Starting phenix.real_space_refine on Sat Sep 12 08:21:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5wpq_8881/09_2026/5wpq_8881.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wpq_8881/09_2026/5wpq_8881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5wpq_8881/09_2026/5wpq_8881.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5wpq_8881/09_2026/5wpq_8881.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5wpq_8881/09_2026/5wpq_8881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wpq_8881/09_2026/5wpq_8881.map" model { file = "/net/cci-nas-00/data/ceres_data/5wpq_8881/09_2026/5wpq_8881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wpq_8881/09_2026/5wpq_8881.cif" } resolution = 3.64 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= 0.012 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 44 residue(s): 0.02s 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: 3.78, per 1000 atoms: 0.25 Number of scatterers: 14889 At special positions: 0 Unit cell: (112.35, 112.35, 116.63, 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: 1.31 Conformation dependent library (CDL) restraints added in 706.7 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: 68 helices and 8 sheets defined 63.4% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 39 through 50 removed outlier: 3.731A pdb=" N ARG A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.952A pdb=" N PHE A 56 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 57 " --> pdb=" O ASP A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 53 through 57' Processing helix chain 'A' and resid 64 through 106 removed outlier: 3.764A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 138 removed outlier: 3.644A pdb=" N LEU A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.845A pdb=" N ILE A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 327 removed outlier: 3.697A pdb=" N CYS A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.627A pdb=" N VAL A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 343 through 349 removed outlier: 3.827A pdb=" N ARG A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 377 Processing helix chain 'A' and resid 383 through 399 Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 408 through 448 removed outlier: 4.153A pdb=" N LEU A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 4.106A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 removed outlier: 4.214A pdb=" N ASN A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.555A pdb=" N THR A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 506 removed outlier: 3.784A pdb=" N TRP A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 526 Processing helix chain 'B' and resid 39 through 50 removed outlier: 3.731A pdb=" N ARG B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 removed outlier: 3.952A pdb=" N PHE B 56 " --> pdb=" O CYS B 53 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 57 " --> pdb=" O ASP B 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 53 through 57' Processing helix chain 'B' and resid 64 through 106 removed outlier: 3.765A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 138 removed outlier: 3.644A pdb=" N LEU B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.846A pdb=" N ILE B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 327 removed outlier: 3.697A pdb=" N CYS B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.628A pdb=" N VAL B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 343 through 349 removed outlier: 3.827A pdb=" N ARG B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 377 Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 401 through 406 Processing helix chain 'B' and resid 408 through 448 removed outlier: 4.154A pdb=" N LEU B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 4.106A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 removed outlier: 4.214A pdb=" N ASN B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 483 removed outlier: 3.555A pdb=" N THR B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 506 removed outlier: 3.785A pdb=" N TRP B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 526 Processing helix chain 'C' and resid 39 through 50 removed outlier: 3.731A pdb=" N ARG C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE C 48 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.951A pdb=" N PHE C 56 " --> pdb=" O CYS C 53 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 57 " --> pdb=" O ASP C 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 53 through 57' Processing helix chain 'C' and resid 64 through 106 removed outlier: 3.764A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 138 removed outlier: 3.643A pdb=" N LEU C 125 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.845A pdb=" N ILE C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 327 removed outlier: 3.697A pdb=" N CYS C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 removed outlier: 3.627A pdb=" N VAL C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 343 through 349 removed outlier: 3.827A pdb=" N ARG C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 377 Processing helix chain 'C' and resid 383 through 399 Processing helix chain 'C' and resid 401 through 406 Processing helix chain 'C' and resid 408 through 448 removed outlier: 4.153A pdb=" N LEU C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 4.105A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 470 removed outlier: 4.214A pdb=" N ASN C 469 " --> pdb=" O PHE C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 483 removed outlier: 3.556A pdb=" N THR C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 506 removed outlier: 3.784A pdb=" N TRP C 491 " --> pdb=" O SER C 487 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 526 Processing helix chain 'D' and resid 39 through 50 removed outlier: 3.732A pdb=" N ARG D 43 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE D 48 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.952A pdb=" N PHE D 56 " --> pdb=" O CYS D 53 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG D 57 " --> pdb=" O ASP