Starting phenix.real_space_refine on Thu Mar 5 04:33:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6n_25720/03_2026/7t6n_25720.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6n_25720/03_2026/7t6n_25720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t6n_25720/03_2026/7t6n_25720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6n_25720/03_2026/7t6n_25720.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6n_25720/03_2026/7t6n_25720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6n_25720/03_2026/7t6n_25720.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 12548 2.51 5 N 3284 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Time building chain proxies: 4.63, per 1000 atoms: 0.24 Number of scatterers: 19412 At special positions: 0 Unit cell: (119.78, 119.78, 120.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3440 8.00 N 3284 7.00 C 12548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 857.1 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 8 sheets defined 68.9% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.754A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 removed outlier: 3.675A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 208 through 223 removed outlier: 3.984A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.790A pdb=" N SER A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.305A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 410 Proline residue: A 405 - end of helix removed outlier: 3.570A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.691A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 488 through 512 removed outlier: 3.979A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.621A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.902A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 608 removed outlier: 4.140A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 30 through 47 Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.763A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 removed outlier: 3.677A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.534A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 208 through 223 removed outlier: 4.149A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.797A pdb=" N SER B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.738A pdb=" N ALA B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.624A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.303A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 410 Proline residue: B 405 - end of helix removed outlier: 3.752A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.699A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 Processing helix chain 'B' and resid 488 through 512 removed outlier: 3.994A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.616A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.872A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 608 removed outlier: 4.077A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET B 608 " --> pdb=" O LEU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.752A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 removed outlier: 4.024A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.764A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 208 through 223 removed outlier: 4.030A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.791A pdb=" N SER C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 301 through 310 removed outlier: 3.741A pdb=" N ALA C 304 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN C 306 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.304A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 410 Proline residue: C 405 - end of helix removed outlier: 3.682A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.700A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 Processing helix chain 'C' and resid 488 through 512 removed outlier: 3.971A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 512 " --> pdb=" O PHE C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.629A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.865A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 608 removed outlier: 4.072A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C 608 " --> pdb=" O LEU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'D' and resid 30 through 47 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.768A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 removed outlier: 3.661A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.566A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 206 Processing helix chain 'D' and resid 208 through 223 removed outlier: 4.019A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.799A pdb=" N SER D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 304 through 310 Processing helix chain 'D' and resid 313 through 324 Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.304A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 410 Proline residue: D 405 - end of helix removed outlier: 3.688A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.691A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 Processing helix chain 'D' and resid 488 through 512 removed outlier: 3.988A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 512 " --> pdb=" O PHE D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.632A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.871A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 