Starting phenix.real_space_refine on Sun May 3 17:25:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5wpt_8882/05_2026/5wpt_8882.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wpt_8882/05_2026/5wpt_8882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5wpt_8882/05_2026/5wpt_8882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wpt_8882/05_2026/5wpt_8882.map" model { file = "/net/cci-nas-00/data/ceres_data/5wpt_8882/05_2026/5wpt_8882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wpt_8882/05_2026/5wpt_8882.cif" } resolution = 3.75 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= 0.010 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: 5 Type Number sf(0) Gaussians S 96 5.16 5 Na 1 4.78 5 C 9772 2.51 5 N 2444 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14889 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "B" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "C" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "D" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 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: "G" 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: "H" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.95, per 1000 atoms: 0.27 Number of scatterers: 14889 At special positions: 0 Unit cell: (110.21, 110.21, 117.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 Na 1 11.00 O 2576 8.00 N 2444 7.00 C 9772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 230 " " NAG F 1 " - " ASN B 230 " " NAG G 1 " - " ASN C 230 " " NAG H 1 " - " ASN D 230 " Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 684.0 milliseconds 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3472 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 4 sheets defined 63.1% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 38 through 49 removed outlier: 3.535A pdb=" N ARG A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 57 removed outlier: 3.612A pdb=" N ARG A 57 " --> pdb=" O CYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 106 removed outlier: 3.955A pdb=" N LEU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.645A pdb=" N ALA A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.718A pdb=" N ILE A 246 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 337 removed outlier: 3.916A pdb=" N VAL A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.577A pdb=" N ARG A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 354 through 376 removed outlier: 3.759A pdb=" N GLU A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 400 removed outlier: 3.875A pdb=" N THR A 392 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 407 removed outlier: 3.784A pdb=" N PHE A 407 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 420 through 447 removed outlier: 4.571A pdb=" N SER A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 removed outlier: 3.520A pdb=" N VAL A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.541A pdb=" N THR A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 487 removed outlier: 3.589A pdb=" N SER A 487 " --> pdb=" O GLN A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 489 through 507 removed outlier: 3.618A pdb=" N LEU A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 505 " --> pdb=" O PHE A 501 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 526 Processing helix chain 'B' and resid 39 through 49 removed outlier: 3.935A pdb=" N LEU B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.612A pdb=" N ARG B 57 " --> pdb=" O CYS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 106 removed outlier: 3.954A pdb=" N LEU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN B 97 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.645A pdb=" N ALA B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.717A pdb=" N ILE B 246 " --> pdb=" O GLN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 337 removed outlier: 3.916A pdb=" N VAL B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.576A pdb=" N ARG B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 354 through 376 removed outlier: 3.758A pdb=" N GLU B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 400 removed outlier: 3.876A pdb=" N THR B 392 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 407 removed outlier: 3.785A pdb=" N PHE B 407 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 420 through 447 removed outlier: 4.570A pdb=" N SER B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 removed outlier: 3.520A pdb=" N VAL B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 483 removed outlier: 3.541A pdb=" N THR B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 487 removed outlier: 3.588A pdb=" N SER B 487 " --> pdb=" O GLN B 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 484 through 487' Processing helix chain 'B' and resid 489 through 507 removed outlier: 3.618A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 505 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 526 Processing helix chain 'C' and resid 39 through 49 removed outlier: 3.935A pdb=" N LEU C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 57 removed outlier: 3.611A pdb=" N ARG C 57 " --> pdb=" O CYS C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 106 removed outlier: 3.955A pdb=" N LEU C 68 " --> pdb=" O CYS C 64 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 138 removed outlier: 3.646A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.717A pdb=" N ILE C 246 " --> pdb=" O GLN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 337 removed outlier: 3.915A pdb=" N VAL C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.577A pdb=" N ARG C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 351 No H-bonds generated for 'chain 'C' and resid 349 through 351' Processing helix chain 'C' and resid 354 through 376 removed outlier: 3.759A pdb=" N GLU C 376 " --> pdb=" O LYS C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 400 removed outlier: 3.875A pdb=" N THR C 392 " --> pdb=" O ILE C 388 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 407 removed