Starting phenix.real_space_refine on Sat Sep 12 08:21:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5wpt_8882/09_2026/5wpt_8882.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wpt_8882/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5wpt_8882/09_2026/5wpt_8882.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5wpt_8882/09_2026/5wpt_8882.cif" model { file = "/net/cci-nas-00/data/ceres_data/5wpt_8882/09_2026/5wpt_8882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wpt_8882/09_2026/5wpt_8882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5wpt_8882/09_2026/5wpt_8882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wpt_8882/09_2026/5wpt_8882.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 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 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: 2.92, per 1000 atoms: 0.20 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: 1.11 Conformation dependent library (CDL) restraints added in 605.7 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: 0.39 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: 2.15 Time building geometry restraints manager: 1.52 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: 8292 15.83 - 31.66: 460 31.66 - 47.48: 116 47.48 - 63.31: 8 63.31 - 79.14: 12 Dihedral angle restraints: 8888 sinusoidal: 3524 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 8885 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.070 Set scattering table: 0.020 Process input model: 12.760 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 11.195 79.141 5416 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/Z covalent geometry : bond 0.00855 / 0.37 (15236) covalent geometry : angle 1.04114 / 0.54 (20652) hydrogen bonds : bond 0.22385 / 14.49 ( 820) hydrogen bonds : angle 7.91974 / 5.45 ( 2376) link_BETA1-4 : bond 0.00872 / 0.44 ( 4) link_BETA1-4 : angle 1.43526 / 0.78 ( 12) link_NAG-ASN : bond 0.00113 / 0.06 ( 4) link_NAG-ASN : angle 7.54995 / 4.03 ( 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 : 0.418 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: 0.1326 time to fit residues: 78.7809 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 : 0.570 ------------------------------------------------------------------------------- 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... 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 = 0.3599 r_free = 0.3599 target = 0.128708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101196 restraints weight = 27898.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103697 restraints weight = 16630.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105319 restraints weight = 12271.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106288 restraints weight = 10173.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106918 restraints weight = 9109.595| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15244 Z= 0.187 Angle : 0.734 8.918 20676 Z= 0.380 Chirality : 0.043 0.156 2420 Planarity : 0.005 0.059 2516 Dihedral : 6.452 45.713 2000 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.80 % Allowed : 10.64 % 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: -2.50 (0.18), residues: 1784 helix: -0.55 (0.15), residues: 1040 sheet: -2.34 (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 0.013 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/Z covalent geometry : bond 0.00409 / 0.19 (15236) covalent geometry : angle 0.72395 / 0.38 (20652) hydrogen bonds : bond 0.07378 / 4.81 ( 820) hydrogen bonds : angle 4.88326 / 3.35 ( 2376) link_BETA1-4 : bond 0.00398 / 0.20 ( 4) link_BETA1-4 : angle 0.89395 / 0.47 ( 12) link_NAG-ASN : bond 0.00036 / 0.02 ( 4) link_NAG-ASN : angle 4.95489 / 2.67 ( 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 323 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 277 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.5891 (mttt) cc_final: 0.5212 (mptt) REVERT: A 63 PRO cc_start: 0.8184 (Cg_endo) cc_final: 0.7830 (Cg_exo) REVERT: A 324 PHE cc_start: 0.8342 (t80) cc_final: 0.7589 (m-80) REVERT: A 340 ARG cc_start: 0.7354 (tpt90) cc_final: 0.7133 (tpt90) REVERT: A 418 LEU cc_start: 0.7224 (pp) cc_final: 0.6994 (tp) REVERT: A 419 ARG cc_start: 0.7104 (ttp-110) cc_final: 0.6287 (tpp-160) REVERT: A 516 LEU cc_start: 0.9002 (mm) cc_final: 0.8738 (mt) REVERT: B 46 LYS cc_start: 0.5860 (mttt) cc_final: 0.5108 (mptt) REVERT: B 63 PRO cc_start: 0.8214 (Cg_endo) cc_final: 0.7812 (Cg_exo) REVERT: B 74 LEU cc_start: 0.8686 (tp) cc_final: 0.8181 (mp) REVERT: B 473 MET cc_start: 0.8046 (ttp) cc_final: 0.7814 (ttm) REVERT: B 516 LEU cc_start: 0.8930 (mm) cc_final: 0.8715 (mt) REVERT: C 46 LYS