608 removed outlier: 4.074A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET D 608 " --> pdb=" O LEU D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.634A pdb=" N LYS A 264 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP A 279 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU A 277 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.625A pdb=" N LYS B 264 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP B 279 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N VAL B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 277 " --> pdb=" O VAL B 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.629A pdb=" N LYS C 264 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP C 279 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VAL C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU C 277 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.631A pdb=" N LYS D 264 " --> pdb=" O ASP D 279 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP D 279 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU D 277 " --> pdb=" O VAL D 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1128 hydrogen bonds defined for protein. 3228 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: 3.25 Time building geometry restraints manager: 2.19 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: 5280 1.34 - 1.46: 4282 1.46 - 1.58: 10066 1.58 - 1.70: 4 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" CG PRO D 362 " pdb=" CD PRO D 362 " ideal model delta sigma weight residual 1.503 1.269 0.234 3.40e-02 8.65e+02 4.72e+01 bond pdb=" CG PRO B 362 " pdb=" CD PRO B 362 " ideal model delta sigma weight residual 1.503 1.269 0.234 3.40e-02 8.65e+02 4.72e+01 bond pdb=" CG PRO A 362 " pdb=" CD PRO A 362 " ideal model delta sigma weight residual 1.503 1.270 0.233 3.40e-02 8.65e+02 4.70e+01 bond pdb=" CG PRO C 362 " pdb=" CD PRO C 362 " ideal model delta sigma weight residual 1.503 1.271 0.232 3.40e-02 8.65e+02 4.67e+01 bond pdb=" CB PRO A 362 " pdb=" CG PRO A 362 " ideal model delta sigma weight residual 1.492 1.653 -0.161 5.00e-02 4.00e+02 1.03e+01 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 26221 2.75 - 5.50: 588 5.50 - 8.25: 99 8.25 - 11.00: 40 11.00 - 13.75: 16 Bond angle restraints: 26964 Sorted by residual: angle pdb=" N PRO C 362 " pdb=" CD PRO C 362 " pdb=" CG PRO C 362 " ideal model delta sigma weight residual 103.20 89.45 13.75 1.50e+00 4.44e-01 8.40e+01 angle pdb=" N PRO D 362 " pdb=" CD PRO D 362 " pdb=" CG PRO D 362 " ideal model delta sigma weight residual 103.20 89.47 13.73 1.50e+00 4.44e-01 8.38e+01 angle pdb=" N PRO B 362 " pdb=" CD PRO B 362 " pdb=" CG PRO B 362 " ideal model delta sigma weight residual 103.20 89.47 13.73 1.50e+00 4.44e-01 8.38e+01 angle pdb=" N PRO A 362 " pdb=" CD PRO A 362 " pdb=" CG PRO A 362 " ideal model delta sigma weight residual 103.20 89.48 13.72 1.50e+00 4.44e-01 8.36e+01 angle pdb=" CA PRO B 362 " pdb=" N PRO B 362 " pdb=" CD PRO B 362 " ideal model delta sigma weight residual 112.00 99.48 12.52 1.40e+00 5.10e-01 8.00e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 10439 15.51 - 31.01: 1101 31.01 - 46.52: 184 46.52 - 62.03: 48 62.03 - 77.54: 40 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA MET D 485 " pdb=" C MET D 485 " pdb=" N ILE D 486 " pdb=" CA ILE D 486 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA MET B 485 " pdb=" C MET B 485 " pdb=" N ILE B 486 " pdb=" CA ILE B 486 " ideal model delta harmonic sigma weight residual 180.00 157.82 22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA GLN B 206 " pdb=" C GLN B 206 " pdb=" N PRO B 207 " pdb=" CA PRO B 207 " ideal model delta harmonic sigma weight residual 180.00 157.95 22.05 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2544 0.066 - 0.133: 423 0.133 - 0.199: 80 0.199 - 0.266: 8 0.266 - 0.332: 17 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB ILE A 429 " pdb=" CA ILE A 429 " pdb=" CG1 ILE A 429 " pdb=" CG2 ILE A 429 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB ILE D 429 " pdb=" CA ILE D 429 " pdb=" CG1 ILE D 429 " pdb=" CG2 ILE D 429 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ASN B 208 " pdb=" N ASN B 208 " pdb=" C ASN B 208 " pdb=" CB ASN B 208 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 361 " 0.109 5.00e-02 4.00e+02 1.54e-01 3.78e+01 pdb=" N PRO B 362 " -0.265 5.00e-02 4.00e+02 pdb=" CA PRO B 362 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO B 362 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 361 " -0.109 5.00e-02 4.00e+02 1.54e-01 3.77e+01 pdb=" N PRO C 362 " 0.265 5.00e-02 4.00e+02 pdb=" CA PRO C 362 " -0.081 5.00e-02 4.00e+02 pdb=" CD PRO C 362 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 361 " 0.109 5.00e-02 4.00e+02 1.53e-01 3.77e+01 pdb=" N PRO D 362 " -0.265 5.00e-02 4.00e+02 pdb=" CA PRO D 362 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO D 362 " 0.075 5.00e-02 4.00e+02 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 6226 2.85 - 3.36: 17894 3.36 - 3.87: 33590 3.87 - 4.39: 38637 4.39 - 4.90: 66052 Nonbonded interactions: 162399 Sorted by model distance: nonbonded pdb=" OE1 GLU D 403 " pdb=" OH TYR D 415 " model vdw 2.335 3.040 nonbonded pdb=" OE1 GLU A 403 " pdb=" OH TYR A 415 " model vdw 2.340 3.040 nonbonded pdb=" OE1 GLU C 403 " pdb=" OH TYR C 415 " model vdw 2.340 3.040 nonbonded pdb=" OE1 GLU B 403 " pdb=" OH TYR B 415 " model vdw 2.356 3.040 nonbonded pdb=" O