outlier: 3.785A pdb=" N PHE C 407 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 420 through 447 removed outlier: 4.571A pdb=" N SER C 424 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.519A pdb=" N VAL C 460 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN C 469 " --> pdb=" O PHE C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 483 removed outlier: 3.541A pdb=" N THR C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 487 removed outlier: 3.590A pdb=" N SER C 487 " --> pdb=" O GLN C 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 484 through 487' Processing helix chain 'C' and resid 489 through 507 removed outlier: 3.618A pdb=" N LEU C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 505 " --> pdb=" O PHE C 501 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 526 Processing helix chain 'D' and resid 39 through 49 removed outlier: 3.935A pdb=" N LEU D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 57 removed outlier: 3.612A pdb=" N ARG D 57 " --> pdb=" O CYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 106 removed outlier: 3.954A pdb=" N LEU D 68 " --> pdb=" O CYS D 64 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 138 removed outlier: 3.646A pdb=" N ALA D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 242 through 246 removed outlier: 3.717A pdb=" N ILE D 246 " --> pdb=" O GLN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 337 removed outlier: 3.916A pdb=" N VAL D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 317 " --> pdb=" O PHE D 313 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 348 removed outlier: 3.576A pdb=" N ARG D 347 " --> pdb=" O SER D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 351 No H-bonds generated for 'chain 'D' and resid 349 through 351' Processing helix chain 'D' and resid 354 through 376 removed outlier: 3.759A pdb=" N GLU D 376 " --> pdb=" O LYS D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 400 removed outlier: 3.875A pdb=" N THR D 392 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D 395 " --> pdb=" O GLY D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 407 removed outlier: 3.785A pdb=" N PHE D 407 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 420 through 447 removed outlier: 4.571A pdb=" N SER D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE D 428 " --> pdb=" O SER D 424 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 470 removed outlier: 3.520A pdb=" N VAL D 460 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN D 469 " --> pdb=" O PHE D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.541A pdb=" N THR D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 487 removed outlier: 3.588A pdb=" N SER D 487 " --> pdb=" O GLN D 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 484 through 487' Processing helix chain 'D' and resid 489 through 507 removed outlier: 3.618A pdb=" N LEU D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE D 505 " --> pdb=" O PHE D 501 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR D 507 " --> pdb=" O SER D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 526 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.600A pdb=" N ILE A 271 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 276 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU A 228 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR A 170 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 163 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 169 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ARG A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.600A pdb=" N ILE B 271 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 276 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU B 228 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR B 170 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 163 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 169 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ARG B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.599A pdb=" N ILE C 271 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU C 276 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU C 228 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR C 170 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 163 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 169 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ARG C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.599A pdb=" N ILE D 271 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU D 276 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU D 228 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR D 170 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 163 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 169 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ARG D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 1.75 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: 4435 1.34 - 1.46: 3038 1.46 - 1.57: 7631 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 15236 Sorted by residual: bond pdb=" CB VAL C 434 " pdb=" CG1 VAL C 434 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.19e+00 bond pdb=" CB VAL B 434 " pdb=" CG1 VAL B 434 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.15e+00 bond pdb=" CB VAL D 434 " pdb=" CG1 VAL D 434 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.11e+00 bond pdb=" CB VAL A 434 " pdb=" CG1 VAL A 434 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.11e+00 bond pdb=" C GLY A 470 " pdb=" N ASP A 471 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.92e-02 2.71e+03 3.65e+00 ... (remaining 15231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 19657 2.16 - 4.32: 846 4.32 - 6.49: 101 6.49 - 8.65: 32 8.65 - 10.81: 16 Bond angle restraints: 20652 Sorted by residual: angle pdb=" C ALA D 421 " pdb=" N LEU D 422 " pdb=" CA LEU D 422 " ideal model delta sigma weight residual 120.06 124.44 -4.38 1.19e+00 7.06e-01 1.35e+01 angle pdb=" C ALA B 421 " pdb=" N LEU B 422 " pdb=" CA LEU B 422 " ideal model delta sigma