Starting phenix.real_space_refine on Mon Apr 6 18:33:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yid_33855/04_2026/7yid_33855.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yid_33855/04_2026/7yid_33855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yid_33855/04_2026/7yid_33855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yid_33855/04_2026/7yid_33855.map" model { file = "/net/cci-nas-00/data/ceres_data/7yid_33855/04_2026/7yid_33855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yid_33855/04_2026/7yid_33855.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 6 8.98 5 S 128 5.16 5 C 13796 2.51 5 N 3544 2.21 5 O 3852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21326 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "B" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "C" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "D" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' K': 6} Classifications: {'undetermined': 6, 'water': 2} Link IDs: {None: 7} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.52, per 1000 atoms: 0.21 Number of scatterers: 21326 At special positions: 0 Unit cell: (157.065, 157.065, 130.746, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 6 19.00 S 128 16.00 O 3852 8.00 N 3544 7.00 C 13796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 940.0 milliseconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 20 sheets defined 54.8% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 15 through 24 removed outlier: 4.039A pdb=" N SER A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.636A pdb=" N ILE A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.317A pdb=" N ARG A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.540A pdb=" N THR A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 248 through 265 removed outlier: 3.942A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 280 through 293 removed outlier: 3.685A pdb=" N ARG A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.870A pdb=" N VAL A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 345 through 375 Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 414 through 429 removed outlier: 3.578A pdb=" N TYR A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 495 removed outlier: 3.519A pdb=" N MET A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 458 " --> pdb=" O MET A 454 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN A 477 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 517 Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.674A pdb=" N VAL A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 527 " --> pdb=" O LYS A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 541 removed outlier: 3.980A pdb=" N ASP A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.821A pdb=" N LYS A 619 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 620 " --> pdb=" O PHE A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 616 through 620' Processing helix chain 'A' and resid 643 through 653 Processing helix chain 'A' and resid 654 through 664 Processing helix chain 'A' and resid 678 through 692 removed outlier: 3.664A pdb=" N GLU A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 24 removed outlier: 4.039A pdb=" N SER B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.636A pdb=" N ILE B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 156 removed outlier: 4.318A pdb=" N ARG B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 153 " --> pdb=" O PHE B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.540A pdb=" N THR B 215 " --> pdb=" O CYS B 211 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.942A pdb=" N SER B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 280 through 293 removed outlier: 3.685A pdb=" N ARG B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET B 286 " --> pdb=" O LYS B 282 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 300 Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.870A pdb=" N VAL B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 345 through 375 Processing helix chain 'B' and resid 387 through 397 Processing helix chain 'B' and resid 414 through 429 removed outlier: 3.578A pdb=" N TYR B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 495 removed outlier: 3.519A pdb=" N MET B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 458 " --> pdb=" O MET B 454 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN B 477 " --> pdb=" O GLN B 473 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 484 " --> pdb=" O ARG B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 517 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.674A pdb=" N VAL B 524 " --> pdb=" O ASP B 520 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE B 527 " --> pdb=" O LYS B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 541 removed outlier: 3.980A pdb=" N ASP B 535 " --> pdb=" O ASP B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.821A pdb=" N LYS B 619 " --> pdb=" O ILE B 616 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 620 " --> pdb=" O PHE B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 620' Processing helix chain 'B' and resid 643 through 653 Processing helix chain 'B' and resid 654 through 664 Processing helix chain 'B' and resid 678 through 692 removed outlier: 3.664A pdb=" N GLU B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 688 " --> pdb=" O LYS B 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 24 removed outlier: 4.039A pdb=" N SER C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.636A pdb=" N ILE C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU C 79 " --> pdb=" O LYS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 156 removed outlier: 4.317A pdb=" N ARG C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 153 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 186 Processing helix chain 'C' and resid 211 through 238 removed outlier: 3.540A pdb=" N THR C 215 " --> pdb=" O CYS C 211 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 248 through 265 removed