PRO C 544 " pdb=" OH TYR C 555 " model vdw 2.398 3.040 ... (remaining 162394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.170 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.234 19860 Z= 0.284 Angle : 1.076 13.745 26964 Z= 0.580 Chirality : 0.057 0.332 3072 Planarity : 0.010 0.154 3416 Dihedral : 13.709 77.537 7236 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.19 % Allowed : 0.33 % Favored : 99.48 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.14), residues: 2408 helix: -2.08 (0.10), residues: 1468 sheet: -2.19 (0.41), residues: 132 loop : -1.40 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 180 TYR 0.021 0.002 TYR A 339 PHE 0.062 0.003 PHE B 456 TRP 0.018 0.002 TRP C 593 HIS 0.006 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00668 (19860) covalent geometry : angle 1.07641 (26964) hydrogen bonds : bond 0.14175 ( 1128) hydrogen bonds : angle 6.46933 ( 3228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 363 time to evaluate : 0.800 Fit side-chains REVERT: A 323 LYS cc_start: 0.8394 (tppp) cc_final: 0.7995 (tppt) REVERT: A 429 ILE cc_start: 0.7665 (mt) cc_final: 0.7428 (mm) REVERT: A 447 MET cc_start: 0.7471 (ptm) cc_final: 0.7269 (ptt) REVERT: A 473 GLN cc_start: 0.8225 (tt0) cc_final: 0.8003 (tt0) REVERT: A 497 MET cc_start: 0.8330 (ttt) cc_final: 0.8106 (ttt) REVERT: B 93 GLU cc_start: 0.8268 (mp0) cc_final: 0.7977 (mp0) REVERT: B 473 GLN cc_start: 0.8229 (tt0) cc_final: 0.8003 (tt0) REVERT: C 323 LYS cc_start: 0.8393 (tppp) cc_final: 0.7982 (tppt) REVERT: C 399 ILE cc_start: 0.6899 (mt) cc_final: 0.6416 (mt) REVERT: C 429 ILE cc_start: 0.7532 (mt) cc_final: 0.7324 (mm) REVERT: C 473 GLN cc_start: 0.8234 (tt0) cc_final: 0.8011 (tt0) REVERT: D 93 GLU cc_start: 0.8272 (mp0) cc_final: 0.7973 (mp0) REVERT: D 177 GLU cc_start: 0.7435 (pm20) cc_final: 0.6799 (tp30) REVERT: D 323 LYS cc_start: 0.8369 (tppp) cc_final: 0.7964 (tppt) REVERT: D 399 ILE cc_start: 0.6876 (mt) cc_final: 0.6375 (mt) REVERT: D 429 ILE cc_start: 0.7586 (mt) cc_final: 0.7375 (mm) REVERT: D 447 MET cc_start: 0.7468 (ptm) cc_final: 0.7268 (ptt) REVERT: D 473 GLN cc_start: 0.8157 (tt0) cc_final: 0.7909 (tt0) outliers start: 4 outliers final: 0 residues processed: 367 average time/residue: 0.6381 time to fit residues: 261.9220 Evaluate side-chains 250 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.0770 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 235 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 185 HIS ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN B 185 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN C 74 GLN C 185 HIS C 208 ASN C 572 ASN D 74 GLN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.167557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.137705 restraints weight = 22383.278| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.56 r_work: 0.3586 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19860 Z= 0.119 Angle : 0.555 6.691 26964 Z= 0.287 Chirality : 0.038 0.178 3072 Planarity : 0.005 0.040 3416 Dihedral : 4.106 17.693 2644 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.05 % Allowed : 8.64 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 2408 helix: -0.05 (0.12), residues: 1504 sheet: -2.03 (0.43), residues: 132 loop : -0.72 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 180 TYR 0.007 0.001 TYR C 559 PHE 0.022 0.001 PHE D 456 TRP 0.013 0.001 TRP A 29 HIS 0.003 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00255 (19860) covalent geometry : angle 0.55501 (26964) hydrogen bonds : bond 0.04090 ( 1128) hydrogen bonds : angle 4.21439 ( 3228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 308 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8086 (ttt90) cc_final: 0.7720 (ttt180) REVERT: A 108 GLU cc_start: 0.7126 (mp0) cc_final: 0.6809 (mp0) REVERT: A 323 LYS cc_start: 0.8565 (tppp) cc_final: 0.8294 (tppt) REVERT: A 615 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8359 (ttt180) REVERT: A 622 GLU cc_start: 0.7610 (tt0) cc_final: 0.6791 (tt0) REVERT: B 107 LYS cc_start: 0.7515 (mptt) cc_final: 0.7314 (mttp) REVERT: B 108 GLU cc_start: 0.7149 (mp0) cc_final: 0.6829 (mp0) REVERT: B 615 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8365 (ttt180) REVERT: C 35 ARG cc_start: 0.8085 (ttt90) cc_final: 0.7789 (ttt180) REVERT: C 323 LYS cc_start: 0.8577 (tppp) cc_final: 0.8305 (tppt) REVERT: C 399 ILE cc_start: 0.7661 (mt) cc_final: 0.7162 (mt) REVERT: C 497 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8325 (ttt) REVERT: C 615 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8335 (ttt180) REVERT: D 177 GLU cc_start: 0.7688 (pm20) cc_final: 0.6973 (tp30) REVERT: D 323 LYS cc_start: 0.8579 (tppp) cc_final: 0.8308 (tppt) REVERT: D 399 ILE cc_start: 0.7641 (mt) cc_final: 0.7141 (mt) REVERT: D 615 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8343 (ttt180) outliers start: 43 outliers final: 6 residues processed: 333 average time/residue: 0.6518 time to fit residues: 242.8175 Evaluate side-chains 254 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 243 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 228 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 217 optimal weight: 0.0470 chunk 110 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 185 HIS A 208 ASN B 67 ASN B 185 HIS B 208 ASN C 67 ASN C 185 HIS C 208 ASN D 67 ASN D 208 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126024 restraints weight = 