weight residual 120.06 124.42 -4.36 1.19e+00 7.06e-01 1.34e+01 angle pdb=" C ALA A 421 " pdb=" N LEU A 422 " pdb=" CA LEU A 422 " ideal model delta sigma weight residual 120.06 124.39 -4.33 1.19e+00 7.06e-01 1.32e+01 angle pdb=" C ALA C 421 " pdb=" N LEU C 422 " pdb=" CA LEU C 422 " ideal model delta sigma weight residual 120.06 124.39 -4.33 1.19e+00 7.06e-01 1.32e+01 angle pdb=" C ILE A 402 " pdb=" N ARG A 403 " pdb=" CA ARG A 403 " ideal model delta sigma weight residual 120.28 125.09 -4.81 1.44e+00 4.82e-01 1.12e+01 ... (remaining 20647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 8434 15.83 - 31.66: 485 31.66 - 47.48: 117 47.48 - 63.31: 8 63.31 - 79.14: 12 Dihedral angle restraints: 9056 sinusoidal: 3692 harmonic: 5364 Sorted by residual: dihedral pdb=" CA ASN D 412 " pdb=" C ASN D 412 " pdb=" N ILE D 413 " pdb=" CA ILE D 413 " ideal model delta harmonic sigma weight residual 180.00 125.16 54.84 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA ASN C 412 " pdb=" C ASN C 412 " pdb=" N ILE C 413 " pdb=" CA ILE C 413 " ideal model delta harmonic sigma weight residual 180.00 125.16 54.84 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA ASN A 412 " pdb=" C ASN A 412 " pdb=" N ILE A 413 " pdb=" CA ILE A 413 " ideal model delta harmonic sigma weight residual 180.00 125.16 54.84 0 5.00e+00 4.00e-02 1.20e+02 ... (remaining 9053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1506 0.046 - 0.092: 707 0.092 - 0.139: 155 0.139 - 0.185: 48 0.185 - 0.231: 4 Chirality restraints: 2420 Sorted by residual: chirality pdb=" CB ILE A 193 " pdb=" CA ILE A 193 " pdb=" CG1 ILE A 193 " pdb=" CG2 ILE A 193 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE B 193 " pdb=" CA ILE B 193 " pdb=" CG1 ILE B 193 " pdb=" CG2 ILE B 193 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE D 193 " pdb=" CA ILE D 193 " pdb=" CG1 ILE D 193 " pdb=" CG2 ILE D 193 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 2417 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 526 " -0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO B 527 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 526 " -0.048 5.00e-02 4.00e+02 7.30e-02 8.54e+00 pdb=" N PRO A 527 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 526 " -0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO D 527 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 527 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 527 " -0.043 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4018 2.80 - 3.33: 13517 3.33 - 3.85: 22826 3.85 - 4.38: 26010 4.38 - 4.90: 44022 Nonbonded interactions: 110393 Sorted by model distance: nonbonded pdb=" O TRP B 335 " pdb=" CG ARG B 338 " model vdw 2.276 3.440 nonbonded pdb=" O TRP A 335 " pdb=" CG ARG A 338 " model vdw 2.277 3.440 nonbonded pdb=" O TRP D 335 " pdb=" CG ARG D 338 " model vdw 2.278 3.440 nonbonded pdb=" O TRP C 335 " pdb=" CG ARG C 338 " model vdw 2.280 3.440 nonbonded pdb=" O PHE D 93 " pdb=" ND2 ASN D 97 " model vdw 2.386 3.120 ... (remaining 110388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 527) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.170 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.009 0.068 15244 Z= 0.367 Angle : 1.057 10.810 20676 Z= 0.546 Chirality : 0.054 0.231 2420 Planarity : 0.008 0.073 2516 Dihedral : 11.173 79.141 5584 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.07 % Favored : 91.70 % Rotamer: Outliers : 0.24 % Allowed : 3.95 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -5.18 (0.13), residues: 1784 helix: -3.19 (0.10), residues: 1028 sheet: -2.71 (0.29), residues: 204 loop : -3.76 (0.19), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 455 TYR 0.026 0.004 TYR A 383 PHE 0.028 0.003 PHE D 407 TRP 0.022 0.003 TRP A 444 HIS 0.011 0.003 HIS D 103 Details of bonding type rmsd covalent geometry : bond 0.00855 (15236) covalent geometry : angle 1.04114 (20652) hydrogen bonds : bond 0.22385 ( 820) hydrogen bonds : angle 7.91974 ( 2376) link_BETA1-4 : bond 0.00872 ( 4) link_BETA1-4 : angle 1.43526 ( 12) link_NAG-ASN : bond 0.00113 ( 4) link_NAG-ASN : angle 7.54995 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 417 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6011 (mttt) cc_final: 0.5321 (mmtt) REVERT: A 62 LYS cc_start: 0.5648 (mttt) cc_final: 0.5069 (tttt) REVERT: A 63 PRO cc_start: 0.8154 (Cg_endo) cc_final: 0.7729 (Cg_exo) REVERT: A 516 LEU cc_start: 0.9064 (mm) cc_final: 0.8812 (mt) REVERT: B 46 LYS cc_start: 0.5998 (mttt) cc_final: 0.5287 (mmtt) REVERT: B 63 PRO cc_start: 0.8018 (Cg_endo) cc_final: 0.7624 (Cg_exo) REVERT: B 226 HIS cc_start: 0.7376 (m-70) cc_final: 0.7168 (p-80) REVERT: B 322 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7824 (ttt180) REVERT: B 324 PHE cc_start: 0.8548 (t80) cc_final: 0.7658 (m-80) REVERT: B 409 HIS cc_start: 0.7580 (t-90) cc_final: 0.7373 (t-90) REVERT: B 516 LEU cc_start: 0.9093 (mm) cc_final: 0.8866 (mt) REVERT: C 46 LYS cc_start: 0.6058 (mttt) cc_final: 0.5250 (mmtt) REVERT: C 63 PRO cc_start: 0.8071 (Cg_endo) cc_final: 0.7674 (Cg_exo) REVERT: C 226 HIS cc_start: 0.7395 (m-70) cc_final: 0.7189 (p-80) REVERT: C 324 PHE cc_start: 0.8560 (t80) cc_final: 0.7770 (m-80) REVERT: C 516 LEU cc_start: 0.9088 (mm) cc_final: 0.8873 (mt) REVERT: D 46 LYS cc_start: 0.6015 (mttt) cc_final: 0.5224 (mmtt) REVERT: D 63 PRO cc_start: 0.8144 (Cg_endo) cc_final: 0.7758 (Cg_exo) REVERT: D 226 HIS cc_start: 0.7366 (m-70) cc_final: 0.7156 (p-80) REVERT: D 324 PHE cc_start: 0.8596 (t80) cc_final: 0.7776 (m-80) REVERT: D 409 HIS cc_start: 0.7626 (t-90) cc_final: 0.7413 (t-90) REVERT: D 516 LEU cc_start: 0.9068 (mm) cc_final: 0.8846 (mt) outliers start: 4 outliers final: 4 residues processed: 421 average time/residue: 0.1550 time to fit residues: 91.0775 Evaluate side-chains 216 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 212 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 352 ASN ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 HIS B 174 HIS B 328 ASN B 352 ASN B 409 HIS B 526 HIS C 174 HIS C 328 ASN C 352 ASN ** C 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS D 174 HIS D 328 ASN D 352 ASN D 409 HIS D 526 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101150 restraints weight = 27901.