outlier: 3.942A pdb=" N SER C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 280 through 293 removed outlier: 3.685A pdb=" N ARG C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 327 through 329 No H-bonds generated for 'chain 'C' and resid 327 through 329' Processing helix chain 'C' and resid 330 through 338 removed outlier: 3.870A pdb=" N VAL C 334 " --> pdb=" O ARG C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 345 through 375 Processing helix chain 'C' and resid 387 through 397 Processing helix chain 'C' and resid 414 through 429 removed outlier: 3.578A pdb=" N TYR C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 495 removed outlier: 3.518A pdb=" N MET C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA C 451 " --> pdb=" O MET C 447 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 458 " --> pdb=" O MET C 454 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET C 474 " --> pdb=" O ILE C 470 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN C 477 " --> pdb=" O GLN C 473 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C 484 " --> pdb=" O ARG C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 517 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.674A pdb=" N VAL C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE C 527 " --> pdb=" O LYS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 541 removed outlier: 3.980A pdb=" N ASP C 535 " --> pdb=" O ASP C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.821A pdb=" N LYS C 619 " --> pdb=" O ILE C 616 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 620 " --> pdb=" O PHE C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 643 through 653 Processing helix chain 'C' and resid 654 through 664 Processing helix chain 'C' and resid 678 through 692 removed outlier: 3.664A pdb=" N GLU C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C 688 " --> pdb=" O LYS C 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 24 removed outlier: 4.039A pdb=" N SER D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 74 through 87 removed outlier: 3.636A pdb=" N ILE D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.318A pdb=" N ARG D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR D 153 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 186 Processing helix chain 'D' and resid 211 through 238 removed outlier: 3.540A pdb=" N THR D 215 " --> pdb=" O CYS D 211 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 248 through 265 removed outlier: 3.942A pdb=" N SER D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.685A pdb=" N ARG D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N MET D 286 " --> pdb=" O LYS D 282 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'D' and resid 321 through 326 Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 330 through 338 removed outlier: 3.870A pdb=" N VAL D 334 " --> pdb=" O ARG D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 345 through 375 Processing helix chain 'D' and resid 387 through 397 Processing helix chain 'D' and resid 414 through 429 removed outlier: 3.578A pdb=" N TYR D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 495 removed outlier: 3.519A pdb=" N MET D 447 " --> pdb=" O ASP D 443 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 458 " --> pdb=" O MET D 454 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET D 474 " --> pdb=" O ILE D 470 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN D 477 " --> pdb=" O GLN D 473 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 517 Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.674A pdb=" N VAL D 524 " --> pdb=" O ASP D 520 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 527 " --> pdb=" O LYS D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 541 removed outlier: 3.980A pdb=" N ASP D 535 " --> pdb=" O ASP D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 555 through 566 Processing helix chain 'D' and resid 616 through 620 removed outlier: 3.821A pdb=" N LYS D 619 " --> pdb=" O ILE D 616 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 620 " --> pdb=" O PHE D 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 616 through 620' Processing helix chain 'D' and resid 643 through 653 Processing helix chain 'D' and resid 654 through 664 Processing helix chain 'D' and resid 678 through 692 removed outlier: 3.664A pdb=" N GLU D 687 " --> pdb=" O LYS D 683 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU D 688 " --> pdb=" O LYS D 684 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.646A pdb=" N LEU A 123 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 568 through 570 removed outlier: 6.514A pdb=" N ASP A 637 " --> pdb=" O VAL A 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS A 668 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 614 " --> pdb=" O CYS A 668 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 576 through 578 removed outlier: 6.870A pdb=" N VAL A 630 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A 595 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE A 606 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 597 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 583 through 584 removed outlier: 3.543A pdb=" N VAL A 584 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA A 624 " --> pdb=" O VAL A 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 32 removed outlier: 4.646A pdb=" N LEU B 123 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 98 Processing sheet with id=AA8, first strand: chain 'B' and resid 568 through 570 removed outlier: 6.514A pdb=" N ASP B 637 " --> pdb=" O VAL B 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS B 668 " --> pdb=" O VAL B 612 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 614 " --> pdb=" O CYS B 668 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 576 through 578 removed outlier: 6.870A pdb=" N VAL B 630 " --> pdb=" O ILE B 577 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU B 595 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE B 606 