Starting phenix.real_space_refine on Wed Jun 18 14:16:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yid_33855/06_2025/7yid_33855.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yid_33855/06_2025/7yid_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_33855/06_2025/7yid_33855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yid_33855/06_2025/7yid_33855.map" model { file = "/net/cci-nas-00/data/ceres_data/7yid_33855/06_2025/7yid_33855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yid_33855/06_2025/7yid_33855.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21326 Number of models: 1 Model: "" Number of chains: 5 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: "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} Restraints were copied for chains: B, C, D Time building chain proxies: 13.87, per 1000 atoms: 0.65 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: 5.45 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.29 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: 6.57 Time building geometry restraints manager: 6.45 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: 3.540 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: 0.910 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 48.830 Find NCS groups from input model: 0.850 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.360 ------------------------------------------------------------------------------- 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 : 7.32 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP B 367 HIS 0.003 0.001 HIS B 118 PHE 0.018 0.002 PHE A 566 TYR 0.033 0.001 TYR B 460 ARG 0.003 0.000 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.15413 ( 1004) hydrogen bonds : angle 5.31572 ( 2916) covalent geometry : bond 0.00271 (21804) covalent geometry : angle 0.55811 (29584) *********************** 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 : 2.249 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: 0.2922 time to fit residues: 113.7430 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 : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.7980 chunk 200 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 206 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 A 570 HIS B 267 HIS B 403 ASN B 570 HIS C 267 HIS C 403 ASN C 570 HIS D 267 HIS D 403 ASN D 570 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.179899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.149235 restraints weight = 21896.927| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.55 r_work: 0.3117 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21804 Z= 0.217 Angle : 0.600 8.393 29584 Z= 0.326 Chirality : 0.045 0.159 3404 Planarity : 0.003 0.039 3668 Dihedral : 4.504 26.557 2864 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.34 % Favored : 92.35 % Rotamer: Outliers : 0.67 % Allowed : 9.41 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.16), residues: 2616 helix: 0.81 (0.14), residues: 1316 sheet: -2.41 (0.37), residues: 148 loop : -2.29 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 388 HIS 0.007 0.001 HIS D 570 PHE 0.017 0.002 PHE D 660 TYR 0.035 0.002 TYR B 460 ARG 0.002 0.000 ARG C 336 Details of bonding type rmsd hydrogen bonds : bond 0.06619 ( 1004) hydrogen bonds : angle 4.42207 ( 2916) covalent geometry : bond 0.00530 (21804) covalent geometry : angle 0.60015 (29584) *********************** 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 204 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 2.442 Fit side-chains REVERT: A 290 LYS cc_start: 0.8270 (ptpt) cc_final: 0.8042 (ptpt) REVERT: A 373 TYR cc_start: 0.8254 (t80) cc_final: 0.7988 (t80) REVERT: A 601 ASP cc_start: 0.7612 (t0) cc_final: 0.7037 (t0) REVERT: B 290 LYS cc_start: 0.8294 (ptpt) cc_final: 0.8066 (ptpt) REVERT: B 373 TYR cc_start: 0.8250 (t80) cc_final: 0.7983 (t80) REVERT: B 601 ASP cc_start: 0.7611 (t0) cc_final: 0.7034 (t0) REVERT: C 290 LYS cc_start: 0.8274 (ptpt) cc_final: 0.8046 (ptpt) REVERT: C 373 TYR cc_start: 0.8260 (t80) cc_final: 0.7991 (t80) REVERT: C 601 ASP cc_start: 0.7636 (t0) cc_final: 0.7055 (t0) REVERT: D 290 LYS cc_start: 0.8288 (ptpt) cc_final: 0.8060 (ptpt) REVERT: D 373 TYR cc_start: 0.8254 (t80) cc_final: 0.7986 (t80) REVERT: D 601 