers : 3.64 % Allowed : 16.77 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.23), residues: 1346 helix: -5.39 (0.25), residues: 6 sheet: 0.89 (0.20), residues: 624 loop : -0.85 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 789 TYR 0.012 0.001 TYR B 405 PHE 0.029 0.002 PHE A 493 TRP 0.009 0.001 TRP A 273 HIS 0.004 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 (10854) covalent geometry : angle 0.57777 / 0.29 (14775) SS BOND : bond 0.00213 / 0.13 ( 12) SS BOND : angle 0.55541 / 0.37 ( 24) hydrogen bonds : bond 0.03003 / 1.98 ( 352) hydrogen bonds : angle 4.89647 / 3.24 ( 906) link_BETA1-4 : bond 0.00354 / 0.18 ( 5) link_BETA1-4 : angle 2.17293 / 1.22 ( 15) link_NAG-ASN : bond 0.00822 / 0.29 ( 7) link_NAG-ASN : angle 5.17908 / 4.22 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 59 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7561 (ppp) cc_final: 0.7357 (ppp) REVERT: A 346 TRP cc_start: 0.9248 (OUTLIER) cc_final: 0.7894 (m-10) REVERT: A 355 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8034 (mpt-90) REVERT: A 427 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8421 (mp) REVERT: A 468 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8418 (m) REVERT: A 579 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7431 (mm) REVERT: A 789 ARG cc_start: -0.1371 (OUTLIER) cc_final: -0.2312 (tmt170) outliers start: 41 outliers final: 27 residues processed: 93 average time/residue: 0.0781 time to fit residues: 10.9579 Evaluate side-chains 89 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 56 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 93 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.189721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.170897 restraints weight = 17374.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.166155 restraints weight = 28523.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.164877 restraints weight = 35725.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.164480 restraints weight = 35933.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.163170 restraints weight = 24918.997| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10878 Z= 0.197 Angle : 0.654 15.746 14835 Z= 0.323 Chirality : 0.047 0.627 1666 Planarity : 0.005 0.075 1930 Dihedral : 5.607 52.910 1701 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.65 % Favored : 94.28 % Rotamer: Outliers : 4.44 % Allowed : 16.86 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.23), residues: 1346 helix: -5.41 (0.24), residues: 6 sheet: 0.84 (0.20), residues: 620 loop : -0.95 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 506 TYR 0.015 0.001 TYR A 109 PHE 0.029 0.002 PHE A 493 TRP 0.033 0.002 TRP A 273 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (10854) covalent geometry : angle 0.62169 / 0.32 (14775) SS BOND : bond 0.00235 / 0.14 ( 12) SS BOND : angle 0.65063 / 0.44 ( 24) hydrogen bonds : bond 0.03339 / 2.20 ( 352) hydrogen bonds : angle 5.06378 / 3.35 ( 906) link_BETA1-4 : bond 0.00350 / 0.17 ( 5) link_BETA1-4 : angle 2.21175 / 1.24 ( 15) link_NAG-ASN : bond 0.00790 / 0.28 ( 7) link_NAG-ASN : angle 5.10207 / 4.20 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 58 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6359 (OUTLIER) cc_final: 0.5975 (m-10) REVERT: A 346 TRP cc_start: 0.9274 (OUTLIER) cc_final: 0.8037 (m-10) REVERT: A 427 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8399 (mp) REVERT: A 468 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8463 (m) REVERT: A 562 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7132 (ttt180) REVERT: A 579 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7389 (mm) REVERT: A 679 MET cc_start: 0.1637 (mpp) cc_final: 0.1135 (tpp) REVERT: A 789 ARG cc_start: -0.1301 (OUTLIER) cc_final: -0.2218 (tmt170) outliers start: 50 outliers final: 35 residues processed: 101 average time/residue: 0.0704 time to fit residues: 10.9909 Evaluate side-chains 99 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 57 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 306 CYS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 9 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.187925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.166927 restraints weight = 17495.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.162510 restraints weight = 33261.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.159652 restraints weight = 37440.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.159691 restraints weight = 37996.