Starting phenix.real_space_refine on Tue Nov 18 16:45:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5wj9_8841/11_2025/5wj9_8841_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wj9_8841/11_2025/5wj9_8841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5wj9_8841/11_2025/5wj9_8841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wj9_8841/11_2025/5wj9_8841.map" model { file = "/net/cci-nas-00/data/ceres_data/5wj9_8841/11_2025/5wj9_8841_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wj9_8841/11_2025/5wj9_8841_neut.cif" } resolution = 3.49 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= 0.015 sd= 0.186 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 10172 2.51 5 N 2584 2.21 5 O 2684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s 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: 15540 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3858 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 18, 'TRANS': 460} Chain breaks: 1 Chain: "B" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3858 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 18, 'TRANS': 460} Chain breaks: 1 Chain: "C" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3858 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 18, 'TRANS': 460} Chain breaks: 1 Chain: "D" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3858 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 18, 'TRANS': 460} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.76, per 1000 atoms: 0.24 Number of scatterers: 15540 At special positions: 0 Unit cell: (109, 109, 120, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2684 8.00 N 2584 7.00 C 10172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 166 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 284 " distance=2.03 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 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 667.6 milliseconds 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3616 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 63.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 41 through 50 removed outlier: 4.046A pdb=" N PHE A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 63 through 106 removed outlier: 3.665A pdb=" N MET A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 138 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 291 through 336 removed outlier: 3.723A pdb=" N ASN A 295 " --> pdb=" O GLN A 291 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.670A pdb=" N GLU A 349 " --> pdb=" O TRP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 378 removed outlier: 3.505A pdb=" N ILE A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 399 removed outlier: 3.690A pdb=" N CYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 removed outlier: 4.105A pdb=" N ARG A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.614A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 448 Proline residue: A 423 - end of helix removed outlier: 4.081A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 468 removed outlier: 3.528A pdb=" N PHE A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 480 removed outlier: 3.921A pdb=" N PHE A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 486 removed outlier: 3.759A pdb=" N GLN A 484 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 485 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 486 " --> pdb=" O GLN A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 481 through 486' Processing helix chain 'A' and resid 487 through 507 removed outlier: 3.554A pdb=" N LEU A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 525 Processing helix chain 'B' and resid 41 through 50 removed outlier: 4.047A pdb=" N PHE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 63 through 106 removed outlier: 3.654A pdb=" N MET B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 138 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 291 through 336 removed outlier: 3.723A pdb=" N ASN B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER B 296 " --> pdb=" O HIS B 292 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLY B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 334 " --> pdb=" O PHE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 removed outlier: 3.639A pdb=" N GLU B 349 " --> pdb=" O TRP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 378 removed outlier: 4.017A pdb=" N ILE B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 399 removed outlier: 3.690A pdb=" N CYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 405 removed outlier: 4.099A pdb=" N ARG B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.614A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 448 Proline residue: B 423 - end of helix removed outlier: 4.082A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.528A pdb=" N PHE B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 480 removed outlier: 3.922A pdb=" N PHE B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 removed outlier: 3.759A pdb=" N GLN B 484 " --> pdb=" O GLN B 481 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY B 485 " --> pdb=" O ALA B 482 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 486 " --> pdb=" O GLN B 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 481 through 486' Processing helix chain 'B' and resid 487 through 507 removed outlier: 3.554A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 525 Processing helix chain 'C' and resid 41 through 50 removed outlier: 4.045A pdb=" N PHE C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 59 Processing helix chain 'C' and resid 63 through 106 removed outlier: 3.659A pdb=" N MET C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 138 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing helix chain 'C' and resid 291 through 336 removed outlier: 3.721A pdb=" N ASN C 295 " --> pdb=" O GLN C 291 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER C 296 " --> pdb=" O HIS C 292 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 299 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 327 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLY C 332 " --> pdb=" O ASN C 328 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET C 334 " --> pdb=" O PHE C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.632A pdb=" N GLU C 349 " --> pdb=" O TRP C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 377 removed outlier: 4.223A pdb=" N ILE C 356 " --> pdb=" O ASN C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 399 removed outlier: 3.692A pdb=" N CYS C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 405 removed outlier: 4.096A pdb=" N ARG C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.612A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 448 Proline residue: C 423 - end of helix removed outlier: 4.083A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 468 removed outlier: 3.528A pdb=" N PHE C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 480 removed outlier: 3.921A pdb=" N PHE C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 486 removed outlier: 3.760A pdb=" N GLN C 484 " --> pdb=" O GLN C 481 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY C 485 " --> pdb=" O ALA C 482 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG C 486 " --> pdb=" O GLN C 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 481 through 486' Processing helix chain 'C' and resid 487 through 507 removed outlier: 3.554A pdb=" N LEU C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 525 Processing helix chain 'D' and resid 41 through 50 removed outlier: 4.048A pdb=" N PHE D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 59 Processing helix chain 'D' and resid 63 through 106 removed outlier: 3.655A pdb=" N