Starting phenix.real_space_refine on Tue Nov 18 14:16:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5wpv_8883/11_2025/5wpv_8883.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wpv_8883/11_2025/5wpv_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5wpv_8883/11_2025/5wpv_8883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wpv_8883/11_2025/5wpv_8883.map" model { file = "/net/cci-nas-00/data/ceres_data/5wpv_8883/11_2025/5wpv_8883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wpv_8883/11_2025/5wpv_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-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14889 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "B" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "C" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "D" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3694 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 12, 'TRANS': 441} Chain breaks: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.62, 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: 1.22 Conformation dependent library (CDL) restraints added in 661.3 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: 0.46 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: 2.36 Time building geometry restraints manager: 1.67 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: 8492 15.64 - 31.27: 399 31.27 - 46.91: 141 46.91 - 62.55: 12 62.55 - 78.18: 12 Dihedral angle restraints: 9056 sinusoidal: 3692 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 9053 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: 0.680 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: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.340 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 11.021 78.184 5584 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 covalent geometry : bond 0.00652 (15236) covalent geometry : angle 0.90872 (20652) hydrogen bonds : bond 0.21291 ( 797) hydrogen bonds : angle 7.84621 ( 2451) link_BETA1-4 : bond 0.00949 ( 4) link_BETA1-4 : angle 0.74180 ( 12) link_NAG-ASN : bond 0.00457 ( 4) link_NAG-ASN : angle 6.77789 ( 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 : 0.554 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: 0.9140 (tp) cc_final: 0.8532 (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: 0.1513 time to fit residues: 95.3412 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 : 0.605 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3664 r_free = 0.3664 target = 0.134465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.102799 restraints weight = 26866.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105530 restraints weight = 15996.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.107328 restraints weight = 11781.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108439 restraints weight = 9800.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109178 restraints weight = 8768.737| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15244 Z= 0.181 Angle : 0.653 7.446 20676 Z= 0.337 Chirality : 0.042 0.147 2420 Planarity : 0.005 0.033 2516 Dihedral : 5.593 34.135 2164 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.89 % Allowed : 10.46 % Favored : 85.64 % 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: -0.88 (0.34), residues: 252 loop : -2.94 (0.23), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 172 TYR 0.025 0.002 TYR C 411 PHE 0.021 0.002 PHE A 474 TRP 0.007 0.001 TRP D 444 HIS 0.004 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00417 (15236) covalent geometry : angle 0.64066 (20652) hydrogen bonds : bond 0.05826 ( 797) hydrogen bonds : angle 4.67368 ( 2451) link_BETA1-4 : bond 0.00691 ( 4) link_BETA1-4 : angle 1.37869 ( 12) link_NAG-ASN : bond 0.00201 ( 4) link_NAG-ASN : angle 5.11866 ( 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 314 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 250 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7946 (m-30) cc_final: 0.7573 (p0) REVERT: A 45 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6698 (tp) REVERT: A 74 LEU cc_start: 0.8959 (tp) cc_final: 0.8693 (mp) REVERT: A 350 PHE cc_start: 0.6568 (t80) cc_final: 0.5957 (t80) REVERT: A 511 SER cc_start: 0.9241 (t) cc_final: 0.9040 (t) REVERT: B 40 ASP cc_start: 0.7957 (m-30) cc_final: 0.7730 (p0) REVERT: B 45 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6583 (tp) REVERT: B 74 LEU cc_start: 0.8878 (tp) cc_final: 0.8521 (mp) REVERT: B 174 HIS cc_start: 0.7180 (t70) cc_final: 0.6804 (t-90) REVERT: B 245 LEU cc_start: 0.6149 (mm) cc_final: 0.5820 (pp) REVERT: B 350 PHE cc_start: 0.6560 (t80) cc_final: 0.5972 (t80) REVERT: B 511 SER cc_start: 0.9247 (t) cc_final: 0.9040 (t) REVERT: C 45 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6650 (tp) REVERT: C 74 LEU cc_start: 0.8931 (tp) cc_final: 0.8537 (mp) REVERT: C 245 LEU cc_start: 0.6145 (mm) cc_final: 0.5845 (pp) REVERT: C 350 PHE cc_start: 0.6521 (t80) cc_final: 0.5951 (t80) REVERT: C 357 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8027 (tp) REVERT: C 511 SER cc_start: 0.9216 (t) cc_final: 0.9013 (t) REVERT: D 40 ASP cc_start: 0.7956 (m-30) cc_final: 0.7731 (p0) REVERT: D 45 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6620 (tp) REVERT: D 74 LEU cc_start: 0.8898 (tp) cc_final: 0.8538 (mp) REVERT: D 174 HIS cc_start: 0.7308 (t70) cc_final: 0.6936 (t-90) REVERT: D 245 LEU cc_start: 0.6119 (mm) cc_final: 0.5791 (pp) REVERT: D 350 PHE cc_start: 0.6532 (t80) cc_final: 0.5933 (t80) REVERT: D 511 SER cc_start: 0.9209 (t) cc_final: 0.9004 (t) outliers start: 64 outliers final: 36 residues processed: 298 average time/residue: 0.0924 time to fit residues: 45.0027 Evaluate side-chains 251 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 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 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: 7.9990 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100910 restraints weight = 27068.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103574 restraints weight = 16261.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.105361 restraints weight = 12049.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106482 restraints weight = 10036.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.107109 restraints weight = 8992.767| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15244 Z= 0.189 Angle : 0.604 6.797 20676 Z= 0.313 Chirality : 0.041 0.139 2420 Planarity : 0.004 0.025 2516 Dihedral : 5.365 36.775 2164 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.68 % Allowed : 12.04 % Favored : 83.27 % 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: -0.98 (0.19), residues: 1784 helix: 0.32 (0.16), residues: 1004 sheet: -0.62 (0.34), residues: 252 loop : -2.49 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 172 TYR 0.027 0.002 TYR C 411 PHE 0.019 0.002 PHE D 474 TRP 0.007 0.001 TRP B 444 HIS 0.003 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00445 (15236) covalent geometry : angle 0.59149 (20652) hydrogen bonds : bond 0.05245 ( 797) hydrogen bonds : angle 4.25991 ( 2451) link_BETA1-4 : bond 0.00465 ( 4) link_BETA1-4 : angle 1.18013 ( 12) link_NAG-ASN : bond 0.00309 ( 4) link_NAG-ASN : angle 5.06333 ( 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 300 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 223 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8040 (m-30) cc_final: 0.7660 (p0) REVERT: A 56 PHE cc_start: 0.5717 (t80) cc_final: 0.4701 (m-10) REVERT: A 74 LEU cc_start: 0.9219 (tp) cc_final: 0.8679 (mp) REVERT: A 274 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8239 (ptp90) REVERT: A 350 PHE cc_start: 0.6670 (t80) cc_final: 0.5992 (t80) REVERT: A 511 SER cc_start: 0.9314 (t) cc_final: 0.9082 (t) REVERT: B 40 ASP cc_start: 0.8086 (m-30) cc_final: 0.7676 (p0) REVERT: B 74 LEU cc_start: 0.9136 (tp) cc_final: 0.8632 (mp) REVERT: B 245 LEU cc_start: 0.6197 (mm) cc_final: 0.5850 (pp) REVERT: B 350 PHE cc_start: 0.6640 (t80) cc_final: 0.5974 (t80) REVERT: B 511 SER cc_start: 0.9323 (t) cc_final: 0.8984 (t) REVERT: C 45 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6473 (tp) REVERT: C 74 LEU cc_start: 0.9151 (tp) cc_final: 0.8634 (mp) REVERT: C 245 LEU cc_start: 0.6206 (mm) cc_final: 0.5973 (pp) REVERT: C 350 PHE cc_start: 0.6597 (t80) cc_final: 0.5901 (t80) REVERT: C 511 SER cc_start: 0.9278 (t) cc_final: 0.8968 (t) REVERT: D 40 ASP cc_start: 0.8076 (m-30) cc_final: 0.7675 (p0) REVERT: D 74 LEU cc_start: 0.9176 (tp) cc_final: 0.8631 (mp) REVERT: D 174 HIS cc_start: 0.7306 (t70) cc_final: 0.6917 (t-90) REVERT: D 245 LEU cc_start: 0.6121 (mm) cc_final: 0.5790 (pp) REVERT: D 274 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8236 (ptp90) REVERT: D 350 PHE cc_start: 0.6639 (t80) cc_final: 0.5993 (t80) REVERT: D 511 SER cc_start: 0.9285 (t) cc_final: 0.9041 (t) outliers start: 77 outliers final: 57 residues processed: 284 average time/residue: 0.1106 time to fit residues: 48.7887 Evaluate side-chains 261 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 201 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 274 ARG 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 283 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 357 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 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 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 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 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 506 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 23 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 27 optimal weight: 0.0270 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103338 restraints weight = 26693.