22510.160| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.60 r_work: 0.3430 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19860 Z= 0.214 Angle : 0.643 7.821 26964 Z= 0.330 Chirality : 0.043 0.195 3072 Planarity : 0.005 0.039 3416 Dihedral : 4.155 15.656 2644 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.29 % Allowed : 11.50 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.17), residues: 2408 helix: 0.66 (0.13), residues: 1504 sheet: -2.16 (0.44), residues: 132 loop : -0.53 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 180 TYR 0.016 0.002 TYR A 559 PHE 0.018 0.002 PHE D 425 TRP 0.012 0.002 TRP C 593 HIS 0.007 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00524 (19860) covalent geometry : angle 0.64264 (26964) hydrogen bonds : bond 0.04916 ( 1128) hydrogen bonds : angle 4.23121 ( 3228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 228 time to evaluate : 0.738 Fit side-chains REVERT: A 177 GLU cc_start: 0.7925 (pm20) cc_final: 0.7444 (tp30) REVERT: A 447 MET cc_start: 0.8444 (ptm) cc_final: 0.8214 (ptp) REVERT: A 473 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: A 615 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8345 (ttt180) REVERT: B 177 GLU cc_start: 0.7889 (pm20) cc_final: 0.7350 (tp30) REVERT: B 473 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: B 615 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8317 (ttt180) REVERT: C 177 GLU cc_start: 0.7848 (pm20) cc_final: 0.7171 (tp30) REVERT: C 180 ARG cc_start: 0.8075 (mtt-85) cc_final: 0.7862 (mtt-85) REVERT: C 215 MET cc_start: 0.9067 (mmm) cc_final: 0.8810 (tpp) REVERT: C 473 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: C 497 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8403 (ttt) REVERT: C 615 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8333 (ttt180) REVERT: D 177 GLU cc_start: 0.7852 (pm20) cc_final: 0.7245 (tp30) REVERT: D 447 MET cc_start: 0.8441 (ptm) cc_final: 0.8203 (ptp) REVERT: D 473 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: D 615 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8334 (ttt180) REVERT: D 622 GLU cc_start: 0.7621 (tt0) cc_final: 0.7173 (tt0) outliers start: 48 outliers final: 14 residues processed: 259 average time/residue: 0.6633 time to fit residues: 191.8028 Evaluate side-chains 249 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 473 GLN Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 208 ASN C 208 ASN D 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.128877 restraints weight = 22295.976| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.58 r_work: 0.3470 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19860 Z= 0.136 Angle : 0.553 6.880 26964 Z= 0.285 Chirality : 0.039 0.183 3072 Planarity : 0.004 0.038 3416 Dihedral : 3.893 14.742 2644 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.62 % Allowed : 12.74 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.17), residues: 2408 helix: 1.18 (0.13), residues: 1504 sheet: -2.10 (0.46), residues: 132 loop : -0.38 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 180 TYR 0.008 0.001 TYR C 559 PHE 0.011 0.001 PHE D 425 TRP 0.012 0.001 TRP C 593 HIS 0.004 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00311 (19860) covalent geometry : angle 0.55251 (26964) hydrogen bonds : bond 0.04128 ( 1128) hydrogen bonds : angle 3.97009 ( 3228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 0.540 Fit side-chains REVERT: A 176 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7997 (mm-30) REVERT: A 177 GLU cc_start: 0.7894 (pm20) cc_final: 0.7490 (tp30) REVERT: A 188 ASP cc_start: 0.7726 (p0) cc_final: 0.7481 (t0) REVERT: A 273 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8025 (pp) REVERT: A 447 MET cc_start: 0.8173 (ptm) cc_final: 0.7945 (ptp) REVERT: A 466 MET cc_start: 0.9028 (mtt) cc_final: 0.8785 (mtt) REVERT: A 615 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8304 (ttt180) REVERT: B 80 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8042 (pt0) REVERT: B 108 GLU cc_start: 0.7354 (mp0) cc_final: 0.7015 (mp0) REVERT: B 177 GLU cc_start: 0.7881 (pm20) cc_final: 0.7523 (tp30) REVERT: B 273 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8091 (pp) REVERT: B 466 MET cc_start: 0.9021 (mtt) cc_final: 0.8805 (mtt) REVERT: B 615 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8292 (ttt180) REVERT: B 622 GLU cc_start: 0.7771 (tt0) cc_final: 0.7376 (tt0) REVERT: C 80 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8040 (pt0) REVERT: C 177 GLU cc_start: 0.7832 (pm20) cc_final: 0.7208 (tp30) REVERT: C 215 MET cc_start: 0.9061 (mmm) cc_final: 0.8860 (tpp) REVERT: C 273 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8084 (pp) REVERT: C 466 MET cc_start: 0.9014 (mtm) cc_final: 0.8770 (mtt) REVERT: C 497 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8578 (ttt) REVERT: C 615 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8297 (ttt180) REVERT: D 35 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7604 (ttt90) REVERT: D 55 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6977 (mm-30) REVERT: D 80 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: D 177 GLU cc_start: 0.7769 (pm20) cc_final: 0.7318 (tp30) REVERT: D 273 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8096 (pp) REVERT: D 447 MET cc_start: 0.8182 (ptm) cc_final: 0.7968 (ptp) REVERT: D 466 MET cc_start: 0.9003 (mtt) cc_final: 0.8752 (mtt) REVERT: D 615 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8293 (ttt180) outliers start: 55 outliers final: 13 residues processed: 272 average time/residue: 0.6000 time to fit residues: 183.5934 Evaluate side-chains 249 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 497 MET Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 29 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 208 ASN C 208 ASN D 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.150840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126986 restraints weight = 21656.809| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.06 r_work: 0.3259 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19860 Z= 0.138 Angle : 0.550 7.000 26964 Z= 0.284 Chirality : 0.039 0.176 3072 Planarity : 0.004 0.038 3416 Dihedral : 3.854 14.339 2644 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.77 % Allowed : 13.26 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.17), residues: 2408 helix: 1.48 (0.13), residues: 1500 sheet: -1.68 (0.51), residues: 112 loop : -0.43 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 180 TYR 0.009 0.001 TYR A 559 PHE 0.012 0.001 PHE B 425 TRP 0.010 0.001 TRP C 593 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00320 (19860) covalent geometry : angle 0.55025 (26964) hydrogen bonds : bond 0.04063 ( 1128) hydrogen bonds : angle 3.90307 ( 3228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 235 time to evaluate : 0.923 Fit side-chains REVERT: A 80 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7916 (pt0) REVERT: A 176 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8087 (mm-30) REVERT: A 273 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8117 (pp) REVERT: A 474 MET cc_start: 0.8090 (ptm) cc_final: 0.7725 (ptm) REVERT: A 615 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8373 (ttt180) REVERT: B 55 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7231 (mm-30) REVERT: B 80 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7871 (pt0) REVERT: B 108 GLU cc_start: 0.7251 (mp0) cc_final: 0.6996 (mp0) REVERT: B 273 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8117 (pp) REVERT: B 615 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8355 (ttt180) REVERT: C 35 ARG cc_start: 0.8296 (ttt90) cc_final: 0.8003 (ttt180) REVERT: C 80 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7948 (pt0) REVERT: C 177 GLU cc_start: 0.7758 (pm20) cc_final: 0.7515 (tp30) REVERT: C 215 MET cc_start: 0.9066 (mmm) cc_final: 0.8865 (tpp) REVERT: C 273 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8150 (pp) REVERT: C 615 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8328 (ttt180) REVERT: D 35 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7647 (ttt90) REVERT: D 55 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7069 (mm-30) REVERT: D 80 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: D 108 GLU cc_start: 0.7259 (mp0) cc_final: 0.6965 (mp0) REVERT: D 177 GLU cc_start: 0.7707 (pm20) cc_final: 0.7346 (tp30) REVERT: D 179 VAL cc_start: 0.8404 (p) cc_final: 0.8145 (t) REVERT: D 273 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8119 (pp) REVERT: D 474 MET cc_start: 0.8226 (ptm) cc_final: 0.7845 (ptm) REVERT: D 615 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8359 (ttt180) outliers start: 58 outliers final: 17 residues processed: 282 average time/residue: 0.6219 time to fit residues: 196.6929 Evaluate side-chains 248 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 637 HIS B 208 ASN C 208 ASN D 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.149747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.128036 restraints weight = 21730.443| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 0.87 r_work: 0.3307 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19860 Z= 0.154 Angle : 0.566 6.882 26964 Z= 0.292 Chirality : 0.040 0.179 3072 Planarity : 0.004 0.038 3416 Dihedral : 3.868 15.593 2644 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.58 % Allowed : 13.98 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2408 helix: 1.53 (0.13), residues: 1500 sheet: -1.79 (0.51), residues: 112 loop : -0.47 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 180 TYR 0.010 0.001 TYR B 559 PHE 0.013 0.001 PHE C 425 TRP 0.009 0.001 TRP C 593 HIS 0.005 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00366 (19860) covalent geometry : angle 0.56646 (26964) hydrogen bonds : bond 0.04178 ( 1128) hydrogen bonds : angle 3.90542 ( 3228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.765 Fit side-chains REVERT: A 55 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7088 (mm-30) REVERT: A 80 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7734 (pt0) REVERT: A 108 GLU cc_start: 0.7243 (mp0) cc_final: 0.6967 (mp0) REVERT: A 176 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7906 (mm-30) REVERT: A 615 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8302 (ttt180) REVERT: B 55 GLU cc_start: 0.7238 (mm-30) cc_final: 0.7024 (mm-30) REVERT: B 80 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7744 (pt0) REVERT: B 108 GLU cc_start: 0.7266 (mp0) cc_final: 0.7013 (mp0) REVERT: B 615 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8295 (ttt180) REVERT: C 55 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7095 (mm-30) REVERT: C 80 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7718 (pt0) REVERT: C 177 GLU cc_start: 0.7676 (pm20) cc_final: 0.7430 (tp30) REVERT: C 215 MET cc_start: 0.9077 (mmm) cc_final: 