MET D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 291 through 336 removed outlier: 3.723A pdb=" N ASN D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER D 296 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 299 " --> pdb=" O ASN D 295 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU D 325 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D 327 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY D 332 " --> pdb=" O ASN D 328 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET D 334 " --> pdb=" O PHE D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 removed outlier: 3.639A pdb=" N GLU D 349 " --> pdb=" O TRP D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 378 removed outlier: 4.009A pdb=" N ILE D 356 " --> pdb=" O ASN D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 399 removed outlier: 3.694A pdb=" N CYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 405 removed outlier: 4.097A pdb=" N ARG D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 416 removed outlier: 3.614A pdb=" N LEU D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 448 Proline residue: D 423 - end of helix removed outlier: 4.081A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 468 removed outlier: 3.528A pdb=" N PHE D 465 " --> pdb=" O SER D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 480 removed outlier: 3.921A pdb=" N PHE D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 486 removed outlier: 3.760A pdb=" N GLN D 484 " --> pdb=" O GLN D 481 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY D 485 " --> pdb=" O ALA D 482 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 486 " --> pdb=" O GLN D 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 481 through 486' Processing helix chain 'D' and resid 487 through 507 removed outlier: 3.554A pdb=" N LEU D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR D 507 " --> pdb=" O SER D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 525 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.574A pdb=" N GLN A 278 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG A 168 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL A 231 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N CYS A 166 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE A 233 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA A 164 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N MET A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.574A pdb=" N GLN A 278 " --> pdb=" O SER A 257 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.572A pdb=" N GLN B 278 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG B 168 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL B 231 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N CYS B 166 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE B 233 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA B 164 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N MET B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.572A pdb=" N GLN B 278 " --> pdb=" O SER B 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.574A pdb=" N GLN C 278 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG C 168 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL C 231 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N CYS C 166 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ILE C 233 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA C 164 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N MET C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.574A pdb=" N GLN C 278 " --> pdb=" O SER C 257 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.574A pdb=" N GLN D 278 " --> pdb=" O SER D 257 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG D 168 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL D 231 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N CYS D 166 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE D 233 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA D 164 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N MET D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.574A pdb=" N GLN D 278 " --> pdb=" O SER D 257 " (cutoff:3.500A) 947 hydrogen bonds defined for protein. 2769 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: 2.54 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: 0.89 - 1.12: 1 1.12 - 1.34: 4699 1.34 - 1.56: 11081 1.56 - 1.78: 26 1.78 - 2.01: 141 Bond restraints: 15948 Sorted by residual: bond pdb=" C PRO B 205 " pdb=" O PRO B 205 " ideal model delta sigma weight residual 1.231 2.007 -0.776 2.00e-02 2.50e+03 1.51e+03 bond pdb=" C HIS D 526 " pdb=" O HIS D 526 " ideal model delta sigma weight residual 1.231 1.761 -0.530 2.00e-02 2.50e+03 7.02e+02 bond pdb=" C HIS A 526 " pdb=" O HIS A 526 " ideal model delta sigma weight residual 1.231 1.678 -0.447 2.00e-02 2.50e+03 5.00e+02 bond pdb=" C HIS C 526 " pdb=" O HIS C 526 " ideal model delta sigma weight residual 1.231 1.668 -0.437 2.00e-02 2.50e+03 4.78e+02 bond pdb=" C PRO D 205 " pdb=" O PRO D 205 " ideal model delta sigma weight residual 1.231 0.893 0.338 2.00e-02 2.50e+03 2.85e+02 ... (remaining 15943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 21388 3.54 - 7.08: 275 7.08 - 10.63: 12 10.63 - 14.17: 2 14.17 - 17.71: 3 Bond angle restraints: 21680 Sorted by residual: angle pdb=" CA HIS A 526 " pdb=" C HIS A 526 " pdb=" O HIS A 526 " ideal model delta sigma weight residual 120.80 138.51 -17.71 1.70e+00 3.46e-01 1.09e+02 angle pdb=" CA HIS D 526 " pdb=" C HIS D 526 " pdb=" O HIS D 526 " ideal model delta sigma weight residual 120.80 136.18 -15.38 1.70e+00 3.46e-01 8.18e+01 angle pdb=" CA HIS B 526 " pdb=" C HIS B 526 " pdb=" O HIS B 526 " ideal model delta sigma weight residual 120.80 135.60 -14.80 1.70e+00 3.46e-01 7.58e+01 angle pdb=" C VAL A 359 " pdb=" CA VAL A 359 " pdb=" CB VAL A 359 " ideal model delta sigma weight residual 112.22 121.95 -9.73 1.38e+00 5.25e-01 4.97e+01 angle pdb=" O GLY D 448 " pdb=" C GLY D 448 " pdb=" N PRO D 449 " ideal model delta sigma weight residual 121.07 123.02 -1.95 3.60e-01 7.72e+00 2.94e+01 ... (remaining 21675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 8392 16.75 - 33.50: 771 33.50 - 50.25: 166 50.25 - 67.00: 39 67.00 - 83.75: 20 Dihedral angle restraints: 9388 sinusoidal: 3776 harmonic: 5612 Sorted by residual: dihedral pdb=" C VAL A 359 " pdb=" N VAL A 359 " pdb=" CA VAL A 359 " pdb=" CB VAL A 359 " ideal model delta harmonic sigma weight residual -122.00 -148.43 26.43 0 2.50e+00 1.60e-01 1.12e+02 dihedral pdb=" N VAL A 359 " pdb=" C VAL A 359 " pdb=" CA VAL A 359 " pdb=" CB VAL A 359 " ideal model delta harmonic sigma weight residual 123.40 146.17 -22.77 0 2.50e+00 1.60e-01 8.30e+01 dihedral pdb=" N PHE B 324 " pdb=" C PHE B 324 " pdb=" CA PHE B 324 " pdb=" CB PHE B 324 " ideal model delta harmonic sigma weight residual 122.80 141.88 -19.08 0 2.50e+00 1.60e-01 5.82e+01 ... (remaining 9385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 2388 0.187 - 0.374: 57 0.374 - 0.561: 4 0.561 - 0.748: 1 0.748 - 0.935: 2 Chirality restraints: 2452 Sorted by residual: chirality pdb=" CA VAL A 359 " pdb=" N VAL A 359 " pdb=" C VAL A 359 " pdb=" CB VAL A 359 " both_signs ideal model delta sigma weight residual False 2.44 1.51 0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" CA PHE B 324 " pdb=" N PHE B 324 " pdb=" C PHE B 324 " pdb=" CB PHE B 324 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA PHE A 350 " pdb=" N PHE A 350 " pdb=" C PHE A 350 " pdb=" CB PHE A 350 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.37e+00 ... (remaining 2449 not shown) Planarity restraints: 2692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 378 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C LYS C 378 