Starting phenix.real_space_refine on Tue Nov 18 14:14:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5wpq_8881/11_2025/5wpq_8881.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wpq_8881/11_2025/5wpq_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 { model { file = "/net/cci-nas-00/data/ceres_data/5wpq_8881/11_2025/5wpq_8881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wpq_8881/11_2025/5wpq_8881.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5wpq_8881/11_2025/5wpq_8881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wpq_8881/11_2025/5wpq_8881.map" } 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-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14889 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "B" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "C" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "D" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.81, per 1000 atoms: 0.26 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: 1.16 Conformation dependent library (CDL) restraints added in 672.5 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: 0.50 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: 2.50 Time building geometry restraints manager: 1.57 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: 8474 15.58 - 31.15: 410 31.15 - 46.73: 132 46.73 - 62.31: 16 62.31 - 77.89: 24 Dihedral angle restraints: 9056 sinusoidal: 3692 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 9053 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.570 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 11.534 77.887 5584 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 covalent geometry : bond 0.00561 (15236) covalent geometry : angle 0.97045 (20652) hydrogen bonds : bond 0.21844 ( 892) hydrogen bonds : angle 8.12583 ( 2748) link_BETA1-4 : bond 0.00555 ( 4) link_BETA1-4 : angle 1.06976 ( 12) link_NAG-ASN : bond 0.00584 ( 4) link_NAG-ASN : angle 6.03761 ( 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 : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8113 (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: 0.8042 (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: 0.8335 (mmpt) cc_final: 0.7551 (ptpt) REVERT: C 299 LEU cc_start: 0.8244 (tp) cc_final: 0.8042 (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: 0.8481 (m-10) REVERT: D 299 LEU cc_start: 0.8122 (tp) cc_final: 0.7902 (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: 0.1332 time to fit residues: 106.2489 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 : 0.590 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3760 r_free = 0.3760 target = 0.149208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121204 restraints weight = 26213.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124005 restraints weight = 15668.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125504 restraints weight = 11215.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.126895 restraints weight = 9163.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127532 restraints weight = 7878.877| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15244 Z= 0.158 Angle : 0.732 10.864 20676 Z= 0.365 Chirality : 0.043 0.158 2420 Planarity : 0.005 0.041 2516 Dihedral : 6.438 59.210 2164 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.59 % Allowed : 13.38 % Favored : 83.03 % 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: -2.02 (0.18), residues: 1784 helix: -0.41 (0.15), residues: 1084 sheet: -1.65 (0.32), residues: 204 loop : -3.10 (0.23), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 403 TYR 0.020 0.002 TYR D 218 PHE 0.015 0.002 PHE C 301 TRP 0.006 0.001 TRP D 398 HIS 0.004 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00327 (15236) covalent geometry : angle 0.72524 (20652) hydrogen bonds : bond 0.07063 ( 892) hydrogen bonds : angle 4.88666 ( 2748) link_BETA1-4 : bond 0.00162 ( 4) link_BETA1-4 : angle 0.80243 ( 12) link_NAG-ASN : bond 0.00019 ( 4) link_NAG-ASN : angle 4.10731 ( 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 338 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 279 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8266 (mmpt) cc_final: 0.7468 (ptpt) REVERT: A 67 MET cc_start: 0.7018 (ttp) cc_final: 0.6540 (ttm) REVERT: A 225 PHE cc_start: 0.8874 (m-80) cc_final: 0.8204 (m-10) REVERT: A 345 TRP cc_start: 0.6975 (t-100) cc_final: 0.6304 (t-100) REVERT: A 349 GLU cc_start: 0.7276 (mt-10) cc_final: 0.7037 (mt-10) REVERT: A 426 MET cc_start: 0.8642 (mmt) cc_final: 0.8382 (mmt) REVERT: B 55 LYS cc_start: 0.8239 (mmpt) cc_final: 0.7446 (ptpt) REVERT: B 345 TRP cc_start: 0.7025 (t-100) cc_final: 0.6361 (t-100) REVERT: B 349 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6971 (mt-10) REVERT: B 426 MET cc_start: 0.8729 (mmt) cc_final: 0.8452 (mmt) REVERT: B 428 PHE cc_start: 0.8682 (t80) cc_final: 0.8404 (t80) REVERT: C 50 MET cc_start: 0.7382 (tpp) cc_final: 0.7064 (mmm) REVERT: C 55 LYS cc_start: 0.8349 (mmpt) cc_final: 0.7636 (ptpt) REVERT: C 426 MET cc_start: 0.8672 (mmt) cc_final: 0.8429 (mmt) REVERT: D 55 LYS cc_start: 0.8264 (mmpt) cc_final: 0.7560 (ptpt) REVERT: D 67 MET cc_start: 0.6955 (ttp) cc_final: 0.6552 (ttm) REVERT: D 225 PHE cc_start: 0.8854 (m-80) cc_final: 0.8196 (m-10) REVERT: D 426 MET cc_start: 0.8694 (mmt) cc_final: 0.8426 (mmt) REVERT: D 459 MET cc_start: 0.8072 (mtt) cc_final: 0.7773 (mtt) outliers start: 59 outliers final: 37 residues processed: 320 average time/residue: 0.1078 time to fit residues: 53.6927 Evaluate side-chains 257 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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: 7.9990 chunk 40 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 0.0870 chunk 96 optimal weight: 0.3980 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 93 optimal weight: 0.5980 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 409 HIS A 412 ASN A 483 GLN B 409 HIS 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.151115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123984 restraints weight = 26168.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126578 restraints weight = 15918.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128265 restraints weight = 11432.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129227 restraints weight = 9242.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130027 restraints weight = 8102.486| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15244 Z= 0.145 Angle : 0.646 9.748 20676 Z= 0.325 Chirality : 0.042 0.173 2420 Planarity : 0.004 0.038 2516 Dihedral : 6.109 58.845 2164 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.41 % Allowed : 16.85 % Favored : 79.74 % 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: -1.14 (0.19), residues: 1784 helix: 0.38 (0.15), residues: 1100 sheet: -1.49 (0.32), residues: 212 loop : -3.03 (0.24), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.021 0.001 TYR D 218 PHE 0.014 0.001 PHE B 235 TRP 0.008 0.001 TRP C 354 HIS 0.010 0.002 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00303 (15236) covalent geometry : angle 0.63891 (20652) hydrogen bonds : bond 0.06177 ( 892) hydrogen bonds : angle 4.52325 ( 2748) link_BETA1-4 : bond 0.00232 ( 4) link_BETA1-4 : angle 0.81301 ( 12) link_NAG-ASN : bond 0.00118 ( 4) link_NAG-ASN : angle 3.87310 ( 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 285 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 229 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8127 (mmpt) cc_final: 0.7375 (ptpt) REVERT: A 67 MET cc_start: 0.7010 (ttp) cc_final: 0.6614 (ttm) REVERT: A 225 PHE cc_start: 0.8908 (m-80) cc_final: 0.8244 (m-10) REVERT: A 426 MET cc_start: 0.8594 (mmt) cc_final: 0.8318 (mmt) REVERT: B 55 LYS cc_start: 0.8162 (mmpt) cc_final: 0.7362 (ptpt) REVERT: B 426 MET cc_start: 0.8617 (mmt) cc_final: 0.8328 (mmt) REVERT: C 50 MET cc_start: 0.7433 (tpp) cc_final: 0.7117 (mmm) REVERT: C 55 LYS cc_start: 0.8273 (mmpt) cc_final: 0.7548 (ptpt) REVERT: C 426 MET cc_start: 0.8623 (mmt) cc_final: 0.8372 (mmt) REVERT: D 55 LYS cc_start: 0.8153 (mmpt) cc_final: 0.7419 (ptpt) REVERT: D 67 MET cc_start: 0.7055 (ttp) cc_final: 0.6656 (ttm) REVERT: D 225 PHE cc_start: 0.8868 (m-80) cc_final: 0.8188 (m-10) REVERT: D 426 MET cc_start: 0.8650 (mmt) cc_final: 0.8376 (mmt) REVERT: D 459 MET cc_start: 0.7988 (mtt) cc_final: 0.7641 (mtt) outliers start: 56 outliers final: 34 residues processed: 271 average time/residue: 0.1123 time to fit residues: 46.7439 Evaluate side-chains 235 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 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 415 ILE 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 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 B residue 445 ILE 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 379 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 445 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 314 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 415 ILE 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: 1.9990 chunk 172 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 0.0370 chunk 157 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3743 r_free = 0.3743 target = 0.144953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118563 restraints weight = 26314.