Starting phenix.real_space_refine on Sat Sep 12 08:27:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5wpv_8883/09_2026/5wpv_8883.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wpv_8883/09_2026/5wpv_8883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5wpv_8883/09_2026/5wpv_8883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wpv_8883/09_2026/5wpv_8883.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5wpv_8883/09_2026/5wpv_8883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wpv_8883/09_2026/5wpv_8883.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5wpv_8883/09_2026/5wpv_8883.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5wpv_8883/09_2026/5wpv_8883.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 96 5.16 5 Na 1 4.78 5 C 9772 2.51 5 N 2444 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14889 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "B" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "C" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "D" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.52, per 1000 atoms: 0.24 Number of scatterers: 14889 At special positions: 0 Unit cell: (110.21, 110.21, 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: 1.15 Conformation dependent library (CDL) restraints added in 694.8 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: 64 helices and 8 sheets defined 61.7% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 38 through 49 Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 67 through 85 removed outlier: 4.137A pdb=" N ILE A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 106 removed outlier: 3.926A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.644A pdb=" N TYR A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 242 through 247 removed outlier: 4.070A pdb=" N ILE A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 337 removed outlier: 3.730A pdb=" N PHE A 301 " --> pdb=" O PHE A 297 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TRP A 335 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 378 removed outlier: 3.635A pdb=" N LEU A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 370 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 removed outlier: 4.337A pdb=" N CYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR A 392 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.860A pdb=" N LEU A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 406' Processing helix chain 'A' and resid 410 through 416 removed outlier: 4.110A pdb=" N LEU A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 447 removed outlier: 4.937A pdb=" N ARG A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 446 " --> pdb=" O CYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 removed outlier: 3.654A pdb=" N ILE A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 482 removed outlier: 3.676A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 526 removed outlier: 4.098A pdb=" N TRP A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 510 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 49 Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 67 through 85 removed outlier: 4.138A pdb=" N ILE B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 106 removed outlier: 3.926A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN B 97 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.644A pdb=" N TYR B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 242 through 247 removed outlier: 4.071A pdb=" N ILE B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 337 removed outlier: 3.731A pdb=" N PHE B 301 " --> pdb=" O PHE B 297 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET B 334 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TRP B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 378 removed outlier: 3.635A pdb=" N LEU B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU B 364 " --> pdb=" O THR B 360 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 400 removed outlier: 4.338A pdb=" N CYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR B 392 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.859A pdb=" N LEU B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 406' Processing helix chain 'B' and resid 410 through 416 removed outlier: 4.110A pdb=" N LEU B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 447 removed outlier: 4.937A pdb=" N ARG B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS B 430 " --> pdb=" O MET B 426 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 446 " --> pdb=" O CYS B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 removed outlier: 3.655A pdb=" N ILE B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 482 removed outlier: 3.676A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 526 removed outlier: 4.098A pdb=" N TRP B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL B 509 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 510 " --> pdb=" O ILE B 506 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 512 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 51 through 59 Processing helix chain 'C' and resid 67 through 85 removed outlier: 4.138A pdb=" N ILE C 73 " --> pdb=" O GLN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 106 removed outlier: 3.926A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 138 removed outlier: 3.644A pdb=" N TYR C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.071A pdb=" N ILE C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 337 removed outlier: 3.731A pdb=" N PHE C 301 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET C 334 " --> pdb=" O PHE C 330 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TRP C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 378 removed outlier: 3.635A pdb=" N LEU C 357 " --> pdb=" O GLY C 353 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU C 364 " --> pdb=" O THR C 360 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 370 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS C 378 " --> pdb=" O GLY C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 400 removed outlier: 4.338A pdb=" N CYS