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS C 378 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN C 379 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 422 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO D 423 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 423 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 423 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 422 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO B 423 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 423 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 423 " 0.028 5.00e-02 4.00e+02 ... (remaining 2689 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 493 2.76 - 3.29: 17407 3.29 - 3.83: 24777 3.83 - 4.36: 31054 4.36 - 4.90: 51414 Nonbonded interactions: 125145 Sorted by model distance: nonbonded pdb=" OG1 THR B 77 " pdb=" CZ2 TRP B 398 " model vdw 2.225 3.340 nonbonded pdb=" O THR B 394 " pdb=" CD1 TRP B 398 " model vdw 2.323 3.260 nonbonded pdb=" O TYR A 439 " pdb=" OH TYR A 497 " model vdw 2.495 3.040 nonbonded pdb=" O TYR B 439 " pdb=" OH TYR B 497 " model vdw 2.496 3.040 nonbonded pdb=" O TYR C 439 " pdb=" OH TYR C 497 " model vdw 2.496 3.040 ... (remaining 125140 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.140 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: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 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 : 0.014 0.776 15956 Z= 0.814 Angle : 1.230 17.712 21696 Z= 0.819 Chirality : 0.075 0.935 2452 Planarity : 0.005 0.051 2692 Dihedral : 14.404 83.745 5748 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.05 % Favored : 90.68 % Rotamer: Outliers : 1.93 % Allowed : 7.55 % Favored : 90.52 % Cbeta Deviations : 0.22 % 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: -3.89 (0.15), residues: 1900 helix: -1.76 (0.12), residues: 1028 sheet: -3.07 (0.32), residues: 196 loop : -3.57 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 403 TYR 0.023 0.002 TYR A 355 PHE 0.027 0.003 PHE C 182 TRP 0.018 0.002 TRP D 345 HIS 0.009 0.002 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.01396 (15948) covalent geometry : angle 1.23016 (21680) SS BOND : bond 0.00226 ( 8) SS BOND : angle 0.72039 ( 16) hydrogen bonds : bond 0.22980 ( 915) hydrogen bonds : angle 8.98952 ( 2769) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 643 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7714 (ttp-170) cc_final: 0.7103 (tpt170) REVERT: A 54 ASP cc_start: 0.9116 (m-30) cc_final: 0.8297 (t0) REVERT: A 57 ARG cc_start: 0.8318 (mtt180) cc_final: 0.8106 (ptm-80) REVERT: A 124 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8846 (tm-30) REVERT: A 174 HIS cc_start: 0.8458 (t70) cc_final: 0.7681 (t-90) REVERT: A 185 ASP cc_start: 0.8643 (p0) cc_final: 0.8341 (p0) REVERT: A 196 ASP cc_start: 0.8794 (p0) cc_final: 0.8510 (p0) REVERT: A 252 ASP cc_start: 0.7618 (m-30) cc_final: 0.7417 (m-30) REVERT: A 346 GLU cc_start: 0.8361 (pt0) cc_final: 0.7954 (pm20) REVERT: A 371 MET cc_start: 0.8658 (mmm) cc_final: 0.8382 (ttp) REVERT: A 409 HIS cc_start: 0.8824 (m90) cc_final: 0.8585 (t-170) REVERT: A 436 TYR cc_start: 0.8963 (t80) cc_final: 0.8531 (t80) REVERT: A 451 HIS cc_start: 0.5961 (m-70) cc_final: 0.5740 (m-70) REVERT: A 464 LEU cc_start: 0.8852 (mt) cc_final: 0.8644 (mt) REVERT: A 486 ARG cc_start: 0.8286 (ptp-170) cc_final: 0.8076 (ptm-80) REVERT: A 487 SER cc_start: 0.8719 (m) cc_final: 0.8496 (p) REVERT: A 491 TRP cc_start: 0.8476 (t60) cc_final: 0.8127 (t60) REVERT: A 505 PHE cc_start: 0.8553 (m-10) cc_final: 0.8321 (m-10) REVERT: A 524 ILE cc_start: 0.8809 (tp) cc_final: 0.8459 (tt) REVERT: B 42 ARG cc_start: 0.7609 (ttp-170) cc_final: 0.7190 (tpt170) REVERT: B 54 ASP cc_start: 0.9170 (m-30) cc_final: 0.8203 (t0) REVERT: B 124 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8836 (tm-30) REVERT: B 174 HIS cc_start: 0.8414 (t70) cc_final: 0.7618 (t-90) REVERT: B 185 ASP cc_start: 0.8626 (p0) cc_final: 0.8308 (p0) REVERT: B 352 ASN cc_start: 0.8614 (m-40) cc_final: 0.8321 (t0) REVERT: B 355 TYR cc_start: 0.8854 (m-80) cc_final: 0.8373 (m-80) REVERT: B 367 SER cc_start: 0.9308 (t) cc_final: 0.9095 (p) REVERT: B 371 MET cc_start: 0.9036 (tpp) cc_final: 0.8810 (ttp) REVERT: B 393 SER cc_start: 0.9536 (t) cc_final: 0.9319 (p) REVERT: B 409 HIS cc_start: 0.8823 (m90) cc_final: 0.8585 (t-170) REVERT: B 436 TYR cc_start: 0.9050 (t80) cc_final: 0.8661 (t80) REVERT: B 451 HIS cc_start: 0.5969 (m-70) cc_final: 0.5732 (m-70) REVERT: B 464 LEU cc_start: 0.8865 (mt) cc_final: 0.8637 (mt) REVERT: B 486 ARG cc_start: 0.8300 (ptp-170) cc_final: 0.8071 (ptm-80) REVERT: B 487 SER cc_start: 0.8715 (m) cc_final: 0.8498 (p) REVERT: B 491 TRP cc_start: 0.8469 (t60) cc_final: 0.8093 (t60) REVERT: B 505 PHE cc_start: 0.8544 (m-10) cc_final: 0.8318 (m-10) REVERT: C 54 ASP cc_start: 0.9103 (m-30) cc_final: 0.8220 (t0) REVERT: C 124 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8830 (tm-30) REVERT: C 185 ASP cc_start: 0.8621 (p0) cc_final: 0.8296 (p0) REVERT: C 252 ASP cc_start: 0.7596 (m-30) cc_final: 0.7382 (m-30) REVERT: C 355 TYR cc_start: 0.8877 (m-80) cc_final: 0.8497 (m-80) REVERT: C 384 ASP cc_start: 0.8591 (p0) cc_final: 0.8374 (p0) REVERT: C 393 SER cc_start: 0.9538 (t) cc_final: 0.9301 (p) REVERT: C 436 TYR cc_start: 0.9071 (t80) cc_final: 0.8712 (t80) REVERT: C 451 HIS cc_start: 0.5988 (m-70) cc_final: 0.5734 (m-70) REVERT: C 464 LEU cc_start: 0.8866 (mt) cc_final: 0.8646 (mt) REVERT: C 486 ARG cc_start: 0.8278 (ptp-170) cc_final: 0.8061 (ptm-80) REVERT: C 487 SER cc_start: 0.8715 (m) cc_final: 0.8494 (p) REVERT: C 491 TRP cc_start: 0.8471 (t60) cc_final: 0.8102 (t60) REVERT: C 505 PHE cc_start: 0.8538 (m-10) cc_final: 0.8338 (m-10) REVERT: D 42 ARG cc_start: 0.7926 (ttp-170) cc_final: 0.7320 (tpt170) REVERT: D 54 ASP cc_start: 0.9235 (m-30) cc_final: 0.8148 (t0) REVERT: D 174 HIS cc_start: 0.8419 (t70) cc_final: 0.7633 (t-90) REVERT: D 185 ASP cc_start: 0.8637 (p0) cc_final: 0.8340 (p0) REVERT: D 294 ASP cc_start: 0.6091 (t70) cc_final: 0.4923 (p0) REVERT: D 346 GLU cc_start: 0.8367 (pt0) cc_final: 0.7933 (pm20) REVERT: D 352 ASN cc_start: 0.8534 (t0) cc_final: 0.7571 (t0) REVERT: D 355 TYR cc_start: 0.8947 (m-80) cc_final: 0.8300 (m-80) REVERT: D 384 ASP cc_start: 0.8585 (p0) cc_final: 0.8366 (p0) REVERT: D 393 SER cc_start: 0.9528 (t) cc_final: 0.9295 (p) REVERT: D 436 TYR cc_start: 0.9077 (t80) cc_final: 0.8700 (t80) REVERT: D 451 HIS cc_start: 0.5976 (m-70) cc_final: 0.5751 (m-70) REVERT: D 464 LEU cc_start: 0.8869 (mt) cc_final: 0.8638 (mt) REVERT: D 486 ARG cc_start: 0.8324 (ptp-170) cc_final: 0.8123 (ptm-80) REVERT: D 487 SER cc_start: 0.8746 (m) cc_final: 0.8522 (p) REVERT: D 491 TRP cc_start: 0.8454 (t60) cc_final: 0.8096 (t60) outliers start: 33 outliers final: 10 residues processed: 658 average time/residue: 0.1157 time to fit residues: 113.7928 Evaluate side-chains 435 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 422 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 325 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN B 69 GLN B 79 GLN B 97 ASN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 79 GLN C 97 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 79 GLN D 97 ASN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.115803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.091886 restraints weight = 40661.920| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.72 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15956 Z= 0.220 Angle : 0.808 12.147 21696 Z= 0.414 Chirality : 0.049 0.206 2452 Planarity : 0.006 0.049 2692 Dihedral : 7.592 68.216 2223 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 3.92 % Allowed : 18.27 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.17), residues: 1900 helix: -0.33 (0.13), residues: 1060 sheet: -1.99 (0.34), residues: 176 loop : -2.63 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 94 TYR 0.012 0.002 TYR D 499 PHE 0.023 0.003 PHE A 350 TRP 0.014 0.002 TRP C 335 HIS 0.008 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00464 (15948) covalent geometry : angle 0.80665 (21680) SS BOND : bond 0.00182 ( 8) SS BOND : angle 1.59942 ( 16) hydrogen bonds : bond 0.06405 ( 915) hydrogen bonds : angle 5.80547 ( 2769) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 423 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7792 (ptp) cc_final: 0.7218 (ptp) REVERT: A 54 ASP cc_start: 0.9026 (m-30) cc_final: 0.8239 (t0) REVERT: A 57 ARG cc_start: 0.8262 (mtt180) cc_final: 0.7937 (mtp85) REVERT: A 252 ASP cc_start: 0.8036 (m-30) cc_final: 0.7669 (m-30) REVERT: A 315 LEU cc_start: 0.9508 (mt) cc_final: 0.9255 (mt) REVERT: A 371 MET cc_start: 0.8821 (mmm) cc_final: 0.8552 (ttp) REVERT: A 436 TYR cc_start: 0.9151 (t80) cc_final: 0.8689 (t80) REVERT: A 464 LEU cc_start: 0.9195 (mt) cc_final: 0.8953 (mt) REVERT: A 491 TRP cc_start: 0.9110 (t60) cc_final: 0.8878 (t60) REVERT: A 524 ILE cc_start: 0.9376 (tp) cc_final: 0.9083 (tt) REVERT: B 50 MET cc_start: 0.7852 (ptp) cc_final: 0.6711 (ptp) REVERT: B 54 ASP cc_start: 0.8914 (m-30) cc_final: 0.8174 (t0) REVERT: B 79 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.8791 (tm-30) REVERT: B 89 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8429 (mp) REVERT: B 315 LEU cc_start: 0.9473 (mt) cc_final: 0.9200 (mt) REVERT: B 324 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7887 (t80) REVERT: B 335 TRP cc_start: 0.7424 (OUTLIER) cc_final: 0.7078 (m-10) REVERT: B 355 TYR cc_start: 0.8684 (m-80) cc_final: 0.8480 (m-80) REVERT: B 376 GLU cc_start: 0.8583 (tt0) cc_final: 0.8328 (tt0) REVERT: B 436 TYR cc_start: 0.9153 (t80) cc_final: 0.8605 (t80) REVERT: B 464 LEU cc_start: 0.9183 (mt) cc_final: 0.8930 (mt) REVERT: B 491 TRP cc_start: 0.9128 (t60) cc_final: 0.8863 (t60) REVERT: B 524 ILE cc_start: 0.9394 (tp) cc_final: 0.9106 (tt) REVERT: C 50 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.6736 (ptt) REVERT: C 54 ASP cc_start: 0.8844 (m-30) cc_final: 0.8147 (t0) REVERT: C 89 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8449 (mp) REVERT: C 252 ASP cc_start: 0.8029 (m-30) cc_final: 0.7791 (m-30) REVERT: C 315 LEU cc_start: 0.9421 (mt) cc_final: 0.9130 (mt) REVERT: C 334 MET cc_start: 0.5973 (mmm) cc_final: 0.5589 (mmt) REVERT: C 355 TYR cc_start: 0.8778 (m-80) cc_final: 0.8426 (m-80) REVERT: C 371 MET cc_start: 0.8685 (ttm) cc_final: 0.8439 (ttp) REVERT: C 436 TYR cc_start: 0.9145 (t80) cc_final: 0.8591 (t80) REVERT: C 464 LEU cc_start: 0.9200 (mt) cc_final: 0.8925 (mt) REVERT: C 491 TRP cc_start: 0.9125 (t60) cc_final: 0.8873 (t60) REVERT: C 524 ILE cc_start: 0.9412 (tp) cc_final: 0.9111 (tt) REVERT: D 54 ASP cc_start: 0.8932 (m-30) cc_final: 0.8138 (t0) REVERT: D 89 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8376 (mp) REVERT: D 315 LEU cc_start: 0.9400 (mt) cc_final: 0.9122 (mt) REVERT: D 352 ASN cc_start: 0.8955 (t0) cc_final: 0.8749 (t0) REVERT: D 355 TYR cc_start: 0.8696 (m-80) cc_final: 0.8379 (m-80) REVERT: D 371 MET cc_start: 0.8705 (ttm) cc_final: 0.8450 (ttp) REVERT: D 380 LEU cc_start: 0.9479 (tp) cc_final: 0.9264 (tt) REVERT: D 436 TYR cc_start: 0.9154 (t80) cc_final: 0.8548 (t80) REVERT: D 464 LEU cc_start: 0.9207 (mt) cc_final: 0.8903 (mt) REVERT: D 491 TRP cc_start: 0.9114 (t60) cc_final: 0.8879 (t60) REVERT: D 524 ILE cc_start: 0.9402 (tp) cc_final: 0.9102 (tt) outliers start: 67 outliers final: 34 residues processed: 451 average time/residue: 0.1103 time to fit residues: 76.6839 Evaluate side-chains 411 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 370 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 324 PHE Chi-restraints excluded: chain B residue 335 TRP Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 445 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 178 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.114886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.091569 restraints weight = 41503.692| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 4.70 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15956 Z= 0.185 Angle : 0.734 8.931 21696 Z= 0.374 Chirality : 0.046 0.191 2452 Planarity : 0.005 0.050 2692 Dihedral : 6.306 45.794 2208 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.42 % Favored : 93.53 % Rotamer: Outliers : 4.92 % Allowed : 18.44 % Favored : 76.64 % 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: -1.35 (0.19), residues: 1900 helix: 0.19 (0.15), residues: 1060 sheet: -1.70 (0.35), residues: 204 loop : -2.41 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.014 0.001 TYR B 411 PHE 0.023 0.002 PHE D 49 TRP 0.030 0.002 TRP D 335 HIS 0.011 0.002 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00397 (15948) covalent geometry : angle 0.73346 (21680) SS BOND : bond 0.00125 ( 8) SS BOND : angle 1.52095 ( 16) hydrogen bonds : bond 0.05491 ( 915) hydrogen bonds : angle 5.38578 ( 2769) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 404 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7731 (ptp) cc_final: 0.7271 (ptp) REVERT: A 54 ASP cc_start: 0.8986 (m-30) cc_final: 0.8247 (t0) REVERT: A 57 ARG cc_start: 0.8213 (mtt180) cc_final: 0.7873 (mtp85) REVERT: A 252 ASP cc_start: 0.8013 (m-30) cc_final: 0.7757 (m-30) REVERT: A 315 LEU cc_start: 0.9510 (mt) cc_final: 0.9270 (mt) REVERT: A 371 MET cc_start: 0.8838 (mmm) cc_final: 0.8603 (ttp) REVERT: A 436 TYR cc_start: 0.9119 (t80) cc_final: 0.8869 (t80) REVERT: A 464 LEU cc_start: 0.9318 (mt) cc_final: 0.9059 (mt) REVERT: A 512 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8573 (mm) REVERT: A 524 ILE cc_start: 0.9414 (tp) cc_final: 0.9122 (tt) REVERT: B 50 MET cc_start: 0.7822 (ptp) cc_final: 0.6730 (ptp) REVERT: B 54 ASP cc_start: 0.8912 (m-30) cc_final: 0.8153 (t0) REVERT: B 115 ASP cc_start: 0.9128 (OUTLIER) cc_final: 0.8732 (p0) REVERT: B 315 LEU cc_start: 0.9475 (mt) cc_final: 0.9188 (mt) REVERT: B 335 TRP cc_start: 0.7408 (OUTLIER) cc_final: 0.7073 (m-10) REVERT: B 355 TYR cc_start: 0.8901 (m-80) cc_final: 0.8650 (m-80) REVERT: B 436 TYR cc_start: 0.9152 (t80) cc_final: 0.8922 (t80) REVERT: B 464 LEU cc_start: 0.9320 (mt) cc_final: 0.9052 (mt) REVERT: B 512 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8607 (mm) REVERT: B 524 ILE cc_start: 0.9413 (tp) cc_final: 0.9137 (tt) REVERT: C 50 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6653 (ptt) REVERT: C 54 ASP cc_start: 0.8802 (m-30) cc_final: 0.8175 (t0) REVERT: C 315 LEU cc_start: 0.9450 (mt) cc_final: 0.9175 (mt) REVERT: C 334 MET cc_start: 0.6062 (mmm) cc_final: 0.5223 (mmt) REVERT: C 371 MET cc_start: 0.8665 (ttm) cc_final: 0.8413 (ttp) REVERT: C 436 TYR cc_start: 0.9147 (t80) cc_final: 0.8921 (t80) REVERT: C 464 LEU cc_start: 0.9361 (mt) cc_final: 0.9061 (mt) REVERT: C 480 MET cc_start: 0.8824 (mmt) cc_final: 0.8598 (mmm) REVERT: C 512 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8588 (mm) REVERT: C 524 ILE cc_start: 0.9412 (tp) cc_final: 0.9124 (tt) REVERT: D 54 ASP cc_start: 0.8835 (m-30) cc_final: 0.8124 (t0) REVERT: D 315 LEU cc_start: 0.9422 (mt) cc_final: 0.9140 (mt) REVERT: D 355 TYR cc_start: 0.8722 (m-80) cc_final: 0.8386 (m-80) REVERT: D 371 MET cc_start: 0.8685 (ttm) cc_final: 0.8433 (ttp) REVERT: D 436 TYR cc_start: 0.9154 (t80) cc_final: 0.8951 (t80) REVERT: D 464 LEU cc_start: 0.9317 (mt) cc_final: 0.9092 (mt) REVERT: D 512 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8598 (mm) REVERT: D 524 ILE cc_start: 0.9407 (tp) cc_final: 0.9118 (tt) outliers start: 84 outliers final: 46 residues processed: 436 average time/residue: 0.0999 time to fit residues: 69.0798 Evaluate side-chains 413 