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106098 restraints weight = 16036.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107917 restraints weight = 11838.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.109078 restraints weight = 9840.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.109796 restraints weight = 8786.286| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3663 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= 0.115 Angle : 0.524 6.798 20676 Z= 0.271 Chirality : 0.039 0.143 2420 Planarity : 0.003 0.024 2516 Dihedral : 4.888 30.817 2164 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.16 % Allowed : 15.02 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.20), residues: 1784 helix: 1.02 (0.17), residues: 1004 sheet: -0.43 (0.33), residues: 268 loop : -2.24 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.024 0.001 TYR B 411 PHE 0.016 0.001 PHE B 474 TRP 0.006 0.001 TRP D 444 HIS 0.002 0.000 HIS B 409 Details of bonding type rmsd covalent geometry : bond 0.00248 (15236) covalent geometry : angle 0.51424 (20652) hydrogen bonds : bond 0.04325 ( 797) hydrogen bonds : angle 3.90731 ( 2451) link_BETA1-4 : bond 0.00725 ( 4) link_BETA1-4 : angle 0.81215 ( 12) link_NAG-ASN : bond 0.00123 ( 4) link_NAG-ASN : angle 4.07636 ( 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 275 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 223 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: 0.7925 (m-30) cc_final: 0.7428 (p0) REVERT: A 56 PHE cc_start: 0.5692 (t80) cc_final: 0.4750 (m-10) REVERT: A 74 LEU cc_start: 0.9193 (tp) cc_final: 0.8647 (mp) REVERT: A 350 PHE cc_start: 0.6521 (t80) cc_final: 0.5915 (t80) REVERT: A 511 SER cc_start: 0.9254 (t) cc_final: 0.8989 (t) REVERT: B 40 ASP cc_start: 0.8102 (m-30) cc_final: 0.7650 (p0) REVERT: B 56 PHE cc_start: 0.5726 (t80) cc_final: 0.4678 (m-10) REVERT: B 74 LEU cc_start: 0.9125 (tp) cc_final: 0.8449 (mp) REVERT: B 86 SER cc_start: 0.9116 (OUTLIER) cc_final: 0.8555 (p) REVERT: B 245 LEU cc_start: 0.6293 (mm) cc_final: 0.5997 (pp) REVERT: B 350 PHE cc_start: 0.6489 (t80) cc_final: 0.5894 (t80) REVERT: B 427 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7032 (mmp-170) REVERT: B 512 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8948 (mm) REVERT: C 45 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6458 (tp) REVERT: C 50 MET cc_start: 0.6460 (ppp) cc_final: 0.6243 (ppp) REVERT: C 56 PHE cc_start: 0.5518 (t80) cc_final: 0.4494 (m-10) REVERT: C 74 LEU cc_start: 0.9110 (tp) cc_final: 0.8462 (mp) REVERT: C 86 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8564 (p) REVERT: C 245 LEU cc_start: 0.6481 (mm) cc_final: 0.6186 (pp) REVERT: C 350 PHE cc_start: 0.6235 (t80) cc_final: 0.5602 (t80) REVERT: D 40 ASP cc_start: 0.8100 (m-30) cc_final: 0.7649 (p0) REVERT: D 56 PHE cc_start: 0.5596 (t80) cc_final: 0.4618 (m-10) REVERT: D 74 LEU cc_start: 0.9171 (tp) cc_final: 0.8485 (mp) REVERT: D 86 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8575 (p) REVERT: D 245 LEU cc_start: 0.6272 (mm) cc_final: 0.5983 (pp) REVERT: D 350 PHE cc_start: 0.6541 (t80) cc_final: 0.5957 (t80) outliers start: 52 outliers final: 34 residues processed: 262 average time/residue: 0.0985 time to fit residues: 41.3056 Evaluate side-chains 243 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 307 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 422 LEU 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 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 427 ARG Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 86 SER 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 430 CYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 86 SER 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 437 LEU Chi-restraints excluded: chain D residue 503 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 66 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 136 optimal weight: 0.0370 chunk 121 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 26 optimal weight: 0.0070 chunk 144 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 overall best weight: 2.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.102159 restraints weight = 26950.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104838 restraints weight = 16252.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106624 restraints weight = 12065.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107705 restraints weight = 10063.