ASP cc_start: 0.7636 (t0) cc_final: 0.7062 (t0) outliers start: 16 outliers final: 12 residues processed: 192 average time/residue: 0.3018 time to fit residues: 94.4527 Evaluate side-chains 196 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 474 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 14 optimal weight: 30.0000 chunk 238 optimal weight: 0.4980 chunk 157 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 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 = 0.3965 r_free = 0.3965 target = 0.183446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.144064 restraints weight = 21684.148| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.23 r_work: 0.2997 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21804 Z= 0.126 Angle : 0.495 5.352 29584 Z= 0.271 Chirality : 0.040 0.142 3404 Planarity : 0.003 0.034 3668 Dihedral : 4.240 23.099 2864 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.42 % Favored : 93.27 % Rotamer: Outliers : 1.18 % Allowed : 11.60 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.16), residues: 2616 helix: 1.04 (0.15), residues: 1340 sheet: -2.28 (0.38), residues: 148 loop : -2.38 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 367 HIS 0.004 0.001 HIS C 176 PHE 0.013 0.001 PHE B 134 TYR 0.021 0.001 TYR A 460 ARG 0.001 0.000 ARG C 336 Details of bonding type rmsd hydrogen bonds : bond 0.05382 ( 1004) hydrogen bonds : angle 3.97870 ( 2916) covalent geometry : bond 0.00282 (21804) covalent geometry : angle 0.49533 (29584) *********************** 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 232 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 2.383 Fit side-chains REVERT: A 119 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7955 (mm-30) REVERT: A 269 THR cc_start: 0.8453 (p) cc_final: 0.8249 (p) REVERT: A 286 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7050 (pmm) REVERT: A 373 TYR cc_start: 0.8157 (t80) cc_final: 0.7910 (t80) REVERT: A 601 ASP cc_start: 0.7536 (t0) cc_final: 0.6956 (t0) REVERT: A 677 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7953 (ttp80) REVERT: B 119 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7957 (mm-30) REVERT: B 269 THR cc_start: 0.8437 (p) cc_final: 0.8228 (p) REVERT: B 286 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7066 (pmm) REVERT: B 373 TYR cc_start: 0.8162 (t80) cc_final: 0.7913 (t80) REVERT: B 601 ASP cc_start: 0.7529 (t0) cc_final: 0.6940 (t0) REVERT: B 677 ARG cc_start: 0.8319 (ttp80) cc_final: 0.7934 (ttp80) REVERT: C 119 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7961 (mm-30) REVERT: C 269 THR cc_start: 0.8439 (p) cc_final: 0.8230 (p) REVERT: C 286 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7076 (pmm) REVERT: C 373 TYR cc_start: 0.8164 (t80) cc_final: 0.7914 (t80) REVERT: C 601 ASP cc_start: 0.7544 (t0) cc_final: 0.6950 (t0) REVERT: C 677 ARG cc_start: 0.8332 (ttp80) cc_final: 0.7950 (ttp80) REVERT: D 119 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7974 (mm-30) REVERT: D 269 THR cc_start: 0.8439 (p) cc_final: 0.8237 (p) REVERT: D 286 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7070 (pmm) REVERT: D 373 TYR cc_start: 0.8165 (t80) cc_final: 0.7915 (t80) REVERT: D 601 ASP cc_start: 0.7542 (t0) cc_final: 0.6955 (t0) REVERT: D 677 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7942 (ttp80) outliers start: 28 outliers final: 8 residues processed: 224 average time/residue: 0.3080 time to fit residues: 111.1929 Evaluate side-chains 204 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 2.147 ------------------------------------------------------------------------------- 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 612 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 394 LEU 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 612 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 394 LEU 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 173 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 246 optimal weight: 0.9980 chunk 233 optimal weight: 0.0060 chunk 199 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.183106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.151587 restraints weight = 22062.858| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.70 r_work: 0.3134 