cc_start: 0.5719 (mttt) cc_final: 0.5067 (mptt) REVERT: C 63 PRO cc_start: 0.8191 (Cg_endo) cc_final: 0.7825 (Cg_exo) REVERT: C 74 LEU cc_start: 0.8648 (tp) cc_final: 0.8147 (mp) REVERT: C 473 MET cc_start: 0.8073 (ttp) cc_final: 0.7852 (ttm) REVERT: C 516 LEU cc_start: 0.8946 (mm) cc_final: 0.8743 (mt) REVERT: D 46 LYS cc_start: 0.5731 (mttt) cc_final: 0.4956 (mptt) REVERT: D 63 PRO cc_start: 0.8170 (Cg_endo) cc_final: 0.7806 (Cg_exo) REVERT: D 313 PHE cc_start: 0.8452 (t80) cc_final: 0.8251 (t80) REVERT: D 473 MET cc_start: 0.8009 (ttp) cc_final: 0.7670 (ttm) REVERT: D 516 LEU cc_start: 0.8960 (mm) cc_final: 0.8753 (mt) outliers start: 46 outliers final: 21 residues processed: 318 average time/residue: 0.1048 time to fit residues: 50.9824 Evaluate side-chains 220 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 0.0270 chunk 96 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 D 486 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.129211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101484 restraints weight = 28361.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103981 restraints weight = 17132.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105558 restraints weight = 12691.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106346 restraints weight = 10611.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106346 restraints weight = 9621.798| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15244 Z= 0.142 Angle : 0.636 8.393 20676 Z= 0.325 Chirality : 0.041 0.159 2420 Planarity : 0.004 0.044 2516 Dihedral : 5.826 46.439 2000 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 2.62 % Allowed : 12.71 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -1.27 (0.20), residues: 1784 helix: 0.50 (0.16), residues: 1048 sheet: -1.96 (0.32), residues: 204 loop : -3.07 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 43 TYR 0.023 0.001 TYR B 218 PHE 0.027 0.002 PHE B 324 TRP 0.011 0.001 TRP A 354 HIS 0.008 0.001 HIS B 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (15236) covalent geometry : angle 0.62903 / 0.32 (20652) hydrogen bonds : bond 0.05716 / 3.72 ( 820) hydrogen bonds : angle 4.29773 / 2.95 ( 2376) link_BETA1-4 : bond 0.00412 / 0.21 ( 4) link_BETA1-4 : angle 0.54078 / 0.28 ( 12) link_NAG-ASN : bond 0.00057 / 0.03 ( 4) link_NAG-ASN : angle 3.95833 / 2.13 ( 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 292 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6116 (mttt) cc_final: 0.5497 (mmtt) REVERT: A 62 LYS cc_start: 0.6113 (mttt) cc_final: 0.5488 (tttt) REVERT: A 261 THR cc_start: 0.9437 (m) cc_final: 0.8965 (p) REVERT: A 483 GLN cc_start: 0.6870 (pm20) cc_final: 0.6379 (tp40) REVERT: A 508 MET cc_start: 0.5781 (ttt) cc_final: 0.5332 (mtp) REVERT: B 46 LYS cc_start: 0.6127 (mttt) cc_final: 0.5198 (mptt) REVERT: B 62 LYS cc_start: 0.5769 (mttt) cc_final: 0.5306 (tttt) REVERT: B 74 LEU cc_start: 0.8787 (tp) cc_final: 0.8268 (mp) REVERT: B 261 THR cc_start: 0.9409 (m) cc_final: 0.8958 (p) REVERT: B 313 PHE cc_start: 0.8447 (t80) cc_final: 0.8239 (t80) REVERT: B 324 PHE cc_start: 0.8305 (t80) cc_final: 0.8093 (t80) REVERT: B 409 HIS cc_start: 0.7681 (t70) cc_final: 0.7462 (t-90) REVERT: B 483 GLN cc_start: 0.7282 (pm20) cc_final: 0.6624 (tp40) REVERT: B 516 LEU cc_start: 0.8925 (mm) cc_final: 0.8725 (mt) REVERT: C 46 LYS cc_start: 0.6031 (mttt) cc_final: 0.5380 (mmtt) REVERT: C 324 PHE cc_start: 0.8282 (t80) cc_final: 0.7477 (m-80) REVERT: C 340 ARG cc_start: 0.7117 (tpt90) cc_final: 0.6910 (tpt90) REVERT: C 473 MET cc_start: 0.7794 (ttp) cc_final: 0.7564 (ttm) REVERT: C 483 GLN cc_start: 0.7295 (pm20) cc_final: 0.6628 (tp40) REVERT: C 516 LEU cc_start: 0.8911 (mm) cc_final: 0.8669 (mt) REVERT: D 46 LYS cc_start: 0.5899 (mttt) cc_final: 0.5376 (mmtt) REVERT: D 324 PHE cc_start: 0.8234 (t80) cc_final: 0.8022 (t80) REVERT: D 340 ARG cc_start: 0.7087 (tpt90) cc_final: 0.6875 (tpt90) REVERT: D 409 HIS cc_start: 0.7742 (t70) cc_final: 0.7530 (t-90) REVERT: D 516 LEU cc_start: 0.8927 (mm) cc_final: 0.8688 (mt) outliers start: 43 outliers final: 31 residues processed: 276 average time/residue: 0.0983 time to fit residues: 43.6319 Evaluate side-chains 243 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 71 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 302 ASP 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: 2.9990 chunk 172 optimal weight: 0.0970 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100823 restraints weight = 28850.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.103507 restraints weight = 16538.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105185 restraints weight = 11900.