C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR C 392 " --> pdb=" O ILE C 388 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.859A pdb=" N LEU C 405 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 401 through 406' Processing helix chain 'C' and resid 410 through 416 removed outlier: 4.110A pdb=" N LEU C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA C 416 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 447 removed outlier: 4.936A pdb=" N ARG C 427 " --> pdb=" O PRO C 423 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS C 430 " --> pdb=" O MET C 426 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL C 446 " --> pdb=" O CYS C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.655A pdb=" N ILE C 468 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN C 469 " --> pdb=" O PHE C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 482 removed outlier: 3.675A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 526 removed outlier: 4.098A pdb=" N TRP C 491 " --> pdb=" O SER C 487 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU C 510 " --> pdb=" O ILE C 506 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 512 " --> pdb=" O MET C 508 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS C 526 " --> pdb=" O ASP C 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 51 through 59 Processing helix chain 'D' and resid 67 through 85 removed outlier: 4.137A pdb=" N ILE D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 106 removed outlier: 3.926A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 138 removed outlier: 3.644A pdb=" N TYR D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 242 through 247 removed outlier: 4.071A pdb=" N ILE D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 337 removed outlier: 3.731A pdb=" N PHE D 301 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 317 " --> pdb=" O PHE D 313 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET D 334 " --> pdb=" O PHE D 330 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TRP D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 378 removed outlier: 3.636A pdb=" N LEU D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU D 364 " --> pdb=" O THR D 360 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL D 370 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS D 378 " --> pdb=" O GLY D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 400 removed outlier: 4.337A pdb=" N CYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR D 392 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.859A pdb=" N LEU D 405 " --> pdb=" O VAL D 401 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 401 through 406' Processing helix chain 'D' and resid 410 through 416 removed outlier: 4.110A pdb=" N LEU D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 447 removed outlier: 4.937A pdb=" N ARG D 427 " --> pdb=" O PRO D 423 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS D 430 " --> pdb=" O MET D 426 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL D 446 " --> pdb=" O CYS D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 470 removed outlier: 3.656A pdb=" N ILE D 468 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN D 469 " --> pdb=" O PHE D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 482 removed outlier: 3.675A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 526 removed outlier: 4.099A pdb=" N TRP D 491 " --> pdb=" O SER D 487 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR D 507 " --> pdb=" O SER D 503 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL D 509 " --> pdb=" O PHE D 505 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU D 510 " --> pdb=" O ILE D 506 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 512 " --> pdb=" O MET D 508 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS D 526 " --> pdb=" O ASP D 522 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.548A pdb=" N GLU A 276 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN A 230 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 167 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ARG A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 149 removed outlier: 3.527A pdb=" N LYS A 238 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.549A pdb=" N GLU B 276 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN B 230 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 167 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ARG B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149 removed outlier: 3.528A pdb=" N LYS B 238 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.548A pdb=" N GLU C 276 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN C 230 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C 167 " --> pdb=" O ASP C 191 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ARG C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.527A pdb=" N LYS C 238 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.548A pdb=" N GLU D 276 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN D 230 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN D 167 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ARG D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 148 through 149 removed outlier: 3.527A pdb=" N LYS D 238 " --> pdb=" O ALA D 148 " (cutoff:3.500A) 837 hydrogen bonds defined for protein. 