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.121293 restraints weight = 15409.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123083 restraints weight = 10817.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124226 restraints weight = 8592.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124850 restraints weight = 7411.085| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15244 Z= 0.135 Angle : 0.618 9.663 20676 Z= 0.308 Chirality : 0.041 0.137 2420 Planarity : 0.004 0.046 2516 Dihedral : 5.697 56.898 2164 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.01 % Allowed : 15.88 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.49 (0.20), residues: 1784 helix: 0.89 (0.16), residues: 1104 sheet: -1.06 (0.32), residues: 212 loop : -2.90 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.025 0.002 TYR B 218 PHE 0.013 0.001 PHE B 235 TRP 0.007 0.001 TRP B 345 HIS 0.008 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00290 (15236) covalent geometry : angle 0.61159 (20652) hydrogen bonds : bond 0.05576 ( 892) hydrogen bonds : angle 4.26429 ( 2748) link_BETA1-4 : bond 0.00295 ( 4) link_BETA1-4 : angle 0.81909 ( 12) link_NAG-ASN : bond 0.00060 ( 4) link_NAG-ASN : angle 3.62197 ( 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: 66 poor density : 223 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: 0.8173 (mmpt) cc_final: 0.7397 (ptpt) REVERT: A 225 PHE cc_start: 0.8894 (m-80) cc_final: 0.8243 (m-10) REVERT: A 330 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7504 (t80) REVERT: A 426 MET cc_start: 0.8584 (mmt) cc_final: 0.8298 (mmt) REVERT: B 55 LYS cc_start: 0.8189 (mmpt) cc_final: 0.7363 (ptpt) REVERT: B 330 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7424 (t80) REVERT: B 345 TRP cc_start: 0.7021 (t-100) cc_final: 0.6504 (t-100) REVERT: B 349 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7264 (mt-10) REVERT: B 426 MET cc_start: 0.8566 (mmt) cc_final: 0.8281 (mmt) REVERT: C 55 LYS cc_start: 0.8305 (mmpt) cc_final: 0.7480 (ptpt) REVERT: C 59 LYS cc_start: 0.5044 (mttt) cc_final: 0.4104 (mmtm) REVERT: C 88 GLN cc_start: 0.7891 (tp40) cc_final: 0.7538 (tp40) REVERT: C 330 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7622 (t80) REVERT: C 426 MET cc_start: 0.8603 (mmt) cc_final: 0.8365 (mmt) REVERT: D 55 LYS cc_start: 0.8195 (mmpt) cc_final: 0.7412 (ptpt) REVERT: D 225 PHE cc_start: 0.8895 (m-80) cc_final: 0.8242 (m-10) REVERT: D 330 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7502 (t80) REVERT: D 426 MET cc_start: 0.8588 (mmt) cc_final: 0.8318 (mmt) REVERT: D 462 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6739 (mt-10) outliers start: 66 outliers final: 39 residues processed: 268 average time/residue: 0.0966 time to fit residues: 42.1372 Evaluate side-chains 238 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 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 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 314 LEU 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 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 364 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 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 445 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: 9.9990 chunk 143 optimal weight: 0.7980 chunk 136 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN C 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 = 0.3763 r_free = 0.3763 target = 0.151710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124804 restraints weight = 26243.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127456 restraints weight = 15861.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129079 restraints weight = 11356.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.130199 restraints weight = 9152.