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106216 restraints weight = 9805.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106640 restraints weight = 8755.777| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15244 Z= 0.150 Angle : 0.631 13.692 20676 Z= 0.315 Chirality : 0.041 0.140 2420 Planarity : 0.004 0.041 2516 Dihedral : 5.650 46.744 2000 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.98 % Allowed : 14.54 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -0.70 (0.20), residues: 1784 helix: 1.01 (0.17), residues: 1048 sheet: -1.66 (0.34), residues: 204 loop : -3.00 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 43 TYR 0.031 0.001 TYR A 218 PHE 0.023 0.002 PHE A 56 TRP 0.023 0.002 TRP A 354 HIS 0.005 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (15236) covalent geometry : angle 0.62498 / 0.31 (20652) hydrogen bonds : bond 0.05243 / 3.42 ( 820) hydrogen bonds : angle 4.06991 / 2.79 ( 2376) link_BETA1-4 : bond 0.00323 / 0.16 ( 4) link_BETA1-4 : angle 0.44145 / 0.23 ( 12) link_NAG-ASN : bond 0.00062 / 0.03 ( 4) link_NAG-ASN : angle 3.72886 / 2.00 ( 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: 49 poor density : 230 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6432 (mttt) cc_final: 0.5726 (mmtt) REVERT: A 61 ARG cc_start: 0.4327 (tpp-160) cc_final: 0.4105 (tpp-160) REVERT: A 62 LYS cc_start: 0.5871 (mttt) cc_final: 0.5549 (tttt) REVERT: A 74 LEU cc_start: 0.8513 (tt) cc_final: 0.7953 (mm) REVERT: A 261 THR cc_start: 0.9421 (m) cc_final: 0.8896 (p) REVERT: A 324 PHE cc_start: 0.8562 (t80) cc_final: 0.8339 (t80) REVERT: A 473 MET cc_start: 0.7537 (ttm) cc_final: 0.7291 (mtp) REVERT: A 483 GLN cc_start: 0.7158 (pm20) cc_final: 0.6278 (tp40) REVERT: A 508 MET cc_start: 0.6106 (ttt) cc_final: 0.5788 (mtp) REVERT: B 46 LYS cc_start: 0.6054 (mttt) cc_final: 0.5480 (mptt) REVERT: B 62 LYS cc_start: 0.5663 (mttt) cc_final: 0.5187 (tttt) REVERT: B 74 LEU cc_start: 0.8768 (tp) cc_final: 0.8265 (mp) REVERT: B 261 THR cc_start: 0.9412 (m) cc_final: 0.8915 (p) REVERT: B 324 PHE cc_start: 0.8262 (t80) cc_final: 0.7996 (t80) REVERT: B 483 GLN cc_start: 0.7453 (pm20) cc_final: 0.6534 (tp40) REVERT: C 46 LYS cc_start: 0.5978 (mttt) cc_final: 0.5488 (mmtt) REVERT: C 62 LYS cc_start: 0.5713 (mttt) cc_final: 0.5179 (tttt) REVERT: C 74 LEU cc_start: 0.8515 (tt) cc_final: 0.7970 (mm) REVERT: C 324 PHE cc_start: 0.8295 (t80) cc_final: 0.8024 (t80) REVERT: C 340 ARG cc_start: 0.7152 (tpt90) cc_final: 0.6908 (tpt90) REVERT: C 483 GLN cc_start: 0.7509 (pm20) cc_final: 0.6617 (tp40) REVERT: D 46 LYS cc_start: 0.5917 (mttt) cc_final: 0.5466 (mmtt) REVERT: D 62 LYS cc_start: 0.5863 (mttt) cc_final: 0.5379 (tttt) REVERT: D 74 LEU cc_start: 0.8484 (tt) cc_final: 0.7935 (mm) REVERT: D 313 PHE cc_start: 0.8351 (t80) cc_final: 0.8056 (t80) REVERT: D 324 PHE cc_start: 0.8285 (t80) cc_final: 0.8051 (t80) REVERT: D 340 ARG cc_start: 0.7181 (tpt90) cc_final: 0.6953 (tpt90) outliers start: 49 outliers final: 40 residues processed: 260 average time/residue: 0.1168 time to fit residues: 46.6561 Evaluate side-chains 250 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 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 452 VAL Chi-restraints excluded: chain A residue 458 SER 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 221 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 LEU 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 452 VAL Chi-restraints excluded: chain B residue 458 SER 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 350 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 SER 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 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 452 VAL Chi-restraints excluded: chain D residue 458 SER 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: 10.0000 chunk 143 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.128523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101373 restraints weight = 28933.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103869 restraints weight = 17159.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105472 restraints weight = 12636.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106472 restraints weight = 10536.