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103687 restraints weight = 16637.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105237 restraints weight = 12188.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106265 restraints weight = 10206.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106740 restraints weight = 9115.448| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15244 Z= 0.191 Angle : 0.733 9.063 20676 Z= 0.380 Chirality : 0.042 0.151 2420 Planarity : 0.005 0.061 2516 Dihedral : 6.602 45.687 2168 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.51 % Favored : 92.43 % Rotamer: Outliers : 3.16 % Allowed : 10.28 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -2.48 (0.18), residues: 1784 helix: -0.54 (0.15), residues: 1040 sheet: -2.32 (0.31), residues: 204 loop : -3.44 (0.21), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 427 TYR 0.015 0.001 TYR A 218 PHE 0.012 0.002 PHE C 235 TRP 0.011 0.002 TRP A 444 HIS 0.004 0.001 HIS C 526 Details of bonding type rmsd covalent geometry : bond 0.00416 (15236) covalent geometry : angle 0.72278 (20652) hydrogen bonds : bond 0.07353 ( 820) hydrogen bonds : angle 4.88469 ( 2376) link_BETA1-4 : bond 0.00154 ( 4) link_BETA1-4 : angle 0.93330 ( 12) link_NAG-ASN : bond 0.00148 ( 4) link_NAG-ASN : angle 4.99951 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 280 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.5894 (mttt) cc_final: 0.5216 (mptt) REVERT: A 63 PRO cc_start: 0.8192 (Cg_endo) cc_final: 0.7832 (Cg_exo) REVERT: A 324 PHE cc_start: 0.8354 (t80) cc_final: 0.7595 (m-80) REVERT: A 340 ARG cc_start: 0.7319 (tpt90) cc_final: 0.7064 (tpt90) REVERT: A 418 LEU cc_start: 0.7224 (pp) cc_final: 0.6993 (tp) REVERT: A 419 ARG cc_start: 0.7110 (ttp-110) cc_final: 0.6289 (tpp-160) REVERT: A 516 LEU cc_start: 0.9005 (mm) cc_final: 0.8739 (mt) REVERT: B 46 LYS cc_start: 0.5856 (mttt) cc_final: 0.5109 (mptt) REVERT: B 63 PRO cc_start: 0.8220 (Cg_endo) cc_final: 0.7815 (Cg_exo) REVERT: B 74 LEU cc_start: 0.8687 (tp) cc_final: 0.8171 (mp) REVERT: B 473 MET cc_start: 0.8066 (ttp) cc_final: 0.7825 (ttm) REVERT: B 516 LEU cc_start: 0.8929 (mm) cc_final: 0.8716 (mt) REVERT: C 46 LYS cc_start: 0.5715 (mttt) cc_final: 0.4950 (mptt) REVERT: C 63 PRO cc_start: 0.8198 (Cg_endo) cc_final: 0.7830 (Cg_exo) REVERT: C 74 LEU cc_start: 0.8687 (tp) cc_final: 0.8164 (mp) REVERT: C 473 MET cc_start: 0.8086 (ttp) cc_final: 0.7870 (ttm) REVERT: C 484 GLN cc_start: 0.6626 (pp30) cc_final: 0.6283 (pm20) REVERT: C 516 LEU cc_start: 0.8946 (mm) cc_final: 0.8746 (mt) REVERT: D 46 LYS cc_start: 0.5731 (mttt) cc_final: 0.4962 (mptt) REVERT: D 63 PRO cc_start: 0.8177 (Cg_endo) cc_final: 0.7806 (Cg_exo) REVERT: D 74 LEU cc_start: 0.8637 (tp) cc_final: 0.8114 (mp) REVERT: D 313 PHE cc_start: 0.8439 (t80) cc_final: 0.8195 (t80) REVERT: D 324 PHE cc_start: 0.8449 (t80) cc_final: 0.7598 (m-80) REVERT: D 473 MET cc_start: 0.8060 (ttp) cc_final: 0.7715 (ttm) REVERT: D 484 GLN cc_start: 0.6553 (pp30) cc_final: 0.6341 (pm20) REVERT: D 516 LEU cc_start: 0.8960 (mm) cc_final: 0.8758 (mt) outliers start: 52 outliers final: 23 residues processed: 325 average time/residue: 0.1157 time to fit residues: 57.2057 Evaluate side-chains 228 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 84 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN B 226 HIS B 327 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.101353 restraints weight = 28348.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.103777 restraints weight = 17109.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105379 restraints weight = 12737.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106226 restraints weight = 10652.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106840 restraints weight = 9629.801| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15244 Z= 0.148 Angle : 0.642 8.463 20676 Z= 0.328 Chirality : 0.041 0.159 2420 Planarity : 0.005 0.045 2516 Dihedral : 6.050 46.600 2168 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.92 % Allowed : 12.71 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -1.30 (0.20), residues: 1784 helix: 0.46 (0.16), residues: 1048 sheet: -1.97 (0.32), residues: 204 loop : -3.07 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 43 TYR 0.024 0.001 TYR B 218 PHE 0.029 0.002 PHE B 324 TRP 0.008 0.001 TRP A 398 HIS 0.007 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00317 (15236) covalent geometry : angle 0.63462 (20652) hydrogen bonds : bond 0.05710 ( 820) hydrogen bonds : angle 4.30795 ( 2376) link_BETA1-4 : bond 0.00284 ( 4) link_BETA1-4 : angle 0.69120 ( 12) link_NAG-ASN : bond 0.00042 ( 4) link_NAG-ASN : angle 3.99745 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 251 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6115 (mttt) cc_final: 0.5507 (mmtt) REVERT: A 62 LYS cc_start: 0.6104 (mttt) cc_final: 0.5496 (tttt) REVERT: A 261 THR cc_start: 0.9435 (m) cc_final: 0.8962 (p) REVERT: A 483 GLN cc_start: 0.6876 (pm20) cc_final: 0.6387 (tp40) REVERT: A 508 MET cc_start: 0.5790 (ttt) cc_final: 0.5334 (mtp) REVERT: B 46 LYS cc_start: 0.6130 (mttt) cc_final: 0.5207 (mptt) REVERT: B 62 LYS cc_start: 0.5755 (mttt) cc_final: 0.5305 (tttt) REVERT: B 74 LEU cc_start: 0.8825 (tp) cc_final: 0.8292 (mp) REVERT: B 261 THR cc_start: 0.9407 (m) cc_final: 0.8959 (p) REVERT: B 324 PHE cc_start: 0.8290 (t80) cc_final: 0.8083 (t80) REVERT: B 409 HIS cc_start: 0.7692 (t70) cc_final: 0.7478 (t-90) REVERT: B 516 LEU cc_start: 0.8928 (mm) cc_final: 0.8720 (mt) REVERT: C 46 LYS cc_start: 0.5902 (mttt) cc_final: 0.5394 (mmtt) REVERT: C 324 PHE cc_start: 0.8288 (t80) cc_final: 0.8082 (t80) REVERT: C 473 MET cc_start: 0.7799 (ttp) cc_final: 0.7595 (ttm) REVERT: D 46 LYS cc_start: 0.5907 (mttt) cc_final: 0.5395 (mmtt) REVERT: D 473 MET cc_start: 0.7878 (ttp) cc_final: 0.7676 (ttp) outliers start: 48 outliers final: 31 residues processed: 282 average time/residue: 0.1006 time to fit residues: 45.4521 Evaluate side-chains 245 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 490 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 23 optimal weight: 7.9990 chunk 172 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 157 optimal weight: 0.0970 chunk 164 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS B 484 GLN B 486 HIS ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.103328 restraints weight = 28475.