2451 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: 2.51 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: 1.23 - 1.34: 4536 1.34 - 1.46: 3605 1.46 - 1.58: 6963 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 1.452 -0.046 2.00e-02 2.50e+03 5.36e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.10e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.94e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.89e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.45e+00 ... (remaining 15231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 19703 1.88 - 3.77: 805 3.77 - 5.65: 95 5.65 - 7.53: 32 7.53 - 9.42: 17 Bond angle restraints: 20652 Sorted by residual: angle pdb=" N ILE B 306 " pdb=" CA ILE B 306 " pdb=" C ILE B 306 " ideal model delta sigma weight residual 112.96 108.32 4.64 1.00e+00 1.00e+00 2.16e+01 angle pdb=" N ILE D 306 " pdb=" CA ILE D 306 " pdb=" C ILE D 306 " ideal model delta sigma weight residual 112.96 108.32 4.64 1.00e+00 1.00e+00 2.16e+01 angle pdb=" N ILE C 306 " pdb=" CA ILE C 306 " pdb=" C ILE C 306 " ideal model delta sigma weight residual 112.96 108.36 4.60 1.00e+00 1.00e+00 2.12e+01 angle pdb=" N ILE A 306 " pdb=" CA ILE A 306 " pdb=" C ILE A 306 " ideal model delta sigma weight residual 112.96 108.37 4.59 1.00e+00 1.00e+00 2.10e+01 angle pdb=" C ILE A 514 " pdb=" N ALA A 515 " pdb=" CA ALA A 515 " ideal model delta sigma weight residual 120.28 125.02 -4.74 1.34e+00 5.57e-01 1.25e+01 ... (remaining 20647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.64: 8340 15.64 - 31.27: 392 31.27 - 46.91: 132 46.91 - 62.55: 12 62.55 - 78.18: 12 Dihedral angle restraints: 8888 sinusoidal: 3524 harmonic: 5364 Sorted by residual: dihedral pdb=" CA THR C 360 " pdb=" C THR C 360 " pdb=" N SER C 361 " pdb=" CA SER C 361 " ideal model delta harmonic sigma weight residual 180.00 159.91 20.09 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA THR A 360 " pdb=" C THR A 360 " pdb=" N SER A 361 " pdb=" CA SER A 361 " ideal model delta harmonic sigma weight residual 180.00 159.92 20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA THR D 360 " pdb=" C THR D 360 " pdb=" N SER D 361 " pdb=" CA SER D 361 " ideal model delta harmonic sigma weight residual 180.00 159.95 20.05 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 8885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1450 0.038 - 0.076: 648 0.076 - 0.114: 230 0.114 - 0.152: 71 0.152 - 0.190: 21 Chirality restraints: 2420 Sorted by residual: chirality pdb=" CB VAL A 452 " pdb=" CA VAL A 452 " pdb=" CG1 VAL A 452 " pdb=" CG2 VAL A 452 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CB VAL D 452 " pdb=" CA VAL D 452 " pdb=" CG1 VAL D 452 " pdb=" CG2 VAL D 452 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CB VAL B 452 " pdb=" CA VAL B 452 " pdb=" CG1 VAL B 452 " pdb=" CG2 VAL B 452 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 2417 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 526 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO D 527 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 527 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 527 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 526 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO B 527 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 526 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.19e+00 pdb=" N PRO A 527 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.034 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4735 2.84 - 3.36: 13526 3.36 - 3.87: 22475 3.87 - 4.39: 25323 4.39 - 4.90: 44296 Nonbonded interactions: 110355 Sorted by model distance: nonbonded pdb=" N PHE A 474 " pdb=" OD2 ASP B 471 " model vdw 2.329 3.120 nonbonded pdb=" O TYR B 439 " pdb=" OH TYR B 497 " model vdw 2.372 3.040 nonbonded pdb=" O TYR C 439 " pdb=" OH TYR C 497 " model vdw 2.373 3.040 nonbonded pdb=" O TYR D 439 " pdb=" OH TYR D 497 " model vdw 2.373 3.040 nonbonded pdb=" O TYR A 439 " pdb=" OH TYR A 497 " model vdw 2.373 3.040 ... (remaining 110350 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 14.430 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 : 0.007 0.056 15244 Z= 0.281 Angle : 0.923 9.418 20676 Z= 0.482 Chirality : 0.051 0.190 2420 Planarity : 0.007 0.057 2516 Dihedral : 11.003 78.184 5416 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.18 % Allowed : 4.93 % Favored : 94.89 % 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: -4.61 (0.15), residues: 1784 helix: -3.23 (0.10), residues: 1024 sheet: -1.30 (0.32), residues: 252 loop : -3.03 (0.22), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 403 TYR 0.025 0.003 TYR A 254 PHE 0.025 0.003 PHE A 474 TRP 0.017 0.003 TRP C 491 HIS 0.005 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.28 (15236) covalent geometry : angle 0.90872 / 0.48 (20652) hydrogen bonds : bond 0.21291 / 14.06 ( 797) hydrogen bonds : angle 7.84621 / 5.38 ( 2451) link_BETA1-4 : bond 0.00949 / 0.48 ( 4) link_BETA1-4 : angle 0.74180 / 0.39 ( 12) link_NAG-ASN : bond 0.00457 / 0.23 ( 4) link_NAG-ASN : angle 6.77789 / 3.63 ( 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 458 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 455 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.9101 (tp) cc_final: 0.8479 (mp) REVERT: A 350 PHE cc_start: 0.6714 (t80) cc_final: 0.6029 (t80) REVERT: A 423 PRO cc_start: 0.7803 (Cg_endo) cc_final: 0.7581 (Cg_exo) REVERT: B 74 LEU cc_start: 0.9047 (tp) cc_final: 0.8398 (mp) REVERT: B 245 LEU cc_start: 0.5930 (mm) cc_final: 0.5701 (pp) REVERT: B 350 PHE cc_start: 0.6656 (t80) cc_final: 0.5995 (t80) REVERT: C 74 LEU cc_start: 0.9139 (tp) cc_final: 0.8531 (mp) REVERT: C 175 VAL cc_start: 0.8041 (t) cc_final: 0.7830 (p) REVERT: C 245 LEU cc_start: 0.6118 (mm) cc_final: 0.5912 (pp) REVERT: C 350 PHE cc_start: 0.6643 (t80) cc_final: 0.6058 (t80) REVERT: D 74 LEU cc_start: 0.9037 (tp) cc_final: 0.8302 (mp) REVERT: D 245 LEU cc_start: 0.5920 (mm) cc_final: 0.5636 (pp) REVERT: D 350 PHE cc_start: 0.6674 (t80) cc_final: 0.6023 (t80) REVERT: D 427 ARG cc_start: 0.7473 (mmt180) cc_final: 0.6554 (mmm-85) outliers start: 3 outliers final: 0 residues processed: 455 average time/residue: 0.1505 time to fit residues: 95.6339 Evaluate side-chains 228 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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: 0.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 GLN A 328 ASN A 379 ASN A 412 ASN B 79 GLN B 328 ASN B 379 ASN B 412 ASN C 79 GLN C 328 ASN C 379 ASN C 412 ASN D 79 GLN D 328 ASN D 379 ASN D 412 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.134211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102474 restraints weight = 26964.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.105196 restraints weight = 16131.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106946 restraints weight = 11946.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107928 restraints weight = 9969.