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.130790 restraints weight = 7957.591| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15244 Z= 0.127 Angle : 0.599 9.542 20676 Z= 0.298 Chirality : 0.040 0.137 2420 Planarity : 0.003 0.034 2516 Dihedral : 5.712 54.848 2164 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.77 % Allowed : 15.75 % Favored : 80.47 % 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: -0.03 (0.20), residues: 1784 helix: 1.24 (0.16), residues: 1104 sheet: -0.70 (0.33), residues: 208 loop : -2.78 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 187 TYR 0.023 0.001 TYR D 218 PHE 0.014 0.001 PHE D 235 TRP 0.007 0.001 TRP A 345 HIS 0.008 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00267 (15236) covalent geometry : angle 0.59080 (20652) hydrogen bonds : bond 0.05276 ( 892) hydrogen bonds : angle 4.12762 ( 2748) link_BETA1-4 : bond 0.00925 ( 4) link_BETA1-4 : angle 2.25233 ( 12) link_NAG-ASN : bond 0.00292 ( 4) link_NAG-ASN : angle 3.61874 ( 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 286 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 224 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8117 (mmpt) cc_final: 0.7387 (ptpt) REVERT: A 225 PHE cc_start: 0.8928 (m-80) cc_final: 0.8320 (m-10) REVERT: A 330 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7569 (t80) REVERT: A 426 MET cc_start: 0.8452 (mmt) cc_final: 0.8198 (mmm) REVERT: B 55 LYS cc_start: 0.8121 (mmpt) cc_final: 0.7351 (ptpt) REVERT: B 330 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7381 (t80) REVERT: B 334 MET cc_start: 0.5909 (OUTLIER) cc_final: 0.4827 (ptp) REVERT: B 426 MET cc_start: 0.8479 (mmt) cc_final: 0.8213 (mmt) REVERT: C 55 LYS cc_start: 0.8183 (mmpt) cc_final: 0.7419 (ptpt) REVERT: C 59 LYS cc_start: 0.5252 (mttt) cc_final: 0.4364 (mmtm) REVERT: C 88 GLN cc_start: 0.7695 (tp40) cc_final: 0.7489 (tp40) REVERT: C 330 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7681 (t80) REVERT: C 426 MET cc_start: 0.8564 (mmt) cc_final: 0.8285 (mmm) REVERT: D 55 LYS cc_start: 0.8161 (mmpt) cc_final: 0.7370 (ptpt) REVERT: D 67 MET cc_start: 0.6489 (ttp) cc_final: 0.6069 (ttm) REVERT: D 225 PHE cc_start: 0.8906 (m-80) cc_final: 0.8311 (m-10) REVERT: D 330 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7588 (t80) REVERT: D 426 MET cc_start: 0.8507 (mmt) cc_final: 0.8239 (mmm) outliers start: 62 outliers final: 43 residues processed: 261 average time/residue: 0.1029 time to fit residues: 42.8944 Evaluate side-chains 244 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 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 489 LEU 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 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 307 LEU Chi-restraints excluded: chain C residue 314 LEU 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 489 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 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 489 LEU 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: 2.9990 chunk 109 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 145 optimal weight: 0.2980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN B 247 ASN C 69 GLN C 412 ASN D 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119898 restraints weight = 26536.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122627 restraints weight = 15594.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124435 restraints weight = 10943.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125594 restraints weight = 8662.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126293 restraints weight = 7460.620| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15244 Z= 0.119 Angle : 0.598 10.273 20676 Z= 0.293 Chirality : 0.040 0.135 2420 Planarity : 0.003 0.034 2516 Dihedral : 5.608 59.734 2164 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.77 % Allowed : 17.27 % 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: 0.31 (0.20), residues: 1784 helix: 1.47 (0.16), residues: 1104 sheet: -0.49 (0.33), residues: 208 loop : -2.59 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.026 0.001 TYR D 218 PHE 0.014 0.001 PHE A 235 TRP 0.008 0.001 TRP B 345 HIS 0.007 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00248 (15236) covalent geometry : angle 0.59219 (20652) hydrogen bonds : bond 0.04958 ( 892) hydrogen bonds : angle 4.04331 ( 2748) link_BETA1-4 : bond 0.00516 ( 4) link_BETA1-4 : angle 0.83835 ( 12) link_NAG-ASN : bond 0.00058 ( 4) link_NAG-ASN : angle 3.35230 ( 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 273 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 211 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8163 (mmpt) cc_final: 0.7199 (mtmt) REVERT: A 225 PHE cc_start: 0.8943 (m-80) cc_final: 0.8383 (m-10) REVERT: A 330 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7684 (t80) REVERT: A 334 MET cc_start: 0.5747 (OUTLIER) cc_final: 0.4893 (ptp) REVERT: A 345 TRP cc_start: 0.6869 (t-100) cc_final: 0.6333 (t-100) REVERT: A 426 MET cc_start: 0.8535 (mmt) cc_final: 0.8281 (mmm) REVERT: A 480 MET cc_start: 0.8508 (mmm) cc_final: 0.8230 (mpp) REVERT: B 55 LYS cc_start: 0.8129 (mmpt) cc_final: 0.7293 (ptpt) REVERT: B 330 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7582 (t80) REVERT: B 334 MET cc_start: 0.5762 (OUTLIER) cc_final: 0.4792 (ptp) REVERT: B 345 TRP cc_start: 0.6963 (t-100) cc_final: 0.6482 (t-100) REVERT: B 480 MET cc_start: 0.8511 (mmm) cc_final: 0.8197 (mpp) REVERT: C 55 LYS cc_start: 0.8091 (mmpt) cc_final: 0.7371 (ptpt) REVERT: C 67 MET cc_start: 0.6857 (ttp) cc_final: 0.6417 (ttm) REVERT: C 330 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7799 (t80) REVERT: C 345 TRP cc_start: 0.6925 (t-100) cc_final: 0.6409 (t-100) REVERT: C 426 MET cc_start: 0.8530 (mmt) cc_final: 0.8252 (mmm) REVERT: D 55 LYS cc_start: 0.8165 (mmpt) cc_final: 0.7346 (ptpt) REVERT: D 67 MET cc_start: 0.6407 (ttp) cc_final: 0.5976 (ttm) REVERT: D 225 PHE cc_start: 0.8907 (m-80) cc_final: 0.8300 (m-10) REVERT: D 330 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7761 (t80) REVERT: D 345 TRP cc_start: 0.6884 (t-100) cc_final: 0.6362 (t-100) REVERT: D 426 MET cc_start: 0.8532 (mmt) cc_final: 0.8269 (mmm) REVERT: D 480 MET cc_start: 0.8408 (mmm) cc_final: 0.8147 (mpp) outliers start: 62 outliers final: 39 residues processed: 248 average time/residue: 0.0956 time to fit residues: 38.6381 Evaluate side-chains 244 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 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 489 LEU 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 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: 0.8980 chunk 83 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN B 69 GLN B 247 ASN B 327 GLN C 327 GLN D 247 ASN D 327 GLN D 412 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116134 restraints weight = 26407.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118826 restraints weight = 15672.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120580 restraints weight = 11065.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121712 restraints weight = 8825.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122394 restraints weight = 7605.330| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15244 Z= 0.169 Angle : 0.645 9.806 20676 Z= 0.319 Chirality : 0.042 0.139 2420 Planarity : 0.004 0.037 2516 Dihedral : 5.575 59.936 2164 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.08 % Allowed : 16.97 % 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: 0.24 (0.20), residues: 1784 helix: 1.48 (0.16), residues: 1104 sheet: -0.67 (0.33), residues: 212 loop : -2.71 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 298 TYR 0.033 0.002 TYR B 218 PHE 0.024 0.002 PHE D 428 TRP 0.007 0.001 TRP C 444 HIS 0.007 0.001 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00391 (15236) covalent geometry : angle 0.63626 (20652) hydrogen bonds : bond 0.05537 ( 892) hydrogen bonds : angle 4.15421 ( 2748) link_BETA1-4 : bond 0.00248 ( 4) link_BETA1-4 : angle 1.36467 ( 12) link_NAG-ASN : bond 0.00327 ( 4) link_NAG-ASN : angle 4.16482 ( 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 277 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 210 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8160 (mmpt) cc_final: 0.7148 (mtmt) REVERT: A 225 PHE cc_start: 0.8958 (m-80) cc_final: 0.8374 (m-10) REVERT: A 330 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7836 (t80) REVERT: A 426 MET cc_start: 0.8538 (mmt) cc_final: 0.8278 (mmm) REVERT: A 480 MET cc_start: 0.8559 (mmm) cc_final: 0.8341 (mpp) REVERT: B 55 LYS cc_start: 0.8136 (mmpt) cc_final: 0.7275 (ptpt) REVERT: B 330 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7778 (t80) REVERT: B 334 MET cc_start: 0.5830 (OUTLIER) cc_final: 0.4897 (ptp) REVERT: B 480 MET cc_start: 0.8563 (mmm) cc_final: 0.8220 (mpp) REVERT: C 55 LYS cc_start: 0.8208 (mmpt) cc_final: 0.7451 (ptpt) REVERT: C 67 MET cc_start: 0.6880 (ttp) cc_final: 0.6434 (ttm) REVERT: C 330 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7948 (t80) REVERT: C 426 MET cc_start: 0.8586 (mmt) cc_final: 0.8287 (mmm) REVERT: D 55 LYS cc_start: 0.8170 (mmpt) cc_final: 0.7153 (mtmt) REVERT: D 67 MET cc_start: 0.6707 (ttp) cc_final: 0.6266 (ttm) REVERT: D 225 PHE cc_start: 0.8921 (m-80) cc_final: 0.8299 (m-10) REVERT: D 330 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7877 (t80) REVERT: D 426 MET cc_start: 0.8581 (mmt) cc_final: 0.8371 (mmt) REVERT: D 480 MET cc_start: 0.8487 (mmm) cc_final: 0.8236 (mpp) outliers start: 67 outliers final: 43 residues processed: 258 average time/residue: 0.0983 time to fit residues: 41.0098 Evaluate side-chains 228 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 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 68 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 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 459 MET 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 307 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 489 LEU 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 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 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: 5.9990 chunk 111 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 92 optimal weight: 0.2980 chunk 178 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 60 optimal weight: 0.0770 chunk 28 optimal weight: 9.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 247 ASN D 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118788 restraints weight = 26781.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.121310 restraints weight = 16230.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.122962 restraints weight = 11720.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123957 restraints weight = 9459.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124715 restraints weight = 8246.358| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15244 Z= 0.125 Angle : 0.607 9.595 20676 Z= 0.296 Chirality : 0.040 0.135 2420 Planarity : 0.003 0.034 2516 Dihedral : 5.403 58.643 2164 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.53 % Allowed : 18.00 % Favored : 78.47 % 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: 0.46 (0.20), residues: 1784 helix: 1.61 (0.16), residues: 1104 sheet: -0.48 (0.34), residues: 212 loop : -2.55 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 187 TYR 0.027 0.001 TYR D 218 PHE 0.019 0.001 PHE D 428 TRP 0.006 0.001 TRP B 345 HIS 0.010 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00268 (15236) covalent geometry : angle 0.60116 (20652) hydrogen bonds : bond 0.05012 ( 892) hydrogen bonds : angle 4.02929 ( 2748) link_BETA1-4 : bond 0.00483 ( 4) link_BETA1-4 : angle 0.94232 ( 12) link_NAG-ASN : bond 0.00022 ( 4) link_NAG-ASN : angle 3.42797 ( 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 259 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 201 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8225 (mmpt) cc_final: 0.7177 (mtmt) REVERT: A 225 PHE cc_start: 0.8913 (m-80) cc_final: 0.8354 (m-10) REVERT: A 313 PHE cc_start: 0.8120 (t80) cc_final: 0.7903 (t80) REVERT: A 330 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7853 (t80) REVERT: A 360 THR cc_start: 0.9067 (t) cc_final: 0.8850 (p) REVERT: A 426 MET cc_start: 0.8455 (mmt) cc_final: 0.8224 (mmm) REVERT: B 55 LYS cc_start: 0.8109 (mmpt) cc_final: 0.7299 (ptpt) REVERT: B 330 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7813 (t80) REVERT: B 334 MET cc_start: 0.5763 (OUTLIER) cc_final: 0.4869 (ptp) REVERT: B 345 TRP cc_start: 0.6932 (t-100) cc_final: 0.6319 (t-100) REVERT: C 55 LYS cc_start: 0.8132 (mmpt) cc_final: 0.7422 (ptpt) REVERT: C 67 MET cc_start: 0.6714 (ttp) cc_final: 0.6269 (ttm) REVERT: C 330 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7980 (t80) REVERT: C 426 MET cc_start: 0.8472 (mmt) cc_final: 0.8211 (mmm) REVERT: D 49 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.6927 (t80) REVERT: D 55 LYS cc_start: 0.8224 (mmpt) cc_final: 0.7157 (mtmt) REVERT: D 67 MET cc_start: 0.6347 (ttp) cc_final: 0.5921 (ttm) REVERT: D 225 PHE cc_start: 0.8875 (m-80) cc_final: 