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 597 " --> pdb=" O VAL B 604 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 583 through 584 removed outlier: 3.543A pdb=" N VAL B 584 " --> pdb=" O ALA B 624 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA B 624 " --> pdb=" O VAL B 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 31 through 32 removed outlier: 4.646A pdb=" N LEU C 123 " --> pdb=" O ILE C 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 93 through 98 Processing sheet with id=AB4, first strand: chain 'C' and resid 568 through 570 removed outlier: 6.514A pdb=" N ASP C 637 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS C 668 " --> pdb=" O VAL C 612 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 614 " --> pdb=" O CYS C 668 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 576 through 578 removed outlier: 6.870A pdb=" N VAL C 630 " --> pdb=" O ILE C 577 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU C 595 " --> pdb=" O ILE C 606 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE C 606 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 597 " --> pdb=" O VAL C 604 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 583 through 584 removed outlier: 3.543A pdb=" N VAL C 584 " --> pdb=" O ALA C 624 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA C 624 " --> pdb=" O VAL C 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 31 through 32 removed outlier: 4.647A pdb=" N LEU D 123 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 93 through 98 Processing sheet with id=AB9, first strand: chain 'D' and resid 568 through 570 removed outlier: 6.514A pdb=" N ASP D 637 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS D 668 " --> pdb=" O VAL D 612 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 614 " --> pdb=" O CYS D 668 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 576 through 578 removed outlier: 6.870A pdb=" N VAL D 630 " --> pdb=" O ILE D 577 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU D 595 " --> pdb=" O ILE D 606 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE D 606 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL D 597 " --> pdb=" O VAL D 604 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 583 through 584 removed outlier: 3.543A pdb=" N VAL D 584 " --> pdb=" O ALA D 624 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA D 624 " --> pdb=" O VAL D 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 1004 hydrogen bonds defined for protein. 2916 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: 2.90 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6668 1.34 - 1.46: 3354 1.46 - 1.57: 11590 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 21804 Sorted by residual: bond pdb=" N GLN B 567 " pdb=" CA GLN B 567 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" N GLN C 567 " pdb=" CA GLN C 567 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" N GLN D 567 " pdb=" CA GLN D 567 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" N GLN A 567 " pdb=" CA GLN A 567 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 bond pdb=" C MET D 474 " pdb=" O MET D 474 " ideal model delta sigma weight residual 1.236 1.250 -0.015 1.28e-02 6.10e+03 1.32e+00 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 28857 1.46 - 2.93: 587 2.93 - 4.39: 92 4.39 - 5.86: 36 5.86 - 7.32: 12 Bond angle restraints: 29584 Sorted by residual: angle pdb=" N ASP B 531 " pdb=" CA ASP B 531 " pdb=" C ASP B 531 " ideal model delta sigma weight residual 113.18 106.81 6.37 1.33e+00 5.65e-01 2.30e+01 angle pdb=" N ASP D 531 " pdb=" CA ASP D 531 " pdb=" C ASP D 531 " ideal model delta sigma weight residual 113.18 106.81 6.37 1.33e+00 5.65e-01 2.30e+01 angle pdb=" N ASP A 531 " pdb=" CA ASP A 531 " pdb=" C ASP A 531 " ideal model delta sigma weight residual 113.18 106.81 6.37 1.33e+00 5.65e-01 2.30e+01 angle pdb=" N ASP C 531 " pdb=" CA ASP C 531 " pdb=" C ASP C 531 " ideal model delta sigma weight residual 113.18 106.81 6.37 1.33e+00 5.65e-01 2.30e+01 angle pdb=" C PHE D 566 " pdb=" N GLN D 567 " pdb=" CA GLN D 567 " ideal model delta sigma weight residual 121.54 128.86 -7.32 1.91e+00 2.74e-01 1.47e+01 ... (remaining 29579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 11596 17.67 - 35.34: 1132 35.34 - 53.01: 168 53.01 - 70.68: 24 70.68 - 88.35: 12 Dihedral angle restraints: 12932 sinusoidal: 5144 harmonic: 7788 Sorted by residual: dihedral pdb=" CA PRO D 529 " pdb=" C PRO D 529 " pdb=" N LYS D 530 " pdb=" CA LYS D 530 " ideal model delta harmonic sigma weight residual -180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO B 529 " pdb=" C PRO B 529 " pdb=" N LYS B 530 " pdb=" CA LYS B 530 " ideal model delta harmonic sigma weight residual -180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO C 529 " pdb=" C PRO C 529 " pdb=" N LYS C 530 " pdb=" CA LYS C 530 " ideal model delta harmonic sigma weight residual 180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 12929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1962 0.030 - 0.060: 953 0.060 - 0.091: 361 0.091 - 0.121: 112 0.121 - 0.151: 16 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CA ILE C 438 " pdb=" N ILE C 438 " pdb=" C ILE C 438 " pdb=" CB ILE C 438 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA MET B 286 " pdb=" N MET B 286 " pdb=" C MET B 286 " pdb=" CB MET B 286 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA MET A 286 " pdb=" N MET A 286 " pdb=" C MET A 286 " pdb=" CB MET A 286 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 3401 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 460 " 0.020 2.00e-02 2.50e+03 1.38e-02 3.81e+00 pdb=" CG TYR B 460 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 460 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 460 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 460 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 460 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 460 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 460 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 460 " 0.020 