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105783 restraints weight = 17004.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107379 restraints weight = 12572.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108319 restraints weight = 10477.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108730 restraints weight = 9414.311| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15244 Z= 0.122 Angle : 0.625 12.898 20676 Z= 0.307 Chirality : 0.040 0.171 2420 Planarity : 0.004 0.039 2516 Dihedral : 5.774 45.875 2168 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.49 % Allowed : 15.15 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -0.76 (0.20), residues: 1784 helix: 0.97 (0.17), residues: 1048 sheet: -1.69 (0.30), residues: 252 loop : -3.15 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 43 TYR 0.029 0.001 TYR A 218 PHE 0.026 0.001 PHE D 324 TRP 0.023 0.002 TRP A 354 HIS 0.005 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00248 (15236) covalent geometry : angle 0.62014 (20652) hydrogen bonds : bond 0.04971 ( 820) hydrogen bonds : angle 4.01759 ( 2376) link_BETA1-4 : bond 0.00394 ( 4) link_BETA1-4 : angle 0.62908 ( 12) link_NAG-ASN : bond 0.00205 ( 4) link_NAG-ASN : angle 3.40774 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 238 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6397 (mttt) cc_final: 0.5644 (mptt) REVERT: A 62 LYS cc_start: 0.5786 (mttt) cc_final: 0.5363 (tttt) REVERT: A 74 LEU cc_start: 0.8472 (tt) cc_final: 0.8028 (mm) REVERT: A 261 THR cc_start: 0.9398 (m) cc_final: 0.9000 (p) REVERT: A 324 PHE cc_start: 0.8514 (t80) cc_final: 0.8279 (t80) REVERT: A 483 GLN cc_start: 0.7111 (pm20) cc_final: 0.6260 (tp40) REVERT: A 508 MET cc_start: 0.6046 (ttt) cc_final: 0.5740 (mtp) REVERT: B 46 LYS cc_start: 0.5975 (mttt) cc_final: 0.5412 (mptt) REVERT: B 62 LYS cc_start: 0.5797 (mttt) cc_final: 0.5326 (tttt) REVERT: B 74 LEU cc_start: 0.8797 (tp) cc_final: 0.8313 (mp) REVERT: B 261 THR cc_start: 0.9395 (m) cc_final: 0.9009 (p) REVERT: B 324 PHE cc_start: 0.8256 (t80) cc_final: 0.7992 (t80) REVERT: B 371 MET cc_start: 0.7668 (ttt) cc_final: 0.7468 (ttt) REVERT: B 516 LEU cc_start: 0.8919 (mm) cc_final: 0.8704 (mt) REVERT: C 46 LYS cc_start: 0.5939 (mttt) cc_final: 0.5492 (mmtt) REVERT: C 62 LYS cc_start: 0.5784 (mttt) cc_final: 0.5364 (tttt) REVERT: C 74 LEU cc_start: 0.8486 (tt) cc_final: 0.8036 (mm) REVERT: C 324 PHE cc_start: 0.8244 (t80) cc_final: 0.7987 (t80) REVERT: C 483 GLN cc_start: 0.6870 (tm-30) cc_final: 0.6190 (tm-30) REVERT: D 46 LYS cc_start: 0.5940 (mttt) cc_final: 0.5496 (mmtt) REVERT: D 61 ARG cc_start: 0.4379 (tpp-160) cc_final: 0.4003 (tpp-160) REVERT: D 62 LYS cc_start: 0.5802 (mttt) cc_final: 0.5498 (tttt) REVERT: D 74 LEU cc_start: 0.8489 (tt) cc_final: 0.8030 (mm) REVERT: D 313 PHE cc_start: 0.8315 (t80) cc_final: 0.8038 (t80) REVERT: D 483 GLN cc_start: 0.6878 (tm-30) cc_final: 0.6222 (tm-30) outliers start: 41 outliers final: 33 residues processed: 262 average time/residue: 0.1071 time to fit residues: 43.9260 Evaluate side-chains 240 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 490 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 66 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 136 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102392 restraints weight = 28917.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104923 restraints weight = 17118.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106581 restraints weight = 12577.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.107573 restraints weight = 10433.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108024 restraints weight = 9332.187| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15244 Z= 0.134 Angle : 0.618 13.555 20676 Z= 0.304 Chirality : 0.041 0.184 2420 Planarity : 0.004 0.038 2516 Dihedral : 5.654 45.557 2168 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.53 % Allowed : 15.82 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.35 (0.21), residues: 1784 helix: 1.31 (0.17), residues: 1048 sheet: -1.46 (0.31), residues: 252 loop : -3.05 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 43 TYR 0.029 0.001 TYR C 218 PHE 0.027 0.001 PHE D 324 TRP 0.024 0.002 TRP B 354 HIS 0.002 0.001 HIS D 409 Details of bonding type rmsd covalent geometry : bond 0.00295 (15236) covalent geometry : angle 0.61255 (20652) hydrogen bonds : bond 0.04786 ( 820) hydrogen bonds : angle 3.91512 ( 2376) link_BETA1-4 : bond 0.00292 ( 4) link_BETA1-4 : angle 0.71293 ( 12) link_NAG-ASN : bond 0.00137 ( 4) link_NAG-ASN : angle 3.45803 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 214 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6361 (mttt) cc_final: 0.5805 (mmtt) REVERT: A 62 LYS cc_start: 0.5886 (mttt) cc_final: 0.5191 (tttt) REVERT: A 65 LYS cc_start: 0.7660 (tptp) cc_final: 0.6577 (mtmm) REVERT: A 74 LEU cc_start: 0.8557 (tt) cc_final: 0.8038 (mm) REVERT: A 261 THR cc_start: 0.9386 (m) cc_final: 0.8932 (p) REVERT: A 265 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8015 (ttpt) REVERT: A 313 PHE cc_start: 0.8370 (t80) cc_final: 0.8103 (t80) REVERT: A 324 PHE cc_start: 0.8191 (t80) cc_final: 0.7854 (t80) REVERT: A 326 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8179 (tt) REVERT: A 426 MET cc_start: 0.8988 (tpp) cc_final: 0.8377 (mpp) REVERT: A 483 GLN cc_start: 0.7116 (pm20) cc_final: 0.6283 (tp40) REVERT: A 508 MET cc_start: 0.6032 (ttt) cc_final: 0.5754 (ttt) REVERT: B 46 LYS cc_start: 0.6402 (mttt) cc_final: 0.5818 (mmtt) REVERT: B 62 LYS cc_start: 0.5831 (mttt) cc_final: 0.5384 (tttt) REVERT: B 74 LEU cc_start: 0.8790 (tp) cc_final: 0.8293 (mp) REVERT: B 261 THR cc_start: 0.9401 (m) cc_final: 0.8961 (p) REVERT: B 313 PHE cc_start: 0.8319 (t80) cc_final: 0.8051 (t80) REVERT: C 46 LYS cc_start: 0.6264 (mttt) cc_final: 0.5747 (mmtt) REVERT: C 62 LYS cc_start: 0.5761 (mttt) cc_final: 0.5348 (tttt) REVERT: C 74 LEU cc_start: 0.8601 (tt) cc_final: 0.8070 (mm) REVERT: C 313 PHE cc_start: 0.8369 (t80) cc_final: 0.8072 (t80) REVERT: C 483 GLN cc_start: 0.6634 (tm-30) cc_final: 0.5988 (tm-30) REVERT: D 46 LYS cc_start: 0.6273 (mttt) cc_final: 0.5752 (mmtt) REVERT: D 62 LYS cc_start: 0.5757 (mttt) cc_final: 0.5351 (tttt) REVERT: D 74 LEU cc_start: 0.8564 (tt) cc_final: 0.8063 (mm) REVERT: D 313 PHE cc_start: 0.8333 (t80) cc_final: 0.8069 (t80) REVERT: D 371 MET cc_start: 0.7672 (ttt) cc_final: 0.7462 (ttt) REVERT: D 483 GLN cc_start: 0.6515 (tm-30) cc_final: 0.5892 (tm-30) outliers start: 58 outliers final: 43 residues processed: 241 average time/residue: 0.1210 time to fit residues: 44.0793 Evaluate side-chains 247 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 383 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 383 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 513 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 145 optimal weight: 0.0030 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS B 243 GLN ** B 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 HIS ** D 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103161 restraints weight = 28698.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105642 restraints weight = 17178.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107248 restraints weight = 12716.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107925 restraints weight = 10620.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108708 restraints weight = 9709.619| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15244 Z= 0.123 Angle : 0.596 10.361 20676 Z= 0.292 Chirality : 0.040 0.162 2420 Planarity : 0.003 0.038 2516 Dihedral : 5.552 44.763 2168 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.59 % Allowed : 16.67 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.15 (0.21), residues: 1784 helix: 1.66 (0.17), residues: 1020 sheet: -1.18 (0.31), residues: 252 loop : -2.48 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 43 TYR 0.024 0.001 TYR C 218 PHE 0.028 0.001 PHE C 56 TRP 0.019 0.001 TRP C 354 HIS 0.008 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00263 (15236) covalent geometry : angle 0.59125 (20652) hydrogen bonds : bond 0.04501 ( 820) hydrogen bonds : angle 3.75841 ( 2376) link_BETA1-4 : bond 0.00414 ( 4) link_BETA1-4 : angle 0.63251 ( 12) link_NAG-ASN : bond 0.00199 ( 4) link_NAG-ASN : angle 3.15494 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 221 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6636 (mttt) cc_final: 0.5956 (mmtt) REVERT: A 62 LYS cc_start: 0.5891 (mttt) cc_final: 0.5395 (tttt) REVERT: A 74 LEU cc_start: 0.8567 (tt) cc_final: 0.7964 (mm) REVERT: A 265 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7881 (ttpt) REVERT: A 313 PHE cc_start: 0.8342 (t80) cc_final: 0.8102 (t80) REVERT: A 324 PHE cc_start: 0.8220 (t80) cc_final: 0.8017 (t80) REVERT: A 341 GLU cc_start: 0.5609 (tt0) cc_final: 0.5120 (mp0) REVERT: A 426 MET cc_start: 0.9010 (tpp) cc_final: 0.8535 (mpp) REVERT: A 483 GLN cc_start: 0.7201 (pm20) cc_final: 0.6369 (tp40) REVERT: A 508 MET cc_start: 0.5824 (ttt) cc_final: 0.5602 (ttt) REVERT: B 46 LYS cc_start: 0.6405 (mttt) cc_final: 0.5839 (mmtt) REVERT: B 62 LYS cc_start: 0.5785 (mttt) cc_final: 0.5261 (tttt) REVERT: B 74 LEU cc_start: 0.8754 (tp) cc_final: 0.8282 (mp) REVERT: B 313 PHE cc_start: 0.8279 (t80) cc_final: 0.8044 (t80) REVERT: B 341 GLU cc_start: 0.5406 (tt0) cc_final: 0.4834 (mp0) REVERT: C 46 LYS cc_start: 0.6343 (mttt) cc_final: 0.5804 (mmtt) REVERT: C 62 LYS cc_start: 0.5891 (mttt) cc_final: 0.5326 (tttt) REVERT: C 74 LEU cc_start: 0.8570 (tt) cc_final: 0.7976 (mm) REVERT: C 341 GLU cc_start: 0.5429 (tt0) cc_final: 0.4349 (mt-10) REVERT: C 371 MET cc_start: 0.7648 (ttt) cc_final: 0.7413 (ttt) REVERT: C 483 GLN cc_start: 0.6780 (tm-30) cc_final: 0.6104 (tm-30) REVERT: D 46 LYS cc_start: 0.6337 (mttt) cc_final: 0.5812 (mmtt) REVERT: D 62 LYS cc_start: 0.5905 (mttt) cc_final: 0.5341 (tttt) REVERT: D 74 LEU cc_start: 0.8575 (tt) cc_final: 0.7990 (mm) REVERT: D 313 PHE cc_start: 0.8291 (t80) cc_final: 0.8055 (t80) REVERT: D 324 PHE cc_start: 0.8032 (t80) cc_final: 0.7797 (t80) REVERT: D 483 GLN cc_start: 0.6770 (tm-30) cc_final: 0.6067 (tm-30) outliers start: 59 outliers final: 46 residues processed: 256 average time/residue: 0.1166 time to fit residues: 46.1524 Evaluate side-chains 242 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 383 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 383 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 513 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 HIS ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.128534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101439 restraints weight = 28410.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103860 restraints weight = 17120.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105347 restraints weight = 12723.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106327 restraints weight = 10765.