Starting phenix.real_space_refine on Mon Jun 16 23:04:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6n_25720/06_2025/7t6n_25720.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6n_25720/06_2025/7t6n_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_25720/06_2025/7t6n_25720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6n_25720/06_2025/7t6n_25720.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6n_25720/06_2025/7t6n_25720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6n_25720/06_2025/7t6n_25720.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.08, per 1000 atoms: 0.67 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: 4.18 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.96 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: 5.82 Time building geometry restraints manager: 5.06 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: 0.10 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 43.650 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.002 TRP C 593 HIS 0.006 0.001 HIS B 201 PHE 0.062 0.003 PHE B 456 TYR 0.021 0.002 TYR A 339 ARG 0.016 0.000 ARG C 180 Details of bonding type rmsd hydrogen bonds : bond 0.14175 ( 1128) hydrogen bonds : angle 6.46933 ( 3228) covalent geometry : bond 0.00668 (19860) covalent geometry : angle 1.07641 (26964) *********************** 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 : 2.332 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: 0.8002 (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: 0.8235 (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: 1.3950 time to fit residues: 574.0695 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 : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 188 optimal weight: 0.4980 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.163986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133470 restraints weight = 22332.727| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.58 r_work: 0.3549 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19860 Z= 0.132 Angle : 0.572 6.842 26964 Z= 0.295 Chirality : 0.039 0.182 3072 Planarity : 0.005 0.040 3416 Dihedral : 4.113 17.335 2644 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.05 % Allowed : 8.83 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2408 helix: -0.04 (0.12), residues: 1504 sheet: -2.04 (0.43), residues: 132 loop : -0.72 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 29 HIS 0.004 0.001 HIS B 84 PHE 0.025 0.001 PHE D 456 TYR 0.009 0.001 TYR C 559 ARG 0.007 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 1128) hydrogen bonds : angle 4.22953 ( 3228) covalent geometry : bond 0.00296 (19860) covalent geometry : angle 0.57227 (26964) *********************** 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 341 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 298 time to evaluate : 2.061 Fit side-chains REVERT: A 35 ARG cc_start: 0.8105 (ttt90) cc_final: 0.7741 (ttt180) REVERT: A 108 GLU cc_start: 0.7182 (mp0) cc_final: 0.6852 (mp0) REVERT: A 323 LYS cc_start: 0.8596 (tppp) cc_final: 0.8322 (tppt) REVERT: A 615 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8287 (ttt180) REVERT: A 622 GLU cc_start: 0.7686 (tt0) cc_final: 0.6846 (tt0) REVERT: B 107 LYS cc_start: 0.7577 (mptt) cc_final: 0.7363 (mttp) REVERT: B 108 GLU cc_start: 0.7204 (mp0) cc_final: 0.6871 (mp0) REVERT: B 615 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8268 (ttt180) REVERT: B 622 GLU cc_start: 0.7648 (tt0) cc_final: 0.7127 (tt0) REVERT: C 35 ARG cc_start: 0.8102 (ttt90) cc_final: 0.7801 (ttt180) REVERT: C 497 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8355 (ttt) REVERT: C 615 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8359 (ttt180) REVERT: D 108 GLU cc_start: 0.7212 (mp0) cc_final: 0.6871 (mp0) REVERT: D 177 GLU cc_start: 0.7720 (pm20) cc_final: 0.6973 (tp30) REVERT: D 323 LYS cc_start: 0.8596 (tppp) cc_final: 0.8321 (tppt) REVERT: D 429 ILE cc_start: 0.8398 (mt) cc_final: 0.8178 (mm) REVERT: D 615 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8351 (ttt180) outliers start: 43 outliers final: 3 residues processed: 324 average time/residue: 1.6513 time to fit residues: 598.6872 Evaluate side-chains 256 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 248 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 615 ARG 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 25 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 192 optimal weight: 0.0470 chunk 113 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 211 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 221 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.8880 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN B 185 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.162456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.132016 restraints weight = 22119.349| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.59 r_work: 0.3516 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2197 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= 0.127 Angle : 0.545 6.769 26964 Z= 0.281 Chirality : 0.039 0.200 3072 Planarity : 0.004 0.036 3416 Dihedral : 3.849 16.031 2644 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.48 % Allowed : 11.74 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2408 helix: 0.93 (0.13), residues: 1504 sheet: -1.98 (0.45), residues: 132 loop : -0.46 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 29 HIS 0.004 0.001 HIS A 201 PHE 0.013 0.001 PHE B 487 TYR 0.008 0.001 TYR C 559 ARG 0.008 0.000 ARG D 180 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 1128) hydrogen bonds : angle 3.90996 ( 3228) covalent geometry : bond 0.00288 (19860) covalent geometry : angle 0.54494 (26964) *********************** 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 287 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 256 