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.158894 restraints weight = 24991.406| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10878 Z= 0.150 Angle : 0.642 15.451 14835 Z= 0.313 Chirality : 0.046 0.608 1666 Planarity : 0.005 0.077 1930 Dihedral : 5.319 52.103 1699 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.13 % Favored : 94.80 % Rotamer: Outliers : 4.70 % Allowed : 16.77 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.23), residues: 1346 helix: -5.42 (0.24), residues: 6 sheet: 0.89 (0.20), residues: 619 loop : -0.91 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 506 TYR 0.011 0.001 TYR A 109 PHE 0.031 0.002 PHE A 493 TRP 0.037 0.001 TRP A 273 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (10854) covalent geometry : angle 0.61115 / 0.31 (14775) SS BOND : bond 0.00201 / 0.13 ( 12) SS BOND : angle 0.52427 / 0.35 ( 24) hydrogen bonds : bond 0.03010 / 1.96 ( 352) hydrogen bonds : angle 4.95159 / 3.27 ( 906) link_BETA1-4 : bond 0.00361 / 0.18 ( 5) link_BETA1-4 : angle 2.21820 / 1.24 ( 15) link_NAG-ASN : bond 0.00793 / 0.27 ( 7) link_NAG-ASN : angle 4.93269 / 4.08 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 59 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6472 (OUTLIER) cc_final: 0.6161 (m-10) REVERT: A 346 TRP cc_start: 0.9240 (OUTLIER) cc_final: 0.7922 (m-10) REVERT: A 355 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7977 (mpt180) REVERT: A 427 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8427 (mp) REVERT: A 468 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8422 (m) REVERT: A 562 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7149 (ttt180) REVERT: A 579 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7476 (mm) REVERT: A 679 MET cc_start: 0.1441 (mpp) cc_final: 0.0792 (tpt) outliers start: 53 outliers final: 38 residues processed: 104 average time/residue: 0.0924 time to fit residues: 14.7684 Evaluate side-chains 98 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 53 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 562 ARG Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 306 CYS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 93 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 131 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.189697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.168090 restraints weight = 17218.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.164366 restraints weight = 33448.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.162145 restraints weight = 34921.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.160646 restraints weight = 37743.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.158569 restraints weight = 34836.186| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10878 Z= 0.167 Angle : 0.652 15.348 14835 Z= 0.319 Chirality : 0.046 0.612 1666 Planarity : 0.005 0.080 1930 Dihedral : 5.307 51.813 1699 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.42 % Favored : 94.50 % Rotamer: Outliers : 4.61 % Allowed : 16.95 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.23), residues: 1346 helix: -5.42 (0.24), residues: 6 sheet: 0.94 (0.20), residues: 622 loop : -0.90 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 506 TYR 0.013 0.001 TYR A 109 PHE 0.030 0.002 PHE A 493 TRP 0.040 0.002 TRP A 273 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (10854) covalent geometry : angle 0.62274 / 0.31 (14775) SS BOND : bond 0.00215 / 0.13 ( 12) SS BOND : angle 0.58494 / 0.39 ( 24) hydrogen bonds : bond 0.03111 / 2.03 ( 352) hydrogen bonds : angle 4.96921 / 3.30 ( 906) link_BETA1-4 : bond 0.00378 / 0.19 ( 5) link_BETA1-4 : angle 2.20942 / 1.23 ( 15) link_NAG-ASN : bond 0.00767 / 0.27 ( 7) link_NAG-ASN : angle 4.88998 / 4.05 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 58 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.6238 (m-10) REVERT: A 355 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7969 (mpt180) REVERT: A 427 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8476 (mp) REVERT: A 468 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8457 (m) outliers start: 52 outliers final: 42 residues processed: 102 average time/residue: 0.0751 time to fit residues: 11.7410 Evaluate side-chains 98 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 52 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 306 CYS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 130 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.187598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.166666 restraints weight = 17562.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.162125 restraints weight = 35957.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.160649 restraints weight = 36258.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.160404 restraints weight = 37232.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.160156 restraints weight = 23815.093| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10878 Z= 0.148 Angle : 0.643 15.127 14835 Z= 0.313 Chirality : 0.046 0.602 1666 Planarity : 0.005 0.084 1930 Dihedral : 5.189 50.659 1699 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.87 % Rotamer: Outliers : 4.26 % Allowed : 17.21 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.23), residues: 1346 helix: -5.42 (0.24), residues: 6 sheet: 0.98 (0.21), residues: 621 loop : -0.85 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 506 TYR 0.012 0.001 TYR A 109 PHE 0.029 0.002 PHE A 493 TRP 0.033 0.001 TRP A 273 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (10854) covalent geometry : angle 0.61457 / 0.31 (14775) SS BOND : bond 0.00214 / 0.13 ( 12) SS BOND : angle 0.53739 / 0.35 ( 24) hydrogen bonds : bond 0.02951 / 1.92 ( 352) hydrogen bonds : angle 4.88579 / 3.24 ( 906) link_BETA1-4 : bond 0.00369 / 0.19 ( 5) link_BETA1-4 : angle 2.19573 / 1.22 ( 15) link_NAG-ASN : bond 0.00764 / 0.26 ( 7) link_NAG-ASN : angle 4.78307 / 3.98 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 57 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8019 (mpt180) REVERT: A 427 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8422 (mp) REVERT: A 468 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8475 (m) outliers start: 48 outliers final: 38 residues processed: 97 average time/residue: 0.0693 time to fit residues: 10.6233 Evaluate side-chains 93 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 52 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 306 CYS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 33 optimal weight: 0.6980 chunk 130 optimal weight: 0.0030 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 59 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.187203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.169735 restraints weight = 17422.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.163928 restraints weight = 24822.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.160158 restraints weight = 30849.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.159663 restraints weight = 37455.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.158691 restraints weight = 27930.199| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10878 Z= 0.164 Angle : 0.661 15.017 14835 Z= 0.322 Chirality : 0.046 0.603 1666 Planarity : 0.005 0.087 1930 Dihedral : 5.255 50.180 1699 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.50 % Favored : 94.43 % Rotamer: Outliers : 4.26 % Allowed : 17.21 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.23), residues: 1346 helix: -5.42 (0.24), residues: 6 sheet: 0.93 (0.21), residues: 609 loop : -0.85 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 314 TYR 0.012 0.001 TYR A 109 PHE 0.028 0.002 PHE A 493 TRP 0.031 0.001 TRP A 273 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.16 (10854) covalent geometry : angle 0.63301 / 0.32 (14775) SS BOND : bond 0.00274 / 0.16 ( 12) SS BOND : angle 0.68407 / 0.42 ( 24) hydrogen bonds : bond 0.03074 / 2.00 ( 352) hydrogen bonds : angle 4.96201 / 3.29 ( 906) link_BETA1-4 : bond 0.00371 / 0.19 ( 5) link_BETA1-4 : angle 2.18734 / 1.22 ( 15) link_NAG-ASN : bond 0.00750 / 0.26 ( 7) link_NAG-ASN : angle 4.75124 / 3.95 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 53 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.6263 (m-10) REVERT: A 355 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7975 (mpt180) REVERT: A 427 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8426 (mp) REVERT: A 468 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8493 (m) REVERT: B 262 PHE cc_start: 0.3341 (OUTLIER) cc_final: 0.2724 (t80) outliers start: 48 outliers final: 37 residues processed: 94 average time/residue: 0.0684 time to fit residues: 10.3364 Evaluate side-chains 94 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 52 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 306 CYS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 31 optimal weight: 0.9980 chunk 129 optimal weight: 20.0000 chunk 122 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 102 optimal weight: 0.2980 chunk 93 optimal weight: 7.9990 chunk 133 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.188719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.171015 restraints weight = 17589.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.165380 restraints weight = 25313.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.161069 restraints weight = 29051.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.160337 restraints weight = 33569.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.159402 restraints weight = 27219.039| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10878 Z= 0.117 Angle : 0.627 14.572 14835 Z= 0.304 Chirality : 0.045 0.578 1666 Planarity : 0.004 0.082 1930 Dihedral : 4.984 47.696 1699 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 3.46 % Allowed : 17.92 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.23), residues: 1346 helix: -5.40 (0.24), residues: 6 sheet: 1.04 (0.21), residues: 612 loop : -0.73 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 506 TYR 0.010 0.001 TYR B 405 PHE 0.029 0.001 PHE A 493 TRP 0.031 0.001 TRP A 273 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10854) covalent geometry : angle 0.60011 / 0.30 (14775) SS BOND : bond 0.00204 / 0.12 ( 12) SS BOND : angle 0.45896 / 0.28 ( 24) hydrogen bonds : bond 0.02641 / 1.72 ( 352) hydrogen bonds : angle 4.76208 / 3.15 ( 906) link_BETA1-4 : bond 0.00387 / 0.19 ( 5) link_BETA1-4 : angle 2.16355 / 1.20 ( 15) link_NAG-ASN : bond 0.00784 / 0.28 ( 7) link_NAG-ASN : angle 4.56149 / 3.80 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1537.75 seconds wall clock time: 27 minutes 12.18 seconds (1632.18 seconds total)