D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 57' Processing helix chain 'D' and resid 64 through 106 removed outlier: 3.764A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 removed outlier: 3.644A pdb=" N LEU D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 247 removed outlier: 3.846A pdb=" N ILE D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 327 removed outlier: 3.696A pdb=" N CYS D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 removed outlier: 3.627A pdb=" N VAL D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 343 through 349 removed outlier: 3.827A pdb=" N ARG D 347 " --> pdb=" O SER D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 377 Processing helix chain 'D' and resid 383 through 399 Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 408 through 448 removed outlier: 4.154A pdb=" N LEU D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 4.106A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 470 removed outlier: 4.214A pdb=" N ASN D 469 " --> pdb=" O PHE D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.556A pdb=" N THR D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 506 removed outlier: 3.785A pdb=" N TRP D 491 " --> pdb=" O SER D 487 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 526 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.826A pdb=" N ASN A 230 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS A 234 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ARG A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLY A 173 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP A 185 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 149 removed outlier: 3.556A pdb=" N CYS A 253 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.826A pdb=" N ASN B 230 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS B 234 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ARG B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY B 173 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP B 185 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149 removed outlier: 3.556A pdb=" N CYS B 253 " --> pdb=" O GLN B 282 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.827A pdb=" N ASN C 230 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS C 234 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ARG C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLY C 173 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP C 185 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.556A pdb=" N CYS C 253 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.826A pdb=" N ASN D 230 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS D 234 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ARG D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY D 173 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP D 185 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 148 through 149 removed outlier: 3.556A pdb=" N CYS D 253 " --> pdb=" O GLN D 282 " (cutoff:3.500A) 932 hydrogen bonds defined for protein. 2748 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: 2.82 Time building geometry restraints manager: 1.74 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: 4457 1.34 - 1.46: 2844 1.46 - 1.58: 7803 1.58 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 15236 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.50e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" C LEU C 139 " pdb=" N PRO C 140 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 2.99e+00 bond pdb=" C LEU D 139 " pdb=" N PRO D 140 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 2.98e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.98e+00 ... (remaining 15231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 20257 2.82 - 5.64: 307 5.64 - 8.46: 72 8.46 - 11.28: 9 11.28 - 14.11: 7 Bond angle restraints: 20652 Sorted by residual: angle pdb=" CA LEU C 380 " pdb=" CB LEU C 380 " pdb=" CG LEU C 380 " ideal model delta sigma weight residual 116.30 130.41 -14.11 3.50e+00 8.16e-02 1.62e+01 angle pdb=" CA LEU B 380 " pdb=" CB LEU B 380 " pdb=" CG LEU B 380 " ideal model delta sigma weight residual 116.30 130.37 -14.07 3.50e+00 8.16e-02 1.62e+01 angle pdb=" CA LEU A 380 " pdb=" CB LEU A 380 " pdb=" CG LEU A 380 " ideal model delta sigma weight residual 116.30 130.34 -14.04 3.50e+00 8.16e-02 1.61e+01 angle pdb=" CA LEU D 380 " pdb=" CB LEU D 380 " pdb=" CG LEU D 380 " ideal model delta sigma weight residual 116.30 130.33 -14.03 3.50e+00 8.16e-02 1.61e+01 angle pdb=" N HIS D 526 " pdb=" CA HIS D 526 " pdb=" C HIS D 526 " ideal model delta sigma weight residual 109.81 117.27 -7.46 2.21e+00 2.05e-01 1.14e+01 ... (remaining 20647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 8330 15.58 - 31.15: 398 31.15 - 46.73: 128 46.73 - 62.31: 8 62.31 - 77.89: 24 Dihedral angle restraints: 8888 sinusoidal: 3524 harmonic: 5364 Sorted by residual: dihedral pdb=" CA GLY B 485 " pdb=" C GLY B 485 " pdb=" N HIS B 486 " pdb=" CA HIS B 486 " ideal model delta harmonic sigma weight residual 180.00 148.09 31.91 0 5.00e+00 4.00e-02 4.07e+01 dihedral pdb=" CA GLY D 485 " pdb=" C GLY D 485 " pdb=" N HIS D 486 " pdb=" CA HIS D 486 " ideal model delta harmonic sigma weight residual 180.00 148.10 31.90 0 5.00e+00 4.00e-02 4.07e+01 dihedral pdb=" CA GLY A 485 " pdb=" C GLY A 485 " pdb=" N HIS A 486 " pdb=" CA HIS A 486 " ideal model delta harmonic sigma weight residual 180.00 148.12 31.88 0 5.00e+00 4.00e-02 4.07e+01 ... (remaining 8885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1570 0.044 - 0.088: 611 0.088 - 0.132: 184 0.132 - 0.175: 35 0.175 - 0.219: 20 Chirality restraints: 2420 Sorted by residual: chirality pdb=" CG LEU B 389 " pdb=" CB LEU B 389 " pdb=" CD1 LEU B 389 " pdb=" CD2 LEU B 389 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CG LEU D 389 " pdb=" CB LEU D 389 " pdb=" CD1 LEU D 389 " pdb=" CD2 LEU D 389 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CG LEU C 389 " pdb=" CB LEU C 389 " pdb=" CD1 LEU C 389 " pdb=" CD2 LEU C 389 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2417 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 448 