time to evaluate : 2.357 Fit side-chains REVERT: A 35 ARG cc_start: 0.8185 (ttt90) cc_final: 0.7817 (ttt180) REVERT: A 108 GLU cc_start: 0.7175 (mp0) cc_final: 0.6864 (mp0) REVERT: A 177 GLU cc_start: 0.7864 (pm20) cc_final: 0.7422 (tp30) REVERT: A 184 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7527 (mt-10) REVERT: A 447 MET cc_start: 0.8127 (ptm) cc_final: 0.7895 (ptp) REVERT: A 615 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8308 (ttt180) REVERT: B 108 GLU cc_start: 0.7192 (mp0) cc_final: 0.6882 (mp0) REVERT: B 177 GLU cc_start: 0.7787 (pm20) cc_final: 0.7352 (tp30) REVERT: B 615 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8299 (ttt180) REVERT: C 177 GLU cc_start: 0.7797 (pm20) cc_final: 0.7070 (tp30) REVERT: C 214 GLN cc_start: 0.8588 (mp-120) cc_final: 0.8380 (mp-120) REVERT: C 215 MET cc_start: 0.9010 (mmm) cc_final: 0.8777 (tpp) REVERT: C 497 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8492 (ptm) REVERT: C 615 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8307 (ttt180) REVERT: D 108 GLU cc_start: 0.7232 (mp0) cc_final: 0.6928 (mp0) REVERT: D 177 GLU cc_start: 0.7772 (pm20) cc_final: 0.7168 (tp30) REVERT: D 447 MET cc_start: 0.8132 (ptm) cc_final: 0.7886 (ptp) REVERT: D 615 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8307 (ttt180) REVERT: D 622 GLU cc_start: 0.7606 (tt0) cc_final: 0.7244 (tt0) outliers start: 31 outliers final: 8 residues processed: 273 average time/residue: 1.5013 time to fit residues: 463.7104 Evaluate side-chains 250 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 237 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP 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 615 ARG Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 111 LEU 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 57 ASP 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 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 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 185 HIS ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 208 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.159227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128456 restraints weight = 22370.944| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.60 r_work: 0.3471 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2516 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= 0.156 Angle : 0.564 7.145 26964 Z= 0.291 Chirality : 0.040 0.187 3072 Planarity : 0.004 0.036 3416 Dihedral : 3.859 14.980 2644 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.05 % Allowed : 12.55 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2408 helix: 1.30 (0.13), residues: 1504 sheet: -2.07 (0.46), residues: 132 loop : -0.35 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 593 HIS 0.005 0.001 HIS C 201 PHE 0.013 0.001 PHE B 425 TYR 0.011 0.001 TYR C 559 ARG 0.007 0.000 ARG D 180 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 1128) hydrogen bonds : angle 3.90127 ( 3228) covalent geometry : bond 0.00368 (19860) covalent geometry : angle 0.56411 (26964) *********************** 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 292 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 3.027 Fit side-chains REVERT: A 108 GLU cc_start: 0.7300 (mp0) cc_final: 0.6958 (mp0) REVERT: A 177 GLU cc_start: 0.7899 (pm20) cc_final: 0.7534 (tp30) REVERT: A 273 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.7970 (pp) REVERT: A 615 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8336 (ttt180) REVERT: B 80 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7890 (pt0) REVERT: B 108 GLU cc_start: 0.7315 (mp0) cc_final: 0.7021 (mp0) REVERT: B 177 GLU cc_start: 0.7890 (pm20) cc_final: 0.7522 (tp30) REVERT: B 273 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.7982 (pp) REVERT: B 615 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8300 (ttt180) REVERT: C 177 GLU cc_start: 0.7868 (pm20) cc_final: 0.7255 (tp30) REVERT: C 215 MET cc_start: 0.9072 (mmm) cc_final: 0.8858 (tpp) REVERT: C 273 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.7964 (pp) REVERT: C 473 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8378 (tt0) REVERT: C 497 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8450 (ttt) REVERT: C 615 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8321 (ttt180) REVERT: D 35 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7656 (ttt90) REVERT: D 108 GLU cc_start: 0.7313 (mp0) cc_final: 0.6975 (mp0) REVERT: D 177 GLU cc_start: 0.7718 (pm20) cc_final: 0.7180 (tp30) REVERT: D 273 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8000 (pp) REVERT: D 466 MET cc_start: 0.9053 (mtt) cc_final: 0.8805 (mtt) REVERT: D 615 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8320 (ttt180) outliers start: 43 outliers final: 11 residues processed: 277 average time/residue: 1.3005 time to fit residues: 408.1594 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 : 2.149 ------------------------------------------------------------------------------- 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 486 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 592 LEU Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain C residue 273 LEU 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 35 ARG Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 273 LEU 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 46 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 65 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 208 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.153412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.133633 restraints weight = 21714.125| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 0.86 r_work: 0.3347 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19860 Z= 0.114 Angle : 0.521 6.588 26964 Z= 0.269 Chirality : 0.038 0.172 3072 Planarity : 0.004 