0.8867 (tpp) REVERT: C 473 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: C 615 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8261 (ttt180) REVERT: D 35 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7422 (ttt90) REVERT: D 80 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7695 (pt0) REVERT: D 177 GLU cc_start: 0.7581 (pm20) cc_final: 0.7274 (tp30) REVERT: D 179 VAL cc_start: 0.8288 (p) cc_final: 0.8078 (t) REVERT: D 273 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8095 (pp) REVERT: D 615 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8297 (ttt180) outliers start: 54 outliers final: 25 residues processed: 256 average time/residue: 0.6227 time to fit residues: 179.2587 Evaluate side-chains 250 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 6.9990 chunk 149 optimal weight: 0.5980 chunk 175 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 637 HIS B 208 ASN C 208 ASN D 208 ASN D 637 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126866 restraints weight = 21614.832| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.04 r_work: 0.3260 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19860 Z= 0.137 Angle : 0.548 6.817 26964 Z= 0.282 Chirality : 0.039 0.172 3072 Planarity : 0.004 0.038 3416 Dihedral : 3.816 15.141 2644 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.72 % Allowed : 14.41 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.17), residues: 2408 helix: 1.64 (0.13), residues: 1508 sheet: -1.83 (0.51), residues: 112 loop : -0.54 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 180 TYR 0.009 0.001 TYR A 559 PHE 0.012 0.001 PHE C 456 TRP 0.011 0.001 TRP A 29 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00319 (19860) covalent geometry : angle 0.54758 (26964) hydrogen bonds : bond 0.04022 ( 1128) hydrogen bonds : angle 3.87873 ( 3228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 217 time to evaluate : 0.595 Fit side-chains REVERT: A 35 ARG cc_start: 0.8209 (ttt90) cc_final: 0.7904 (ttt180) REVERT: A 55 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7162 (mm-30) REVERT: A 80 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7825 (pt0) REVERT: A 108 GLU cc_start: 0.7237 (mp0) cc_final: 0.6987 (mp0) REVERT: A 273 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8141 (pp) REVERT: A 366 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8817 (m) REVERT: A 466 MET cc_start: 0.8836 (mtm) cc_final: 0.8601 (mtt) REVERT: A 615 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8334 (ttt180) REVERT: B 35 ARG cc_start: 0.8251 (ttt90) cc_final: 0.7943 (ttt180) REVERT: B 80 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7823 (pt0) REVERT: B 108 GLU cc_start: 0.7242 (mp0) cc_final: 0.7001 (mp0) REVERT: B 273 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8163 (pp) REVERT: B 366 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8804 (m) REVERT: B 474 MET cc_start: 0.8196 (ptm) cc_final: 0.7818 (ptm) REVERT: B 615 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8331 (ttt180) REVERT: C 55 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7209 (mm-30) REVERT: C 80 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7885 (pt0) REVERT: C 177 GLU cc_start: 0.7786 (pm20) cc_final: 0.7582 (tp30) REVERT: C 215 MET cc_start: 0.9081 (mmm) cc_final: 0.8879 (tpp) REVERT: C 273 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8124 (pp) REVERT: C 366 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8815 (m) REVERT: C 466 MET cc_start: 0.8868 (mtm) cc_final: 0.8648 (mtt) REVERT: C 474 MET cc_start: 0.8143 (ptm) cc_final: 0.7756 (ptm) REVERT: C 497 MET cc_start: 0.8502 (ttt) cc_final: 0.8289 (ttt) REVERT: C 615 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8297 (ttt180) REVERT: D 35 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7619 (ttt90) REVERT: D 80 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7828 (pt0) REVERT: D 177 GLU cc_start: 0.7706 (pm20) cc_final: 0.7378 (tp30) REVERT: D 179 VAL cc_start: 0.8435 (p) cc_final: 0.8088 (t) REVERT: D 273 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8151 (pp) REVERT: D 366 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8813 (m) REVERT: D 466 MET cc_start: 0.8818 (mtt) cc_final: 0.8545 (mtt) REVERT: D 474 MET cc_start: 0.8245 (ptm) cc_final: 0.7929 (ptt) REVERT: D 615 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8344 (ttt180) outliers start: 57 outliers final: 20 residues processed: 261 average time/residue: 0.5977 time to fit residues: 175.6367 Evaluate side-chains 247 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 220 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.151592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130399 restraints weight = 21673.618| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 0.89 r_work: 0.3316 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19860 Z= 0.125 Angle : 0.541 6.733 26964 Z= 0.278 Chirality : 0.039 0.166 3072 Planarity : 0.004 0.037 3416 Dihedral : 3.747 15.542 2644 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.43 % Allowed : 14.65 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.17), residues: 2408 helix: 1.76 (0.13), residues: 1508 sheet: -1.93 (0.50), residues: 112 loop : -0.53 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 180 TYR 0.008 0.001 TYR C 559 PHE 0.011 0.001 PHE C 487 TRP 0.012 0.001 TRP B 29 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00284 (19860) covalent geometry : angle 0.54050 (26964) hydrogen bonds : bond 0.03827 ( 1128) hydrogen bonds : angle 3.82060 ( 3228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 0.505 Fit side-chains REVERT: A 35 ARG cc_start: 0.8018 (ttt90) cc_final: 0.7711 (ttt180) REVERT: A 55 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6899 (mm-30) REVERT: A 80 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7684 (pt0) REVERT: A 108 GLU cc_start: 0.7172 (mp0) cc_final: 0.6925 (mp0) REVERT: A 273 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8163 (pp) REVERT: A 366 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8739 (m) REVERT: A 466 MET cc_start: 0.8778 (mtm) cc_final: 0.8530 (mtt) REVERT: A 474 MET cc_start: 0.8077 (ptm) cc_final: 0.7779 (ptt) REVERT: A 615 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8266 (ttt180) REVERT: B 35 ARG cc_start: 0.8060 (ttt90) cc_final: 0.7732 (ttt180) REVERT: B 80 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7687 (pt0) REVERT: B 108 GLU cc_start: 0.7185 (mp0) cc_final: 0.6951 (mp0) REVERT: B 273 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8064 (pp) REVERT: B 366 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8750 (m) REVERT: B 474 MET cc_start: 0.8102 (ptm) cc_final: 0.7686 (ptm) REVERT: B 615 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8240 (ttt180) REVERT: C 55 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6936 (mm-30) REVERT: C 80 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7698 (pt0) REVERT: C 177 GLU cc_start: 0.7718 (pm20) cc_final: 0.7497 (tp30) REVERT: C 273 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8048 (pp) REVERT: C 366 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8741 (m) REVERT: C 466 MET cc_start: 0.8757 (mtm) cc_final: 0.8546 (mtt) REVERT: C 615 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8251 (ttt180) REVERT: D 35 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7415 (ttt90) REVERT: D 80 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: D 108 GLU cc_start: 0.7187 (mp0) cc_final: 0.6946 (mp0) REVERT: D 177 GLU cc_start: 0.7624 (pm20) cc_final: 0.7357 (tp30) REVERT: D 179 VAL cc_start: 0.8300 (p) cc_final: 0.8053 (t) REVERT: D 273 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8128 (pp) REVERT: D 366 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8731 (m) REVERT: D 466 MET cc_start: 0.8721 (mtt) cc_final: 0.8442 (mtt) REVERT: D 474 MET cc_start: 0.8078 (ptm) cc_final: 0.7704 (ptm) REVERT: D 497 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8169 (ttt) REVERT: D 615 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8266 (ttt180) outliers start: 51 outliers final: 22 residues processed: 257 average time/residue: 0.6075 time to fit residues: 175.2141 Evaluate side-chains 255 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 194 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 209 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 229 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN C 637 HIS ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.152433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131252 restraints weight = 21510.526| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 0.89 r_work: 0.3329 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19860 Z= 0.118 Angle : 0.531 6.710 26964 Z= 0.273 Chirality : 0.039 0.162 3072 Planarity : 0.004 0.037 3416 Dihedral : 3.690 16.502 2644 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.29 % Allowed : 15.17 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.18), residues: 2408 helix: 1.89 (0.13), residues: 1508 sheet: -1.93 (0.50), residues: 112 loop : -0.52 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 180 TYR 0.007 0.001 TYR A 559 PHE 0.011 0.001 PHE B 456 TRP 0.014 0.001 TRP A 29 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00263 (19860) covalent geometry : angle 0.53052 (26964) hydrogen bonds : bond 0.03738 ( 1128) hydrogen bonds : angle 3.78938 ( 3228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 0.716 Fit side-chains REVERT: A 35 ARG cc_start: 0.8009 (ttt90) cc_final: 0.7702 (ttt180) REVERT: A 55 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6891 (mm-30) REVERT: A 80 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: A 108 GLU cc_start: 0.7195 (mp0) cc_final: 0.6949 (mp0) REVERT: A 273 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8155 (pp) REVERT: A 366 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8749 (m) REVERT: A 466 MET cc_start: 0.8786 (mtm) cc_final: 0.8556 (mtt) REVERT: A 615 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8262 (ttt180) REVERT: B 35 ARG cc_start: 0.8042 (ttt90) cc_final: 0.7718 (ttt180) REVERT: B 55 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6917 (mm-30) REVERT: B 80 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7625 (pt0) REVERT: B 108 GLU cc_start: 0.7198 (mp0) cc_final: 0.6954 (mp0) REVERT: B 273 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8155 (pp) REVERT: B 366 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8738 (m) REVERT: B 466 MET cc_start: 0.8730 (mtm) cc_final: 0.8471 (mtt) REVERT: B 615 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8249 (ttt180) REVERT: C 55 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6902 (mm-30) REVERT: C 80 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7636 (pt0) REVERT: C 273 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8151 (pp) REVERT: C 366 