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108763 restraints weight = 8987.305| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15244 Z= 0.183 Angle : 0.659 7.150 20676 Z= 0.342 Chirality : 0.042 0.149 2420 Planarity : 0.005 0.034 2516 Dihedral : 5.022 20.988 1996 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.71 % Allowed : 10.77 % Favored : 85.52 % 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: -2.27 (0.18), residues: 1784 helix: -0.88 (0.15), residues: 1044 sheet: -0.90 (0.33), residues: 256 loop : -2.93 (0.23), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 172 TYR 0.025 0.002 TYR C 411 PHE 0.021 0.002 PHE A 474 TRP 0.007 0.002 TRP A 491 HIS 0.004 0.001 HIS C 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (15236) covalent geometry : angle 0.64757 / 0.34 (20652) hydrogen bonds : bond 0.05861 / 3.79 ( 797) hydrogen bonds : angle 4.69329 / 3.20 ( 2451) link_BETA1-4 : bond 0.00593 / 0.30 ( 4) link_BETA1-4 : angle 1.09956 / 0.60 ( 12) link_NAG-ASN : bond 0.00224 / 0.11 ( 4) link_NAG-ASN : angle 5.03497 / 2.70 ( 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 310 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 249 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7961 (m-30) cc_final: 0.7573 (p0) REVERT: A 45 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6658 (tp) REVERT: A 74 LEU cc_start: 0.8962 (tp) cc_final: 0.8701 (mp) REVERT: A 350 PHE cc_start: 0.6566 (t80) cc_final: 0.5961 (t80) REVERT: A 511 SER cc_start: 0.9282 (t) cc_final: 0.9053 (t) REVERT: B 40 ASP cc_start: 0.8018 (m-30) cc_final: 0.7776 (p0) REVERT: B 45 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6609 (tp) REVERT: B 74 LEU cc_start: 0.8902 (tp) cc_final: 0.8400 (mp) REVERT: B 174 HIS cc_start: 0.7209 (t70) cc_final: 0.6855 (t-90) REVERT: B 245 LEU cc_start: 0.6128 (mm) cc_final: 0.5815 (pp) REVERT: B 350 PHE cc_start: 0.6582 (t80) cc_final: 0.5997 (t80) REVERT: B 511 SER cc_start: 0.9303 (t) cc_final: 0.9100 (t) REVERT: C 45 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6641 (tp) REVERT: C 74 LEU cc_start: 0.8937 (tp) cc_final: 0.8577 (mp) REVERT: C 245 LEU cc_start: 0.6128 (mm) cc_final: 0.5841 (pp) REVERT: C 350 PHE cc_start: 0.6512 (t80) cc_final: 0.5946 (t80) REVERT: C 357 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8031 (tp) REVERT: D 40 ASP cc_start: 0.8049 (m-30) cc_final: 0.7783 (p0) REVERT: D 45 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6616 (tp) REVERT: D 74 LEU cc_start: 0.8922 (tp) cc_final: 0.8413 (mp) REVERT: D 174 HIS cc_start: 0.7298 (t70) cc_final: 0.6931 (t-90) REVERT: D 245 LEU cc_start: 0.6102 (mm) cc_final: 0.5786 (pp) REVERT: D 350 PHE cc_start: 0.6509 (t80) cc_final: 0.5950 (t80) REVERT: D 511 SER cc_start: 0.9271 (t) cc_final: 0.9065 (t) outliers start: 61 outliers final: 35 residues processed: 297 average time/residue: 0.0962 time to fit residues: 46.7239 Evaluate side-chains 248 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 432 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 84 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.130072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.098136 restraints weight = 27266.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100760 restraints weight = 16492.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.102487 restraints weight = 12265.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103559 restraints weight = 10241.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.104245 restraints weight = 9206.783| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 15244 Z= 0.276 Angle : 0.693 6.890 20676 Z= 0.356 Chirality : 0.044 0.149 2420 Planarity : 0.004 0.033 2516 Dihedral : 4.892 18.398 1996 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.99 % Allowed : 12.23 % Favored : 82.79 % 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: -1.26 (0.19), residues: 1784 helix: 0.10 (0.16), residues: 1012 sheet: -0.81 (0.33), residues: 248 loop : -2.59 (0.23), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 427 TYR 0.026 0.002 TYR C 411 PHE 0.021 0.002 PHE B 474 TRP 0.010 0.002 TRP B 444 HIS 0.004 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.28 (15236) covalent geometry : angle 0.67869 / 0.35 (20652) hydrogen bonds : bond 0.05814 / 3.77 ( 797) hydrogen bonds : angle 4.42181 / 3.03 ( 2451) link_BETA1-4 : bond 0.00419 / 0.21 ( 4) link_BETA1-4 : angle 1.38661 / 0.75 ( 12) link_NAG-ASN : bond 0.00660 / 0.33 ( 4) link_NAG-ASN : angle 5.63476 / 3.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 210 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7987 (m-30) cc_final: 0.7588 (p0) REVERT: A 45 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6545 (tp) REVERT: A 74 LEU cc_start: 0.9216 (tp) cc_final: 0.8690 (mp) REVERT: A 511 SER cc_start: 0.9341 (t) cc_final: 0.9127 (t) REVERT: B 40 ASP cc_start: 0.8074 (m-30) cc_final: 0.7602 (p0) REVERT: B 45 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6587 (tp) REVERT: B 74 LEU cc_start: 0.9159 (tp) cc_final: 0.8621 (mp) REVERT: B 245 LEU cc_start: 0.6105 (mm) cc_final: 0.5732 (pp) REVERT: B 511 SER cc_start: 0.9336 (t) cc_final: 0.9037 (t) REVERT: C 45 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6609 (tp) REVERT: C 74 LEU cc_start: 0.9229 (tp) cc_final: 0.8686 (mp) REVERT: C 245 LEU cc_start: 0.6032 (mm) cc_final: 0.5707 (pp) REVERT: C 274 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8181 (ptp90) REVERT: D 40 ASP cc_start: 0.8074 (m-30) cc_final: 0.7615 (p0) REVERT: D 45 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6522 (tp) REVERT: D 74 LEU cc_start: 0.9147 (tp) cc_final: 0.8574 (mp) REVERT: D 174 HIS cc_start: 0.7418 (t70) cc_final: 0.7025 (t-90) REVERT: D 245 LEU cc_start: 0.6110 (mm) cc_final: 0.5749 (pp) REVERT: D 511 SER cc_start: 0.9307 (t) cc_final: 0.9086 (t) outliers start: 82 outliers final: 59 residues processed: 278 average time/residue: 0.1030 time to fit residues: 45.9488 Evaluate side-chains 249 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 185 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 509 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 23 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 469 ASN C 481 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.132803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.101028 restraints weight = 26841.