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO B 449 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 449 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 449 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 448 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO D 449 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 449 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 449 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 448 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO C 449 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 449 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 449 " -0.031 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4388 2.83 - 3.35: 13270 3.35 - 3.86: 23074 3.86 - 4.38: 25280 4.38 - 4.90: 44093 Nonbonded interactions: 110105 Sorted by model distance: nonbonded pdb=" O TYR A 439 " pdb=" OH TYR A 497 " model vdw 2.310 3.040 nonbonded pdb=" O TYR D 439 " pdb=" OH TYR D 497 " model vdw 2.310 3.040 nonbonded pdb=" O TYR C 439 " pdb=" OH TYR C 497 " model vdw 2.310 3.040 nonbonded pdb=" O TYR B 439 " pdb=" OH TYR B 497 " model vdw 2.310 3.040 nonbonded pdb=" O LEU B 414 " pdb=" OG1 THR B 417 " model vdw 2.327 3.040 ... (remaining 110100 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: 0.900 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.340 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.006 0.056 15244 Z= 0.244 Angle : 0.981 14.105 20676 Z= 0.501 Chirality : 0.054 0.219 2420 Planarity : 0.007 0.057 2516 Dihedral : 11.402 77.887 5416 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.49 % Allowed : 3.89 % Favored : 95.62 % 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: -4.69 (0.14), residues: 1784 helix: -3.01 (0.10), residues: 1040 sheet: -2.15 (0.32), residues: 204 loop : -3.21 (0.21), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 102 TYR 0.022 0.003 TYR B 254 PHE 0.028 0.003 PHE A 101 TRP 0.014 0.003 TRP B 444 HIS 0.006 0.002 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (15236) covalent geometry : angle 0.97045 / 0.50 (20652) hydrogen bonds : bond 0.21844 / 14.01 ( 892) hydrogen bonds : angle 8.12583 / 5.62 ( 2748) link_BETA1-4 : bond 0.00555 / 0.28 ( 4) link_BETA1-4 : angle 1.06976 / 0.51 ( 12) link_NAG-ASN : bond 0.00584 / 0.29 ( 4) link_NAG-ASN : angle 6.03761 / 3.20 ( 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 557 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 549 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8114 (mmpt) cc_final: 0.7437 (ptpt) REVERT: A 225 PHE cc_start: 0.8986 (m-80) cc_final: 0.8494 (m-10) REVERT: A 299 LEU cc_start: 0.8244 (tp) cc_final: 0.8033 (tp) REVERT: A 349 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6677 (mt-10) REVERT: A 426 MET cc_start: 0.8838 (mmt) cc_final: 0.8614 (mmm) REVERT: B 55 LYS cc_start: 0.8041 (mmpt) cc_final: 0.7353 (pttt) REVERT: B 299 LEU cc_start: 0.8231 (tp) cc_final: 0.8018 (tp) REVERT: B 349 GLU cc_start: 0.7609 (mt-10) cc_final: 0.6753 (mt-10) REVERT: B 426 MET cc_start: 0.8845 (mmt) cc_final: 0.8634 (mmm) REVERT: C 55 LYS cc_start: 0.8336 (mmpt) cc_final: 0.7551 (ptpt) REVERT: C 299 LEU cc_start: 0.8243 (tp) cc_final: 0.8041 (tp) REVERT: C 349 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6335 (mt-10) REVERT: C 426 MET cc_start: 0.8797 (mmt) cc_final: 0.8569 (mmm) REVERT: D 55 LYS cc_start: 0.8106 (mmpt) cc_final: 0.7432 (ptpt) REVERT: D 225 PHE cc_start: 0.8950 (m-80) cc_final: 0.8480 (m-10) REVERT: D 299 LEU cc_start: 0.8122 (tp) cc_final: 0.7903 (tp) REVERT: D 349 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6575 (mt-10) REVERT: D 426 MET cc_start: 0.8868 (mmt) cc_final: 0.8649 (mmm) REVERT: D 459 MET cc_start: 0.8075 (mtt) cc_final: 0.7797 (mtt) REVERT: D 473 MET cc_start: 0.8082 (mtt) cc_final: 0.7864 (mtt) outliers start: 8 outliers final: 0 residues processed: 553 average time/residue: 0.1204 time to fit residues: 97.3335 Evaluate side-chains 237 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.0670 chunk 149 optimal weight: 9.9990 overall best weight: 1.8924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN A 79 GLN A 234 HIS A 247 ASN A 267 HIS A 328 ASN A 409 HIS A 481 GLN A 483 GLN B 69 GLN B 79 GLN B 234 HIS B 267 HIS B 328 ASN B 409 HIS B 481 GLN B 483 GLN C 69 GLN C 79 GLN C 135 GLN C 234 HIS C 247 ASN C 267 HIS C 328 ASN C 409 HIS C 481 GLN C 483 GLN D 69 GLN D 79 GLN D 234 HIS D 247 ASN D 267 HIS D 328 ASN D 409 HIS D 481 GLN D 483 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120633 restraints weight = 26213.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123332 restraints weight = 15749.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125068 restraints weight = 11246.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126069 restraints weight = 9115.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126943 restraints weight = 8030.699| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3164 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= 0.159 Angle : 0.736 11.505 20676 Z= 0.367 Chirality : 0.043 0.161 2420 Planarity : 0.005 0.041 2516 Dihedral : 5.256 24.853 1996 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.59 % Allowed : 13.32 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.18), residues: 1784 helix: -0.36 (0.15), residues: 1084 sheet: -1.64 (0.32), residues: 204 loop : -3.09 (0.23), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 403 TYR 0.021 0.002 TYR D 218 PHE 0.015 0.002 PHE B 101 TRP 0.006 0.001 TRP D 398 HIS 0.004 0.001 HIS D 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (15236) covalent geometry : angle 0.72932 / 0.37 (20652) hydrogen bonds : bond 0.06831 / 4.34 ( 892) hydrogen bonds : angle 4.84353 / 3.35 ( 2748) link_BETA1-4 : bond 0.00312 / 0.15 ( 4) link_BETA1-4 : angle 0.86390 / 0.42 ( 12) link_NAG-ASN : bond 0.00038 / 0.02 ( 4) link_NAG-ASN : angle 4.20377 / 2.23 ( 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 340 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 281 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8256 (mmpt) cc_final: 0.7476 (ptpt) REVERT: A 67 MET cc_start: 0.6937 (ttp) cc_final: 0.6427 (ttm) REVERT: A 225 PHE cc_start: 0.8872 (m-80) cc_final: 0.8192 (m-10) REVERT: A 345 TRP cc_start: 0.7012 (t-100) cc_final: 0.6351 (t-100) REVERT: A 349 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7046 (mt-10) REVERT: A 426 MET cc_start: 0.8638 (mmt) cc_final: 0.8374 (mmt) REVERT: B 55 LYS cc_start: 0.8235 (mmpt) cc_final: 0.7450 (ptpt) REVERT: B 426 MET cc_start: 0.8726 (mmt) cc_final: 0.8442 (mmt) REVERT: B 428 PHE cc_start: 0.8675 (t80) cc_final: 0.8407 (t80) REVERT: C 50 MET cc_start: 0.7376 (tpp) cc_final: 0.7056 (mmm) REVERT: C 55 LYS cc_start: 0.8347 (mmpt) cc_final: 0.7637 (ptpt) REVERT: C 426 MET cc_start: 0.8668 (mmt) cc_final: 0.8426 (mmt) REVERT: D 55 LYS cc_start: 0.8255 (mmpt) cc_final: 0.7552 (ptpt) REVERT: D 67 MET cc_start: 0.6959 (ttp) cc_final: 0.6553 (ttm) REVERT: D 225 PHE cc_start: 0.8850 (m-80) cc_final: 0.8184 (m-10) REVERT: D 426 MET cc_start: 0.8697 (mmt) cc_final: 0.8426 (mmt) REVERT: D 459 MET cc_start: 0.8083 (mtt) cc_final: 0.7778 (mtt) outliers start: 59 outliers final: 37 residues processed: 321 average time/residue: 0.1016 time to fit residues: 51.0410 Evaluate side-chains 255 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 440 CYS Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 440 CYS Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 440 CYS Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 409 HIS Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 445 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 84 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 93 optimal weight: 0.3980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 ASN A 409 HIS A 412 ASN A 483 GLN B 412 ASN C 247 ASN C 409 HIS C 412 ASN C 483 GLN D 247 ASN D 409 HIS D 412 ASN D 483 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.152118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124935 restraints weight = 26102.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127684 restraints weight = 15739.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.129419 restraints weight = 11118.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130975 restraints weight = 8845.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131341 restraints weight = 7448.296| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15244 Z= 0.135 Angle : 0.633 9.913 20676 Z= 0.318 Chirality : 0.041 0.171 2420 Planarity : 0.004 0.037 2516 Dihedral : 4.974 22.668 1996 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.10 % Allowed : 17.09 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.19), residues: 1784 helix: 0.39 (0.15), residues: 1108 sheet: -1.41 (0.32), residues: 212 loop : -3.00 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.021 0.001 TYR D 218 PHE 0.013 0.001 PHE A 235 TRP 0.008 0.001 TRP C 354 HIS 0.006 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (15236) covalent geometry : angle 0.62731 / 0.32 (20652) hydrogen bonds : bond 0.05988 / 3.81 ( 892) hydrogen bonds : angle 4.48356 / 3.10 ( 2748) link_BETA1-4 : bond 0.00275 / 0.14 ( 4) link_BETA1-4 : angle 0.70387 / 0.34 ( 12) link_NAG-ASN : bond 0.00035 / 0.02 ( 4) link_NAG-ASN : angle 3.58952 / 1.89 ( 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 293 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 242 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8145 (mmpt) cc_final: 0.7359 (ptpt) REVERT: A 67 MET cc_start: 0.7025 (ttp) cc_final: 0.6668 (ttm) REVERT: A 225 PHE cc_start: 0.8902 (m-80) cc_final: 0.8221 (m-10) REVERT: A 345 TRP cc_start: 0.7194 (t-100) cc_final: 0.6216 (t-100) REVERT: A 349 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6832 (mt-10) REVERT: A 426 MET cc_start: 0.8606 (mmt) cc_final: 0.8325 (mmt) REVERT: B 55 LYS cc_start: 0.8180 (mmpt) cc_final: 0.7394 (ptpt) REVERT: B 345 TRP cc_start: 0.7192 (t-100) cc_final: 0.6305 (t-100) REVERT: B 426 MET cc_start: 0.8611 (mmt) cc_final: 0.8326 (mmt) REVERT: C 55 LYS cc_start: 0.8269 (mmpt) cc_final: 0.7566 (ptpt) REVERT: C 67 MET cc_start: 0.6590 (ttp) cc_final: 0.6174 (ttm) REVERT: C 426 MET cc_start: 0.8617 (mmt) cc_final: 0.8359 (mmt) REVERT: D 55 LYS cc_start: 0.8160 (mmpt) cc_final: 0.7402 (ptpt) REVERT: D 67 MET cc_start: 0.7050 (ttp) cc_final: 0.6669 (ttm) REVERT: D 225 PHE cc_start: 0.8884 (m-80) cc_final: 0.8212 (m-10) REVERT: D 426 MET cc_start: 0.8627 (mmt) cc_final: 0.8347 (mmt) REVERT: D 459 MET cc_start: 0.8045 (mtt) cc_final: 0.7676 (mtt) outliers start: 51 outliers final: 31 residues processed: 279 average time/residue: 0.1078 time to fit residues: 46.0047 Evaluate side-chains 231 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 445 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 23 optimal weight: 0.5980 chunk 172 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 91 optimal weight: 0.0980 chunk 157 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 ASN A 267 HIS B 247 ASN B 267 HIS C 247 ASN C 267 HIS C 483 GLN D 247 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.146468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.120258 restraints weight = 26306.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123061 restraints weight = 15290.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.124901 restraints weight = 10634.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.125903 restraints weight = 8372.