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21804 Z= 0.121 Angle : 0.484 6.423 29584 Z= 0.263 Chirality : 0.040 0.139 3404 Planarity : 0.003 0.029 3668 Dihedral : 4.134 24.176 2864 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.80 % Favored : 92.89 % Rotamer: Outliers : 1.68 % Allowed : 11.43 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2616 helix: 1.20 (0.15), residues: 1340 sheet: -2.13 (0.40), residues: 148 loop : -2.29 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 367 HIS 0.002 0.001 HIS A 539 PHE 0.012 0.001 PHE B 93 TYR 0.019 0.001 TYR B 460 ARG 0.001 0.000 ARG B 336 Details of bonding type rmsd hydrogen bonds : bond 0.05109 ( 1004) hydrogen bonds : angle 3.82150 ( 2916) covalent geometry : bond 0.00268 (21804) covalent geometry : angle 0.48359 (29584) *********************** 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 238 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 2.310 Fit side-chains REVERT: A 119 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8027 (mm-30) REVERT: A 286 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.6951 (pmm) REVERT: A 344 TYR cc_start: 0.7883 (m-80) cc_final: 0.7602 (m-80) REVERT: A 373 TYR cc_start: 0.8197 (t80) cc_final: 0.7929 (t80) REVERT: A 601 ASP cc_start: 0.7564 (t0) cc_final: 0.6967 (t0) REVERT: A 677 ARG cc_start: 0.8298 (ttp80) cc_final: 0.7979 (ttp80) REVERT: B 119 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8041 (mm-30) REVERT: B 269 THR cc_start: 0.8494 (p) cc_final: 0.8259 (p) REVERT: B 286 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.6951 (pmm) REVERT: B 344 TYR cc_start: 0.7893 (m-80) cc_final: 0.7611 (m-80) REVERT: B 373 TYR cc_start: 0.8196 (t80) cc_final: 0.7924 (t80) REVERT: B 601 ASP cc_start: 0.7580 (t0) cc_final: 0.6975 (t0) REVERT: B 677 ARG cc_start: 0.8278 (ttp80) cc_final: 0.7957 (ttp80) REVERT: C 119 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8043 (mm-30) REVERT: C 269 THR cc_start: 0.8486 (p) cc_final: 0.8251 (p) REVERT: C 286 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.6962 (pmm) REVERT: C 344 TYR cc_start: 0.7894 (m-80) cc_final: 0.7614 (m-80) REVERT: C 373 TYR cc_start: 0.8198 (t80) cc_final: 0.7926 (t80) REVERT: C 601 ASP cc_start: 0.7603 (t0) cc_final: 0.6995 (t0) REVERT: C 677 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7981 (ttp80) REVERT: D 119 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8062 (mm-30) REVERT: D 286 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.6971 (pmm) REVERT: D 344 TYR cc_start: 0.7895 (m-80) cc_final: 0.7620 (m-80) REVERT: D 373 TYR cc_start: 0.8193 (t80) cc_final: 0.7922 (t80) REVERT: D 601 ASP cc_start: 0.7578 (t0) cc_final: 0.6982 (t0) REVERT: D 677 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7971 (ttp80) outliers start: 40 outliers final: 24 residues processed: 230 average time/residue: 0.3126 time to fit residues: 114.4389 Evaluate side-chains 226 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 298 LEU 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 612 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 298 LEU 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 612 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 298 LEU 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 612 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 298 LEU 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 612 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 83 optimal weight: 9.9990 chunk 255 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 25 optimal weight: 0.6980 chunk 206 optimal weight: 5.9990 chunk 253 optimal weight: 0.9990 chunk 232 optimal weight: 0.0770 chunk 106 optimal weight: 0.3980 chunk 247 optimal weight: 3.