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106765 restraints weight = 9674.569| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15244 Z= 0.159 Angle : 0.631 9.812 20676 Z= 0.311 Chirality : 0.041 0.182 2420 Planarity : 0.004 0.038 2516 Dihedral : 5.603 44.342 2168 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 4.38 % Allowed : 16.79 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.31 (0.21), residues: 1784 helix: 1.76 (0.17), residues: 1020 sheet: -1.02 (0.30), residues: 268 loop : -2.46 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 338 TYR 0.025 0.001 TYR D 218 PHE 0.028 0.002 PHE B 324 TRP 0.013 0.002 TRP C 354 HIS 0.008 0.001 HIS D 409 Details of bonding type rmsd covalent geometry : bond 0.00363 (15236) covalent geometry : angle 0.62505 (20652) hydrogen bonds : bond 0.04750 ( 820) hydrogen bonds : angle 3.80236 ( 2376) link_BETA1-4 : bond 0.00256 ( 4) link_BETA1-4 : angle 0.70583 ( 12) link_NAG-ASN : bond 0.00058 ( 4) link_NAG-ASN : angle 3.53100 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 199 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6679 (mttt) cc_final: 0.5994 (mmtt) REVERT: A 62 LYS cc_start: 0.5657 (mttt) cc_final: 0.5291 (tttt) REVERT: A 265 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7947 (ttpt) REVERT: A 324 PHE cc_start: 0.8219 (t80) cc_final: 0.7975 (t80) REVERT: A 426 MET cc_start: 0.9058 (tpp) cc_final: 0.8367 (mpp) REVERT: A 483 GLN cc_start: 0.7142 (pm20) cc_final: 0.6273 (tp40) REVERT: A 508 MET cc_start: 0.5822 (ttt) cc_final: 0.5594 (ttt) REVERT: B 46 LYS cc_start: 0.6440 (mttt) cc_final: 0.5888 (mmtt) REVERT: B 62 LYS cc_start: 0.5698 (mttt) cc_final: 0.5279 (tttt) REVERT: B 324 PHE cc_start: 0.8304 (t80) cc_final: 0.8099 (t80) REVERT: C 46 LYS cc_start: 0.6363 (mttt) cc_final: 0.5833 (mmtt) REVERT: C 62 LYS cc_start: 0.5721 (mttt) cc_final: 0.5302 (tttt) REVERT: C 483 GLN cc_start: 0.6538 (tm-30) cc_final: 0.5918 (tm-30) REVERT: D 46 LYS cc_start: 0.6360 (mttt) cc_final: 0.5840 (mmtt) REVERT: D 62 LYS cc_start: 0.5735 (mttt) cc_final: 0.5319 (tttt) REVERT: D 324 PHE cc_start: 0.8011 (t80) cc_final: 0.7721 (t80) outliers start: 72 outliers final: 55 residues processed: 240 average time/residue: 0.1062 time to fit residues: 40.3386 Evaluate side-chains 245 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 189 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 383 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 383 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 513 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 0.0020 chunk 28 optimal weight: 9.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS B 409 HIS ** B 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102082 restraints weight = 28658.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104552 restraints weight = 17191.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106137 restraints weight = 12724.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106962 restraints weight = 10653.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107661 restraints weight = 9637.279| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15244 Z= 0.135 Angle : 0.632 10.385 20676 Z= 0.307 Chirality : 0.041 0.200 2420 Planarity : 0.004 0.039 2516 Dihedral : 5.507 42.881 2168 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.08 % Allowed : 18.00 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.35 (0.21), residues: 1784 helix: 1.73 (0.17), residues: 1044 sheet: -0.91 (0.30), residues: 268 loop : -2.53 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 43 TYR 0.024 0.001 TYR A 218 PHE 0.037 0.002 PHE C 324 TRP 0.024 0.002 TRP B 354 HIS 0.005 0.001 HIS D 409 Details of bonding type rmsd covalent geometry : bond 0.00299 (15236) covalent geometry : angle 0.62804 (20652) hydrogen bonds : bond 0.04516 ( 820) hydrogen bonds : angle 3.72434 ( 2376) link_BETA1-4 : bond 0.00371 ( 4) link_BETA1-4 : angle 0.58598 ( 12) link_NAG-ASN : bond 0.00188 ( 4) link_NAG-ASN : angle 3.16569 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 202 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6662 (mttt) cc_final: 0.5997 (mmtt) REVERT: A 62 LYS cc_start: 0.5956 (mttt) cc_final: 0.5463 (tttt) REVERT: A 265 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7873 (ttpt) REVERT: A 324 PHE cc_start: 0.8232 (t80) cc_final: 0.8000 (t80) REVERT: A 483 GLN cc_start: 0.7169 (pm20) cc_final: 0.6289 (tp40) REVERT: B 46 LYS cc_start: 0.6499 (mttt) cc_final: 0.5944 (mmtt) REVERT: B 62 LYS cc_start: 0.5930 (mttt) cc_final: 0.5399 (tttt) REVERT: B 74 LEU cc_start: 0.8585 (tt) cc_final: 0.8037 (mm) REVERT: C 46 LYS cc_start: 0.6353 (mttt) cc_final: 0.5850 (mmtt) REVERT: C 62 LYS cc_start: 0.5738 (mttt) cc_final: 0.5236 (tttt) REVERT: C 324 PHE cc_start: 0.8699 (t80) cc_final: 0.8485 (t80) REVERT: C 483 GLN cc_start: 0.6695 (tm-30) cc_final: 0.5932 (tm-30) REVERT: D 46 LYS cc_start: 0.6473 (mttt) cc_final: 0.5958 (mmtt) REVERT: D 62 LYS cc_start: 0.5740 (mttt) cc_final: 0.5283 (tttt) REVERT: D 324 PHE cc_start: 0.8016 (t80) cc_final: 0.7739 (t80) REVERT: D 483 GLN cc_start: 0.6465 (tm-30) cc_final: 0.5655 (tm-30) outliers start: 67 outliers final: 53 residues processed: 244 average time/residue: 0.1099 time to fit residues: 41.9132 Evaluate side-chains 236 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 182 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 383 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 513 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 91 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101371 restraints weight = 28768.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103836 restraints weight = 17388.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105359 restraints weight = 12927.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106342 restraints weight = 10858.