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103755 restraints weight = 16112.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.105556 restraints weight = 11924.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106664 restraints weight = 9921.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.107060 restraints weight = 8882.667| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15244 Z= 0.135 Angle : 0.564 6.743 20676 Z= 0.290 Chirality : 0.040 0.144 2420 Planarity : 0.003 0.025 2516 Dihedral : 4.584 18.541 1996 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.83 % Allowed : 14.96 % Favored : 81.20 % 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: 0.77 (0.17), residues: 1004 sheet: -0.43 (0.32), residues: 268 loop : -2.35 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.023 0.001 TYR D 411 PHE 0.018 0.001 PHE B 474 TRP 0.007 0.001 TRP B 444 HIS 0.002 0.001 HIS C 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (15236) covalent geometry : angle 0.55425 / 0.29 (20652) hydrogen bonds : bond 0.04776 / 3.09 ( 797) hydrogen bonds : angle 4.10795 / 2.84 ( 2451) link_BETA1-4 : bond 0.00569 / 0.28 ( 4) link_BETA1-4 : angle 0.94166 / 0.52 ( 12) link_NAG-ASN : bond 0.00016 / 0.01 ( 4) link_NAG-ASN : angle 4.38823 / 2.35 ( 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 272 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7954 (m-30) cc_final: 0.7463 (p0) REVERT: A 56 PHE cc_start: 0.5443 (t80) cc_final: 0.4462 (m-10) REVERT: A 74 LEU cc_start: 0.9205 (tp) cc_final: 0.8680 (mp) REVERT: A 511 SER cc_start: 0.9264 (t) cc_final: 0.9018 (t) REVERT: B 40 ASP cc_start: 0.8006 (m-30) cc_final: 0.7511 (p0) REVERT: B 74 LEU cc_start: 0.9012 (tp) cc_final: 0.8537 (mp) REVERT: B 245 LEU cc_start: 0.6200 (mm) cc_final: 0.5884 (pp) REVERT: B 350 PHE cc_start: 0.6441 (t80) cc_final: 0.5745 (t80) REVERT: B 511 SER cc_start: 0.9244 (t) cc_final: 0.8925 (t) REVERT: C 45 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6423 (tp) REVERT: C 74 LEU cc_start: 0.9194 (tp) cc_final: 0.8553 (mp) REVERT: C 245 LEU cc_start: 0.6170 (mm) cc_final: 0.5882 (pp) REVERT: C 274 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8136 (ptp90) REVERT: C 350 PHE cc_start: 0.6436 (t80) cc_final: 0.5691 (t80) REVERT: D 40 ASP cc_start: 0.8001 (m-30) cc_final: 0.7505 (p0) REVERT: D 74 LEU cc_start: 0.9029 (tp) cc_final: 0.8419 (mp) REVERT: D 245 LEU cc_start: 0.6183 (mm) cc_final: 0.5873 (pp) REVERT: D 274 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8247 (ptp90) REVERT: D 350 PHE cc_start: 0.6449 (t80) cc_final: 0.5736 (t80) outliers start: 63 outliers final: 52 residues processed: 253 average time/residue: 0.1055 time to fit residues: 42.3003 Evaluate side-chains 249 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 194 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 509 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 66 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 451 HIS C 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.099114 restraints weight = 27124.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.101752 restraints weight = 16391.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.103432 restraints weight = 12193.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.104544 restraints weight = 10217.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105206 restraints weight = 9153.348| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15244 Z= 0.197 Angle : 0.594 6.833 20676 Z= 0.306 Chirality : 0.041 0.139 2420 Planarity : 0.003 0.024 2516 Dihedral : 4.535 17.400 1996 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.99 % Allowed : 15.51 % Favored : 79.50 % 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: 0.89 (0.17), residues: 1020 sheet: -0.53 (0.32), residues: 264 loop : -2.10 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 427 TYR 0.022 0.002 TYR D 411 PHE 0.017 0.002 PHE D 56 TRP 0.007 0.001 TRP C 444 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (15236) covalent geometry : angle 0.58216 / 0.30 (20652) hydrogen bonds : bond 0.04949 / 3.22 ( 797) hydrogen bonds : angle 4.02675 / 2.79 ( 2451) link_BETA1-4 : bond 0.00537 / 0.27 ( 4) link_BETA1-4 : angle 1.04520 / 0.57 ( 12) link_NAG-ASN : bond 0.00346 / 0.17 ( 4) link_NAG-ASN : angle 4.77488 / 2.55 ( 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 266 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 184 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7933 (m-30) cc_final: 0.7320 (p0) REVERT: A 74 LEU cc_start: 0.9229 (tp) cc_final: 0.8695 (mp) REVERT: A 511 SER cc_start: 0.9301 (t) cc_final: 0.9062 (t) REVERT: B 40 ASP cc_start: 0.8043 (m-30) cc_final: 0.7401 (p0) REVERT: B 56 PHE cc_start: 0.5687 (t80) cc_final: 0.4469 (m-10) REVERT: B 74 LEU cc_start: 0.9072 (tp) cc_final: 0.8566 (mp) REVERT: B 245 LEU cc_start: 0.6273 (mm) cc_final: 0.5820 (pp) REVERT: B 511 SER cc_start: 0.9330 (t) cc_final: 0.8987 (t) REVERT: C 45 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6480 (tp) REVERT: C 56 PHE cc_start: 0.5715 (t80) cc_final: 0.4441 (m-10) REVERT: C 74 LEU cc_start: 0.9196 (tp) cc_final: 0.8669 (mp) REVERT: C 245 LEU cc_start: 0.6247 (mm) cc_final: 0.5819 (pp) REVERT: C 274 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8038 (ptp90) REVERT: D 56 PHE cc_start: 0.5641 (t80) cc_final: 0.4454 (m-10) REVERT: D 74 LEU cc_start: 0.9059 (tp) cc_final: 0.8530 (mp) REVERT: D 245 LEU cc_start: 0.6261 (mm) cc_final: 0.5828 (pp) REVERT: D 274 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8315 (ptp90) outliers start: 82 outliers final: 59 residues processed: 250 average time/residue: 0.1016 time to fit residues: 40.9473 Evaluate side-chains 244 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 182 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 509 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.132992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.101565 restraints weight = 26807.