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8747 (m) REVERT: C 466 MET cc_start: 0.8777 (mtm) cc_final: 0.8575 (mtt) REVERT: C 474 MET cc_start: 0.7970 (ptm) cc_final: 0.7645 (ptt) REVERT: C 615 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8240 (ttt180) REVERT: D 35 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7462 (ttt90) REVERT: D 80 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7626 (pt0) REVERT: D 108 GLU cc_start: 0.7216 (mp0) cc_final: 0.6975 (mp0) REVERT: D 177 GLU cc_start: 0.7621 (pm20) cc_final: 0.7353 (tp30) REVERT: D 273 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8125 (pp) REVERT: D 366 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8737 (m) REVERT: D 466 MET cc_start: 0.8719 (mtt) cc_final: 0.8425 (mtt) REVERT: D 474 MET cc_start: 0.8071 (ptm) cc_final: 0.7752 (ptt) REVERT: D 497 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8158 (ttt) REVERT: D 615 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8263 (ttt180) outliers start: 48 outliers final: 24 residues processed: 258 average time/residue: 0.6145 time to fit residues: 177.5813 Evaluate side-chains 257 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 165 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 HIS B 73 GLN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.135097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.105274 restraints weight = 22970.435| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.57 r_work: 0.3152 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19860 Z= 0.175 Angle : 0.600 7.114 26964 Z= 0.308 Chirality : 0.041 0.182 3072 Planarity : 0.004 0.038 3416 Dihedral : 3.892 21.128 2644 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.15 % Allowed : 16.03 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.17), residues: 2408 helix: 1.67 (0.13), residues: 1508 sheet: -1.35 (0.59), residues: 92 loop : -0.58 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 180 TYR 0.012 0.001 TYR C 559 PHE 0.017 0.002 PHE D 456 TRP 0.014 0.001 TRP A 29 HIS 0.006 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00424 (19860) covalent geometry : angle 0.60038 (26964) hydrogen bonds : bond 0.04329 ( 1128) hydrogen bonds : angle 3.95052 ( 3228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 212 time to evaluate : 0.694 Fit side-chains REVERT: A 80 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7748 (pt0) REVERT: A 273 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8109 (pp) REVERT: A 366 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8771 (m) REVERT: A 474 MET cc_start: 0.8352 (ptm) cc_final: 0.7936 (ptm) REVERT: A 615 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8301 (ttt180) REVERT: B 80 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7790 (pt0) REVERT: B 273 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8096 (pp) REVERT: B 366 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8781 (m) REVERT: B 615 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8233 (ttt180) REVERT: C 80 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7790 (pt0) REVERT: C 273 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8091 (pp) REVERT: C 366 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8802 (m) REVERT: C 466 MET cc_start: 0.9042 (mtm) cc_final: 0.8840 (mtt) REVERT: C 474 MET cc_start: 0.8224 (ptm) cc_final: 0.7883 (ptt) REVERT: C 615 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8258 (ttt180) REVERT: D 35 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7615 (ttt90) REVERT: D 80 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7737 (pt0) REVERT: D 177 GLU cc_start: 0.7913 (pm20) cc_final: 0.7502 (tp30) REVERT: D 273 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8128 (pp) REVERT: D 366 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8765 (m) REVERT: D 466 MET cc_start: 0.8979 (mtt) cc_final: 0.8722 (mtt) REVERT: D 474 MET cc_start: 0.8329 (ptm) cc_final: 0.7917 (ptm) REVERT: D 615 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8291 (ttt180) outliers start: 45 outliers final: 23 residues processed: 238 average time/residue: 0.6087 time to fit residues: 162.0959 Evaluate side-chains 244 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 615 ARG Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 16 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 185 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.137289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.107316 restraints weight = 22851.993| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.61 r_work: 0.3213 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19860 Z= 0.126 Angle : 0.554 7.391 26964 Z= 0.285 Chirality : 0.039 0.169 3072 Planarity : 0.004 0.038 3416 Dihedral : 3.801 23.289 2644 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.96 % Allowed : 16.03 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.18), residues: 2408 helix: 1.83 (0.13), residues: 1508 sheet: -1.93 (0.50), residues: 112 loop : -0.51 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 180 TYR 0.007 0.001 TYR A 336 PHE 0.014 0.001 PHE D 456 TRP 0.017 0.001 TRP A 29 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00286 (19860) covalent geometry : angle 0.55414 (26964) hydrogen bonds : bond 0.03878 ( 1128) hydrogen bonds : angle 3.84466 ( 3228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6109.88 seconds wall clock time: 105 minutes 8.69 seconds (6308.69 seconds total)