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126768 restraints weight = 7242.344| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15244 Z= 0.119 Angle : 0.600 9.987 20676 Z= 0.299 Chirality : 0.040 0.138 2420 Planarity : 0.003 0.046 2516 Dihedral : 4.679 20.118 1996 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.28 % Allowed : 16.12 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.30 (0.20), residues: 1784 helix: 0.98 (0.16), residues: 1104 sheet: -0.88 (0.32), residues: 212 loop : -2.72 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.027 0.001 TYR D 218 PHE 0.013 0.001 PHE D 235 TRP 0.010 0.001 TRP C 345 HIS 0.006 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (15236) covalent geometry : angle 0.59529 / 0.30 (20652) hydrogen bonds : bond 0.05210 / 3.33 ( 892) hydrogen bonds : angle 4.17800 / 2.89 ( 2748) link_BETA1-4 : bond 0.00391 / 0.20 ( 4) link_BETA1-4 : angle 0.72747 / 0.35 ( 12) link_NAG-ASN : bond 0.00104 / 0.05 ( 4) link_NAG-ASN : angle 3.05894 / 1.61 ( 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 289 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 235 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8130 (mmpt) cc_final: 0.7384 (ptpt) REVERT: A 67 MET cc_start: 0.6718 (ttp) cc_final: 0.6233 (ttm) REVERT: A 225 PHE cc_start: 0.8909 (m-80) cc_final: 0.8315 (m-10) REVERT: A 330 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7518 (t80) REVERT: A 345 TRP cc_start: 0.7150 (t-100) cc_final: 0.6191 (t-100) REVERT: A 349 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6995 (mt-10) REVERT: A 426 MET cc_start: 0.8536 (mmt) cc_final: 0.8320 (mmm) REVERT: B 55 LYS cc_start: 0.8158 (mmpt) cc_final: 0.7346 (ptpt) REVERT: B 330 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7267 (t80) REVERT: B 334 MET cc_start: 0.5867 (OUTLIER) cc_final: 0.4839 (ptp) REVERT: B 345 TRP cc_start: 0.7231 (t-100) cc_final: 0.6609 (t-100) REVERT: B 426 MET cc_start: 0.8547 (mmt) cc_final: 0.8245 (mmt) REVERT: C 50 MET cc_start: 0.7438 (tpp) cc_final: 0.6852 (mmm) REVERT: C 55 LYS cc_start: 0.8213 (mmpt) cc_final: 0.7588 (ptpt) REVERT: C 67 MET cc_start: 0.6583 (ttp) cc_final: 0.6142 (ttm) REVERT: C 88 GLN cc_start: 0.7752 (tp40) cc_final: 0.7447 (tp40) REVERT: C 330 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7645 (t80) REVERT: C 345 TRP cc_start: 0.7112 (t-100) cc_final: 0.6646 (t-100) REVERT: C 426 MET cc_start: 0.8554 (mmt) cc_final: 0.8297 (mmt) REVERT: D 55 LYS cc_start: 0.8114 (mmpt) cc_final: 0.7406 (ptpt) REVERT: D 225 PHE cc_start: 0.8894 (m-80) cc_final: 0.8221 (m-10) REVERT: D 330 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7519 (t80) REVERT: D 345 TRP cc_start: 0.7226 (t-100) cc_final: 0.6684 (t-100) REVERT: D 349 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7076 (mt-10) REVERT: D 426 MET cc_start: 0.8555 (mmt) cc_final: 0.8255 (mmt) outliers start: 54 outliers final: 32 residues processed: 270 average time/residue: 0.0891 time to fit residues: 39.1376 Evaluate side-chains 240 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 510 LEU 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: 8.9990 chunk 136 optimal weight: 0.0670 chunk 121 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.153174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126273 restraints weight = 26321.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.129016 restraints weight = 15335.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130797 restraints weight = 10756.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.131928 restraints weight = 8537.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132541 restraints weight = 7358.911| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15244 Z= 0.117 Angle : 0.592 9.610 20676 Z= 0.290 Chirality : 0.040 0.134 2420 Planarity : 0.003 0.032 2516 Dihedral : 4.585 18.360 1996 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.89 % Allowed : 15.69 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.20), residues: 1784 helix: 1.29 (0.16), residues: 1104 sheet: -0.54 (0.34), residues: 208 loop : -2.65 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 187 TYR 0.023 0.001 TYR D 218 PHE 0.015 0.001 PHE B 235 TRP 0.008 0.001 TRP C 354 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (15236) covalent geometry : angle 0.58605 / 0.29 (20652) hydrogen bonds : bond 0.04936 / 3.15 ( 892) hydrogen bonds : angle 4.05228 / 2.80 ( 2748) link_BETA1-4 : bond 0.00563 / 0.28 ( 4) link_BETA1-4 : angle 1.51437 / 0.74 ( 12) link_NAG-ASN : bond 0.00271 / 0.14 ( 4) link_NAG-ASN : angle 3.29678 / 1.75 ( 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 279 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 215 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8132 (mmpt) cc_final: 0.7357 (ptpt) REVERT: A 67 MET cc_start: 0.6767 (ttp) cc_final: 0.6368 (ttm) REVERT: A 194 GLN cc_start: 0.6972 (mm-40) cc_final: 0.6498 (tp40) REVERT: A 225 PHE cc_start: 0.8921 (m-80) cc_final: 0.8301 (m-10) REVERT: A 330 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7564 (t80) REVERT: A 334 MET cc_start: 0.5753 (OUTLIER) cc_final: 0.4740 (ptm) REVERT: B 55 LYS cc_start: 0.8094 (mmpt) cc_final: 0.7285 (ptpt) REVERT: B 194 GLN cc_start: 0.6951 (mm-40) cc_final: 0.6469 (tp40) REVERT: B 330 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7507 (t80) REVERT: B 334 MET cc_start: 0.5789 (OUTLIER) cc_final: 0.4807 (ptp) REVERT: B 345 TRP cc_start: 0.7216 (t-100) cc_final: 0.6623 (t-100) REVERT: C 50 MET cc_start: 0.7465 (tpp) cc_final: 0.6820 (mmm) REVERT: C 55 LYS cc_start: 0.8167 (mmpt) cc_final: 0.7546 (ptpt) REVERT: C 88 GLN cc_start: 0.7682 (tp40) cc_final: 0.7427 (tp40) REVERT: C 330 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7721 (t80) REVERT: C 345 TRP cc_start: 0.7135 (t-100) cc_final: 0.6786 (t-100) REVERT: C 426 MET cc_start: 0.8490 (mmt) cc_final: 0.8230 (mmm) REVERT: D 55 LYS cc_start: 0.8168 (mmpt) cc_final: 0.7354 (ptpt) REVERT: D 194 GLN cc_start: 0.7033 (mm-40) cc_final: 0.6552 (tp40) REVERT: D 225 PHE cc_start: 0.8886 (m-80) cc_final: 0.8252 (m-10) REVERT: D 330 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7580 (t80) REVERT: D 334 MET cc_start: 0.5744 (OUTLIER) cc_final: 0.4773 (ptp) REVERT: D 345 TRP cc_start: 0.7203 (t-100) cc_final: 0.6701 (t-100) REVERT: D 349 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7031 (mt-10) REVERT: D 426 MET cc_start: 0.8499 (mmt) cc_final: 0.8264 (mmm) outliers start: 64 outliers final: 38 residues processed: 253 average time/residue: 0.0883 time to fit residues: 36.5391 Evaluate side-chains 241 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 145 optimal weight: 0.4980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 ASN A 412 ASN C 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119484 restraints weight = 26521.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122205 restraints weight = 15630.