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.104230 restraints weight = 16184.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.105967 restraints weight = 12029.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.107088 restraints weight = 10063.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.107712 restraints weight = 9009.463| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15244 Z= 0.126 Angle : 0.530 6.828 20676 Z= 0.273 Chirality : 0.039 0.142 2420 Planarity : 0.003 0.024 2516 Dihedral : 4.357 16.797 1996 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.38 % Allowed : 16.18 % Favored : 79.44 % 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: 0.11 (0.20), residues: 1784 helix: 1.23 (0.17), residues: 1004 sheet: -0.36 (0.32), residues: 268 loop : -2.00 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.020 0.001 TYR D 411 PHE 0.017 0.001 PHE A 56 TRP 0.005 0.001 TRP C 444 HIS 0.002 0.000 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (15236) covalent geometry : angle 0.52080 / 0.27 (20652) hydrogen bonds : bond 0.04341 / 2.82 ( 797) hydrogen bonds : angle 3.85418 / 2.67 ( 2451) link_BETA1-4 : bond 0.00600 / 0.30 ( 4) link_BETA1-4 : angle 0.71155 / 0.37 ( 12) link_NAG-ASN : bond 0.00021 / 0.01 ( 4) link_NAG-ASN : angle 3.99085 / 2.14 ( 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 269 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 197 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7944 (m-30) cc_final: 0.7256 (p0) REVERT: A 50 MET cc_start: 0.4729 (OUTLIER) cc_final: 0.4506 (tmm) REVERT: A 56 PHE cc_start: 0.5626 (t80) cc_final: 0.4431 (m-10) REVERT: A 74 LEU cc_start: 0.9186 (tp) cc_final: 0.8683 (mp) REVERT: A 86 SER cc_start: 0.9151 (OUTLIER) cc_final: 0.8536 (p) REVERT: A 511 SER cc_start: 0.9246 (t) cc_final: 0.8989 (t) REVERT: B 40 ASP cc_start: 0.8075 (m-30) cc_final: 0.7374 (p0) REVERT: B 50 MET cc_start: 0.5810 (ppp) cc_final: 0.5567 (ppp) REVERT: B 56 PHE cc_start: 0.5666 (t80) cc_final: 0.4461 (m-10) REVERT: B 74 LEU cc_start: 0.8962 (tp) cc_final: 0.8479 (mp) REVERT: B 86 SER cc_start: 0.9137 (OUTLIER) cc_final: 0.8573 (p) REVERT: B 245 LEU cc_start: 0.6308 (mm) cc_final: 0.5888 (pp) REVERT: C 50 MET cc_start: 0.5846 (ppp) cc_final: 0.5604 (ppp) REVERT: C 56 PHE cc_start: 0.5744 (t80) cc_final: 0.4544 (m-10) REVERT: C 74 LEU cc_start: 0.9142 (tp) cc_final: 0.8670 (mp) REVERT: C 86 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8579 (p) REVERT: C 245 LEU cc_start: 0.6281 (mm) cc_final: 0.5889 (pp) REVERT: D 50 MET cc_start: 0.5942 (ppp) cc_final: 0.5697 (ppp) REVERT: D 56 PHE cc_start: 0.5643 (t80) cc_final: 0.4471 (m-10) REVERT: D 74 LEU cc_start: 0.9012 (tp) cc_final: 0.8523 (mp) REVERT: D 86 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8577 (p) REVERT: D 245 LEU cc_start: 0.6310 (mm) cc_final: 0.5900 (pp) REVERT: D 274 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8244 (ptp90) outliers start: 72 outliers final: 47 residues processed: 249 average time/residue: 0.1042 time to fit residues: 41.7980 Evaluate side-chains 234 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 503 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 92 optimal weight: 0.0970 chunk 141 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.135425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103783 restraints weight = 26508.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106493 restraints weight = 15909.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108319 restraints weight = 11826.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.109345 restraints weight = 9845.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.110173 restraints weight = 8836.951| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15244 Z= 0.097 Angle : 0.500 7.153 20676 Z= 0.257 Chirality : 0.038 0.142 2420 Planarity : 0.003 0.023 2516 Dihedral : 4.122 16.768 1996 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.59 % Allowed : 18.00 % 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: 0.47 (0.20), residues: 1784 helix: 1.53 (0.17), residues: 1004 sheet: -0.30 (0.32), residues: 268 loop : -1.81 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 427 TYR 0.029 0.001 TYR B 411 PHE 0.016 0.001 PHE A 56 TRP 0.003 0.000 TRP B 398 HIS 0.002 0.000 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (15236) covalent geometry : angle 0.49336 / 0.26 (20652) hydrogen bonds : bond 0.03858 / 2.50 ( 797) hydrogen bonds : angle 3.67102 / 2.55 ( 2451) link_BETA1-4 : bond 0.00613 / 0.31 ( 4) link_BETA1-4 : angle 0.54599 / 0.26 ( 12) link_NAG-ASN : bond 0.00167 / 0.08 ( 4) link_NAG-ASN : angle 3.31281 / 1.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7920 (m-30) cc_final: 0.7231 (p0) REVERT: A 50 MET cc_start: 0.5019 (OUTLIER) cc_final: 0.4734 (tmm) REVERT: A 56 PHE cc_start: 0.5484 (t80) cc_final: 0.4415 (m-10) REVERT: A 74 LEU cc_start: 0.9155 (tp) cc_final: 0.8647 (mp) REVERT: A 86 SER cc_start: 0.9054 (OUTLIER) cc_final: 0.8576 (p) REVERT: A 350 PHE cc_start: 0.6422 (t80) cc_final: 0.5796 (t80) REVERT: A 511 SER cc_start: 0.9223 (t) cc_final: 0.8965 (t) REVERT: B 40 ASP cc_start: 0.7900 (m-30) cc_final: 0.7104 (p0) REVERT: B 50 MET cc_start: 0.6089 (ppp) cc_final: 0.5814 (ppp) REVERT: B 56 PHE cc_start: 0.5632 (t80) cc_final: 0.4583 (m-10) REVERT: B 74 LEU cc_start: 0.9003 (tp) cc_final: 0.8471 (mp) REVERT: B 86 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8585 (p) REVERT: B 245 LEU cc_start: 0.6292 (mm) cc_final: 0.5863 (pp) REVERT: B 350 PHE cc_start: 0.6501 (t80) cc_final: 0.5738 (t80) REVERT: C 45 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6481 (tp) REVERT: C 50 MET cc_start: 0.6172 (ppp) cc_final: 0.5934 (ppp) REVERT: C 56 PHE cc_start: 0.5714 (t80) cc_final: 0.4679 (m-10) REVERT: C 74 LEU cc_start: 0.9136 (tp) cc_final: 0.8621 (mp) REVERT: C 86 SER cc_start: 0.9076 (OUTLIER) cc_final: 0.8617 (p) REVERT: C 245 LEU cc_start: 0.6467 (mm) cc_final: 0.6033 (pp) REVERT: C 350 PHE cc_start: 0.6411 (t80) cc_final: 0.5610 (t80) REVERT: D 40 ASP cc_start: 0.7930 (m-30) cc_final: 0.7138 (p0) REVERT: D 50 MET cc_start: 0.6104 (ppp) cc_final: 0.5855 (ppp) REVERT: D 56 PHE cc_start: 0.5565 (t80) cc_final: 0.4598 (m-10) REVERT: D 74 LEU cc_start: 0.9045 (tp) cc_final: 0.8515 (mp) REVERT: D 86 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8594 (p) REVERT: D 245 LEU cc_start: 0.6483 (mm) cc_final: 0.6109 (pp) REVERT: D 274 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8159 (ptp90) outliers start: 59 outliers final: 29 residues processed: 251 average time/residue: 0.0993 time to fit residues: 40.5957 Evaluate side-chains 226 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 503 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 60 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.102459 restraints weight = 26908.