0.035 3416 Dihedral : 3.724 15.108 2644 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.05 % Allowed : 13.22 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.17), residues: 2408 helix: 1.66 (0.13), residues: 1500 sheet: -1.72 (0.49), residues: 112 loop : -0.40 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 593 HIS 0.003 0.001 HIS C 201 PHE 0.009 0.001 PHE B 487 TYR 0.007 0.001 TYR C 336 ARG 0.006 0.000 ARG D 180 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 1128) hydrogen bonds : angle 3.75751 ( 3228) covalent geometry : bond 0.00249 (19860) covalent geometry : angle 0.52078 (26964) *********************** 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 289 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 246 time to evaluate : 2.076 Fit side-chains REVERT: A 55 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7018 (mm-30) REVERT: A 80 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7722 (pt0) REVERT: A 466 MET cc_start: 0.8792 (mtt) cc_final: 0.8515 (mtt) REVERT: A 497 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8168 (ttm) REVERT: A 615 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8321 (ttt180) REVERT: B 55 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7007 (mm-30) REVERT: B 497 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8137 (ttm) REVERT: B 615 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8275 (ttt180) REVERT: C 55 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7043 (mm-30) REVERT: C 80 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7758 (pt0) REVERT: C 108 GLU cc_start: 0.7118 (mp0) cc_final: 0.6914 (mp0) REVERT: C 466 MET cc_start: 0.8793 (mtm) cc_final: 0.8559 (mtt) REVERT: C 615 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8283 (ttt180) REVERT: D 35 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7442 (ttt90) REVERT: D 55 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7265 (mm-30) REVERT: D 80 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7738 (pt0) REVERT: D 108 GLU cc_start: 0.7170 (mp0) cc_final: 0.6930 (mp0) REVERT: D 177 GLU cc_start: 0.7671 (pm20) cc_final: 0.7344 (tp30) REVERT: D 466 MET cc_start: 0.8799 (mtt) cc_final: 0.8590 (mtt) REVERT: D 497 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8110 (ttm) REVERT: D 615 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8301 (ttt180) outliers start: 43 outliers final: 12 residues processed: 271 average time/residue: 1.4012 time to fit residues: 429.4216 Evaluate side-chains 247 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU 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 497 MET Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 497 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 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 419 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 9 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127123 restraints weight = 21731.263| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 0.93 r_work: 0.3095 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19860 Z= 0.155 Angle : 0.568 7.128 26964 Z= 0.293 Chirality : 0.040 0.184 3072 Planarity : 0.004 0.036 3416 Dihedral : 3.832 15.296 2644 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.72 % Allowed : 13.17 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.17), residues: 2408 helix: 1.64 (0.13), residues: 1500 sheet: -2.28 (0.45), residues: 132 loop : -0.35 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 593 HIS 0.005 0.001 HIS A 201 PHE 0.014 0.001 PHE A 425 TYR 0.011 0.001 TYR C 559 ARG 0.006 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 1128) hydrogen bonds : angle 3.85480 ( 3228) covalent geometry : bond 0.00368 (19860) covalent geometry : angle 0.56759 (26964) *********************** 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 276 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 219 time to evaluate : 2.175 Fit side-chains REVERT: A 55 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6803 (mm-30) REVERT: A 80 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7709 (pt0) REVERT: A 273 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7942 (pp) REVERT: A 466 MET cc_start: 0.8939 (mtt) cc_final: 0.8658 (mtt) REVERT: A 497 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8119 (ttt) REVERT: A 615 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8242 (ttt180) REVERT: B 55 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6808 (mm-30) REVERT: B 273 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.7946 (pp) REVERT: B 497 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8111 (ttt) REVERT: B 615 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8222 (ttt180) REVERT: C 55 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6831 (mm-30) REVERT: C 80 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7734 (pt0) REVERT: C 615 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8214 (ttt180) REVERT: D 35 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7391 (ttt90) REVERT: D 55 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7258 (mm-30) REVERT: D 80 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7748 (pt0) REVERT: D 177 GLU cc_start: 0.7699 (pm20) cc_final: 0.7331 (tp30) REVERT: D 273 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7965 (pp) REVERT: D 497 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8089 (ttt) REVERT: D 590 ASP cc_start: 0.6859 (m-30) cc_final: 0.6631 (m-30) REVERT: D 615 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8220 (ttt180) outliers start: 57 outliers final: 13 residues processed: 257 average time/residue: 1.2848 time to fit residues: 373.2104 Evaluate side-chains 239 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 497 MET 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 273 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 497 