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106899 restraints weight = 9443.309| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15244 Z= 0.146 Angle : 0.612 13.017 20676 Z= 0.303 Chirality : 0.040 0.143 2420 Planarity : 0.004 0.038 2516 Dihedral : 5.520 45.955 2000 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.01 % Allowed : 15.45 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -0.18 (0.21), residues: 1784 helix: 1.47 (0.17), residues: 1020 sheet: -1.56 (0.31), residues: 252 loop : -2.68 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 43 TYR 0.029 0.001 TYR C 218 PHE 0.016 0.001 PHE D 324 TRP 0.023 0.002 TRP D 354 HIS 0.008 0.001 HIS B 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (15236) covalent geometry : angle 0.60628 / 0.30 (20652) hydrogen bonds : bond 0.04948 / 3.23 ( 820) hydrogen bonds : angle 3.93982 / 2.70 ( 2376) link_BETA1-4 : bond 0.00336 / 0.17 ( 4) link_BETA1-4 : angle 0.36037 / 0.18 ( 12) link_NAG-ASN : bond 0.00101 / 0.05 ( 4) link_NAG-ASN : angle 3.41915 / 1.84 ( 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 278 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 212 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6367 (mttt) cc_final: 0.5800 (mmtt) REVERT: A 62 LYS cc_start: 0.5791 (mttt) cc_final: 0.5389 (tttt) REVERT: A 74 LEU cc_start: 0.8575 (tt) cc_final: 0.7981 (mm) REVERT: A 265 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8008 (ttpt) REVERT: A 324 PHE cc_start: 0.8231 (t80) cc_final: 0.7996 (t80) REVERT: A 483 GLN cc_start: 0.7133 (pm20) cc_final: 0.6338 (tp40) REVERT: A 508 MET cc_start: 0.5918 (ttt) cc_final: 0.5685 (ttt) REVERT: B 46 LYS cc_start: 0.6370 (mttt) cc_final: 0.5784 (mmtt) REVERT: B 62 LYS cc_start: 0.5727 (mttt) cc_final: 0.5317 (tttt) REVERT: B 74 LEU cc_start: 0.8791 (tp) cc_final: 0.8291 (mp) REVERT: B 483 GLN cc_start: 0.7557 (pm20) cc_final: 0.6542 (tp40) REVERT: B 516 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8689 (mt) REVERT: C 46 LYS cc_start: 0.6113 (mttt) cc_final: 0.5681 (mmtt) REVERT: C 62 LYS cc_start: 0.5753 (mttt) cc_final: 0.5345 (tttt) REVERT: C 74 LEU cc_start: 0.8577 (tt) cc_final: 0.7993 (mm) REVERT: C 313 PHE cc_start: 0.8380 (t80) cc_final: 0.8129 (t80) REVERT: C 483 GLN cc_start: 0.7618 (pm20) cc_final: 0.6653 (tp40) REVERT: D 46 LYS cc_start: 0.6049 (mttt) cc_final: 0.5634 (mmtt) REVERT: D 62 LYS cc_start: 0.5776 (mttt) cc_final: 0.5362 (tttt) REVERT: D 74 LEU cc_start: 0.8627 (tt) cc_final: 0.8005 (mm) REVERT: D 313 PHE cc_start: 0.8355 (t80) cc_final: 0.8085 (t80) REVERT: D 324 PHE cc_start: 0.8292 (t80) cc_final: 0.8043 (t80) outliers start: 66 outliers final: 50 residues processed: 249 average time/residue: 0.1062 time to fit residues: 41.9195 Evaluate side-chains 255 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 265 LYS Chi-restraints excluded: chain A residue 302 ASP 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 422 LEU 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 245 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 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 452 VAL Chi-restraints excluded: chain B residue 458 SER 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 B residue 516 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 304 VAL 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 452 VAL 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 71 VAL Chi-restraints excluded: chain D residue 221 LEU 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 383 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 508 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 0.0980 chunk 109 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 145 optimal weight: 0.1980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 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 = 0.3634 r_free = 0.3634 target = 0.131365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104611 restraints weight = 28573.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107152 restraints weight = 16770.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.108811 restraints weight = 12261.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.109785 restraints weight = 10167.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110241 restraints weight = 9108.673| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15244 Z= 0.111 Angle : 0.579 10.527 20676 Z= 0.287 Chirality : 0.039 0.154 2420 Planarity : 0.003 0.039 2516 Dihedral : 5.304 44.354 2000 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.16 % Allowed : 16.91 % Favored : 79.93 % 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: 0.06 (0.21), residues: 1784 helix: 1.59 (0.17), residues: 1040 sheet: -1.01 (0.30), residues: 268 loop : -2.91 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 43 TYR 0.022 0.001 TYR C 218 PHE 0.027 0.001 PHE C 56 TRP 0.025 0.002 TRP B 354 HIS 0.004 0.000 HIS B 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (15236) covalent geometry : angle 0.57573 / 0.29 (20652) hydrogen bonds : bond 0.04351 / 2.84 ( 820) hydrogen bonds : angle 3.71430 / 2.55 ( 2376) link_BETA1-4 : bond 0.00637 / 