0.8283 (m-10) REVERT: D 330 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7883 (t80) REVERT: D 426 MET cc_start: 0.8458 (mmt) cc_final: 0.8187 (mmm) outliers start: 58 outliers final: 38 residues processed: 237 average time/residue: 0.0931 time to fit residues: 36.4045 Evaluate side-chains 232 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 489 LEU 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 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 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 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 489 LEU 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: 5.9990 chunk 50 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** B 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.140566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114189 restraints weight = 26835.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116647 restraints weight = 16512.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118240 restraints weight = 11982.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119274 restraints weight = 9766.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119700 restraints weight = 8546.635| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15244 Z= 0.227 Angle : 0.702 9.994 20676 Z= 0.347 Chirality : 0.044 0.135 2420 Planarity : 0.004 0.045 2516 Dihedral : 5.644 59.850 2164 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.04 % Allowed : 19.16 % Favored : 77.80 % 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: 1.35 (0.16), residues: 1112 sheet: -0.84 (0.33), residues: 212 loop : -2.72 (0.24), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 419 TYR 0.036 0.002 TYR D 218 PHE 0.015 0.002 PHE C 333 TRP 0.011 0.001 TRP D 444 HIS 0.008 0.002 HIS D 234 Details of bonding type rmsd covalent geometry : bond 0.00541 (15236) covalent geometry : angle 0.69285 (20652) hydrogen bonds : bond 0.05979 ( 892) hydrogen bonds : angle 4.30304 ( 2748) link_BETA1-4 : bond 0.00185 ( 4) link_BETA1-4 : angle 1.35061 ( 12) link_NAG-ASN : bond 0.00603 ( 4) link_NAG-ASN : angle 4.67265 ( 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 244 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8260 (mmpt) cc_final: 0.7365 (ptpt) REVERT: A 225 PHE cc_start: 0.8945 (m-80) cc_final: 0.8379 (m-10) REVERT: A 330 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7921 (t80) REVERT: A 426 MET cc_start: 0.8561 (mmt) cc_final: 0.8344 (mmt) REVERT: B 55 LYS cc_start: 0.8245 (mmpt) cc_final: 0.7400 (ptpt) REVERT: B 330 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7899 (t80) REVERT: B 457 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8292 (tt) REVERT: C 50 MET cc_start: 0.7482 (tpp) cc_final: 0.7152 (mmm) REVERT: C 55 LYS cc_start: 0.8194 (mmpt) cc_final: 0.7425 (ptpt) REVERT: C 67 MET cc_start: 0.6819 (ttp) cc_final: 0.6285 (ttm) REVERT: C 330 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7974 (t80) REVERT: D 49 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.6928 (t80) REVERT: D 55 LYS cc_start: 0.8273 (mmpt) cc_final: 0.7303 (ptpt) REVERT: D 67 MET cc_start: 0.6882 (ttp) cc_final: 0.6468 (ttm) REVERT: D 225 PHE cc_start: 0.8915 (m-80) cc_final: 0.8330 (m-10) REVERT: D 330 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7968 (t80) REVERT: D 457 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8133 (tt) outliers start: 50 outliers final: 36 residues processed: 232 average time/residue: 0.0948 time to fit residues: 36.1724 Evaluate side-chains 219 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 445 ILE Chi-restraints excluded: chain B residue 457 LEU 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 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 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 364 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 457 LEU 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: 1.9990 chunk 106 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 60 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 92 optimal weight: 0.3980 chunk 121 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 267 HIS ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN B 247 ASN B 483 GLN D 483 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120067 restraints weight = 26538.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122859 restraints weight = 16361.