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.185641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.158909 restraints weight = 21903.775| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.26 r_work: 0.3259 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21804 Z= 0.101 Angle : 0.477 9.324 29584 Z= 0.252 Chirality : 0.039 0.135 3404 Planarity : 0.003 0.026 3668 Dihedral : 4.002 23.118 2864 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.27 % Favored : 93.43 % Rotamer: Outliers : 1.51 % Allowed : 11.72 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2616 helix: 1.41 (0.15), residues: 1332 sheet: -1.89 (0.41), residues: 148 loop : -2.21 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 513 HIS 0.002 0.000 HIS A 639 PHE 0.010 0.001 PHE C 471 TYR 0.014 0.001 TYR A 460 ARG 0.001 0.000 ARG C 336 Details of bonding type rmsd hydrogen bonds : bond 0.04572 ( 1004) hydrogen bonds : angle 3.63560 ( 2916) covalent geometry : bond 0.00210 (21804) covalent geometry : angle 0.47660 (29584) *********************** 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 236 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 2.150 Fit side-chains REVERT: A 119 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8030 (mm-30) REVERT: A 286 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.6806 (pmm) REVERT: A 344 TYR cc_start: 0.7837 (m-80) cc_final: 0.7573 (m-80) REVERT: A 373 TYR cc_start: 0.8171 (t80) cc_final: 0.7907 (t80) REVERT: A 601 ASP cc_start: 0.7480 (t0) cc_final: 0.6900 (t0) REVERT: A 677 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7939 (ttp80) REVERT: B 119 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8033 (mm-30) REVERT: B 286 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.6773 (pmm) REVERT: B 344 TYR cc_start: 0.7851 (m-80) cc_final: 0.7580 (m-80) REVERT: B 373 TYR cc_start: 0.8168 (t80) cc_final: 0.7903 (t80) REVERT: B 601 ASP cc_start: 0.7496 (t0) cc_final: 0.6914 (t0) REVERT: B 677 ARG cc_start: 0.8256 (ttp80) cc_final: 0.7920 (ttp80) REVERT: C 119 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8042 (mm-30) REVERT: C 286 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.6806 (pmm) REVERT: C 344 TYR cc_start: 0.7853 (m-80) cc_final: 0.7586 (m-80) REVERT: C 373 TYR cc_start: 0.8159 (t80) cc_final: 0.7897 (t80) REVERT: C 601 ASP cc_start: 0.7536 (t0) cc_final: 0.6948 (t0) REVERT: C 677 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7940 (ttp80) REVERT: D 119 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8048 (mm-30) REVERT: D 286 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.6812 (pmm) REVERT: D 344 TYR cc_start: 0.7860 (m-80) cc_final: 0.7593 (m-80) REVERT: D 373 TYR cc_start: 0.8157 (t80) cc_final: 0.7896 (t80) REVERT: D 601 ASP cc_start: 0.7486 (t0) cc_final: 0.6907 (t0) REVERT: D 677 ARG cc_start: 0.8267 (ttp80) cc_final: 0.7934 (ttp80) outliers start: 36 outliers final: 16 residues processed: 228 average time/residue: 0.3018 time to fit residues: 109.2482 Evaluate side-chains 208 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 2.082 ------------------------------------------------------------------------------- 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 566 PHE Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 286 MET 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 105 VAL Chi-restraints excluded: chain C residue 286 MET 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 105 VAL Chi-restraints excluded: chain D residue 286 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 41 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 49 optimal weight: 0.0040 chunk 83 optimal weight: 6.9990 chunk 30 optimal weight: 0.0070 chunk 188 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 51 optimal weight: 0.4980 overall best weight: 0.6812 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.184082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.152856 restraints weight = 21846.307| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.59 r_work: 0.3176 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 21804 Z= 0.115 Angle : 0.479 7.421 29584 Z= 0.257 Chirality : 0.040 0.134 3404 Planarity : 0.003 0.026 3668 Dihedral : 3.976 24.237 2864 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.73 % Favored : 92.97 % Rotamer: Outliers : 2.02 % Allowed : 11.51 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2616 helix: 1.41 (0.15), residues: 1332 sheet: -1.93 (0.42), residues: 148 loop : -2.18 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 367 HIS 0.002 0.000 HIS D 539 PHE 0.013 0.001 PHE D 93 TYR 0.016 0.001 TYR A 460 ARG 0.001 0.000 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.04795 ( 1004) hydrogen bonds : angle 3.64822 ( 2916) covalent geometry : bond 0.00255 (21804) covalent geometry : angle 