0.32 ( 4) link_BETA1-4 : angle 0.43379 / 0.22 ( 12) link_NAG-ASN : bond 0.00248 / 0.12 ( 4) link_NAG-ASN : angle 2.64288 / 1.42 ( 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 296 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6615 (mttt) cc_final: 0.5927 (mmtt) REVERT: A 62 LYS cc_start: 0.5934 (mttt) cc_final: 0.5381 (tttt) REVERT: A 74 LEU cc_start: 0.8553 (tt) cc_final: 0.8030 (mm) REVERT: A 265 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7853 (ttpt) REVERT: A 313 PHE cc_start: 0.8292 (t80) cc_final: 0.8073 (t80) REVERT: A 324 PHE cc_start: 0.8265 (t80) cc_final: 0.8054 (t80) REVERT: A 341 GLU cc_start: 0.5594 (tt0) cc_final: 0.4685 (mt-10) REVERT: A 483 GLN cc_start: 0.7191 (pm20) cc_final: 0.6279 (tp40) REVERT: B 46 LYS cc_start: 0.6380 (mttt) cc_final: 0.5835 (mmtt) REVERT: B 62 LYS cc_start: 0.5800 (mttt) cc_final: 0.5264 (tttt) REVERT: B 74 LEU cc_start: 0.8752 (tp) cc_final: 0.8279 (mp) REVERT: B 313 PHE cc_start: 0.8266 (t80) cc_final: 0.8053 (t80) REVERT: B 341 GLU cc_start: 0.5394 (tt0) cc_final: 0.4343 (mt-10) REVERT: B 483 GLN cc_start: 0.7503 (pm20) cc_final: 0.6444 (tp40) REVERT: B 516 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8692 (mt) REVERT: C 46 LYS cc_start: 0.6298 (mttt) cc_final: 0.5777 (mmtt) REVERT: C 62 LYS cc_start: 0.5892 (mttt) cc_final: 0.5323 (tttt) REVERT: C 74 LEU cc_start: 0.8562 (tt) cc_final: 0.8074 (mm) REVERT: C 313 PHE cc_start: 0.8283 (t80) cc_final: 0.8031 (t80) REVERT: C 341 GLU cc_start: 0.5429 (tt0) cc_final: 0.4378 (mt-10) REVERT: C 371 MET cc_start: 0.7674 (ttt) cc_final: 0.7455 (ttt) REVERT: C 483 GLN cc_start: 0.7502 (pm20) cc_final: 0.6505 (tp40) REVERT: D 46 LYS cc_start: 0.6307 (mttt) cc_final: 0.5794 (mmtt) REVERT: D 62 LYS cc_start: 0.5914 (mttt) cc_final: 0.5348 (tttt) REVERT: D 74 LEU cc_start: 0.8560 (tt) cc_final: 0.8051 (mm) REVERT: D 313 PHE cc_start: 0.8284 (t80) cc_final: 0.8069 (t80) REVERT: D 341 GLU cc_start: 0.5450 (tt0) cc_final: 0.4385 (mt-10) outliers start: 52 outliers final: 39 residues processed: 276 average time/residue: 0.1125 time to fit residues: 48.4359 Evaluate side-chains 239 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 350 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 490 VAL 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 306 ILE Chi-restraints excluded: chain B residue 326 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 422 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 311 LEU 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 D residue 45 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 71 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 422 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 508 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 GLN ** 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 ** 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 = 0.3585 r_free = 0.3585 target = 0.127526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100317 restraints weight = 28670.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102746 restraints weight = 17317.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104289 restraints weight = 12853.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105248 restraints weight = 10795.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105547 restraints weight = 9725.312| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.005 0.034 15244 Z= 0.194 Angle : 0.659 9.733 20676 Z= 0.327 Chirality : 0.042 0.203 2420 Planarity : 0.004 0.037 2516 Dihedral : 5.442 45.618 2000 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.95 % Allowed : 17.70 % Favored : 78.35 % 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: 0.19 (0.21), residues: 1784 helix: 1.67 (0.17), residues: 1032 sheet: -1.13 (0.30), residues: 268 loop : -2.59 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 43 TYR 0.027 0.002 TYR A 218 PHE 0.023 0.002 PHE D 56 TRP 0.020 0.002 TRP C 354 HIS 0.007 0.001 HIS B 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (15236) covalent geometry : angle 0.65331 / 0.33 (20652) hydrogen bonds : bond 0.04923 / 3.22 ( 820) hydrogen bonds : angle 3.86116 / 2.64 ( 2376) link_BETA1-4 : bond 0.00268 / 0.13 ( 4) link_BETA1-4 : angle 0.46414 / 0.23 ( 12) link_NAG-ASN : bond 0.00085 / 0.04 ( 4) link_NAG-ASN : angle 3.54946 / 1.90 ( 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 269 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 204 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6682 (mttt) cc_final: 0.5985 (mmtt) REVERT: A 62 LYS cc_start: 0.5763 (mttt) cc_final: 0.5295 (tttt) REVERT: A 265 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7989 (ttpt) REVERT: A 324 PHE cc_start: 0.8314 (t80) cc_final: 0.8072 (t80) REVERT: A 341 GLU cc_start: 0.5471 (tt0) cc_final: 0.5271 (mp0) REVERT: A 483 GLN cc_start: 0.7137 (pm20) cc_final: 0.6235 (tp40) REVERT: B 46 LYS cc_start: 0.6414 (mttt) cc_final: 0.5855 (mmtt) REVERT: B 62 LYS cc_start: 0.5728 (mttt) cc_final: 0.5303 (tttt) REVERT: B 74 LEU cc_start: 0.8786 (tp) cc_final: 0.8303 (mp) REVERT: B 341 GLU cc_start: 0.5294 (tt0) cc_final: 0.5032 (mp0) REVERT: B 483 GLN cc_start: 0.7543 (pm20) cc_final: 0.6414 (tp40) REVERT: C 46 LYS cc_start: 0.6363 (mttt) cc_final: 0.5835 (mmtt) REVERT: C 62 LYS cc_start: 0.5729 (mttt) cc_final: 0.5310 (tttt) REVERT: C 341 GLU cc_start: 0.5307 (tt0) cc_final: 0.5010 (mp0) REVERT: C 483 GLN cc_start: 0.7527 (pm20) cc_final: 0.6425 (tp40) REVERT: D 46 LYS cc_start: 0.6380 (mttt) cc_final: 0.5856 (mmtt) REVERT: D 62 LYS cc_start: 0.5731 (mttt) cc_final: 0.5279 (tttt) REVERT: D 341 GLU cc_start: 0.5312 (tt0) cc_final: 0.5020 (mp0) outliers start: 65 outliers final: 49 residues processed: 243 average time/residue: 0.1088 time to fit residues: 41.8630 Evaluate side-chains 236 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 304 VAL 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 409 HIS Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 422 LEU 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 300 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 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 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 71 VAL Chi-restraints excluded: chain C residue 304 VAL 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 409 HIS Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 422 LEU 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 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 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: 3.9990 chunk 111 optimal weight: 7.9990 chunk 149 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 60 optimal weight: 0.0670 chunk 28 optimal weight: 3.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 HIS ** B 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104070 restraints weight = 28486.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106667 restraints weight = 16702.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108289 restraints weight = 12170.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109264 restraints weight = 10087.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109669 restraints weight = 9028.191| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15244 Z= 0.114 Angle : 0.619 12.993 20676 Z= 0.298 Chirality : 0.040 0.199 2420 Planarity : 0.003 0.037 2516 Dihedral : 5.202 43.125 2000 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.04 % Allowed : 19.22 % Favored : 77.74 % 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: 0.42 (0.21), residues: 1784 helix: 1.79 (0.17), residues: 1040 sheet: -0.81 (0.31), residues: 268 loop : -2.56 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 43 TYR 0.021 0.001 TYR A 218 PHE 0.030 0.001 PHE A 56 TRP 0.025 0.002 TRP D 354 HIS 0.002 0.000 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (15236) covalent geometry : angle 0.61646 / 0.30 (20652) hydrogen bonds : bond 0.04234 / 2.76 ( 820) hydrogen bonds : angle 3.66080 / 2.51 ( 2376) link_BETA1-4 : bond 0.00449 / 0.22 ( 4) link_BETA1-4 : angle 0.24741 / 0.12 ( 12) link_NAG-ASN : bond 0.00269 / 0.13 ( 4) link_NAG-ASN : angle 2.49007 / 1.34 ( 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 263 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6625 (mttt) cc_final: 0.6037 (mmtt) REVERT: A 62 LYS cc_start: 0.5762 (mttt) cc_final: 0.5327 (tttt) REVERT: A 265 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7822 (ttpt) REVERT: A 313 PHE cc_start: 0.8333 (t80) cc_final: 0.8122 (t80) REVERT: A 324 PHE cc_start: 0.8265 (t80) cc_final: 0.8033 (t80) REVERT: A 483 GLN cc_start: 0.7136 (pm20) cc_final: 0.6244 (tp40) REVERT: B 46 LYS cc_start: 0.6504 (mttt) cc_final: 0.5867 (mmtt) REVERT: B 62 LYS cc_start: 0.5891 (mttt) cc_final: 0.5035 (tttt) REVERT: B 65 LYS cc_start: 0.7657 (tptp) cc_final: 0.6671 (mtmm) REVERT: B 74 LEU cc_start: 0.8730 (tp) cc_final: 0.8255 (mp) REVERT: B 313 PHE cc_start: 0.8340 (t80) cc_final: 0.8131 (t80) REVERT: B 483 GLN cc_start: 0.7517 (pm20) cc_final: 0.6471 (tp40) REVERT: C 46 LYS cc_start: 0.6472 (mttt) cc_final: 0.5945 (mmtt) REVERT: C 62 LYS cc_start: 0.5662 (mttt) cc_final: 0.5249 (tttt) REVERT: C 313 PHE cc_start: 0.8287 (t80) cc_final: 0.8051 (t80) REVERT: C 483 GLN cc_start: 0.7570 (pm20) cc_final: 0.6526 (tp40) REVERT: D 46 LYS cc_start: 0.6478 (mttt) cc_final: 0.5962 (mmtt) REVERT: D 62 LYS cc_start: 0.5741 (mttt) cc_final: 0.5285 (tttt) outliers start: 50 outliers final: 37 residues processed: 249 average time/residue: 0.1084 time to fit residues: 42.6103 Evaluate side-chains 238 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 265 LYS 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 409 HIS Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 422 LEU 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 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 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 C residue 68 LEU 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 490 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 221 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 91 optimal weight: 0.2980 chunk 50 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 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 409 HIS ** 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 = 0.3622 r_free = 0.3622 target = 0.130524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.103463 restraints weight = 28628.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105972 restraints weight = 16838.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.107387 restraints weight = 12318.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108551 restraints weight = 10314.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.109004 restraints weight = 9199.546| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15244 Z= 0.133 Angle : 0.638 14.436 20676 Z= 0.307 Chirality : 0.041 0.196 2420 Planarity : 0.003 0.035 2516 Dihedral : 5.168 43.373 2000 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.49 % Allowed : 19.59 % 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: 0.47 (0.21), residues: 1784 helix: 1.79 (0.17), residues: 1044 sheet: -0.81 (0.31), residues: 268 loop : -2.45 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 43 TYR 0.025 0.001 TYR A 218 PHE 0.030 0.001 PHE B 56 TRP 0.022 0.002 TRP D 354 HIS 0.006 0.001 HIS B 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (15236) covalent geometry : angle 0.63503 / 0.31 (20652) hydrogen bonds : bond 0.04362 / 2.87 ( 820) hydrogen bonds : angle 3.70913 / 2.54 ( 2376) link_BETA1-4 : bond 0.00420 / 0.21 ( 4) link_BETA1-4 : angle 0.44216 / 0.22 ( 12) link_NAG-ASN : bond 0.00136 / 0.07 ( 4) link_NAG-ASN : angle 2.79865 / 1.50 ( 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 246 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6736 (mttt) cc_final: 0.6163 (mmtt) REVERT: A 62 LYS cc_start: 0.5694 (mttt) cc_final: 0.5374 (tttt) REVERT: A 265 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7833 (ttpt) REVERT: A 313 PHE cc_start: 0.8339 (t80) cc_final: 0.8133 (t80) REVERT: A 483 GLN cc_start: 0.7179 (pm20) cc_final: 0.6273 (tp40) REVERT: B 46 LYS cc_start: 0.6645 (mttt) cc_final: 0.5977 (mmtt) REVERT: B 62 LYS cc_start: 0.5874 (mttt) cc_final: 0.5123 (tttt) REVERT: B 65 LYS cc_start: 0.7665 (tptp) cc_final: 0.6687 (mtmm) REVERT: B 74 LEU cc_start: 0.8774 (tp) cc_final: 0.8306 (mp) REVERT: B 483 GLN cc_start: 0.7570 (pm20) cc_final: 0.6344 (tp40) REVERT: B 516 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8700 (mt) REVERT: C 46 LYS cc_start: 0.6650 (mttt) cc_final: 0.6002 (mmtt) REVERT: C 62 LYS cc_start: 0.5797 (mttt) cc_final: 0.5389 (tttt) REVERT: C 313 PHE cc_start: 0.8300 (t80) cc_final: 0.8036 (t80) REVERT: C 483 GLN cc_start: 0.7609 (pm20) cc_final: 0.6399 (tp40) REVERT: D 46 LYS cc_start: 0.6680 (mttt) cc_final: 0.6049 (mmtt) REVERT: D 62 LYS cc_start: 0.5844 (mttt) cc_final: 0.5407 (tttt) outliers start: 41 outliers final: 37 residues processed: 236 average time/residue: 0.1101 time to fit residues: 40.9267 Evaluate side-chains 231 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 342 ILE 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 409 HIS Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 384 ASP 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 516 LEU Chi-restraints excluded: chain C residue 68 LEU 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 409 HIS Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 221 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 138 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 177 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN B 69 GLN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101684 restraints weight = 28613.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.104159 restraints weight = 17093.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105750 restraints weight = 12627.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106621 restraints weight = 10533.