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.105139 restraints weight = 16262.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106939 restraints weight = 12128.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.108060 restraints weight = 10118.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.108808 restraints weight = 9079.200| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15244 Z= 0.121 Angle : 0.525 7.404 20676 Z= 0.267 Chirality : 0.039 0.156 2420 Planarity : 0.003 0.023 2516 Dihedral : 4.080 15.604 1996 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.28 % Allowed : 18.13 % Favored : 78.59 % 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: 0.55 (0.20), residues: 1784 helix: 1.61 (0.17), residues: 1004 sheet: -0.26 (0.33), residues: 268 loop : -1.83 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 427 TYR 0.028 0.001 TYR C 411 PHE 0.022 0.001 PHE B 474 TRP 0.005 0.001 TRP C 398 HIS 0.002 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (15236) covalent geometry : angle 0.51752 / 0.27 (20652) hydrogen bonds : bond 0.03970 / 2.59 ( 797) hydrogen bonds : angle 3.65437 / 2.54 ( 2451) link_BETA1-4 : bond 0.00520 / 0.26 ( 4) link_BETA1-4 : angle 0.58834 / 0.29 ( 12) link_NAG-ASN : bond 0.00046 / 0.02 ( 4) link_NAG-ASN : angle 3.57699 / 1.91 ( 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 246 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 192 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7894 (m-30) cc_final: 0.7168 (p0) REVERT: A 56 PHE cc_start: 0.5464 (t80) cc_final: 0.4414 (m-10) REVERT: A 74 LEU cc_start: 0.9165 (tp) cc_final: 0.8652 (mp) REVERT: A 86 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8596 (p) REVERT: A 350 PHE cc_start: 0.6502 (t80) cc_final: 0.5835 (t80) REVERT: A 511 SER cc_start: 0.9257 (t) cc_final: 0.8976 (t) REVERT: B 40 ASP cc_start: 0.7934 (m-30) cc_final: 0.7090 (p0) REVERT: B 50 MET cc_start: 0.6182 (ppp) cc_final: 0.5844 (ppp) REVERT: B 56 PHE cc_start: 0.5563 (t80) cc_final: 0.4560 (m-10) REVERT: B 74 LEU cc_start: 0.9046 (tp) cc_final: 0.8499 (mp) REVERT: B 86 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8586 (p) REVERT: B 245 LEU cc_start: 0.6236 (mm) cc_final: 0.5815 (pp) REVERT: C 45 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6487 (tp) REVERT: C 50 MET cc_start: 0.6193 (ppp) cc_final: 0.5946 (ppp) REVERT: C 56 PHE cc_start: 0.5702 (t80) cc_final: 0.4683 (m-10) REVERT: C 74 LEU cc_start: 0.9128 (tp) cc_final: 0.8602 (mp) REVERT: C 86 SER cc_start: 0.9085 (OUTLIER) cc_final: 0.8639 (p) REVERT: C 245 LEU cc_start: 0.6316 (mm) cc_final: 0.5836 (pp) REVERT: C 350 PHE cc_start: 0.6463 (t80) cc_final: 0.5644 (t80) REVERT: D 40 ASP cc_start: 0.7997 (m-30) cc_final: 0.7152 (p0) REVERT: D 50 MET cc_start: 0.6202 (ppp) cc_final: 0.5922 (ppp) REVERT: D 56 PHE cc_start: 0.5595 (t80) cc_final: 0.4624 (m-10) REVERT: D 74 LEU cc_start: 0.9067 (tp) cc_final: 0.8514 (mp) REVERT: D 86 SER cc_start: 0.9051 (OUTLIER) cc_final: 0.8609 (p) REVERT: D 245 LEU cc_start: 0.6226 (mm) cc_final: 0.5812 (pp) REVERT: D 274 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8200 (ptp90) outliers start: 54 outliers final: 39 residues processed: 228 average time/residue: 0.0935 time to fit residues: 35.7196 Evaluate side-chains 231 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 503 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.133954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.102311 restraints weight = 26900.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.104958 restraints weight = 16277.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106746 restraints weight = 12122.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.107814 restraints weight = 10116.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108552 restraints weight = 9092.483| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4299 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= 0.123 Angle : 0.524 6.899 20676 Z= 0.268 Chirality : 0.039 0.157 2420 Planarity : 0.003 0.023 2516 Dihedral : 4.047 15.562 1996 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.22 % Allowed : 18.49 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1784 helix: 1.69 (0.17), residues: 1004 sheet: -0.28 (0.33), residues: 268 loop : -1.72 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 298 TYR 0.027 0.001 TYR A 411 PHE 0.021 0.001 PHE B 474 TRP 0.004 0.001 TRP B 444 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (15236) covalent geometry : angle 0.51632 / 0.27 (20652) hydrogen bonds : bond 0.04015 / 2.61 ( 797) hydrogen bonds : angle 3.63879 / 2.53 ( 2451) link_BETA1-4 : bond 0.00541 / 0.27 ( 4) link_BETA1-4 : angle 0.67136 / 0.34 ( 12) link_NAG-ASN : bond 0.00037 / 0.02 ( 4) link_NAG-ASN : angle 3.60410 / 1.92 ( 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 236 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 183 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7894 (m-30) cc_final: 0.7153 (p0) REVERT: A 56 PHE cc_start: 0.5523 (t80) cc_final: 0.4418 (m-10) REVERT: A 74 LEU cc_start: 0.9163 (tp) cc_final: 0.8666 (mp) REVERT: A 86 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8612 (p) REVERT: B 40 ASP cc_start: 0.7969 (m-30) cc_final: 0.7126 (p0) REVERT: B 50 MET cc_start: 0.6120 (ppp) cc_final: 0.5916 (ppp) REVERT: B 56 PHE cc_start: 0.5612 (t80) cc_final: 0.4587 (m-10) REVERT: B 74 LEU cc_start: 0.9048 (tp) cc_final: 0.8509 (mp) REVERT: B 86 