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.108437 restraints weight = 9036.390| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15244 Z= 0.135 Angle : 0.528 6.823 20676 Z= 0.272 Chirality : 0.039 0.136 2420 Planarity : 0.003 0.022 2516 Dihedral : 4.674 25.826 2164 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.83 % Allowed : 16.18 % Favored : 79.99 % 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: 0.19 (0.20), residues: 1784 helix: 1.33 (0.17), residues: 1004 sheet: -0.37 (0.33), residues: 268 loop : -2.03 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.024 0.001 TYR B 411 PHE 0.014 0.001 PHE A 474 TRP 0.005 0.001 TRP B 444 HIS 0.002 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00313 (15236) covalent geometry : angle 0.51768 (20652) hydrogen bonds : bond 0.04356 ( 797) hydrogen bonds : angle 3.78099 ( 2451) link_BETA1-4 : bond 0.00519 ( 4) link_BETA1-4 : angle 0.94357 ( 12) link_NAG-ASN : bond 0.00077 ( 4) link_NAG-ASN : angle 4.28044 ( 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 276 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 213 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7912 (m-30) cc_final: 0.7395 (p0) REVERT: A 56 PHE cc_start: 0.5766 (t80) cc_final: 0.4784 (m-10) REVERT: A 74 LEU cc_start: 0.9206 (tp) cc_final: 0.8683 (mp) REVERT: A 86 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8541 (p) REVERT: A 350 PHE cc_start: 0.6352 (t80) cc_final: 0.5690 (t80) REVERT: A 511 SER cc_start: 0.9294 (t) cc_final: 0.9015 (t) REVERT: B 40 ASP cc_start: 0.8040 (m-30) cc_final: 0.7540 (p0) REVERT: B 56 PHE cc_start: 0.5786 (t80) cc_final: 0.4758 (m-10) REVERT: B 74 LEU cc_start: 0.9156 (tp) cc_final: 0.8622 (mp) REVERT: B 86 SER cc_start: 0.9115 (OUTLIER) cc_final: 0.8574 (p) REVERT: B 245 LEU cc_start: 0.6083 (mm) cc_final: 0.5797 (pp) REVERT: B 350 PHE cc_start: 0.6332 (t80) cc_final: 0.5687 (t80) REVERT: B 427 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6882 (mmp-170) REVERT: C 56 PHE cc_start: 0.5636 (t80) cc_final: 0.4564 (m-10) REVERT: C 74 LEU cc_start: 0.9122 (tp) cc_final: 0.8593 (mp) REVERT: C 86 SER cc_start: 0.9098 (OUTLIER) cc_final: 0.8567 (p) REVERT: C 245 LEU cc_start: 0.6158 (mm) cc_final: 0.5938 (pp) REVERT: C 350 PHE cc_start: 0.6253 (t80) cc_final: 0.5605 (t80) REVERT: D 40 ASP cc_start: 0.7996 (m-30) cc_final: 0.7500 (p0) REVERT: D 56 PHE cc_start: 0.5714 (t80) cc_final: 0.4704 (m-10) REVERT: D 74 LEU cc_start: 0.9155 (tp) cc_final: 0.8596 (mp) REVERT: D 86 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8581 (p) REVERT: D 245 LEU cc_start: 0.6074 (mm) cc_final: 0.5769 (pp) REVERT: D 350 PHE cc_start: 0.6333 (t80) cc_final: 0.5703 (t80) outliers start: 63 outliers final: 45 residues processed: 254 average time/residue: 0.0949 time to fit residues: 39.7060 Evaluate side-chains 251 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 201 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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 388 ILE 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 506 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 357 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 426 MET Chi-restraints excluded: chain B residue 427 ARG 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 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 430 CYS Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 320 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 437 LEU Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3641 r_free = 0.3641 target = 0.133245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.101238 restraints weight = 26783.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.103905 restraints weight = 16181.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.105657 restraints weight = 12054.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.106665 restraints weight = 10080.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107459 restraints weight = 9074.755| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15244 Z= 0.151 Angle : 0.540 6.862 20676 Z= 0.279 Chirality : 0.039 0.136 2420 Planarity : 0.003 0.024 2516 Dihedral : 4.658 23.648 2164 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.81 % Allowed : 14.90 % Favored : 80.29 % 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: 0.34 (0.21), residues: 1784 helix: 1.42 (0.17), residues: 1000 sheet: -0.32 (0.33), residues: 268 loop : -1.86 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 427 TYR 0.027 0.001 TYR D 411 PHE 0.013 0.001 PHE B 474 TRP 0.006 0.001 TRP D 444 HIS 0.003 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00356 (15236) covalent geometry : angle 0.52891 (20652) hydrogen bonds : bond 0.04418 ( 797) hydrogen bonds : angle 3.74298 ( 2451) link_BETA1-4 : bond 0.00555 ( 4) link_BETA1-4 : angle 1.05357 ( 12) link_NAG-ASN : bond 0.00120 ( 4) link_NAG-ASN : angle 4.39501 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 201 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7818 (m-30) cc_final: 0.7221 (p0) REVERT: A 50 MET cc_start: 0.5288 (ttp) cc_final: 0.4977 (tmm) REVERT: A 56 