2.00e-02 2.50e+03 1.37e-02 3.76e+00 pdb=" CG TYR A 460 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 460 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 460 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 460 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 460 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 460 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 460 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 460 " 0.020 2.00e-02 2.50e+03 1.35e-02 3.65e+00 pdb=" CG TYR C 460 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR C 460 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 460 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 460 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 460 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 460 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 460 " 0.004 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 5406 2.80 - 3.39: 23084 3.39 - 3.97: 37651 3.97 - 4.56: 52724 4.56 - 5.14: 79781 Nonbonded interactions: 198646 Sorted by model distance: nonbonded pdb=" O LYS A 144 " pdb=" OG1 THR A 147 " model vdw 2.216 3.040 nonbonded pdb=" O LYS C 144 " pdb=" OG1 THR C 147 " model vdw 2.216 3.040 nonbonded pdb=" O LYS B 144 " pdb=" OG1 THR B 147 " model vdw 2.216 3.040 nonbonded pdb=" O LYS D 144 " pdb=" OG1 THR D 147 " model vdw 2.216 3.040 nonbonded pdb=" OE2 GLU A 596 " pdb=" OH TYR C 195 " model vdw 2.257 3.040 ... (remaining 198641 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 692) 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=1.00 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: 4.020 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.230 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.003 0.037 21804 Z= 0.129 Angle : 0.558 7.324 29584 Z= 0.312 Chirality : 0.041 0.151 3404 Planarity : 0.003 0.040 3668 Dihedral : 13.957 88.352 7884 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.57 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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 (0.17), residues: 2616 helix: 1.00 (0.15), residues: 1276 sheet: -1.61 (0.31), residues: 260 loop : -2.09 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 677 TYR 0.033 0.001 TYR B 460 PHE 0.018 0.002 PHE A 566 TRP 0.007 0.001 TRP B 367 HIS 0.003 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00271 (21804) covalent geometry : angle 0.55811 (29584) hydrogen bonds : bond 0.15413 ( 1004) hydrogen bonds : angle 5.31572 ( 2916) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.734 Fit side-chains REVERT: A 601 ASP cc_start: 0.6927 (t0) cc_final: 0.6485 (t0) REVERT: B 601 ASP cc_start: 0.6939 (t0) cc_final: 0.6496 (t0) REVERT: C 601 ASP cc_start: 0.6918 (t0) cc_final: 0.6480 (t0) REVERT: D 601 ASP cc_start: 0.6925 (t0) cc_final: 0.6485 (t0) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1341 time to fit residues: 52.4096 Evaluate side-chains 204 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.0030 chunk 111 optimal weight: 2.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 403 ASN B 267 HIS B 403 ASN C 267 HIS C 403 ASN D 267 HIS D 403 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.184490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.163476 restraints weight = 22176.941| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.68 r_work: 0.3266 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21804 Z= 0.144 Angle : 0.536 8.596 29584 Z= 0.290 Chirality : 0.042 0.150 3404 Planarity : 0.003 0.036 3668 Dihedral : 4.281 24.647 2864 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.03 % Favored : 92.66 % Rotamer: Outliers : 0.17 % Allowed : 8.57 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.17), residues: 2616 helix: 0.95 (0.15), residues: 1344 sheet: -1.66 (0.31), residues: 260 loop : -2.38 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.029 0.001 TYR B 460 PHE 0.013 0.002 PHE C 471 TRP 0.007 0.001 TRP B 367 HIS 0.005 0.001 HIS D 570 Details of bonding type rmsd covalent geometry : bond 0.00329 (21804) covalent geometry : angle 0.53605 (29584) hydrogen bonds : bond 0.05679 ( 1004) hydrogen bonds : angle 4.26703 ( 2916) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 0.542 Fit side-chains REVERT: A 290 LYS cc_start: 0.8365 (ptpt) cc_final: 0.8145 (ptpt) REVERT: A 373 TYR cc_start: 0.8313 (t80) cc_final: 0.8087 (t80) REVERT: A 484 MET cc_start: 0.8749 (tmm) cc_final: 0.8526 (tmm) REVERT: A 601 ASP cc_start: 0.7827 (t0) cc_final: 0.7189 (t0) REVERT: B 290 LYS cc_start: 0.8384 (ptpt) cc_final: 0.8168 (ptpt) REVERT: B 373 TYR cc_start: 0.8320 (t80) cc_final: 0.8095 (t80) REVERT: B 484 MET cc_start: 0.8751 (tmm) cc_final: 0.8531 (tmm) REVERT: B 601 ASP cc_start: 0.7804 (t0) cc_final: 0.7165 (t0) REVERT: C 290 LYS cc_start: 0.8378 (ptpt) cc_final: 0.8159 (ptpt) REVERT: C 373 TYR cc_start: 0.8311 (t80) cc_final: 0.8083 (t80) REVERT: C 484 MET cc_start: 0.8744 (tmm) cc_final: 0.8515 (tmm) REVERT: C 601 ASP cc_start: 0.7813 (t0) cc_final: 0.7171 (t0) REVERT: D 290 LYS cc_start: 0.8388 (ptpt) cc_final: 0.8171 (ptpt) REVERT: D 373 TYR cc_start: 0.8307 (t80) cc_final: 0.8079 (t80) REVERT: D 484 MET cc_start: 0.8741 (tmm) cc_final: 0.8513 (tmm) REVERT: D 601 ASP cc_start: 0.7827 (t0) cc_final: 0.7186 (t0) outliers start: 4 outliers final: 4 residues processed: 192 average time/residue: 0.1358 time to fit residues: 42.2173 Evaluate side-chains 196 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 394 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 30 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 146 optimal weight: 40.0000 chunk 190 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.177896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.144274 restraints weight = 22090.193| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.73 r_work: 0.3040 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21804 Z= 0.257 Angle : 0.620 5.631 29584 Z= 0.339 Chirality : 0.046 0.151 3404 Planarity : 0.003 0.038 3668 Dihedral : 4.625 27.537 2864 