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 360 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 335 TRP Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 174 optimal weight: 1.9990 chunk 165 optimal weight: 0.0170 chunk 30 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 142 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.114119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.090940 restraints weight = 41360.035| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 4.69 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15956 Z= 0.176 Angle : 0.715 8.906 21696 Z= 0.359 Chirality : 0.046 0.316 2452 Planarity : 0.005 0.045 2692 Dihedral : 6.098 54.161 2202 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 5.21 % Allowed : 19.96 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.19), residues: 1900 helix: 0.24 (0.15), residues: 1072 sheet: -1.33 (0.36), residues: 204 loop : -2.39 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 455 TYR 0.012 0.001 TYR A 497 PHE 0.029 0.002 PHE A 49 TRP 0.024 0.002 TRP D 335 HIS 0.016 0.002 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00375 (15948) covalent geometry : angle 0.71418 (21680) SS BOND : bond 0.00146 ( 8) SS BOND : angle 1.57505 ( 16) hydrogen bonds : bond 0.05000 ( 915) hydrogen bonds : angle 5.23837 ( 2769) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 389 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7737 (ptp) cc_final: 0.7270 (ptp) REVERT: A 54 ASP cc_start: 0.8986 (m-30) cc_final: 0.8279 (t0) REVERT: A 57 ARG cc_start: 0.8214 (mtt180) cc_final: 0.7841 (mtp85) REVERT: A 115 ASP cc_start: 0.9157 (p0) cc_final: 0.8788 (p0) REVERT: A 252 ASP cc_start: 0.8078 (m-30) cc_final: 0.7802 (m-30) REVERT: A 355 TYR cc_start: 0.9111 (m-80) cc_final: 0.8711 (m-80) REVERT: A 371 MET cc_start: 0.8867 (mmm) cc_final: 0.8588 (ttp) REVERT: A 451 HIS cc_start: 0.6215 (m-70) cc_final: 0.5800 (m-70) REVERT: A 459 MET cc_start: 0.9032 (mmm) cc_final: 0.8822 (mmm) REVERT: A 512 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8617 (mm) REVERT: A 524 ILE cc_start: 0.9379 (tp) cc_final: 0.9094 (tt) REVERT: B 50 MET cc_start: 0.7789 (ptp) cc_final: 0.6680 (ptp) REVERT: B 54 ASP cc_start: 0.8907 (m-30) cc_final: 0.8190 (t0) REVERT: B 115 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8743 (p0) REVERT: B 335 TRP cc_start: 0.7373 (OUTLIER) cc_final: 0.7113 (m-10) REVERT: B 436 TYR cc_start: 0.9134 (t80) cc_final: 0.8711 (t80) REVERT: B 451 HIS cc_start: 0.6332 (m-70) cc_final: 0.5899 (m-70) REVERT: B 464 LEU cc_start: 0.9355 (mt) cc_final: 0.9069 (mt) REVERT: B 512 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8621 (mm) REVERT: B 524 ILE cc_start: 0.9394 (tp) cc_final: 0.9120 (tt) REVERT: C 41 LEU cc_start: 0.8970 (tp) cc_final: 0.8652 (tp) REVERT: C 50 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.6745 (ptt) REVERT: C 54 ASP cc_start: 0.8815 (m-30) cc_final: 0.8203 (t0) REVERT: C 115 ASP cc_start: 0.9141 (OUTLIER) cc_final: 0.8746 (p0) REVERT: C 334 MET cc_start: 0.5681 (mmm) cc_final: 0.5310 (mmt) REVERT: C 371 MET cc_start: 0.8629 (ttm) cc_final: 0.8383 (ttp) REVERT: C 436 TYR cc_start: 0.9139 (t80) cc_final: 0.8744 (t80) REVERT: C 464 LEU cc_start: 0.9376 (mt) cc_final: 0.9093 (mt) REVERT: C 512 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8618 (mm) REVERT: C 524 ILE cc_start: 0.9377 (tp) cc_final: 0.9093 (tt) REVERT: D 54 ASP cc_start: 0.8874 (m-30) cc_final: 0.8334 (t0) REVERT: D 115 ASP cc_start: 0.9138 (p0) cc_final: 0.8771 (p0) REVERT: D 335 TRP cc_start: 0.7444 (OUTLIER) cc_final: 0.6785 (m100) REVERT: D 355 TYR cc_start: 0.8871 (m-80) cc_final: 0.8581 (m-80) REVERT: D 371 MET cc_start: 0.8641 (ttm) cc_final: 0.8421 (ttp) REVERT: D 436 TYR cc_start: 0.9144 (t80) cc_final: 0.8799 (t80) REVERT: D 464 LEU cc_start: 0.9342 (mt) cc_final: 0.9091 (mt) REVERT: D 512 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8656 (mm) REVERT: D 524 ILE cc_start: 0.9375 (tp) cc_final: 0.9087 (tt) outliers start: 89 outliers final: 53 residues processed: 430 average time/residue: 0.0974 time to fit residues: 65.8921 Evaluate side-chains 422 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 360 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 TRP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 335 TRP Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 155 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.114341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.091433 restraints weight = 40847.990| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 4.66 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15956 Z= 0.156 Angle : 0.726 14.026 21696 Z= 0.356 Chirality : 0.046 0.357 2452 Planarity : 0.004 0.038 2692 Dihedral : 5.867 54.768 2202 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 5.50 % Allowed : 21.43 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.19), residues: 1900 helix: 0.39 (0.15), residues: 1064 sheet: -1.07 (0.36), residues: 204 loop : -2.34 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 338 TYR 0.012 0.001 TYR A 436 PHE 0.031 0.002 PHE B 235 TRP 0.023 0.001 TRP D 335 HIS 0.014 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00333 (15948) covalent geometry : angle 0.72489 (21680) SS BOND : bond 0.00133 ( 8) SS BOND : angle 1.60590 ( 16) hydrogen bonds : bond 0.04771 ( 915) hydrogen bonds : angle 5.09480 ( 2769) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 390 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7779 (ptp) cc_final: 0.7331 (ptp) REVERT: A 54 ASP cc_start: 0.8990 (m-30) cc_final: 0.8249 (t0) REVERT: A 57 ARG cc_start: 0.8242 (mtt180) cc_final: 0.7847 (mtp85) REVERT: A 88 GLN cc_start: 0.8726 (pt0) cc_final: 0.8189 (tm-30) REVERT: A 115 ASP cc_start: 0.9197 (p0) cc_final: 0.8833 (p0) REVERT: A 355 TYR cc_start: 0.9127 (m-80) cc_final: 0.8395 (m-80) REVERT: A 371 MET cc_start: 0.8846 (mmm) cc_final: 0.8437 (ttp) REVERT: A 435 ILE cc_start: 0.9546 (mt) cc_final: 0.9314 (tt) REVERT: A 459 MET cc_start: 0.9080 (mmm) cc_final: 0.8849 (mmm) REVERT: A 512 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8647 (mm) REVERT: A 524 ILE cc_start: 0.9371 (tp) cc_final: 0.9066 (tt) REVERT: B 50 MET cc_start: 0.7735 (ptp) cc_final: 0.6599 (ptp) REVERT: B 54 ASP cc_start: 0.8883 (m-30) cc_final: 0.8157 (t0) REVERT: B 115 ASP cc_start: 0.9197 (OUTLIER) cc_final: 0.8825 (p0) REVERT: B 335 TRP cc_start: 0.7285 (OUTLIER) cc_final: 0.6930 (m-10) REVERT: B 393 SER cc_start: 0.9626 (p) cc_final: 0.9320 (p) REVERT: B 435 ILE cc_start: 0.9563 (mt) cc_final: 0.9331 (tt) REVERT: B 436 TYR cc_start: 0.9135 (t80) cc_final: 0.8814 (t80) REVERT: B 464 LEU cc_start: 0.9362 (mt) cc_final: 0.9114 (mt) REVERT: B 512 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8637 (mm) REVERT: B 524 ILE cc_start: 0.9379 (tp) cc_final: 0.9080 (tt) REVERT: C 50 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.6761 (ptt) REVERT: C 54 ASP cc_start: 0.8795 (m-30) cc_final: 0.8164 (t0) REVERT: C 115 ASP cc_start: 0.9185 (OUTLIER) cc_final: 0.8806 (p0) REVERT: C 334 MET cc_start: 0.5867 (mmm) cc_final: 0.5581 (mmt) REVERT: C 371 MET cc_start: 0.8642 (ttm) cc_final: 0.8387 (ttp) REVERT: C 436 TYR cc_start: 0.9146 (t80) cc_final: 0.8830 (t80) REVERT: C 464 LEU cc_start: 0.9348 (mt) cc_final: 0.9097 (mt) REVERT: C 512 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8641 (mm) REVERT: C 524 ILE cc_start: 0.9364 (tp) cc_final: 0.9052 (tt) REVERT: D 54 ASP cc_start: 0.8921 (m-30) cc_final: 0.8321 (t0) REVERT: D 115 ASP cc_start: 0.9159 (p0) cc_final: 0.8795 (p0) REVERT: D 335 TRP cc_start: 0.7643 (OUTLIER) cc_final: 0.6758 (m100) REVERT: D 371 MET cc_start: 0.8644 (ttm) cc_final: 0.8396 (ttp) REVERT: D 393 SER cc_start: 0.9723 (OUTLIER) cc_final: 0.9347 (p) REVERT: D 436 TYR cc_start: 