PHE cc_start: 0.5917 (t80) cc_final: 0.4810 (m-10) REVERT: A 74 LEU cc_start: 0.9208 (tp) cc_final: 0.8695 (mp) REVERT: A 86 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8576 (p) REVERT: A 350 PHE cc_start: 0.6456 (t80) cc_final: 0.5760 (t80) REVERT: A 511 SER cc_start: 0.9325 (t) cc_final: 0.9038 (t) REVERT: B 40 ASP cc_start: 0.8056 (m-30) cc_final: 0.7377 (p0) REVERT: B 56 PHE cc_start: 0.5817 (t80) cc_final: 0.4625 (m-10) REVERT: B 74 LEU cc_start: 0.9133 (tp) cc_final: 0.8628 (mp) REVERT: B 86 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8607 (p) REVERT: B 245 LEU cc_start: 0.6188 (mm) cc_final: 0.5810 (pp) REVERT: B 350 PHE cc_start: 0.6427 (t80) cc_final: 0.5756 (t80) REVERT: B 427 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6823 (mmp-170) REVERT: B 512 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8916 (mm) REVERT: C 56 PHE cc_start: 0.5959 (t80) cc_final: 0.4757 (m-10) REVERT: C 74 LEU cc_start: 0.9143 (tp) cc_final: 0.8628 (mp) REVERT: C 86 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8593 (p) REVERT: C 245 LEU cc_start: 0.6177 (mm) cc_final: 0.5890 (pp) REVERT: C 350 PHE cc_start: 0.6441 (t80) cc_final: 0.5675 (t80) REVERT: D 40 ASP cc_start: 0.8053 (m-30) cc_final: 0.7367 (p0) REVERT: D 56 PHE cc_start: 0.5602 (t80) cc_final: 0.4524 (m-10) REVERT: D 74 LEU cc_start: 0.9149 (tp) cc_final: 0.8607 (mp) REVERT: D 86 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8601 (p) REVERT: D 245 LEU cc_start: 0.6181 (mm) cc_final: 0.5880 (pp) REVERT: D 350 PHE cc_start: 0.6431 (t80) cc_final: 0.5768 (t80) outliers start: 79 outliers final: 48 residues processed: 261 average time/residue: 0.0942 time to fit residues: 40.6426 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 : 0.589 ------------------------------------------------------------------------------- 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 326 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 426 MET 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 509 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 86 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 401 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 512 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 189 VAL 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 437 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 86 SER 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 437 LEU Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.135775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.104050 restraints weight = 26424.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.106810 restraints weight = 15868.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108628 restraints weight = 11738.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109657 restraints weight = 9759.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.110420 restraints weight = 8768.891| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15244 Z= 0.101 Angle : 0.511 7.190 20676 Z= 0.258 Chirality : 0.038 0.136 2420 Planarity : 0.003 0.027 2516 Dihedral : 4.314 20.150 2164 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.59 % Allowed : 16.18 % Favored : 80.23 % 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: 0.60 (0.21), residues: 1784 helix: 1.64 (0.17), residues: 1000 sheet: -0.24 (0.32), residues: 268 loop : -1.75 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.024 0.001 TYR D 411 PHE 0.012 0.001 PHE B 474 TRP 0.003 0.000 TRP D 444 HIS 0.002 0.000 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00218 (15236) covalent geometry : angle 0.50370 (20652) hydrogen bonds : bond 0.03837 ( 797) hydrogen bonds : angle 3.61145 ( 2451) link_BETA1-4 : bond 0.00650 ( 4) link_BETA1-4 : angle 0.71122 ( 12) link_NAG-ASN : bond 0.00184 ( 4) link_NAG-ASN : angle 3.63275 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 210 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7771 (m-30) cc_final: 0.7188 (p0) REVERT: A 56 PHE cc_start: 0.5909 (t80) cc_final: 0.4839 (m-10) REVERT: A 74 LEU cc_start: 0.9176 (tp) cc_final: 0.8669 (mp) REVERT: A 86 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8588 (p) REVERT: A 350 PHE cc_start: 0.6386 (t80) cc_final: 0.5757 (t80) REVERT: A 511 SER cc_start: 0.9260 (t) cc_final: 0.8996 (t) REVERT: B 40 ASP cc_start: 0.7932 (m-30) cc_final: 0.7206 (p0) REVERT: B 56 PHE cc_start: 0.5848 (t80) cc_final: 0.4718 (m-10) REVERT: B 74 LEU cc_start: 0.9114 (tp) cc_final: 0.8491 (mp) REVERT: B 86 SER cc_start: 0.9057 (OUTLIER) cc_final: 0.8612 (p) REVERT: B 245 LEU cc_start: 0.6442 (mm) cc_final: 0.6089 (pp) REVERT: B 350 PHE cc_start: 0.6348 (t80) cc_final: 0.5735 (t80) REVERT: B 427 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6879 (mmp-170) REVERT: B 512 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8645 (mp) REVERT: C 56 PHE cc_start: 0.5666 (t80) cc_final: 0.4553 (m-10) REVERT: C 74 LEU cc_start: 0.9089 (tp) cc_final: 0.8567 (mp) REVERT: C 86 SER cc_start: 0.9060 (OUTLIER) cc_final: 0.8608 (p) REVERT: C 245 LEU cc_start: 0.6417 (mm) cc_final: 0.6070 (pp) REVERT: C 350 PHE cc_start: 0.6368 (t80) cc_final: 0.5597 (t80) REVERT: D 40 ASP cc_start: 0.7898 (m-30) cc_final: 0.7149 (p0) REVERT: D 56 PHE cc_start: 0.5557 (t80) cc_final: 0.4564 (m-10) REVERT: D 74 LEU cc_start: 0.9114 (tp) cc_final: 0.8468 (mp) REVERT: D 86 SER cc_start: 0.9057 (OUTLIER) cc_final: 0.8604 (p) REVERT: D 245 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6066 (pp) REVERT: D 350 PHE cc_start: 0.6347 (t80) cc_final: 0.5720 (t80) outliers start: 59 outliers final: 30 residues processed: 251 average time/residue: 0.0953 time to fit residues: 39.0503 Evaluate side-chains 230 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 307 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 388 ILE 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 B residue 45 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 189 VAL 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 426 MET Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 245 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 437 LEU Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 92 optimal weight: 0.0980 chunk 178 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.133946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102007 restraints weight = 26848.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.104719 restraints weight = 16189.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106503 restraints weight = 12012.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.107678 restraints weight = 10018.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108159 restraints weight = 8938.955| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4183 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= 0.140 Angle : 0.540 7.501 20676 Z= 0.274 Chirality : 0.039 0.136 2420 Planarity : 0.003 0.028 2516 Dihedral : 4.343 21.059 2164 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.22 % Allowed : 16.97 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.21), residues: 1784 helix: 1.57 (0.17), residues: 1012 sheet: -0.26 (0.33), residues: 268 loop : -1.76 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 419 TYR 0.024 0.001 TYR B 411 PHE 0.020 0.001 PHE A 474 TRP 0.006 0.001 TRP A 398 HIS 0.002 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00331 (15236) covalent geometry : angle 0.53078 (20652) hydrogen bonds : bond 0.04147 ( 797) hydrogen bonds : angle 3.63192 ( 2451) link_BETA1-4 : bond 0.00531 ( 4) link_BETA1-4 : angle 0.97986 ( 12) link_NAG-ASN : bond 0.00109 ( 4) link_NAG-ASN : angle 4.13810 ( 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: 53 poor density : 193 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7865 (m-30) cc_final: 0.7166 (p0) REVERT: A 56 PHE cc_start: 0.5864 (t80) cc_final: 0.4744 (m-10) REVERT: A 74 LEU cc_start: 0.9199 (tp) cc_final: 0.8694 (mp) REVERT: A 86 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8619 (p) REVERT: A 350 PHE cc_start: 0.6521 (t80) cc_final: 0.5833 (t80) REVERT: A 511 SER cc_start: 0.9329 (t) cc_final: 0.9060 (t) REVERT: B 40 ASP cc_start: 0.7871 (m-30) cc_final: 0.7049 (p0) REVERT: B 56 PHE cc_start: 0.5860 (t80) cc_final: 0.4725 (m-10) REVERT: B 74 LEU cc_start: 0.9167 (tp) cc_final: 0.8660 (mp) REVERT: B 86 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8635 (p) REVERT: B 245 LEU cc_start: 0.6211 (mm) cc_final: 0.5823 (pp) REVERT: B 350 PHE cc_start: 0.6465 (t80) cc_final: 0.5792 (t80) REVERT: B 427 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6825 (mmp-170) REVERT: C 56 PHE cc_start: 0.5731 (t80) cc_final: 0.4583 (m-10) REVERT: C 74 LEU cc_start: 0.9130 (tp) cc_final: 0.8607 (mp) REVERT: C 86 SER cc_start: 0.9085 (OUTLIER) cc_final: 0.8638 (p) REVERT: C 245 LEU cc_start: 0.6181 (mm) cc_final: 0.5787 (pp) REVERT: C 350 PHE cc_start: 0.6412 (t80) cc_final: 0.5735 (t80) REVERT: D 40 ASP cc_start: 0.7922 (m-30) cc_final: 0.7122 (p0) REVERT: D 56 PHE cc_start: 0.5826 (t80) cc_final: 0.4703 (m-10) REVERT: D 74 LEU cc_start: 0.9138 (tp) cc_final: 0.8598 (mp) REVERT: D 86 SER cc_start: 0.9083 (OUTLIER) cc_final: 0.8633 (p) REVERT: D 245 LEU cc_start: 0.6189 (mm) cc_final: 0.5800 (pp) REVERT: D 350 PHE cc_start: 0.6505 (t80) cc_final: 0.5801 (t80) outliers start: 53 outliers final: 38 residues processed: 232 average time/residue: 0.0945 time to fit residues: 36.1824 Evaluate side-chains 234 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 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 388 ILE 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 B residue 45 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 189 VAL 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 426 MET Chi-restraints excluded: chain B residue 427 ARG 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 189 VAL 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 426 MET Chi-restraints excluded: chain C residue 430 CYS 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 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 437 LEU Chi-restraints excluded: chain D residue 459 MET 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: 5.9990 chunk 50 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.101234 restraints weight = 26880.