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.10 % Favored : 91.59 % Rotamer: Outliers : 1.34 % Allowed : 11.60 % Favored : 87.06 % 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: -1.21 (0.16), residues: 2616 helix: 0.63 (0.14), residues: 1352 sheet: -2.51 (0.37), residues: 148 loop : -2.43 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 22 TYR 0.034 0.002 TYR C 460 PHE 0.022 0.002 PHE C 660 TRP 0.010 0.001 TRP A 388 HIS 0.007 0.001 HIS D 570 Details of bonding type rmsd covalent geometry : bond 0.00638 (21804) covalent geometry : angle 0.61997 (29584) hydrogen bonds : bond 0.07052 ( 1004) hydrogen bonds : angle 4.39032 ( 2916) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.806 Fit side-chains REVERT: A 119 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8096 (mm-30) REVERT: A 286 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7267 (pmm) REVERT: A 290 LYS cc_start: 0.8286 (ptpt) cc_final: 0.8062 (ptpt) REVERT: A 373 TYR cc_start: 0.8249 (t80) cc_final: 0.7980 (t80) REVERT: A 601 ASP cc_start: 0.7678 (t0) cc_final: 0.7081 (t0) REVERT: B 119 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8095 (mm-30) REVERT: B 286 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7269 (pmm) REVERT: B 290 LYS cc_start: 0.8293 (ptpt) cc_final: 0.8068 (ptpt) REVERT: B 373 TYR cc_start: 0.8247 (t80) cc_final: 0.7980 (t80) REVERT: B 601 ASP cc_start: 0.7695 (t0) cc_final: 0.7095 (t0) REVERT: C 119 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8087 (mm-30) REVERT: C 286 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7276 (pmm) REVERT: C 290 LYS cc_start: 0.8275 (ptpt) cc_final: 0.8051 (ptpt) REVERT: C 373 TYR cc_start: 0.8250 (t80) cc_final: 0.7981 (t80) REVERT: C 601 ASP cc_start: 0.7658 (t0) cc_final: 0.7066 (t0) REVERT: D 119 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8097 (mm-30) REVERT: D 286 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7271 (pmm) REVERT: D 290 LYS cc_start: 0.8298 (ptpt) cc_final: 0.8073 (ptpt) REVERT: D 373 TYR cc_start: 0.8251 (t80) cc_final: 0.7982 (t80) REVERT: D 601 ASP cc_start: 0.7645 (t0) cc_final: 0.7057 (t0) outliers start: 32 outliers final: 12 residues processed: 220 average time/residue: 0.1321 time to fit residues: 47.9415 Evaluate side-chains 212 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 251 optimal weight: 0.9990 chunk 54 optimal weight: 0.0870 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 39 optimal weight: 0.6980 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.180946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.147995 restraints weight = 21976.316| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.81 r_work: 0.3095 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21804 Z= 0.140 Angle : 0.511 6.208 29584 Z= 0.279 Chirality : 0.041 0.140 3404 Planarity : 0.003 0.033 3668 Dihedral : 4.353 23.865 2864 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.46 % Favored : 93.23 % Rotamer: Outliers : 1.51 % Allowed : 12.61 % Favored : 85.88 % 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: -0.86 (0.17), residues: 2616 helix: 1.00 (0.15), residues: 1340 sheet: -2.31 (0.40), residues: 148 loop : -2.37 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 336 TYR 0.018 0.001 TYR A 460 PHE 0.013 0.002 PHE D 471 TRP 0.009 0.001 TRP A 367 HIS 0.005 0.001 HIS D 570 Details of bonding type rmsd covalent geometry : bond 0.00320 (21804) covalent geometry : angle 0.51101 (29584) hydrogen bonds : bond 0.05695 ( 1004) hydrogen bonds : angle 4.00370 ( 2916) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.785 Fit side-chains REVERT: A 119 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8085 (mm-30) REVERT: A 286 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7042 (pmm) REVERT: A 373 TYR cc_start: 0.8250 (t80) cc_final: 0.7995 (t80) REVERT: A 601 ASP cc_start: 0.7673 (t0) cc_final: 0.7064 (t0) REVERT: A 677 ARG cc_start: 0.8325 (ttp80) cc_final: 0.8033 (ttp80) REVERT: B 119 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8107 (mm-30) REVERT: B 286 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7050 (pmm) REVERT: B 373 TYR cc_start: 0.8246 (t80) cc_final: 0.7990 (t80) REVERT: B 601 ASP cc_start: 0.7715 (t0) cc_final: 0.7099 (t0) REVERT: B 677 ARG cc_start: 0.8310 (ttp80) cc_final: 0.8011 (ttp80) REVERT: C 119 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8104 (mm-30) REVERT: C 286 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7060 (pmm) REVERT: C 373 TYR cc_start: 0.8255 (t80) cc_final: 0.7999 (t80) REVERT: C 601 ASP cc_start: 0.7682 (t0) cc_final: 0.7066 (t0) REVERT: C 677 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8049 (ttp80) REVERT: D 119 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8113 (mm-30) REVERT: D 286 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7076 (pmm) REVERT: D 373 TYR cc_start: 0.8252 (t80) cc_final: 0.7996 (t80) REVERT: D 601 ASP cc_start: 0.7689 (t0) cc_final: 0.7077 (t0) REVERT: D 677 ARG cc_start: 0.8322 (ttp80) cc_final: 0.8026 (ttp80) outliers start: 36 outliers final: 20 residues processed: 234 average time/residue: 0.1395 time to fit residues: 52.0690 Evaluate side-chains 214 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 598 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 258 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.179255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.145597 restraints weight = 22044.015| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.82 r_work: 0.3048 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21804 Z= 0.174 Angle : 0.548 9.120 29584 Z= 0.296 Chirality : 0.043 0.144 3404 Planarity : 0.003 0.035 3668 Dihedral : 4.398 25.759 2864 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.80 % Favored : 91.90 % Rotamer: Outliers : 2.02 % Allowed : 13.03 % Favored : 84.96 % 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: -0.73 (0.17), residues: 2616 helix: 1.08 (0.15), residues: 1316 sheet: -2.37 (0.39), residues: 148 loop : -2.17 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 333 TYR 0.021 0.001 TYR A 