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123985 restraints weight = 10986.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125116 restraints weight = 8746.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125722 restraints weight = 7546.347| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15244 Z= 0.127 Angle : 0.592 10.166 20676 Z= 0.292 Chirality : 0.040 0.133 2420 Planarity : 0.003 0.033 2516 Dihedral : 4.507 18.196 1996 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.89 % Allowed : 17.15 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.20), residues: 1784 helix: 1.56 (0.16), residues: 1104 sheet: -0.47 (0.34), residues: 212 loop : -2.57 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 347 TYR 0.028 0.002 TYR B 218 PHE 0.013 0.001 PHE C 235 TRP 0.010 0.001 TRP A 345 HIS 0.008 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (15236) covalent geometry : angle 0.58688 / 0.29 (20652) hydrogen bonds : bond 0.04956 / 3.17 ( 892) hydrogen bonds : angle 4.00539 / 2.78 ( 2748) link_BETA1-4 : bond 0.00301 / 0.15 ( 4) link_BETA1-4 : angle 0.84630 / 0.41 ( 12) link_NAG-ASN : bond 0.00137 / 0.07 ( 4) link_NAG-ASN : angle 3.34159 / 1.74 ( 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 276 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 212 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8107 (mmpt) cc_final: 0.7129 (mtmt) REVERT: A 225 PHE cc_start: 0.8925 (m-80) cc_final: 0.8364 (m-10) REVERT: A 330 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7663 (t80) REVERT: A 334 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.4793 (ptp) REVERT: A 345 TRP cc_start: 0.7248 (t-100) cc_final: 0.6865 (t-100) REVERT: B 55 LYS cc_start: 0.8090 (mmpt) cc_final: 0.7254 (ptpt) REVERT: B 330 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7609 (t80) REVERT: B 334 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.4744 (ptp) REVERT: B 345 TRP cc_start: 0.7306 (t-100) cc_final: 0.6616 (t-100) REVERT: B 480 MET cc_start: 0.8439 (mmm) cc_final: 0.8186 (mpp) REVERT: C 55 LYS cc_start: 0.8052 (mmpt) cc_final: 0.7324 (ptpt) REVERT: C 59 LYS cc_start: 0.5134 (mttt) cc_final: 0.4287 (mmtm) REVERT: C 330 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7817 (t80) REVERT: C 345 TRP cc_start: 0.7086 (t-100) cc_final: 0.6714 (t-100) REVERT: C 426 MET cc_start: 0.8548 (mmt) cc_final: 0.8266 (mmm) REVERT: D 55 LYS cc_start: 0.8108 (mmpt) cc_final: 0.7149 (mtmt) REVERT: D 225 PHE cc_start: 0.8902 (m-80) cc_final: 0.8323 (m-10) REVERT: D 330 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7711 (t80) REVERT: D 334 MET cc_start: 0.5734 (OUTLIER) cc_final: 0.4897 (ptp) REVERT: D 345 TRP cc_start: 0.7145 (t-100) cc_final: 0.6548 (t-100) REVERT: D 349 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7069 (mt-10) REVERT: D 426 MET cc_start: 0.8511 (mmt) cc_final: 0.8308 (mmm) REVERT: D 480 MET cc_start: 0.8440 (mmm) cc_final: 0.8149 (mpp) outliers start: 64 outliers final: 41 residues processed: 252 average time/residue: 0.0915 time to fit residues: 37.1241 Evaluate side-chains 246 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 ASN A 327 GLN B 247 ASN B 327 GLN C 69 GLN C 327 GLN C 412 ASN D 247 ASN D 327 GLN D 412 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.143868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117529 restraints weight = 26421.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120015 restraints weight = 16325.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121654 restraints weight = 11884.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.122728 restraints weight = 9617.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123293 restraints weight = 8413.760| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15244 Z= 0.162 Angle : 0.618 9.759 20676 Z= 0.308 Chirality : 0.041 0.142 2420 Planarity : 0.004 0.033 2516 Dihedral : 4.615 19.390 1996 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.83 % Allowed : 16.91 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.20), residues: 1784 helix: 1.61 (0.16), residues: 1104 sheet: -0.53 (0.34), residues: 212 loop : -2.67 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 455 TYR 0.032 0.002 TYR B 218 PHE 0.014 0.001 PHE C 235 TRP 0.007 0.001 TRP A 444 HIS 0.010 0.002 HIS C 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (15236) covalent geometry : angle 0.61121 / 0.31 (20652) hydrogen bonds : bond 0.05325 / 3.40 ( 892) hydrogen bonds : angle 4.08582 / 2.83 ( 2748) link_BETA1-4 : bond 0.00211 / 0.11 ( 4) link_BETA1-4 : angle 1.02161 / 0.50 ( 12) link_NAG-ASN : bond 0.00299 / 0.15 ( 4) link_NAG-ASN : angle 3.84259 / 2.01 ( 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 268 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 205 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8128 (mmpt) cc_final: 0.7302 (ptpt) REVERT: A 225 PHE cc_start: 0.8920 (m-80) cc_final: 0.8312 (m-10) REVERT: A 330 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7833 (t80) REVERT: A 480 MET cc_start: 0.8385 (mpp) cc_final: 0.8131 (mpp) REVERT: B 55 LYS cc_start: 0.8104 (mmpt) cc_final: 0.7256 (ptpt) REVERT: B 330 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7771 (t80) REVERT: B 334 MET cc_start: 0.5807 (OUTLIER) cc_final: 0.4916 (ptp) REVERT: B 345 TRP cc_start: 0.7352 (t-100) cc_final: 0.6560 (t-100) REVERT: B 480 MET cc_start: 0.8445 (mmm) cc_final: 0.8160 (mpp) REVERT: C 49 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6671 (t80) REVERT: C 55 LYS cc_start: 0.8206 (mmpt) cc_final: 0.7447 (ptpt) REVERT: C 67 MET cc_start: 0.6741 (ttp) cc_final: 0.6238 (ttm) REVERT: C 330 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7928 (t80) REVERT: C 345 TRP cc_start: 0.7155 (t-100) cc_final: 0.6644 (t-100) REVERT: C 426 MET cc_start: 0.8503 (mmt) cc_final: 0.8220 (mmm) REVERT: D 49 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.6977 (t80) REVERT: D 55 LYS cc_start: 0.8138 (mmpt) cc_final: 0.7301 (ptpt) REVERT: D 67 MET cc_start: 0.6305 (ttp) cc_final: 0.5891 (ttm) REVERT: D 225 PHE cc_start: 0.8903 (m-80) cc_final: 0.8364 (m-10) REVERT: D 330 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7853 (t80) REVERT: D 426 MET cc_start: 0.8489 (mmt) cc_final: 0.8240 (mmt) REVERT: D 480 MET cc_start: 0.8464 (mmm) cc_final: 0.8187 (mpp) outliers start: 63 outliers final: 37 residues processed: 251 average time/residue: 0.0978 time to fit residues: 39.1805 Evaluate side-chains 223 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 74 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 178 optimal weight: 0.1980 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 ASN B 171 HIS B 247 ASN D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.146965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.120784 restraints weight = 26632.