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106900 restraints weight = 9783.013| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15244 Z= 0.154 Angle : 0.648 9.304 20676 Z= 0.317 Chirality : 0.041 0.210 2420 Planarity : 0.004 0.038 2516 Dihedral : 5.520 43.257 2168 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.83 % Allowed : 17.88 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.37 (0.21), residues: 1784 helix: 1.70 (0.17), residues: 1048 sheet: -0.92 (0.30), residues: 268 loop : -2.47 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 338 TYR 0.027 0.001 TYR C 218 PHE 0.037 0.002 PHE B 324 TRP 0.023 0.002 TRP C 354 HIS 0.006 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00352 (15236) covalent geometry : angle 0.64371 (20652) hydrogen bonds : bond 0.04618 ( 820) hydrogen bonds : angle 3.78037 ( 2376) link_BETA1-4 : bond 0.00263 ( 4) link_BETA1-4 : angle 0.59982 ( 12) link_NAG-ASN : bond 0.00115 ( 4) link_NAG-ASN : angle 3.33128 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 190 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6756 (mttt) cc_final: 0.6099 (mmtt) REVERT: A 62 LYS cc_start: 0.5866 (mttt) cc_final: 0.5457 (tttt) REVERT: A 265 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7903 (ttpt) REVERT: A 483 GLN cc_start: 0.7248 (pm20) cc_final: 0.6372 (tp40) REVERT: B 46 LYS cc_start: 0.6668 (mttt) cc_final: 0.5985 (mmtt) REVERT: B 62 LYS cc_start: 0.5841 (mttt) cc_final: 0.5426 (tttt) REVERT: B 74 LEU cc_start: 0.8639 (tt) cc_final: 0.8076 (mp) REVERT: C 46 LYS cc_start: 0.6511 (mttt) cc_final: 0.5980 (mmtt) REVERT: C 62 LYS cc_start: 0.5887 (mttt) cc_final: 0.5440 (tttt) REVERT: D 46 LYS cc_start: 0.6487 (mttt) cc_final: 0.5979 (mmtt) REVERT: D 62 LYS cc_start: 0.5837 (mttt) cc_final: 0.5402 (tttt) REVERT: D 324 PHE cc_start: 0.8000 (t80) cc_final: 0.7727 (t80) REVERT: D 483 GLN cc_start: 0.6399 (tm-30) cc_final: 0.5537 (tm-30) outliers start: 63 outliers final: 53 residues processed: 232 average time/residue: 0.1105 time to fit residues: 40.3894 Evaluate side-chains 233 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 179 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 383 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 490 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 138 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN C 69 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.129504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102543 restraints weight = 28425.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105061 restraints weight = 16862.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106664 restraints weight = 12398.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107618 restraints weight = 10305.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.108240 restraints weight = 9265.029| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15244 Z= 0.135 Angle : 0.644 9.299 20676 Z= 0.314 Chirality : 0.041 0.204 2420 Planarity : 0.004 0.039 2516 Dihedral : 5.445 42.345 2168 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.41 % Allowed : 18.67 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.44 (0.21), residues: 1784 helix: 1.76 (0.17), residues: 1044 sheet: -0.83 (0.31), residues: 268 loop : -2.43 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 338 TYR 0.025 0.001 TYR A 218 PHE 0.033 0.002 PHE B 324 TRP 0.028 0.002 TRP D 354 HIS 0.006 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00300 (15236) covalent geometry : angle 0.63982 (20652) hydrogen bonds : bond 0.04470 ( 820) hydrogen bonds : angle 3.74488 ( 2376) link_BETA1-4 : bond 0.00336 ( 4) link_BETA1-4 : angle 0.57073 ( 12) link_NAG-ASN : bond 0.00185 ( 4) link_NAG-ASN : angle 3.10416 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6736 (mttt) cc_final: 0.6152 (mmtt) REVERT: A 62 LYS cc_start: 0.6051 (mttt) cc_final: 0.5590 (tttt) REVERT: A 74 LEU cc_start: 0.8551 (tt) cc_final: 0.8078 (mp) REVERT: A 265 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7845 (ttpt) REVERT: A 483 GLN cc_start: 0.7251 (pm20) cc_final: 0.6343 (tp40) REVERT: B 46 LYS cc_start: 0.6660 (mttt) cc_final: 0.5988 (mmtt) REVERT: B 62 LYS cc_start: 0.5929 (mttt) cc_final: 0.5531 (tttt) REVERT: B 74 LEU cc_start: 0.8620 (tt) cc_final: 0.8061 (mp) REVERT: B 462 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7299 (mt-10) REVERT: C 46 LYS cc_start: 0.6708 (mttt) cc_final: 0.6056 (mmtt) REVERT: C 62 LYS cc_start: 0.6044 (mttt) cc_final: 0.5610 (tttt) REVERT: C 74 LEU cc_start: 0.8546 (tt) cc_final: 0.8079 (mp) REVERT: C 473 MET cc_start: 0.7369 (ttm) cc_final: 0.7168 (mtp) REVERT: D 46 LYS cc_start: 0.6676 (mttt) cc_final: 0.6054 (mmtt) REVERT: D 62 LYS cc_start: 0.6000 (mttt) cc_final: 0.5516 (tttt) REVERT: D 74 LEU cc_start: 0.8560 (tt) cc_final: 0.8078 (mp) REVERT: D 324 PHE cc_start: 0.8079 (t80) cc_final: 0.7780 (t80) REVERT: D 483 GLN cc_start: 0.6402 (tm-30) cc_final: 0.5590 (tm-30) outliers start: 56 outliers final: 48 residues processed: 226 average time/residue: 0.1069 time to fit residues: 37.9107 Evaluate side-chains 226 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 177 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 350 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 383 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 350 PHE Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 490 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 175 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN B 483 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.099292 restraints weight = 28841.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101716 restraints weight = 17533.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103289 restraints weight = 13073.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104207 restraints weight = 10984.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104702 restraints weight = 9930.750| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15244 Z= 0.208 Angle : 0.702 8.850 20676 Z= 0.348 Chirality : 0.043 0.248 2420 Planarity : 0.004 0.039 2516 Dihedral : 5.657 43.538 2168 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.53 % Allowed : 18.55 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.27 (0.21), residues: 1784 helix: 1.66 (0.17), residues: 1044 sheet: -0.97 (0.30), residues: 268 loop : -2.55 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 338 TYR 0.033 0.002 TYR B 218 PHE 0.031 0.002 PHE B 56 TRP 0.022 0.002 TRP D 354 HIS 0.007 0.001 HIS D 409 Details of bonding type rmsd covalent geometry : bond 0.00485 (15236) covalent geometry : angle 0.69669 (20652) hydrogen bonds : bond 0.05007 ( 820) hydrogen bonds : angle 3.94086 ( 2376) link_BETA1-4 : bond 0.00211 ( 4) link_BETA1-4 : angle 0.66020 ( 12) link_NAG-ASN : bond 0.00028 ( 4) link_NAG-ASN : angle 3.77692 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2207.26 seconds wall clock time: 39 minutes 22.11 seconds (2362.11 seconds total)