460 PHE 0.013 0.002 PHE C 660 TRP 0.008 0.001 TRP A 367 HIS 0.005 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00418 (21804) covalent geometry : angle 0.54848 (29584) hydrogen bonds : bond 0.05999 ( 1004) hydrogen bonds : angle 4.03369 ( 2916) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 0.824 Fit side-chains REVERT: A 286 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7066 (pmm) REVERT: A 344 TYR cc_start: 0.8083 (m-80) cc_final: 0.7845 (m-80) REVERT: A 373 TYR cc_start: 0.8286 (t80) cc_final: 0.7977 (t80) REVERT: A 601 ASP cc_start: 0.7663 (t0) cc_final: 0.7045 (t0) REVERT: A 677 ARG cc_start: 0.8317 (ttp80) cc_final: 0.7966 (ttp80) REVERT: B 286 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7072 (pmm) REVERT: B 344 TYR cc_start: 0.8078 (m-80) cc_final: 0.7842 (m-80) REVERT: B 373 TYR cc_start: 0.8280 (t80) cc_final: 0.7969 (t80) REVERT: B 601 ASP cc_start: 0.7710 (t0) cc_final: 0.7089 (t0) REVERT: B 677 ARG cc_start: 0.8294 (ttp80) cc_final: 0.7933 (ttp80) REVERT: C 286 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7081 (pmm) REVERT: C 344 TYR cc_start: 0.8091 (m-80) cc_final: 0.7854 (m-80) REVERT: C 373 TYR cc_start: 0.8282 (t80) cc_final: 0.7971 (t80) REVERT: C 601 ASP cc_start: 0.7685 (t0) cc_final: 0.7065 (t0) REVERT: C 677 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7970 (ttp80) REVERT: D 286 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7086 (pmm) REVERT: D 344 TYR cc_start: 0.8087 (m-80) cc_final: 0.7853 (m-80) REVERT: D 373 TYR cc_start: 0.8278 (t80) cc_final: 0.7967 (t80) REVERT: D 601 ASP cc_start: 0.7704 (t0) cc_final: 0.7087 (t0) REVERT: D 677 ARG cc_start: 0.8319 (ttp80) cc_final: 0.7964 (ttp80) outliers start: 48 outliers final: 32 residues processed: 225 average time/residue: 0.1409 time to fit residues: 51.1749 Evaluate side-chains 216 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 254 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 214 optimal weight: 30.0000 chunk 2 optimal weight: 0.0980 chunk 154 optimal weight: 0.6980 chunk 236 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.183588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.146971 restraints weight = 21869.232| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.83 r_work: 0.3046 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21804 Z= 0.116 Angle : 0.489 7.563 29584 Z= 0.263 Chirality : 0.040 0.143 3404 Planarity : 0.003 0.030 3668 Dihedral : 4.168 23.022 2864 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.42 % Favored : 93.27 % Rotamer: Outliers : 2.02 % Allowed : 13.66 % Favored : 84.33 % 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: -0.59 (0.17), residues: 2616 helix: 1.25 (0.15), residues: 1340 sheet: -2.07 (0.41), residues: 148 loop : -2.28 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 671 TYR 0.014 0.001 TYR A 460 PHE 0.013 0.001 PHE A 93 TRP 0.009 0.001 TRP C 367 HIS 0.004 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00256 (21804) covalent geometry : angle 0.48863 (29584) hydrogen bonds : bond 0.05006 ( 1004) hydrogen bonds : angle 3.76020 ( 2916) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 193 time to evaluate : 0.747 Fit side-chains REVERT: A 286 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.6907 (pmm) REVERT: A 344 TYR cc_start: 0.7935 (m-80) cc_final: 0.7705 (m-80) REVERT: A 373 TYR cc_start: 0.8153 (t80) cc_final: 0.7879 (t80) REVERT: A 601 ASP cc_start: 0.7551 (t0) cc_final: 0.6930 (t0) REVERT: A 677 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7840 (ttp80) REVERT: B 286 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6909 (pmm) REVERT: B 373 TYR cc_start: 0.8146 (t80) cc_final: 0.7872 (t80) REVERT: B 601 ASP cc_start: 0.7597 (t0) cc_final: 0.6969 (t0) REVERT: B 677 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7828 (ttp80) REVERT: C 286 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6913 (pmm) REVERT: C 373 TYR cc_start: 0.8141 (t80) cc_final: 0.7867 (t80) REVERT: C 601 ASP cc_start: 0.7610 (t0) cc_final: 0.6991 (t0) REVERT: C 677 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7838 (ttp80) REVERT: D 286 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.6917 (pmm) REVERT: D 344 TYR cc_start: 0.7941 (m-80) cc_final: 0.7713 (m-80) REVERT: D 373 TYR cc_start: 0.8147 (t80) cc_final: 0.7873 (t80) REVERT: D 601 ASP cc_start: 0.7589 (t0) cc_final: 0.6975 (t0) REVERT: D 677 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7842 (ttp80) outliers start: 48 outliers final: 24 residues processed: 233 average time/residue: 0.1338 time to fit residues: 50.4506 Evaluate side-chains 202 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.4980 chunk 151 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 263 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 104 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.182288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.153453 restraints weight = 21932.600| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.55 r_work: 0.3164 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21804 Z= 0.122 Angle : 0.512 9.380 29584 Z= 0.269 Chirality : 0.041 0.135 3404 Planarity : 0.003 0.030 3668 Dihedral : 4.140 24.127 2864 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.42 % Favored : 93.27 % Rotamer: Outliers : 1.85 % Allowed : 14.12 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.17), residues: 2616 helix: 1.28 (0.15), residues: 1340 sheet: -1.94 (0.42), residues: 148 loop : -2.25 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 115 TYR 0.014 0.001 TYR A 460 PHE 0.011 0.001 PHE B 471 TRP 0.008 0.001 TRP D 367 HIS 0.004 0.001 HIS D 570 Details of bonding type rmsd covalent geometry : bond 0.00274 (21804) covalent geometry : angle 0.51216 (29584) hydrogen bonds : bond 0.05064 ( 1004) hydrogen bonds : angle 3.75342 ( 2916) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.808 Fit side-chains REVERT: A 286 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.6907 (pmm) REVERT: A 344 TYR cc_start: 0.8036 (m-80) cc_final: 0.7801 (m-80) REVERT: A 373 TYR cc_start: 0.8296 (t80) cc_final: 0.7937 (t80) REVERT: A 601 ASP cc_start: 0.7697 (t0) cc_final: 0.7062 (t0) REVERT: A 677 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7865 (ttp80) REVERT: B 286 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.6907 (pmm) REVERT: B 344 TYR cc_start: 0.8049 (m-80) cc_final: 0.7810 (m-80) REVERT: B 373 TYR cc_start: 0.8304 (t80) cc_final: 0.7946 (t80) REVERT: B 601 ASP cc_start: 0.7767 (t0) cc_final: 0.7121 (t0) REVERT: B 677 ARG cc_start: 0.8263 (ttp80) cc_final: 0.7843 (ttp80) REVERT: C 286 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.6916 (pmm) REVERT: C 344 TYR cc_start: 0.8052 (m-80) cc_final: 0.7821 (m-80) REVERT: C 373 TYR cc_start: 0.8286 (t80) cc_final: 0.7924 (t80) REVERT: C 601 ASP cc_start: 0.7747 (t0) cc_final: 0.7111 (t0) REVERT: C 677 ARG cc_start: 0.8280 (ttp80) cc_final: 0.7861 (ttp80) REVERT: D 286 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.6903 (pmm) REVERT: D 344 TYR cc_start: 0.8050 (m-80) cc_final: 0.7816 (m-80) REVERT: D 373 TYR cc_start: 0.8285 (t80) cc_final: 0.7925 (t80) REVERT: D 601 ASP cc_start: 0.7733 (t0) cc_final: 0.7097 (t0) REVERT: D 677 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7852 (ttp80) outliers start: 44 outliers final: 28 residues processed: 220 average time/residue: 0.1351 time to fit residues: 48.2120 Evaluate side-chains 208 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 138 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 260 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 246 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 232 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.181169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.151675 restraints weight = 21930.427| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.54 r_work: 0.3142 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21804 Z= 0.146 Angle : 0.537 8.614 29584 Z= 0.282 Chirality : 0.042 0.151 3404 Planarity : 0.003 0.030 3668 Dihedral : 4.174 24.638 2864 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.34 % Favored : 92.35 % Rotamer: Outliers : 1.34 % Allowed : 14.29 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.17), residues: 2616 helix: 1.18 (0.15), residues: 1348 sheet: -2.00 (0.42), residues: 148 loop : -2.24 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 333 TYR 0.015 0.001 TYR A 460 PHE 0.013 0.002 PHE C 93 TRP 0.007 0.001 TRP C 367 HIS 0.004 0.001 HIS D 570 Details of bonding type rmsd covalent geometry : bond 0.00342 (21804) covalent geometry : angle 0.53726 (29584) hydrogen bonds : bond 0.05430 ( 1004) hydrogen bonds : angle 3.83462 ( 2916) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.693 Fit side-chains REVERT: A 107 PHE cc_start: 0.7850 (m-80) cc_final: 0.7609 (m-80) REVERT: A 286 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.6921 (pmm) REVERT: A 344 TYR cc_start: 0.8082 (m-80) cc_final: 0.7846 (m-80) REVERT: A 373 TYR cc_start: 0.8305 (t80) cc_final: 0.7941 (t80) REVERT: A 601 ASP cc_start: 0.7687 (t0) cc_final: 0.7066 (t0) REVERT: A 677 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7861 (ttp80) REVERT: B 107 PHE cc_start: 0.7816 (m-80) cc_final: 0.7571 (m-80) REVERT: B 286 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.6940 (pmm) REVERT: B 344 TYR cc_start: 0.8090 (m-80) cc_final: 0.7848 (m-80) REVERT: B 373 TYR cc_start: 0.8295 (t80) cc_final: 0.7931 (t80) REVERT: B 601 ASP cc_start: 0.7739 (t0) cc_final: 0.7102 (t0) REVERT: B 677 ARG cc_start: 0.8276 (ttp80) cc_final: 0.7827 (ttp80) REVERT: C 107 PHE cc_start: 0.7822 (m-80) cc_final: 0.7581 (m-80) REVERT: C 286 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.6945 (pmm) REVERT: C 344 TYR cc_start: 0.8097 (m-80) cc_final: 0.7861 (m-80) REVERT: C 373 TYR cc_start: 0.8297 (t80) cc_final: 0.7929 (t80) REVERT: C 601 ASP cc_start: 0.7717 (t0) cc_final: 0.7091 (t0) REVERT: C 677 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7853 (ttp80) REVERT: D 107 PHE cc_start: 0.7812 (m-80) cc_final: 0.7569 (m-80) REVERT: D 286 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.6942 (pmm) REVERT: D 344 TYR cc_start: 0.8095 (m-80) cc_final: 0.7858 (m-80) REVERT: D 373 TYR cc_start: 0.8296 (t80) cc_final: 0.7930 (t80) REVERT: D 601 ASP cc_start: 0.7711 (t0) cc_final: 0.7091 (t0) REVERT: D 677 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7839 (ttp80) outliers start: 32 outliers final: 28 residues processed: 220 average time/residue: 0.1447 time to fit residues: 50.6155 Evaluate side-chains 224 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 172 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 178 optimal weight: 0.3980 chunk 136 optimal weight: 0.4980 chunk 31 optimal weight: 9.9990 chunk 235 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.183238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.159532 restraints weight = 21824.762| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.13 r_work: 0.3272 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21804 Z= 0.112 Angle : 0.502 8.225 29584 Z= 0.263 Chirality : 0.040 0.157 3404 Planarity : 0.003 0.028 3668 Dihedral : 4.039 23.201 2864 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.57 % Favored : 93.12 % Rotamer: Outliers : 1.68 % Allowed : 14.12 % Favored : 84.20 % 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: -0.45 (0.17), residues: 2616 helix: 1.35 (0.15), residues: 1344 sheet: -2.00 (0.42), residues: 148 loop : -2.21 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 330 TYR 0.012 0.001 TYR C 460 PHE 0.010 0.001 PHE B 471 TRP 0.009 0.001 TRP D 367 HIS 0.004 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00246 (21804) covalent geometry : angle 0.50223 (29584) hydrogen bonds : bond 0.04789 ( 1004) hydrogen bonds : angle 3.66960 ( 2916) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 0.773 Fit side-chains REVERT: A 107 PHE cc_start: 0.7738 (m-80) cc_final: 0.7491 (m-80) REVERT: A 286 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.6819 (pmm) REVERT: A 344 TYR cc_start: 0.7942 (m-80) cc_final: 0.7706 (m-80) REVERT: A 373 TYR cc_start: 0.8140 (t80) cc_final: 0.7765 (t80) REVERT: A 601 ASP cc_start: 0.7498 (t0) cc_final: 0.6904 (t0) REVERT: A 677 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7776 (ttp80) REVERT: B 107 PHE cc_start: 0.7701 (m-80) cc_final: 0.7452 (m-80) REVERT: B 286 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.6820 (pmm) REVERT: B 344 TYR cc_start: 0.7949 (m-80) cc_final: 0.7711 (m-80) REVERT: B 373 TYR cc_start: 0.8140 (t80) cc_final: 0.7765 (t80) REVERT: B 601 ASP cc_start: 0.7572 (t0) cc_final: 0.6959 (t0) REVERT: B 677 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7753 (ttp80) REVERT: C 107 PHE cc_start: 0.7717 (m-80) cc_final: 0.7467 (m-80) REVERT: C 286 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.6828 (pmm) REVERT: C 344 TYR cc_start: 0.7954 (m-80) cc_final: 0.7722 (m-80) REVERT: C 373 TYR cc_start: 0.8132 (t80) cc_final: 0.7759 (t80) REVERT: C 601 ASP cc_start: 0.7557 (t0) cc_final: 0.6958 (t0) REVERT: C 677 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7772 (ttp80) REVERT: D 107 PHE cc_start: 0.7698 (m-80) cc_final: 0.7450 (m-80) REVERT: D 286 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.6834 (pmm) REVERT: D 344 TYR cc_start: 0.7945 (m-80) cc_final: 0.7711 (m-80) REVERT: D 373 TYR cc_start: 0.8136 (t80) cc_final: 0.7758 (t80) REVERT: D 601 ASP cc_start: 0.7541 (t0) cc_final: 0.6943 (t0) REVERT: D 677 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7770 (ttp80) outliers start: 40 outliers final: 28 residues processed: 236 average time/residue: 0.1343 time to fit residues: 50.6833 Evaluate side-chains 220 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 124 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 154 optimal weight: 0.9980 chunk 106 optimal weight: 0.0970 chunk 200 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 253 optimal weight: 0.5980 chunk 164 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.183715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.155299 restraints weight = 21909.204| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.30 r_work: 0.3232 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21804 Z= 0.111 Angle : 0.510 8.357 29584 Z= 0.266 Chirality : 0.040 0.144 3404 Planarity : 0.003 0.029 3668 Dihedral : 4.006 23.478 2864 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.96 % Favored : 92.74 % Rotamer: Outliers : 1.34 % Allowed : 14.29 % Favored : 84.37 % 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: -0.39 (0.17), residues: 2616 helix: 1.39 (0.15), residues: 1336 sheet: -1.92 (0.42), residues: 148 loop : -2.16 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.012 0.001 TYR C 460 PHE 0.014 0.001 PHE B 93 TRP 0.008 0.001 TRP C 367 HIS 0.004 0.001 HIS C 570 Details of bonding type rmsd covalent geometry : bond 0.00243 (21804) covalent geometry : angle 0.50995 (29584) hydrogen bonds : bond 0.04729 ( 1004) hydrogen bonds : angle 3.67069 ( 2916) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.976 Fit side-chains REVERT: A 107 PHE cc_start: 0.7755 (m-80) cc_final: 0.7501 (m-80) REVERT: A 286 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.6820 (pmm) REVERT: A 373 TYR cc_start: 0.8211 (t80) cc_final: 0.7839 (t80) REVERT: A 601 ASP cc_start: 0.7543 (t0) cc_final: 0.6934 (t0) REVERT: A 677 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7953 (ttp80) REVERT: B 107 PHE cc_start: 0.7719 (m-80) cc_final: 0.7462 (m-80) REVERT: B 286 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.6798 (pmm) REVERT: B 373 TYR cc_start: 0.8201 (t80) cc_final: 0.7830 (t80) REVERT: B 601 ASP cc_start: 0.7585 (t0) cc_final: 0.6963 (t0) REVERT: B 677 ARG cc_start: 0.8199 (ttp80) cc_final: 0.7940 (ttp80) REVERT: C 107 PHE cc_start: 0.7745 (m-80) cc_final: 0.7491 (m-80) REVERT: C 286 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.6830 (pmm) REVERT: C 373 TYR cc_start: 0.8197 (t80) cc_final: 0.7826 (t80) REVERT: C 601 ASP cc_start: 0.7594 (t0) cc_final: 0.6980 (t0) REVERT: C 677 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7946 (ttp80) REVERT: D 107 PHE cc_start: 0.7724 (m-80) cc_final: 0.7471 (m-80) REVERT: D 286 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.6831 (pmm) REVERT: D 373 TYR cc_start: 0.8200 (t80) cc_final: 0.7828 (t80) REVERT: D 601 ASP cc_start: 0.7571 (t0) cc_final: 0.6958 (t0) REVERT: D 677 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7946 (ttp80) outliers start: 32 outliers final: 28 residues processed: 214 average time/residue: 0.1431 time to fit residues: 48.7565 Evaluate side-chains 214 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 567 GLN Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 119 optimal weight: 0.9980 chunk 233 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 chunk 198 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 219 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 82 optimal weight: 30.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.183125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.155894 restraints weight = 21871.277| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.32 r_work: 0.3204 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21804 Z= 0.122 Angle : 0.515 8.092 29584 Z= 0.270 Chirality : 0.041 0.151 3404 Planarity : 0.003 0.031 3668 Dihedral : 4.016 23.920 2864 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.03 % Favored : 92.66 % Rotamer: Outliers : 1.34 % Allowed : 14.37 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.17), residues: 2616 helix: 1.36 (0.15), residues: 1336 sheet: -1.98 (0.42), residues: 148 loop : -2.15 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 336 TYR 0.012 0.001 TYR D 460 PHE 0.011 0.001 PHE B 471 TRP 0.008 0.001 TRP C 367 HIS 0.004 0.001 HIS C 570 Details of bonding type rmsd covalent geometry : bond 0.00276 (21804) covalent geometry : angle 0.51523 (29584) hydrogen bonds : bond 0.04876 ( 1004) hydrogen bonds : angle 3.70736 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5150.02 seconds wall clock time: 88 minutes 56.21 seconds (5336.21 seconds total)