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103923 restraints weight = 16171.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.105649 restraints weight = 11989.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.106814 restraints weight = 10026.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107501 restraints weight = 8952.659| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15244 Z= 0.152 Angle : 0.551 6.947 20676 Z= 0.280 Chirality : 0.040 0.135 2420 Planarity : 0.003 0.028 2516 Dihedral : 4.475 22.059 2164 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.16 % Allowed : 17.09 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.21), residues: 1784 helix: 1.37 (0.16), residues: 1040 sheet: -0.27 (0.32), residues: 268 loop : -1.93 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 419 TYR 0.024 0.001 TYR B 411 PHE 0.024 0.001 PHE A 474 TRP 0.006 0.001 TRP D 444 HIS 0.002 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00360 (15236) covalent geometry : angle 0.54142 (20652) hydrogen bonds : bond 0.04289 ( 797) hydrogen bonds : angle 3.65529 ( 2451) link_BETA1-4 : bond 0.00570 ( 4) link_BETA1-4 : angle 1.02781 ( 12) link_NAG-ASN : bond 0.00130 ( 4) link_NAG-ASN : angle 4.27377 ( 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 237 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 185 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7888 (m-30) cc_final: 0.7157 (p0) REVERT: A 56 PHE cc_start: 0.5949 (t80) cc_final: 0.4725 (m-10) REVERT: A 74 LEU cc_start: 0.9173 (tp) cc_final: 0.8676 (mp) REVERT: A 86 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 511 SER cc_start: 0.9336 (t) cc_final: 0.9005 (t) REVERT: B 40 ASP cc_start: 0.7933 (m-30) cc_final: 0.7094 (p0) REVERT: B 56 PHE cc_start: 0.5886 (t80) cc_final: 0.4699 (m-10) REVERT: B 74 LEU cc_start: 0.9117 (tp) cc_final: 0.8646 (mp) REVERT: B 86 SER cc_start: 0.9103 (OUTLIER) cc_final: 0.8632 (p) REVERT: B 245 LEU cc_start: 0.6300 (mm) cc_final: 0.5833 (pp) REVERT: B 427 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.7124 (mmt180) REVERT: C 56 PHE cc_start: 0.5961 (t80) cc_final: 0.4726 (m-10) REVERT: C 74 LEU cc_start: 0.9119 (tp) cc_final: 0.8632 (mp) REVERT: C 86 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8638 (p) REVERT: C 245 LEU cc_start: 0.6280 (mm) cc_final: 0.5818 (pp) REVERT: C 419 ARG cc_start: 0.6691 (ttp80) cc_final: 0.4703 (ttm-80) REVERT: D 40 ASP cc_start: 0.7919 (m-30) cc_final: 0.7096 (p0) REVERT: D 56 PHE cc_start: 0.5872 (t80) cc_final: 0.4732 (m-10) REVERT: D 74 LEU cc_start: 0.9160 (tp) cc_final: 0.8662 (mp) REVERT: D 86 SER cc_start: 0.9105 (OUTLIER) cc_final: 0.8607 (p) REVERT: D 245 LEU cc_start: 0.6238 (mm) cc_final: 0.5873 (pp) outliers start: 52 outliers final: 38 residues processed: 222 average time/residue: 0.0910 time to fit residues: 33.0950 Evaluate side-chains 227 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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 388 ILE 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 B residue 45 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 189 VAL 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 426 MET Chi-restraints excluded: chain B residue 427 ARG 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 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 426 MET 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 86 SER Chi-restraints excluded: chain D residue 143 SER 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 503 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 138 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 92 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.135054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.103307 restraints weight = 26569.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.106027 restraints weight = 15940.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107840 restraints weight = 11788.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108987 restraints weight = 9796.