0.9116 (t80) cc_final: 0.8813 (t80) REVERT: D 464 LEU cc_start: 0.9345 (mt) cc_final: 0.9102 (mt) REVERT: D 480 MET cc_start: 0.8360 (mmp) cc_final: 0.8016 (mmp) REVERT: D 512 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8632 (mm) REVERT: D 524 ILE cc_start: 0.9372 (tp) cc_final: 0.9068 (tt) outliers start: 94 outliers final: 54 residues processed: 434 average time/residue: 0.0984 time to fit residues: 67.8363 Evaluate side-chains 429 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 365 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 335 TRP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 335 TRP Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 21 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN B 194 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.114996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.091957 restraints weight = 41032.891| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 4.72 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15956 Z= 0.147 Angle : 0.716 12.659 21696 Z= 0.351 Chirality : 0.046 0.398 2452 Planarity : 0.004 0.037 2692 Dihedral : 5.659 54.877 2200 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.16 % Favored : 93.79 % Rotamer: Outliers : 5.68 % Allowed : 22.89 % Favored : 71.43 % 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: -0.95 (0.19), residues: 1900 helix: 0.36 (0.15), residues: 1080 sheet: -0.74 (0.37), residues: 196 loop : -2.29 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 338 TYR 0.018 0.001 TYR C 411 PHE 0.025 0.002 PHE A 493 TRP 0.022 0.001 TRP D 335 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00311 (15948) covalent geometry : angle 0.71530 (21680) SS BOND : bond 0.00143 ( 8) SS BOND : angle 1.63632 ( 16) hydrogen bonds : bond 0.04614 ( 915) hydrogen bonds : angle 5.03050 ( 2769) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 392 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7764 (ptp) cc_final: 0.7300 (ptp) REVERT: A 54 ASP cc_start: 0.8974 (m-30) cc_final: 0.8212 (t0) REVERT: A 57 ARG cc_start: 0.8269 (mtt180) cc_final: 0.7873 (mtp85) REVERT: A 88 GLN cc_start: 0.8745 (pt0) cc_final: 0.8256 (tm-30) REVERT: A 115 ASP cc_start: 0.9197 (p0) cc_final: 0.8846 (p0) REVERT: A 355 TYR cc_start: 0.9159 (m-80) cc_final: 0.8756 (m-80) REVERT: A 371 MET cc_start: 0.8888 (mmm) cc_final: 0.8470 (ttp) REVERT: A 459 MET cc_start: 0.9086 (mmm) cc_final: 0.8880 (mmm) REVERT: A 512 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8645 (mm) REVERT: A 524 ILE cc_start: 0.9364 (tp) cc_final: 0.9061 (tt) REVERT: B 50 MET cc_start: 0.7702 (ptp) cc_final: 0.6555 (ptp) REVERT: B 54 ASP cc_start: 0.8876 (m-30) cc_final: 0.8139 (t0) REVERT: B 115 ASP cc_start: 0.9206 (OUTLIER) cc_final: 0.8826 (p0) REVERT: B 335 TRP cc_start: 0.7183 (OUTLIER) cc_final: 0.6811 (m-10) REVERT: B 436 TYR cc_start: 0.9133 (t80) cc_final: 0.8865 (t80) REVERT: B 464 LEU cc_start: 0.9368 (mt) cc_final: 0.9121 (mt) REVERT: B 480 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.8021 (mmp) REVERT: B 512 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8637 (mm) REVERT: B 524 ILE cc_start: 0.9367 (tp) cc_final: 0.9057 (tt) REVERT: C 50 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6785 (ptt) REVERT: C 54 ASP cc_start: 0.8787 (m-30) cc_final: 0.8148 (t0) REVERT: C 115 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8792 (p0) REVERT: C 249 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8060 (tp30) REVERT: C 334 MET cc_start: 0.5900 (mmm) cc_final: 0.5611 (mmt) REVERT: C 371 MET cc_start: 0.8630 (ttm) cc_final: 0.8384 (ttp) REVERT: C 435 ILE cc_start: 0.9556 (mt) cc_final: 0.9339 (tt) REVERT: C 436 TYR cc_start: 0.9136 (t80) cc_final: 0.8875 (t80) REVERT: C 464 LEU cc_start: 0.9353 (mt) cc_final: 0.9118 (mt) REVERT: C 512 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8647 (mm) REVERT: C 524 ILE cc_start: 0.9359 (tp) cc_final: 0.9046 (tt) REVERT: D 54 ASP cc_start: 0.8898 (m-30) cc_final: 0.8096 (t0) REVERT: D 57 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8408 (ptm160) REVERT: D 88 GLN cc_start: 0.8757 (pt0) cc_final: 0.8301 (tm-30) REVERT: D 115 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8808 (p0) REVERT: D 289 VAL cc_start: -0.0501 (OUTLIER) cc_final: -0.1300 (m) REVERT: D 309 CYS cc_start: 0.9189 (m) cc_final: 0.8906 (m) REVERT: D 335 TRP cc_start: 0.7745 (OUTLIER) cc_final: 0.6906 (m100) REVERT: D 371 MET cc_start: 0.8598 (ttm) cc_final: 0.8361 (ttp) REVERT: D 436 TYR cc_start: 0.9118 (t80) cc_final: 0.8839 (t80) REVERT: D 464 LEU cc_start: 0.9345 (mt) cc_final: 0.9115 (mt) REVERT: D 512 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8651 (mm) REVERT: D 524 ILE cc_start: 0.9382 (tp) cc_final: 0.9077 (tt) outliers start: 97 outliers final: 56 residues processed: 432 average time/residue: 0.0929 time to fit residues: 64.0067 Evaluate side-chains 430 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 361 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 TRP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 335 TRP Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 115 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 148 optimal weight: 0.0020 chunk 46 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 GLN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.115845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093183 restraints weight = 40527.858| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 4.68 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15956 Z= 0.145 Angle : 0.742 15.467 21696 Z= 0.360 Chirality : 0.046 0.399 2452 Planarity : 0.004 0.037 2692 Dihedral : 5.603 53.057 2200 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.11 % Favored : 93.84 % Rotamer: Outliers : 4.80 % Allowed : 25.00 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.19), residues: 1900 helix: 0.38 (0.15), residues: 1088 sheet: -0.41 (0.40), residues: 196 loop : -2.25 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 44 TYR 0.018 0.001 TYR C 411 PHE 0.023 0.002 PHE D 493 TRP 0.022 0.002 TRP D 335 HIS 0.008 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00308 (15948) covalent geometry : angle 0.74120 (21680) SS BOND : bond 0.00169 ( 8) SS BOND : angle 1.70706 ( 16) hydrogen bonds : bond 0.04585 ( 915) hydrogen bonds : angle 4.99484 ( 2769) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 380 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7622 (ptp) cc_final: 0.7239 (ptp) REVERT: A 54 ASP cc_start: 0.8978 (m-30) cc_final: 0.8088 (t0) REVERT: A 88 GLN cc_start: 0.8721 (pt0) cc_final: 0.8270 (tm-30) REVERT: A 115 ASP cc_start: 0.9163 (p0) cc_final: 0.8790 (p0) REVERT: A 355 TYR cc_start: 0.9142 (m-80) cc_final: 0.8671 (m-80) REVERT: A 371 MET cc_start: 0.8887 (mmm) cc_final: 0.8438 (ttp) REVERT: A 459 MET cc_start: 0.9103 (mmm) cc_final: 0.8892 (mmm) REVERT: A 512 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8662 (mm) REVERT: A 524 ILE cc_start: 0.9393 (tp) cc_final: 0.9099 (tt) REVERT: B 50 MET cc_start: 0.7669 (ptp) cc_final: 0.6526 (ptp) REVERT: B 54 ASP cc_start: 0.8842 (m-30) cc_final: 0.8097 (t0) REVERT: B 88 GLN cc_start: 0.8719 (pt0) cc_final: 0.8266 (tm-30) REVERT: B 115 ASP cc_start: 0.9165 (OUTLIER) cc_final: 0.8790 (p0) REVERT: B 335 TRP cc_start: 0.7202 (OUTLIER) cc_final: 0.6856 (m-10) REVERT: B 464 LEU cc_start: 0.9357 (mt) cc_final: 0.9128 (mt) REVERT: B 512 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8645 (mm) REVERT: B 524 ILE cc_start: 0.9394 (tp) cc_final: 0.9096 (tt) REVERT: C 50 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6597 (ptt) REVERT: C 54 ASP cc_start: 0.8757 (m-30) cc_final: 0.8111 (t0) REVERT: C 88 GLN cc_start: 0.8746 (pt0) cc_final: 0.8290 (tm-30) REVERT: C 115 ASP cc_start: 0.9131 (OUTLIER) cc_final: 0.8750 (p0) REVERT: C 249 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7419 (tm-30) REVERT: C 289 VAL cc_start: -0.1333 (OUTLIER) cc_final: -0.2143 (m) REVERT: C 309 CYS cc_start: 0.9177 (m) cc_final: 0.8857 (m) REVERT: C 334 MET cc_start: 0.5807 (mmm) cc_final: 0.5512 (mmt) REVERT: C 371 MET cc_start: 0.8616 (ttm) cc_final: 0.8389 (ttp) REVERT: C 512 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8663 (mm) REVERT: C 524 ILE cc_start: 0.9379 (tp) cc_final: 0.9075 (tt) REVERT: D 50 MET cc_start: 0.8369 (tpp) cc_final: 0.8149 (tpp) REVERT: D 54 ASP cc_start: 0.8869 (m-30) cc_final: 0.8301 (t0) REVERT: D 88 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: D 115 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8764 (p0) REVERT: D 147 TYR cc_start: 0.8118 (m-80) cc_final: 0.7918 (m-80) REVERT: D 289 VAL cc_start: -0.0658 (OUTLIER) cc_final: -0.1468 (m) REVERT: D 309 CYS cc_start: 0.9164 (m) cc_final: 0.8389 (p) REVERT: D 335 TRP cc_start: 0.7821 (OUTLIER) cc_final: 0.6898 (m100) REVERT: D 371 MET cc_start: 0.8591 (ttm) cc_final: 0.8345 (ttp) REVERT: D 435 ILE cc_start: 0.9561 (mt) cc_final: 0.9350 (tt) REVERT: D 436 TYR cc_start: 0.9107 (t80) cc_final: 0.8855 (t80) REVERT: D 464 LEU cc_start: 0.9330 (mt) cc_final: 0.9120 (mt) REVERT: D 512 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8665 (mm) REVERT: D 524 ILE cc_start: 0.9391 (tp) cc_final: 0.9097 (tt) outliers start: 82 outliers final: 59 residues processed: 419 average time/residue: 0.0940 time to fit residues: 62.8397 Evaluate side-chains 429 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 357 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 TRP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 335 TRP Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 89 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 137 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 chunk 40 optimal weight: 0.0070 chunk 22 optimal weight: 3.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.116693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.094127 restraints weight = 40545.521| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 4.69 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15956 Z= 0.142 Angle : 0.764 14.796 21696 Z= 0.365 Chirality : 0.046 0.441 2452 Planarity : 0.004 0.037 2692 Dihedral : 5.552 51.536 2200 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.84 % Favored : 94.11 % Rotamer: Outliers : 4.86 % Allowed : 25.47 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.19), residues: 1900 helix: 0.39 (0.15), residues: 1088 sheet: -0.22 (0.40), residues: 196 loop : -2.21 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 338 TYR 0.026 0.001 TYR B 436 PHE 0.021 0.002 PHE B 493 TRP 0.023 0.002 TRP D 444 HIS 0.005 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00302 (15948) covalent geometry : angle 0.76333 (21680) SS BOND : bond 0.00166 ( 8) SS BOND : angle 1.63419 ( 16) hydrogen bonds : bond 0.04557 ( 915) hydrogen bonds : angle 4.96976 ( 2769) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 392 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7537 (ptp) cc_final: 0.7187 (ptp) REVERT: A 54 ASP cc_start: 0.8956 (m-30) cc_final: 0.8031 (t0) REVERT: A 88 GLN cc_start: 0.8645 (pt0) cc_final: 0.8258 (tm-30) REVERT: A 115 ASP cc_start: 0.9157 (p0) cc_final: 0.8798 (p0) REVERT: A 355 TYR cc_start: 0.9119 (m-80) cc_final: 0.8652 (m-80) REVERT: A 371 MET cc_start: 0.8899 (mmm) cc_final: 0.8425 (ttp) REVERT: A 459 MET cc_start: 0.9109 (mmm) cc_final: 0.8907 (mmm) REVERT: A 512 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8640 (mm) REVERT: A 524 ILE cc_start: 0.9354 (tp) cc_final: 0.9059 (tt) REVERT: B 50 MET cc_start: 0.7720 (ptp) cc_final: 0.6619 (ptt) REVERT: B 54 ASP cc_start: 0.8849 (m-30) cc_final: 0.8039 (t0) REVERT: B 88 GLN cc_start: 0.8714 (pt0) cc_final: 0.8465 (tm-30) REVERT: B 115 ASP cc_start: 0.9161 (OUTLIER) cc_final: 0.8795 (p0) REVERT: B 147 TYR cc_start: 0.8127 (m-80) cc_final: 0.7911 (m-80) REVERT: B 309 CYS cc_start: 0.9138 (m) cc_final: 0.8827 (m) REVERT: B 335 TRP cc_start: 0.7108 (OUTLIER) cc_final: 0.6808 (m-10) REVERT: B 371 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8675 (ppp) REVERT: B 512 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8633 (mm) REVERT: B 524 ILE cc_start: 0.9391 (tp) cc_final: 0.9087 (tt) REVERT: C 50 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6628 (ptt) REVERT: C 54 ASP cc_start: 0.8732 (m-30) cc_final: 0.8113 (t0) REVERT: C 88 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8309 (tm-30) REVERT: C 115 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8737 (p0) REVERT: C 249 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7379 (tm-30) REVERT: C 289 VAL cc_start: -0.1446 (OUTLIER) cc_final: -0.1860 (t) REVERT: C 309 CYS cc_start: 0.9175 (m) cc_final: 0.8848 (m) REVERT: C 334 MET cc_start: 0.5770 (mmm) cc_final: 0.5494 (mmt) REVERT: C 512 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8625 (mm) REVERT: C 524 ILE cc_start: 0.9370 (tp) cc_final: 0.9060 (tt) REVERT: D 50 MET cc_start: 0.8291 (tpp) cc_final: 0.8083 (tpp) REVERT: D 54 ASP cc_start: 0.8824 (m-30) cc_final: 0.8293 (t0) REVERT: D 88 GLN cc_start: 0.8659 (pt0) cc_final: 0.8443 (tm-30) REVERT: D 115 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8770 (p0) REVERT: D 147 TYR cc_start: 0.8120 (m-80) cc_final: 0.7904 (m-80) REVERT: D 289 VAL cc_start: -0.0507 (OUTLIER) cc_final: -0.0748 (t) REVERT: D 309 CYS cc_start: 0.9170 (m) cc_final: 0.8401 (p) REVERT: D 335 TRP cc_start: 0.7830 (OUTLIER) cc_final: 0.6945 (m100) REVERT: D 371 MET cc_start: 0.8553 (ttm) cc_final: 0.8301 (ttp) REVERT: D 436 TYR cc_start: 0.9083 (t80) cc_final: 0.8881 (t80) REVERT: D 512 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8680 (mm) REVERT: D 524 ILE cc_start: 0.9385 (tp) cc_final: 0.9083 (tt) outliers start: 83 outliers final: 53 residues processed: 430 average time/residue: 0.0943 time to fit residues: 65.8149 Evaluate side-chains 442 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 375 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 TRP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 335 TRP Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 33 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.114068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.091723 restraints weight = 40923.606| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 4.60 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15956 Z= 0.207 Angle : 0.799 13.704 21696 Z= 0.387 Chirality : 0.048 0.468 2452 Planarity : 0.004 0.038 2692 Dihedral : 5.476 53.788 2198 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 5.04 % Allowed : 26.00 % Favored : 68.97 % 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: -0.81 (0.20), residues: 1900 helix: 0.36 (0.15), residues: 1088 sheet: -0.42 (0.41), residues: 208 loop : -2.15 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 338 TYR 0.023 0.002 TYR B 411 PHE 0.020 0.002 PHE C 501 TRP 0.026 0.002 TRP D 444 HIS 0.005 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00453 (15948) covalent geometry : angle 0.79831 (21680) SS BOND : bond 0.00128 ( 8) SS BOND : angle 1.69863 ( 16) hydrogen bonds : bond 0.04578 ( 915) hydrogen bonds : angle 5.08273 ( 2769) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 361 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7602 (ptp) cc_final: 0.7381 (ptp) REVERT: A 54 ASP cc_start: 0.8985 (m-30) cc_final: 0.8162 (t0) REVERT: A 88 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8459 (tm-30) REVERT: A 355 TYR cc_start: 0.9166 (m-80) cc_final: 0.8664 (m-80) REVERT: A 371 MET cc_start: 0.8963 (mmm) cc_final: 0.8476 (ttp) REVERT: A 459 MET cc_start: 0.9167 (mmm) cc_final: 0.8926 (mmm) REVERT: A 512 