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107276 restraints weight = 9548.128| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15244 Z= 0.161 Angle : 0.672 12.698 20676 Z= 0.326 Chirality : 0.041 0.233 2420 Planarity : 0.004 0.036 2516 Dihedral : 5.244 43.390 2000 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.86 % Allowed : 19.59 % Favored : 77.55 % 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: 0.41 (0.21), residues: 1784 helix: 1.68 (0.17), residues: 1052 sheet: -0.85 (0.30), residues: 268 loop : -2.39 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 338 TYR 0.027 0.001 TYR C 218 PHE 0.028 0.002 PHE B 56 TRP 0.020 0.002 TRP D 354 HIS 0.006 0.001 HIS B 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (15236) covalent geometry : angle 0.66773 / 0.33 (20652) hydrogen bonds : bond 0.04654 / 3.06 ( 820) hydrogen bonds : angle 3.80826 / 2.60 ( 2376) link_BETA1-4 : bond 0.00346 / 0.17 ( 4) link_BETA1-4 : angle 0.40837 / 0.20 ( 12) link_NAG-ASN : bond 0.00037 / 0.02 ( 4) link_NAG-ASN : angle 3.08612 / 1.65 ( 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 231 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6755 (mttt) cc_final: 0.6183 (mmtt) REVERT: A 62 LYS cc_start: 0.5773 (mttt) cc_final: 0.5424 (tttt) REVERT: A 74 LEU cc_start: 0.8567 (tt) cc_final: 0.8095 (mp) REVERT: A 265 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7919 (ttpt) REVERT: A 313 PHE cc_start: 0.8316 (t80) cc_final: 0.8093 (t80) REVERT: A 483 GLN cc_start: 0.7248 (pm20) cc_final: 0.6329 (tp40) REVERT: B 46 LYS cc_start: 0.6687 (mttt) cc_final: 0.6024 (mmtt) REVERT: B 62 LYS cc_start: 0.5890 (mttt) cc_final: 0.5516 (tttt) REVERT: B 74 LEU cc_start: 0.8707 (tp) cc_final: 0.8251 (mp) REVERT: B 483 GLN cc_start: 0.7536 (pm20) cc_final: 0.6246 (tp40) REVERT: C 46 LYS cc_start: 0.6736 (mttt) cc_final: 0.6096 (mmtt) REVERT: C 62 LYS cc_start: 0.5884 (mttt) cc_final: 0.5499 (tttt) REVERT: C 74 LEU cc_start: 0.8575 (tt) cc_final: 0.8102 (mp) REVERT: C 313 PHE cc_start: 0.8345 (t80) cc_final: 0.8071 (t80) REVERT: C 483 GLN cc_start: 0.7580 (pm20) cc_final: 0.6341 (tp40) REVERT: D 46 LYS cc_start: 0.6692 (mttt) cc_final: 0.6049 (mmtt) REVERT: D 62 LYS cc_start: 0.5859 (mttt) cc_final: 0.5477 (tttt) REVERT: D 74 LEU cc_start: 0.8583 (tt) cc_final: 0.8096 (mp) outliers start: 47 outliers final: 39 residues processed: 220 average time/residue: 0.1092 time to fit residues: 37.8612 Evaluate side-chains 217 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 265 LYS 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 401 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 422 LEU 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 221 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 384 ASP 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 513 PHE Chi-restraints excluded: chain C residue 300 LEU 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 409 HIS 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 221 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 321 LEU 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 422 LEU 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: 6.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.101087 restraints weight = 28669.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103484 restraints weight = 17162.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105070 restraints weight = 12762.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105857 restraints weight = 10673.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106531 restraints weight = 9679.336| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15244 Z= 0.168 Angle : 0.682 12.608 20676 Z= 0.331 Chirality : 0.041 0.211 2420 Planarity : 0.004 0.037 2516 Dihedral : 5.306 42.941 2000 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.74 % Allowed : 19.71 % Favored : 77.55 % 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: 0.36 (0.21), residues: 1784 helix: 1.66 (0.17), residues: 1048 sheet: -0.83 (0.31), residues: 268 loop : -2.43 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 43 TYR 0.031 0.001 TYR D 218 PHE 0.030 0.002 PHE C 56 TRP 0.019 0.002 TRP C 354 HIS 0.007 0.001 HIS B 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (15236) covalent geometry : angle 0.67773 / 0.33 (20652) hydrogen bonds : bond 0.04719 / 3.11 ( 820) hydrogen bonds : angle 3.83411 / 2.62 ( 2376) link_BETA1-4 : bond 0.00325 / 0.16 ( 4) link_BETA1-4 : angle 0.33952 / 0.17 ( 12) link_NAG-ASN : bond 0.00028 / 0.01 ( 4) link_NAG-ASN : angle 3.10871 / 1.66 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.45 seconds wall clock time: 39 minutes 28.46 seconds (2368.46 seconds total)