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109611 restraints weight = 8750.237| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15244 Z= 0.108 Angle : 0.519 7.719 20676 Z= 0.263 Chirality : 0.038 0.134 2420 Planarity : 0.003 0.029 2516 Dihedral : 4.218 20.718 2164 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.07 % Allowed : 18.25 % Favored : 79.68 % 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: 0.60 (0.21), residues: 1784 helix: 1.59 (0.17), residues: 1032 sheet: -0.20 (0.33), residues: 268 loop : -1.85 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 419 TYR 0.020 0.001 TYR D 411 PHE 0.018 0.001 PHE A 474 TRP 0.003 0.001 TRP A 398 HIS 0.002 0.000 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00242 (15236) covalent geometry : angle 0.51185 (20652) hydrogen bonds : bond 0.03840 ( 797) hydrogen bonds : angle 3.55538 ( 2451) link_BETA1-4 : bond 0.00641 ( 4) link_BETA1-4 : angle 0.70190 ( 12) link_NAG-ASN : bond 0.00110 ( 4) link_NAG-ASN : angle 3.65835 ( 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 229 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7860 (m-30) cc_final: 0.7135 (p0) REVERT: A 50 MET cc_start: 0.4950 (tmm) cc_final: 0.4714 (tmm) REVERT: A 56 PHE cc_start: 0.6121 (t80) cc_final: 0.4908 (m-10) REVERT: A 74 LEU cc_start: 0.9094 (tp) cc_final: 0.8644 (mp) REVERT: A 86 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8590 (p) REVERT: A 350 PHE cc_start: 0.6497 (t80) cc_final: 0.5732 (t80) REVERT: B 40 ASP cc_start: 0.7908 (m-30) cc_final: 0.7053 (p0) REVERT: B 56 PHE cc_start: 0.5877 (t80) cc_final: 0.4762 (m-10) REVERT: B 74 LEU cc_start: 0.9098 (tp) cc_final: 0.8492 (mp) REVERT: B 86 SER cc_start: 0.9077 (OUTLIER) cc_final: 0.8679 (p) REVERT: B 245 LEU cc_start: 0.6162 (mm) cc_final: 0.5776 (pp) REVERT: B 350 PHE cc_start: 0.6593 (t80) cc_final: 0.5761 (t80) REVERT: B 427 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.7091 (mmt180) REVERT: C 56 PHE cc_start: 0.5783 (t80) cc_final: 0.4666 (m-10) REVERT: C 74 LEU cc_start: 0.9091 (tp) cc_final: 0.8606 (mp) REVERT: C 86 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8622 (p) REVERT: C 245 LEU cc_start: 0.6114 (mm) cc_final: 0.5747 (pp) REVERT: C 350 PHE cc_start: 0.6538 (t80) cc_final: 0.5740 (t80) REVERT: C 419 ARG cc_start: 0.6689 (ttp80) cc_final: 0.4784 (ttm-80) REVERT: C 427 ARG cc_start: 0.7403 (mmt180) cc_final: 0.7009 (mmp-170) REVERT: D 56 PHE cc_start: 0.5862 (t80) cc_final: 0.4747 (m-10) REVERT: D 74 LEU cc_start: 0.9115 (tp) cc_final: 0.8500 (mp) REVERT: D 86 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8666 (p) REVERT: D 245 LEU cc_start: 0.6131 (mm) cc_final: 0.5748 (pp) REVERT: D 350 PHE cc_start: 0.6542 (t80) cc_final: 0.5749 (t80) outliers start: 34 outliers final: 24 residues processed: 219 average time/residue: 0.0951 time to fit residues: 33.9712 Evaluate side-chains 220 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 326 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 422 LEU 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 B residue 45 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 427 ARG 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 384 ASP 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 384 ASP Chi-restraints excluded: chain D residue 426 MET 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: 0.0770 chunk 40 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 62 optimal weight: 0.0050 overall best weight: 0.9154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.136080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.104620 restraints weight = 26553.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107293 restraints weight = 15996.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.109108 restraints weight = 11869.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110308 restraints weight = 9857.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110938 restraints weight = 8778.951| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15244 Z= 0.099 Angle : 0.508 7.134 20676 Z= 0.257 Chirality : 0.038 0.136 2420 Planarity : 0.003 0.028 2516 Dihedral : 4.054 19.536 2164 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.07 % Allowed : 18.86 % Favored : 79.08 % 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: 0.77 (0.21), residues: 1784 helix: 1.74 (0.17), residues: 1024 sheet: -0.14 (0.33), residues: 268 loop : -1.78 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.019 0.001 TYR D 411 PHE 0.019 0.001 PHE A 474 TRP 0.004 0.000 TRP D 398 HIS 0.002 0.000 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00216 (15236) covalent geometry : angle 0.50164 (20652) hydrogen bonds : bond 0.03662 ( 797) hydrogen bonds : angle 3.47934 ( 2451) link_BETA1-4 : bond 0.00563 ( 4) link_BETA1-4 : angle 0.70886 ( 12) link_NAG-ASN : bond 0.00152 ( 4) link_NAG-ASN : angle 3.40523 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2213.31 seconds wall clock time: 39 minutes 10.69 seconds (2350.69 seconds total)