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8719 (mm) REVERT: A 524 ILE cc_start: 0.9399 (tp) cc_final: 0.9095 (tt) REVERT: B 50 MET cc_start: 0.7763 (ptp) cc_final: 0.6653 (ptp) REVERT: B 54 ASP cc_start: 0.8866 (m-30) cc_final: 0.8128 (t0) REVERT: B 88 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8390 (tm-30) REVERT: B 115 ASP cc_start: 0.9215 (OUTLIER) cc_final: 0.8842 (p0) REVERT: B 335 TRP cc_start: 0.7155 (OUTLIER) cc_final: 0.6870 (m-10) REVERT: B 371 MET cc_start: 0.8888 (tmm) cc_final: 0.8644 (ppp) REVERT: B 393 SER cc_start: 0.9669 (OUTLIER) cc_final: 0.9322 (t) REVERT: B 434 VAL cc_start: 0.9620 (t) cc_final: 0.9407 (p) REVERT: B 512 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8713 (mm) REVERT: B 524 ILE cc_start: 0.9403 (tp) cc_final: 0.9096 (tt) REVERT: C 50 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6816 (ptt) REVERT: C 54 ASP cc_start: 0.8774 (m-30) cc_final: 0.7825 (t0) REVERT: C 88 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8296 (tm-30) REVERT: C 115 ASP cc_start: 0.9172 (OUTLIER) cc_final: 0.8792 (p0) REVERT: C 249 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7245 (tm-30) REVERT: C 512 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8695 (mm) REVERT: C 524 ILE cc_start: 0.9386 (tp) cc_final: 0.9077 (tt) REVERT: D 54 ASP cc_start: 0.8804 (m-30) cc_final: 0.8392 (t0) REVERT: D 88 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8512 (tm-30) REVERT: D 115 ASP cc_start: 0.9183 (OUTLIER) cc_final: 0.8766 (p0) REVERT: D 309 CYS cc_start: 0.9195 (m) cc_final: 0.8846 (m) REVERT: D 335 TRP cc_start: 0.7906 (OUTLIER) cc_final: 0.6952 (m100) REVERT: D 371 MET cc_start: 0.8651 (ttm) cc_final: 0.8404 (ttp) REVERT: D 436 TYR cc_start: 0.9137 (t80) cc_final: 0.8897 (t80) REVERT: D 512 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8711 (mm) REVERT: D 524 ILE cc_start: 0.9398 (tp) cc_final: 0.9090 (tt) outliers start: 86 outliers final: 67 residues processed: 404 average time/residue: 0.0958 time to fit residues: 62.2770 Evaluate side-chains 424 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 342 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 TRP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 335 TRP Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 134 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 139 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS A 409 HIS ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 HIS ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.115606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.093169 restraints weight = 40666.074| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.66 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15956 Z= 0.154 Angle : 0.788 13.540 21696 Z= 0.377 Chirality : 0.050 0.536 2452 Planarity : 0.004 0.038 2692 Dihedral : 5.417 52.467 2198 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.11 % Favored : 93.84 % Rotamer: Outliers : 4.63 % Allowed : 27.17 % Favored : 68.21 % 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: -0.75 (0.20), residues: 1900 helix: 0.39 (0.15), residues: 1088 sheet: -0.24 (0.41), residues: 204 loop : -2.18 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 338 TYR 0.019 0.001 TYR A 411 PHE 0.030 0.002 PHE D 501 TRP 0.025 0.002 TRP D 444 HIS 0.006 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00337 (15948) covalent geometry : angle 0.78734 (21680) SS BOND : bond 0.00155 ( 8) SS BOND : angle 1.66197 ( 16) hydrogen bonds : bond 0.04558 ( 915) hydrogen bonds : angle 5.04018 ( 2769) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 369 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8976 (m-30) cc_final: 0.8107 (t0) REVERT: A 88 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8488 (tm-30) REVERT: A 249 GLU cc_start: 0.7841 (tp30) cc_final: 0.7554 (mp0) REVERT: A 355 TYR cc_start: 0.9119 (m-80) cc_final: 0.8636 (m-80) REVERT: A 371 MET cc_start: 0.8946 (mmm) cc_final: 0.8465 (ttp) REVERT: A 455 ARG cc_start: 0.8738 (mmt-90) cc_final: 0.8464 (mmt180) REVERT: A 459 MET cc_start: 0.9142 (mmm) cc_final: 0.8911 (mmm) REVERT: A 512 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8705 (mm) REVERT: A 524 ILE cc_start: 0.9397 (tp) cc_final: 0.9076 (tt) REVERT: B 50 MET cc_start: 0.7750 (ptp) cc_final: 0.6637 (ptt) REVERT: B 54 ASP cc_start: 0.8852 (m-30) cc_final: 0.8060 (t0) REVERT: B 88 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8387 (tm-30) REVERT: B 115 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8819 (p0) REVERT: B 309 CYS cc_start: 0.9160 (m) cc_final: 0.8841 (m) REVERT: B 335 TRP cc_start: 0.7122 (OUTLIER) cc_final: 0.6833 (m-10) REVERT: B 393 SER cc_start: 0.9659 (OUTLIER) cc_final: 0.9309 (t) REVERT: B 434 VAL cc_start: 0.9642 (t) cc_final: 0.9420 (p) REVERT: B 512 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8681 (mm) REVERT: B 524 ILE cc_start: 0.9403 (tp) cc_final: 0.9089 (tt) REVERT: C 50 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.6685 (ptt) REVERT: C 54 ASP cc_start: 0.8756 (m-30) cc_final: 0.8118 (t0) REVERT: C 88 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: C 115 ASP cc_start: 0.9167 (OUTLIER) cc_final: 0.8790 (p0) REVERT: C 309 CYS cc_start: 0.9162 (m) cc_final: 0.8793 (m) REVERT: C 512 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8659 (mm) REVERT: C 524 ILE cc_start: 0.9391 (tp) cc_final: 0.9063 (tt) REVERT: D 54 ASP cc_start: 0.8778 (m-30) cc_final: 0.8251 (t0) REVERT: D 88 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8486 (tm-30) REVERT: D 115 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8750 (p0) REVERT: D 335 TRP cc_start: 0.7904 (OUTLIER) cc_final: 0.6999 (m100) REVERT: D 371 MET cc_start: 0.8621 (ttm) cc_final: 0.8394 (ttp) REVERT: D 455 ARG cc_start: 0.8753 (mmt-90) cc_final: 0.8526 (mmt180) REVERT: D 512 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8696 (mm) REVERT: D 524 ILE cc_start: 0.9391 (tp) cc_final: 0.9071 (tt) outliers start: 79 outliers final: 62 residues processed: 404 average time/residue: 0.0931 time to fit residues: 60.4076 Evaluate side-chains 437 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 360 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 TRP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 335 TRP Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 512 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 101 optimal weight: 7.9990 chunk 36 optimal weight: 0.2980 chunk 60 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 0.2980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** B 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.116620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.094352 restraints weight = 40638.446| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 4.67 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15956 Z= 0.147 Angle : 0.787 13.312 21696 Z= 0.376 Chirality : 0.049 0.462 2452 Planarity : 0.004 0.039 2692 Dihedral : 5.335 54.329 2198 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 94.00 % Rotamer: Outliers : 4.63 % Allowed : 27.17 % Favored : 68.21 % 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: -0.74 (0.20), residues: 1900 helix: 0.41 (0.15), residues: 1088 sheet: -0.30 (0.41), residues: 208 loop : -2.16 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 338 TYR 0.020 0.001 TYR A 411 PHE 0.024 0.002 PHE D 501 TRP 0.023 0.002 TRP D 444 HIS 0.004 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00320 (15948) covalent geometry : angle 0.78570 (21680) SS BOND : bond 0.00194 ( 8) SS BOND : angle 1.63567 ( 16) hydrogen bonds : bond 0.04526 ( 915) hydrogen bonds : angle 5.02604 ( 2769) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2533.49 seconds wall clock time: 44 minutes 43.20 seconds (2683.20 seconds total)