0.47939 (29584) *********************** 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 240 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 2.160 Fit side-chains REVERT: A 107 PHE cc_start: 0.7688 (m-80) cc_final: 0.7338 (m-80) REVERT: A 119 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8055 (mm-30) REVERT: A 286 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6884 (pmm) REVERT: A 344 TYR cc_start: 0.7810 (m-80) cc_final: 0.7530 (m-80) REVERT: A 373 TYR cc_start: 0.8200 (t80) cc_final: 0.7927 (t80) REVERT: A 601 ASP cc_start: 0.7572 (t0) cc_final: 0.6957 (t0) REVERT: A 677 ARG cc_start: 0.8283 (ttp80) cc_final: 0.7884 (ttp80) REVERT: B 107 PHE cc_start: 0.7658 (m-80) cc_final: 0.7307 (m-80) REVERT: B 119 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8054 (mm-30) REVERT: B 286 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.6872 (pmm) REVERT: B 344 TYR cc_start: 0.7820 (m-80) cc_final: 0.7536 (m-80) REVERT: B 373 TYR cc_start: 0.8193 (t80) cc_final: 0.7915 (t80) REVERT: B 601 ASP cc_start: 0.7578 (t0) cc_final: 0.6957 (t0) REVERT: B 677 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7862 (ttp80) REVERT: C 107 PHE cc_start: 0.7670 (m-80) cc_final: 0.7321 (m-80) REVERT: C 119 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8058 (mm-30) REVERT: C 286 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6885 (pmm) REVERT: C 344 TYR cc_start: 0.7815 (m-80) cc_final: 0.7539 (m-80) REVERT: C 373 TYR cc_start: 0.8192 (t80) cc_final: 0.7915 (t80) REVERT: C 601 ASP cc_start: 0.7618 (t0) cc_final: 0.6993 (t0) REVERT: C 677 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7882 (ttp80) REVERT: D 107 PHE cc_start: 0.7660 (m-80) cc_final: 0.7307 (m-80) REVERT: D 119 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8077 (mm-30) REVERT: D 286 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.6886 (pmm) REVERT: D 344 TYR cc_start: 0.7812 (m-80) cc_final: 0.7536 (m-80) REVERT: D 373 TYR cc_start: 0.8193 (t80) cc_final: 0.7917 (t80) REVERT: D 601 ASP cc_start: 0.7589 (t0) cc_final: 0.6974 (t0) REVERT: D 677 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7880 (ttp80) outliers start: 48 outliers final: 24 residues processed: 236 average time/residue: 0.2971 time to fit residues: 113.8314 Evaluate side-chains 212 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 2.231 ------------------------------------------------------------------------------- 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 107 optimal weight: 0.8980 chunk 236 optimal weight: 0.5980 chunk 238 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 0.0060 chunk 58 optimal weight: 1.9990 chunk 229 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.183434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.153147 restraints weight = 21819.993| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.54 r_work: 0.3175 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 21804 Z= 0.115 Angle : 0.491 8.671 29584 Z= 0.259 Chirality : 0.040 0.143 3404 Planarity : 0.003 0.025 3668 Dihedral : 3.956 23.931 2864 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.27 % Favored : 93.43 % Rotamer: Outliers : 1.85 % Allowed : 12.31 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2616 helix: 1.44 (0.15), residues: 1332 sheet: -1.94 (0.41), residues: 148 loop : -2.15 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 367 HIS 0.002 0.000 HIS A 118 PHE 0.010 0.001 PHE C 471 TYR 0.014 0.001 TYR A 460 ARG 0.001 0.000 ARG D 151 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 1004) hydrogen bonds : angle 3.63836 ( 2916) covalent geometry : bond 0.00257 (21804) covalent geometry : angle 0.49067 (29584) *********************** 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 : 2.451 Fit side-chains REVERT: A 107 PHE cc_start: 0.7714 (m-80) cc_final: 0.7358 (m-80) REVERT: A 119 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8019 (mm-30) REVERT: A 286 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6872 (pmm) REVERT: A 373 TYR cc_start: 0.8254 (t80) cc_final: 0.7983 (t80) REVERT: A 601 ASP cc_start: 0.7565 (t0) cc_final: 0.6944 (t0) REVERT: A 677 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7869 (ttp80) REVERT: B 107 PHE cc_start: 0.7675 (m-80) cc_final: 0.7314 (m-80) REVERT: B 119 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8037 (mm-30) REVERT: B 286 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6872 (pmm) REVERT: B 373 TYR cc_start: 0.8252 (t80) cc_final: 0.7978 (t80) REVERT: B 601 ASP cc_start: 0.7571 (t0) cc_final: 0.6944 (t0) REVERT: B 677 ARG cc_start: 0.8256 (ttp80) cc_final: 0.7837 (ttp80) REVERT: C 107 PHE cc_start: 0.7687 (m-80) cc_final: 0.7330 (m-80) REVERT: C 119 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8030 (mm-30) REVERT: C 286 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.6870 (pmm) REVERT: C 373 TYR cc_start: 0.8249 (t80) cc_final: 0.7926 (t80) REVERT: C 601 ASP cc_start: 0.7602 (t0) cc_final: 0.6972 (t0) REVERT: C 677 ARG cc_start: 0.8276 (ttp80) cc_final: 0.7861 (ttp80) REVERT: D 107 PHE cc_start: 0.7688 (m-80) cc_final: 0.7329 (m-80) REVERT: D 119 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8038 (mm-30) REVERT: D 286 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.6885 (pmm) REVERT: D 373 TYR cc_start: 0.8249 (t80) cc_final: 0.7976 (t80) REVERT: D 601 ASP cc_start: 0.7588 (t0) cc_final: 0.6967 (t0) REVERT: D 677 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7851 (ttp80) outliers start: 44 outliers final: 28 residues processed: 220 average time/residue: 0.3256 time to fit residues: 114.8856 Evaluate side-chains 212 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 2.420 ------------------------------------------------------------------------------- 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 27 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 183 optimal weight: 0.0270 chunk 26 optimal weight: 0.8980 chunk 49 optimal weight: 0.0070 chunk 214 optimal weight: 30.0000 chunk 263 optimal weight: 0.9980 chunk 230 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.184939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.156102 restraints weight = 21874.651| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.37 r_work: 0.3223 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21804 Z= 0.107 Angle : 0.480 7.985 29584 Z= 0.254 Chirality : 0.040 0.149 3404 Planarity : 0.002 0.024 3668 Dihedral : 3.891 23.620 2864 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.38 % Favored : 93.31 % Rotamer: Outliers : 1.34 % Allowed : 12.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2616 helix: 1.49 (0.15), residues: 1336 sheet: -1.93 (0.41), residues: 148 loop : -2.08 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 367 HIS 0.002 0.000 HIS D 539 PHE 0.009 0.001 PHE C 471 TYR 0.013 0.001 TYR A 460 ARG 0.001 0.000 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 1004) hydrogen bonds : angle 3.57147 ( 2916) covalent geometry : bond 0.00233 (21804) covalent geometry : angle 0.47998 (29584) *********************** 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 235 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 2.495 Fit side-chains REVERT: A 98 TYR cc_start: 0.7528 (m-10) cc_final: 0.7207 (m-10) REVERT: A 107 PHE cc_start: 0.7696 (m-80) cc_final: 0.7381 (m-80) REVERT: A 119 GLU cc_start: 0.8235 (mm-30) cc_final: 0.8018 (mm-30) REVERT: A 286 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.6807 (pmm) REVERT: A 344 TYR cc_start: 0.7847 (m-80) cc_final: 0.7578 (m-80) REVERT: A 373 TYR cc_start: 0.8247 (t80) cc_final: 0.7915 (t80) REVERT: A 601 ASP cc_start: 0.7564 (t0) cc_final: 0.6964 (t0) REVERT: B 98 TYR cc_start: 0.7535 (m-10) cc_final: 0.7208 (m-10) REVERT: B 107 PHE cc_start: 0.7659 (m-80) cc_final: 0.7341 (m-80) REVERT: B 119 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8038 (mm-30) REVERT: B 286 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.6801 (pmm) REVERT: B 344 TYR cc_start: 0.7860 (m-80) cc_final: 0.7584 (m-80) REVERT: B 373 TYR cc_start: 0.8248 (t80) cc_final: 0.7912 (t80) REVERT: B 601 ASP cc_start: 0.7581 (t0) cc_final: 0.6974 (t0) REVERT: C 98 TYR cc_start: 0.7522 (m-10) cc_final: 0.7205 (m-10) REVERT: C 107 PHE cc_start: 0.7669 (m-80) cc_final: 0.7353 (m-80) REVERT: C 119 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8036 (mm-30) REVERT: C 286 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.6816 (pmm) REVERT: C 344 TYR cc_start: 0.7858 (m-80) cc_final: 0.7592 (m-80) REVERT: C 373 TYR cc_start: 0.8217 (t80) cc_final: 0.7887 (t80) REVERT: C 601 ASP cc_start: 0.7615 (t0) cc_final: 0.7006 (t0) REVERT: D 98 TYR cc_start: 0.7502 (m-10) cc_final: 0.7177 (m-10) REVERT: D 107 PHE cc_start: 0.7675 (m-80) cc_final: 0.7358 (m-80) REVERT: D 119 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8036 (mm-30) REVERT: D 286 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6825 (pmm) REVERT: D 344 TYR cc_start: 0.7862 (m-80) cc_final: 0.7592 (m-80) REVERT: D 373 TYR cc_start: 0.8243 (t80) cc_final: 0.7910 (t80) REVERT: D 601 ASP cc_start: 0.7593 (t0) cc_final: 0.6993 (t0) outliers start: 32 outliers final: 28 residues processed: 231 average time/residue: 0.3085 time to fit residues: 114.3130 Evaluate side-chains 221 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 2.155 ------------------------------------------------------------------------------- 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 262 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 237 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 249 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 chunk 146 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 220 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.183342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.157170 restraints weight = 21688.212| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.34 r_work: 0.3239 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1624 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= 0.120 Angle : 0.500 7.764 29584 Z= 0.263 Chirality : 0.040 0.150 3404 Planarity : 0.003 0.025 3668 Dihedral : 3.929 24.066 2864 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.57 % Favored : 93.12 % Rotamer: Outliers : 1.43 % Allowed : 12.52 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.17), residues: 2616 helix: 1.45 (0.15), residues: 1336 sheet: -1.48 (0.34), residues: 260 loop : -2.07 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 388 HIS 0.002 0.000 HIS B 118 PHE 0.010 0.001 PHE B 471 TYR 0.014 0.001 TYR D 460 ARG 0.003 0.000 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 1004) hydrogen bonds : angle 3.62546 ( 2916) covalent geometry : bond 0.00271 (21804) covalent geometry : angle 0.50016 (29584) *********************** 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 210 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 2.247 Fit side-chains REVERT: A 107 PHE cc_start: 0.7718 (m-80) cc_final: 0.7407 (m-80) REVERT: A 119 GLU cc_start: 0.8228 (mm-30) cc_final: 0.8013 (mm-30) REVERT: A 286 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6858 (pmm) REVERT: A 373 TYR cc_start: 0.8239 (t80) cc_final: 0.7909 (t80) REVERT: A 601 ASP cc_start: 0.7566 (t0) cc_final: 0.6952 (t0) REVERT: B 107 PHE cc_start: 0.7689 (m-80) cc_final: 0.7377 (m-80) REVERT: B 119 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8027 (mm-30) REVERT: B 286 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.6829 (pmm) REVERT: B 373 TYR cc_start: 0.8229 (t80) cc_final: 0.7894 (t80) REVERT: B 601 ASP cc_start: 0.7577 (t0) cc_final: 0.6958 (t0) REVERT: C 107 PHE cc_start: 0.7713 (m-80) cc_final: 0.7399 (m-80) REVERT: C 119 GLU cc_start: 0.8235 (mm-30) cc_final: 0.8018 (mm-30) REVERT: C 286 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.6854 (pmm) REVERT: C 373 TYR cc_start: 0.8221 (t80) cc_final: 0.7899 (t80) REVERT: C 601 ASP cc_start: 0.7623 (t0) cc_final: 0.7002 (t0) REVERT: D 107 PHE cc_start: 0.7698 (m-80) cc_final: 0.7383 (m-80) REVERT: D 119 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8037 (mm-30) REVERT: D 286 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.6862 (pmm) REVERT: D 373 TYR cc_start: 0.8226 (t80) cc_final: 0.7894 (t80) REVERT: D 601 ASP cc_start: 0.7605 (t0) cc_final: 0.6987 (t0) outliers start: 34 outliers final: 28 residues processed: 206 average time/residue: 0.2965 time to fit residues: 100.5100 Evaluate side-chains 204 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 2.374 ------------------------------------------------------------------------------- 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 76 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 160 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 104 optimal weight: 0.0670 overall best weight: 0.8722 ------------------------------------------------------------------------------- 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 = 0.182552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.153594 restraints weight = 21949.128| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.54 r_work: 0.3176 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21804 Z= 0.129 Angle : 0.505 7.586 29584 Z= 0.268 Chirality : 0.041 0.156 3404 Planarity : 0.003 0.028 3668 Dihedral : 3.968 24.581 2864 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.73 % Favored : 92.97 % Rotamer: Outliers : 1.85 % Allowed : 12.10 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.17), residues: 2616 helix: 1.38 (0.15), residues: 1344 sheet: -1.51 (0.34), residues: 260 loop : -2.08 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 38 HIS 0.002 0.000 HIS B 118 PHE 0.010 0.001 PHE A 471 TYR 0.014 0.001 TYR B 460 ARG 0.004 0.000 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.05016 ( 1004) hydrogen bonds : angle 3.68206 ( 2916) covalent geometry : bond 0.00297 (21804) covalent geometry : angle 0.50528 (29584) ********************** 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 224 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 2.221 Fit side-chains REVERT: A 107 PHE cc_start: 0.7879 (m-80) cc_final: 0.7589 (m-80) REVERT: A 286 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.6850 (pmm) REVERT: A 373 TYR cc_start: 0.8333 (t80) cc_final: 0.8001 (t80) REVERT: A 601 ASP cc_start: 0.7703 (t0) cc_final: 0.7080 (t0) REVERT: B 107 PHE cc_start: 0.7858 (m-80) cc_final: 0.7561 (m-80) REVERT: B 286 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.6860 (pmm) REVERT: B 373 TYR cc_start: 0.8332 (t80) cc_final: 0.8000 (t80) REVERT: B 601 ASP cc_start: 0.7743 (t0) cc_final: 0.7111 (t0) REVERT: C 107 PHE cc_start: 0.7862 (m-80) cc_final: 0.7568 (m-80) REVERT: C 286 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.6895 (pmm) REVERT: C 373 TYR cc_start: 0.8299 (t80) cc_final: 0.7990 (t80) REVERT: C 601 ASP cc_start: 0.7784 (t0) cc_final: 0.7147 (t0) REVERT: D 107 PHE cc_start: 0.7859 (m-80) cc_final: 0.7564 (m-80) REVERT: D 286 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.6861 (pmm) REVERT: D 373 TYR cc_start: 0.8331 (t80) cc_final: 0.8000 (t80) REVERT: D 601 ASP cc_start: 0.7764 (t0) cc_final: 0.7132 (t0) outliers start: 44 outliers final: 28 residues processed: 220 average time/residue: 0.2875 time to fit residues: 103.8369 Evaluate side-chains 204 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 286 MET 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 191 ILE Chi-restraints excluded: chain B residue 286 MET 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 191 ILE Chi-restraints excluded: chain C residue 286 MET 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 191 ILE Chi-restraints excluded: chain D residue 286 MET 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 224 optimal weight: 0.0770 chunk 87 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 217 optimal weight: 0.3980 chunk 191 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 219 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.184377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.160735 restraints weight = 21873.443| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.13 r_work: 0.3299 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21804 Z= 0.106 Angle : 0.489 7.192 29584 Z= 0.258 Chirality : 0.040 0.151 3404 Planarity : 0.003 0.025 3668 Dihedral : 3.900 23.226 2864 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.88 % Favored : 92.81 % Rotamer: Outliers : 1.43 % Allowed : 12.61 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2616 helix: 1.50 (0.15), residues: 1336 sheet: -1.48 (0.34), residues: 260 loop : -2.01 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 367 HIS 0.003 0.000 HIS A 118 PHE 0.011 0.001 PHE C 448 TYR 0.012 0.001 TYR D 460 ARG 0.004 0.000 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 1004) hydrogen bonds : angle 3.57708 ( 2916) covalent geometry : bond 0.00228 (21804) covalent geometry : angle 0.48928 (29584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11719.31 seconds wall clock time: 204 minutes 59.36 seconds (12299.36 seconds total)