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124244 restraints weight = 11613.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.125505 restraints weight = 9413.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126012 restraints weight = 8295.852| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15244 Z= 0.118 Angle : 0.625 11.532 20676 Z= 0.301 Chirality : 0.041 0.244 2420 Planarity : 0.003 0.034 2516 Dihedral : 5.225 52.581 2164 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.49 % Allowed : 19.10 % Favored : 78.41 % 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: 0.50 (0.20), residues: 1784 helix: 1.57 (0.16), residues: 1108 sheet: -0.32 (0.35), residues: 212 loop : -2.46 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 427 TYR 0.027 0.001 TYR C 218 PHE 0.026 0.001 PHE A 428 TRP 0.007 0.001 TRP B 345 HIS 0.009 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00235 (15236) covalent geometry : angle 0.62143 (20652) hydrogen bonds : bond 0.04804 ( 892) hydrogen bonds : angle 4.00654 ( 2748) link_BETA1-4 : bond 0.00663 ( 4) link_BETA1-4 : angle 0.74678 ( 12) link_NAG-ASN : bond 0.00167 ( 4) link_NAG-ASN : angle 2.96853 ( 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 240 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8257 (mmpt) cc_final: 0.7317 (ptpt) REVERT: A 225 PHE cc_start: 0.8886 (m-80) cc_final: 0.8258 (m-10) REVERT: A 426 MET cc_start: 0.8399 (mmt) cc_final: 0.8184 (mmm) REVERT: A 428 PHE cc_start: 0.8363 (t80) cc_final: 0.8134 (t80) REVERT: A 459 MET cc_start: 0.7688 (mtm) cc_final: 0.7478 (mtm) REVERT: B 55 LYS cc_start: 0.8227 (mmpt) cc_final: 0.7281 (ptpt) REVERT: B 330 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7897 (t80) REVERT: B 345 TRP cc_start: 0.6854 (t-100) cc_final: 0.6465 (t-100) REVERT: C 50 MET cc_start: 0.7460 (tpp) cc_final: 0.6861 (mmm) REVERT: C 55 LYS cc_start: 0.8141 (mmpt) cc_final: 0.7270 (mtmt) REVERT: C 67 MET cc_start: 0.6508 (ttp) cc_final: 0.5949 (ttm) REVERT: C 459 MET cc_start: 0.7664 (mtm) cc_final: 0.7438 (mtm) REVERT: D 49 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.6977 (t80) REVERT: D 55 LYS cc_start: 0.8244 (mmpt) cc_final: 0.7273 (ptpt) REVERT: D 67 MET cc_start: 0.6767 (ttp) cc_final: 0.6257 (ttm) REVERT: D 225 PHE cc_start: 0.8892 (m-80) cc_final: 0.8226 (m-10) outliers start: 41 outliers final: 29 residues processed: 226 average time/residue: 0.0896 time to fit residues: 33.4775 Evaluate side-chains 220 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 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 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 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 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 334 MET Chi-restraints excluded: chain D residue 379 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** D 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.140275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112845 restraints weight = 26553.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.115402 restraints weight = 16145.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117071 restraints weight = 11661.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118142 restraints weight = 9502.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118660 restraints weight = 8329.872| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15244 Z= 0.251 Angle : 0.747 12.458 20676 Z= 0.366 Chirality : 0.046 0.244 2420 Planarity : 0.005 0.052 2516 Dihedral : 5.509 51.546 2164 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.76 % Allowed : 20.13 % Favored : 78.10 % 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: 1.32 (0.16), residues: 1112 sheet: -0.85 (0.33), residues: 212 loop : -2.64 (0.24), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 57 TYR 0.038 0.002 TYR C 218 PHE 0.026 0.002 PHE C 350 TRP 0.013 0.002 TRP C 444 HIS 0.009 0.002 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00602 (15236) covalent geometry : angle 0.73690 (20652) hydrogen bonds : bond 0.06073 ( 892) hydrogen bonds : angle 4.36437 ( 2748) link_BETA1-4 : bond 0.00258 ( 4) link_BETA1-4 : angle 1.62207 ( 12) link_NAG-ASN : bond 0.00747 ( 4) link_NAG-ASN : angle 4.85423 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2322.45 seconds wall clock time: 41 minutes 9.03 seconds (2469.03 seconds total)