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8654 (p) REVERT: B 245 LEU cc_start: 0.6270 (mm) cc_final: 0.5724 (pp) REVERT: C 45 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6527 (tp) REVERT: C 50 MET cc_start: 0.6205 (ppp) cc_final: 0.5925 (ppp) REVERT: C 56 PHE cc_start: 0.5692 (t80) cc_final: 0.4682 (m-10) REVERT: C 74 LEU cc_start: 0.9163 (tp) cc_final: 0.8657 (mp) REVERT: C 86 SER cc_start: 0.9083 (OUTLIER) cc_final: 0.8644 (p) REVERT: C 245 LEU cc_start: 0.6282 (mm) cc_final: 0.5750 (pp) REVERT: D 40 ASP cc_start: 0.7968 (m-30) cc_final: 0.7128 (p0) REVERT: D 45 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6966 (tp) REVERT: D 50 MET cc_start: 0.6181 (ppp) cc_final: 0.5897 (ppp) REVERT: D 56 PHE cc_start: 0.5644 (t80) cc_final: 0.4657 (m-10) REVERT: D 74 LEU cc_start: 0.9074 (tp) cc_final: 0.8521 (mp) REVERT: D 86 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8603 (p) REVERT: D 245 LEU cc_start: 0.6263 (mm) cc_final: 0.5730 (pp) REVERT: D 274 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8204 (ptp90) outliers start: 53 outliers final: 40 residues processed: 219 average time/residue: 0.0856 time to fit residues: 31.2280 Evaluate side-chains 222 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 175 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 503 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 138 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.102584 restraints weight = 26631.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.105260 restraints weight = 16020.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107072 restraints weight = 11914.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.108208 restraints weight = 9920.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.108993 restraints weight = 8871.260| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15244 Z= 0.116 Angle : 0.522 8.353 20676 Z= 0.267 Chirality : 0.039 0.158 2420 Planarity : 0.003 0.024 2516 Dihedral : 4.005 15.454 1996 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.10 % Allowed : 18.67 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.20), residues: 1784 helix: 1.74 (0.17), residues: 1004 sheet: -0.28 (0.33), residues: 268 loop : -1.64 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.033 0.001 TYR A 411 PHE 0.021 0.001 PHE B 474 TRP 0.004 0.001 TRP A 398 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (15236) covalent geometry : angle 0.51537 / 0.27 (20652) hydrogen bonds : bond 0.03917 / 2.55 ( 797) hydrogen bonds : angle 3.60630 / 2.51 ( 2451) link_BETA1-4 : bond 0.00525 / 0.26 ( 4) link_BETA1-4 : angle 0.64736 / 0.32 ( 12) link_NAG-ASN : bond 0.00008 / 0.00 ( 4) link_NAG-ASN : angle 3.51284 / 1.87 ( 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 232 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7861 (m-30) cc_final: 0.7060 (p0) REVERT: A 56 PHE cc_start: 0.5579 (t80) cc_final: 0.4442 (m-10) REVERT: A 74 LEU cc_start: 0.9151 (tp) cc_final: 0.8654 (mp) REVERT: A 86 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8610 (p) REVERT: B 50 MET cc_start: 0.6179 (ppp) cc_final: 0.5889 (ppp) REVERT: B 56 PHE cc_start: 0.5586 (t80) cc_final: 0.4587 (m-10) REVERT: B 74 LEU cc_start: 0.9023 (tp) cc_final: 0.8491 (mp) REVERT: B 86 SER cc_start: 0.9052 (OUTLIER) cc_final: 0.8648 (p) REVERT: B 245 LEU cc_start: 0.6251 (mm) cc_final: 0.5708 (pp) REVERT: C 45 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6518 (tp) REVERT: C 50 MET cc_start: 0.6277 (ppp) cc_final: 0.5970 (ppp) REVERT: C 56 PHE cc_start: 0.5698 (t80) cc_final: 0.4666 (m-10) REVERT: C 74 LEU cc_start: 0.9152 (tp) cc_final: 0.8641 (mp) REVERT: C 86 SER cc_start: 0.9105 (OUTLIER) cc_final: 0.8702 (p) REVERT: C 245 LEU cc_start: 0.6249 (mm) cc_final: 0.5705 (pp) REVERT: D 40 ASP cc_start: 0.7966 (m-30) cc_final: 0.7124 (p0) REVERT: D 45 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6856 (tp) REVERT: D 50 MET cc_start: 0.6204 (ppp) cc_final: 0.5914 (ppp) REVERT: D 56 PHE cc_start: 0.5617 (t80) cc_final: 0.4644 (m-10) REVERT: D 74 LEU cc_start: 0.9059 (tp) cc_final: 0.8506 (mp) REVERT: D 86 SER cc_start: 0.9071 (OUTLIER) cc_final: 0.8662 (p) REVERT: D 245 LEU cc_start: 0.6232 (mm) cc_final: 0.5709 (pp) REVERT: D 274 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8208 (ptp90) outliers start: 51 outliers final: 42 residues processed: 214 average time/residue: 0.1017 time to fit residues: 35.7535 Evaluate side-chains 229 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 503 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 0.0170 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 175 optimal weight: 0.0980 chunk 119 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.102599 restraints weight = 26716.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.105318 restraints weight = 16052.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107101 restraints weight = 11891.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108257 restraints weight = 9937.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108941 restraints weight = 8878.919| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15244 Z= 0.119 Angle : 0.524 7.640 20676 Z= 0.267 Chirality : 0.039 0.159 2420 Planarity : 0.003 0.027 2516 Dihedral : 3.986 15.381 1996 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.35 % Allowed : 18.49 % Favored : 78.16 % 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: 0.78 (0.20), residues: 1784 helix: 1.79 (0.16), residues: 1000 sheet: -0.27 (0.33), residues: 268 loop : -1.62 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 427 TYR 0.026 0.001 TYR B 411 PHE 0.021 0.001 PHE B 474 TRP 0.004 0.001 TRP A 398 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (15236) covalent geometry : angle 0.51749 / 0.27 (20652) hydrogen bonds : bond 0.03926 / 2.56 ( 797) hydrogen bonds : angle 3.59756 / 2.50 ( 2451) link_BETA1-4 : bond 0.00524 / 0.26 ( 4) link_BETA1-4 : angle 0.67374 / 0.34 ( 12) link_NAG-ASN : bond 0.00023 / 0.01 ( 4) link_NAG-ASN : angle 3.50106 / 1.86 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2283.15 seconds wall clock time: 40 minutes 36.89 seconds (2436.89 seconds total)