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123353 restraints weight = 16272.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125050 restraints weight = 11714.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126140 restraints weight = 9421.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126739 restraints weight = 8194.784| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15244 Z= 0.115 Angle : 0.584 9.562 20676 Z= 0.289 Chirality : 0.040 0.132 2420 Planarity : 0.003 0.034 2516 Dihedral : 4.466 16.606 1996 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.04 % Allowed : 18.73 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1784 helix: 1.73 (0.16), residues: 1112 sheet: -0.25 (0.35), residues: 212 loop : -2.39 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.025 0.001 TYR C 218 PHE 0.014 0.001 PHE C 235 TRP 0.011 0.001 TRP A 345 HIS 0.010 0.001 HIS C 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (15236) covalent geometry : angle 0.58047 / 0.29 (20652) hydrogen bonds : bond 0.04673 / 2.96 ( 892) hydrogen bonds : angle 3.92578 / 2.73 ( 2748) link_BETA1-4 : bond 0.00460 / 0.23 ( 4) link_BETA1-4 : angle 0.61067 / 0.29 ( 12) link_NAG-ASN : bond 0.00098 / 0.05 ( 4) link_NAG-ASN : angle 2.83639 / 1.49 ( 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 252 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8131 (mmpt) cc_final: 0.7107 (mtmt) REVERT: A 67 MET cc_start: 0.6399 (ttp) cc_final: 0.5815 (ttm) REVERT: A 225 PHE cc_start: 0.8852 (m-80) cc_final: 0.8263 (m-10) REVERT: A 330 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7815 (t80) REVERT: A 334 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.4893 (ptp) REVERT: A 345 TRP cc_start: 0.6873 (t-100) cc_final: 0.6467 (t-100) REVERT: B 55 LYS cc_start: 0.8107 (mmpt) cc_final: 0.7286 (ptpt) REVERT: B 330 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7804 (t80) REVERT: B 334 MET cc_start: 0.5715 (OUTLIER) cc_final: 0.4790 (ptp) REVERT: B 345 TRP cc_start: 0.7328 (t-100) cc_final: 0.6934 (t-100) REVERT: C 49 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6623 (t80) REVERT: C 50 MET cc_start: 0.7424 (tpp) cc_final: 0.6936 (mmm) REVERT: C 55 LYS cc_start: 0.8086 (mmpt) cc_final: 0.7457 (ptpt) REVERT: C 67 MET cc_start: 0.6527 (ttp) cc_final: 0.5970 (ttm) REVERT: C 345 TRP cc_start: 0.7088 (t-100) cc_final: 0.6674 (t-100) REVERT: C 426 MET cc_start: 0.8444 (mmt) cc_final: 0.8195 (mmm) REVERT: D 49 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.6919 (t80) REVERT: D 55 LYS cc_start: 0.8117 (mmpt) cc_final: 0.7227 (ptpt) REVERT: D 67 MET cc_start: 0.6262 (ttp) cc_final: 0.5846 (ttm) REVERT: D 225 PHE cc_start: 0.8859 (m-80) cc_final: 0.8259 (m-10) REVERT: D 330 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7844 (t80) REVERT: D 334 MET cc_start: 0.5711 (OUTLIER) cc_final: 0.4872 (ptp) REVERT: D 345 TRP cc_start: 0.6905 (t-100) cc_final: 0.6393 (t-100) REVERT: D 349 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7200 (mt-10) outliers start: 50 outliers final: 32 residues processed: 235 average time/residue: 0.0905 time to fit residues: 34.8557 Evaluate side-chains 230 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 91 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 247 ASN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.146298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.119858 restraints weight = 26739.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.122414 restraints weight = 16336.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124115 restraints weight = 11819.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125158 restraints weight = 9535.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125602 restraints weight = 8293.705| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15244 Z= 0.125 Angle : 0.602 9.595 20676 Z= 0.294 Chirality : 0.040 0.132 2420 Planarity : 0.003 0.032 2516 Dihedral : 4.449 16.538 1996 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.98 % Allowed : 18.80 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1784 helix: 1.80 (0.16), residues: 1104 sheet: -0.10 (0.35), residues: 212 loop : -2.34 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 419 TYR 0.028 0.001 TYR C 218 PHE 0.013 0.001 PHE D 235 TRP 0.008 0.001 TRP A 345 HIS 0.008 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (15236) covalent geometry : angle 0.59750 / 0.29 (20652) hydrogen bonds : bond 0.04774 / 3.04 ( 892) hydrogen bonds : angle 3.95105 / 2.75 ( 2748) link_BETA1-4 : bond 0.00230 / 0.11 ( 4) link_BETA1-4 : angle 0.87178 / 0.43 ( 12) link_NAG-ASN : bond 0.00089 / 0.04 ( 4) link_NAG-ASN : angle 3.09355 / 1.61 ( 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 247 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8158 (mmpt) cc_final: 0.7231 (ptpt) REVERT: A 67 MET cc_start: 0.6412 (ttp) cc_final: 0.5976 (ttm) REVERT: A 225 PHE cc_start: 0.8863 (m-80) cc_final: 0.8296 (m-10) REVERT: A 330 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7910 (t80) REVERT: A 334 MET cc_start: 0.5815 (OUTLIER) cc_final: 0.4979 (ptp) REVERT: A 345 TRP cc_start: 0.6877 (t-100) cc_final: 0.6466 (t-100) REVERT: B 55 LYS cc_start: 0.8152 (mmpt) cc_final: 0.7282 (ptpt) REVERT: B 330 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7845 (t80) REVERT: B 334 MET cc_start: 0.5825 (OUTLIER) cc_final: 0.4932 (ptp) REVERT: B 459 MET cc_start: 0.7811 (mtm) cc_final: 0.7607 (mtm) REVERT: C 49 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.6634 (t80) REVERT: C 50 MET cc_start: 0.7444 (tpp) cc_final: 0.6929 (mmm) REVERT: C 55 LYS cc_start: 0.8183 (mmpt) cc_final: 0.7487 (ptpt) REVERT: C 67 MET cc_start: 0.6538 (ttp) cc_final: 0.5953 (ttm) REVERT: C 345 TRP cc_start: 0.7053 (t-100) cc_final: 0.6570 (t-100) REVERT: C 349 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7099 (mt-10) REVERT: C 426 MET cc_start: 0.8456 (mmt) cc_final: 0.8204 (mmm) REVERT: D 49 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.6962 (t80) REVERT: D 55 LYS cc_start: 0.8155 (mmpt) cc_final: 0.7231 (ptpt) REVERT: D 67 MET cc_start: 0.6223 (ttp) cc_final: 0.5801 (ttm) REVERT: D 225 PHE cc_start: 0.8872 (m-80) cc_final: 0.8282 (m-10) REVERT: D 330 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7862 (t80) REVERT: D 334 MET cc_start: 0.5772 (OUTLIER) cc_final: 0.4941 (ptp) REVERT: D 345 TRP cc_start: 0.6888 (t-100) cc_final: 0.6485 (t-100) outliers start: 49 outliers final: 34 residues processed: 230 average time/residue: 0.0901 time to fit residues: 33.8244 Evaluate side-chains 232 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 191 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 138 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 92 optimal weight: 0.0070 chunk 121 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 overall best weight: 3.0804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 247 ASN ** C 267 HIS ** 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 = 0.3735 r_free = 0.3735 target = 0.144114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116778 restraints weight = 26581.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119481 restraints weight = 15867.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121267 restraints weight = 11274.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122364 restraints weight = 9027.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123162 restraints weight = 7824.921| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15244 Z= 0.168 Angle : 0.660 9.836 20676 Z= 0.321 Chirality : 0.042 0.182 2420 Planarity : 0.004 0.034 2516 Dihedral : 4.568 18.210 1996 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.98 % Allowed : 18.73 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.20), residues: 1784 helix: 1.70 (0.16), residues: 1104 sheet: -0.28 (0.35), residues: 212 loop : -2.37 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.032 0.002 TYR C 218 PHE 0.018 0.002 PHE D 101 TRP 0.013 0.001 TRP B 345 HIS 0.007 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (15236) covalent geometry : angle 0.65361 / 0.32 (20652) hydrogen bonds : bond 0.05298 / 3.38 ( 892) hydrogen bonds : angle 4.07721 / 2.83 ( 2748) link_BETA1-4 : bond 0.00112 / 0.06 ( 4) link_BETA1-4 : angle 0.97951 / 0.48 ( 12) link_NAG-ASN : bond 0.00351 / 0.18 ( 4) link_NAG-ASN : angle 3.69185 / 1.93 ( 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 234 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8228 (mmpt) cc_final: 0.7241 (ptpt) REVERT: A 67 MET cc_start: 0.6615 (ttp) cc_final: 0.6195 (ttm) REVERT: A 225 PHE cc_start: 0.8914 (m-80) cc_final: 0.8337 (m-10) REVERT: A 227 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.6383 (ptmt) REVERT: A 345 TRP cc_start: 0.6939 (t-100) cc_final: 0.6534 (t-100) REVERT: A 480 MET cc_start: 0.8417 (mmm) cc_final: 0.8199 (mpp) REVERT: B 55 LYS cc_start: 0.8231 (mmpt) cc_final: 0.7315 (ptpt) REVERT: B 345 TRP cc_start: 0.7214 (t-100) cc_final: 0.6912 (t-100) REVERT: B 459 MET cc_start: 0.7847 (mtm) cc_final: 0.7634 (mtm) REVERT: C 49 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.6581 (t80) REVERT: C 55 LYS cc_start: 0.8255 (mmpt) cc_final: 0.7431 (ptpt) REVERT: C 345 TRP cc_start: 0.7193 (t-100) cc_final: 0.6716 (t-100) REVERT: C 426 MET cc_start: 0.8569 (mmt) cc_final: 0.8270 (mmm) REVERT: D 49 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.6938 (t80) REVERT: D 55 LYS cc_start: 0.8235 (mmpt) cc_final: 0.7256 (ptpt) REVERT: D 67 MET cc_start: 0.6438 (ttp) cc_final: 0.5974 (ttm) REVERT: D 225 PHE cc_start: 0.8938 (m-80) cc_final: 0.8402 (m-10) REVERT: D 345 TRP cc_start: 0.6871 (t-100) cc_final: 0.6284 (t-100) outliers start: 49 outliers final: 36 residues processed: 221 average time/residue: 0.0910 time to fit residues: 32.3019 Evaluate side-chains 214 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 0.0670 chunk 127 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 129 optimal weight: 0.0570 chunk 62 optimal weight: 4.9990 overall best weight: 0.6036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.148186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121445 restraints weight = 26663.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124282 restraints weight = 15473.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126094 restraints weight = 10787.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127261 restraints weight = 8541.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.128059 restraints weight = 7354.577| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5028 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= 0.112 Angle : 0.611 9.529 20676 Z= 0.292 Chirality : 0.040 0.165 2420 Planarity : 0.003 0.034 2516 Dihedral : 4.391 16.559 1996 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.37 % Allowed : 19.59 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.20), residues: 1784 helix: 1.85 (0.16), residues: 1104 sheet: 0.08 (0.36), residues: 212 loop : -2.04 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 322 TYR 0.027 0.001 TYR C 218 PHE 0.015 0.001 PHE C 235 TRP 0.012 0.001 TRP B 345 HIS 0.014 0.001 HIS C 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (15236) covalent geometry : angle 0.60806 / 0.29 (20652) hydrogen bonds : bond 0.04464 / 2.83 ( 892) hydrogen bonds : angle 3.86444 / 2.69 ( 2748) link_BETA1-4 : bond 0.00555 / 0.28 ( 4) link_BETA1-4 : angle 0.65896 / 0.33 ( 12) link_NAG-ASN : bond 0.00149 / 0.07 ( 4) link_NAG-ASN : angle 2.53333 / 1.33 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2262.99 seconds wall clock time: 40 minutes 7.90 seconds (2407.90 seconds total)