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 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 273 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 577 MET 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 171 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 161 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.152860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.130640 restraints weight = 21579.864| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 0.92 r_work: 0.3337 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19860 Z= 0.117 Angle : 0.520 6.651 26964 Z= 0.268 Chirality : 0.038 0.167 3072 Planarity : 0.004 0.036 3416 Dihedral : 3.699 15.607 2644 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.24 % Allowed : 13.45 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2408 helix: 1.83 (0.13), residues: 1500 sheet: -2.29 (0.45), residues: 132 loop : -0.30 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 29 HIS 0.003 0.001 HIS B 201 PHE 0.009 0.001 PHE B 487 TYR 0.007 0.001 TYR A 336 ARG 0.007 0.000 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 1128) hydrogen bonds : angle 3.75207 ( 3228) covalent geometry : bond 0.00264 (19860) covalent geometry : angle 0.52013 (26964) *********************** 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 279 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 2.041 Fit side-chains REVERT: A 55 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6868 (mm-30) REVERT: A 80 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7645 (pt0) REVERT: A 273 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8134 (pp) REVERT: A 466 MET cc_start: 0.8820 (mtt) cc_final: 0.8589 (mtt) REVERT: A 474 MET cc_start: 0.8024 (ptm) cc_final: 0.7715 (ptt) REVERT: A 497 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8150 (ttm) REVERT: A 615 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8283 (ttt180) REVERT: B 35 ARG cc_start: 0.8056 (ttt90) cc_final: 0.7732 (ttt180) REVERT: B 55 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6906 (mm-30) REVERT: B 80 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7687 (pt0) REVERT: B 273 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8132 (pp) REVERT: B 366 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8770 (m) REVERT: B 474 MET cc_start: 0.8066 (ptm) cc_final: 0.7685 (ptm) REVERT: B 497 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8136 (ttm) REVERT: B 615 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8274 (ttt180) REVERT: C 55 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6896 (mm-30) REVERT: C 80 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7630 (pt0) REVERT: C 177 GLU cc_start: 0.7387 (tp30) cc_final: 0.7184 (tp30) REVERT: C 273 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8167 (pp) REVERT: C 615 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8275 (ttt180) REVERT: D 35 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7461 (ttt90) REVERT: D 80 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7690 (pt0) REVERT: D 108 GLU cc_start: 0.7211 (mp0) cc_final: 0.6970 (mp0) REVERT: D 273 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8130 (pp) REVERT: D 474 MET cc_start: 0.8039 (ptm) cc_final: 0.7723 (ptt) REVERT: D 497 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8126 (ttm) REVERT: D 615 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8279 (ttt180) outliers start: 47 outliers final: 14 residues processed: 258 average time/residue: 1.2641 time to fit residues: 370.4766 Evaluate side-chains 249 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 2.051 ------------------------------------------------------------------------------- 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 419 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 497 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 497 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 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 419 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 109 optimal weight: 0.0060 chunk 89 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 229 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 215 optimal weight: 4.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.153524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 119)---------------| | r_work = 0.3493 r_free = 0.3493 target = 0.131526 restraints weight = 21683.931| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 0.89 r_work: 0.3352 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19860 Z= 0.114 Angle : 0.523 6.603 26964 Z= 0.270 Chirality : 0.038 0.157 3072 Planarity : 0.004 0.035 3416 Dihedral : 3.634 15.419 2644 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.62 % Allowed : 13.60 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.18), residues: 2408 helix: 1.97 (0.13), residues: 1504 sheet: -2.26 (0.45), residues: 132 loop : -0.29 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 29 HIS 0.003 0.001 HIS B 201 PHE 0.013 0.001 PHE C 456 TYR 0.007 0.001 TYR A 336 ARG 0.007 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 1128) hydrogen bonds : angle 3.70881 ( 3228) covalent geometry : bond 0.00253 (19860) covalent geometry : angle 0.52286 (26964) *********************** 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 285 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 230 time to evaluate : 2.073 Fit side-chains REVERT: A 55 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6835 (mm-30) REVERT: A 80 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7581 (pt0) REVERT: A 273 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8110 (pp) REVERT: A 366 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8747 (m) REVERT: A 466 MET cc_start: 0.8863 (mtt) cc_final: 0.8654 (mtt) REVERT: A 497 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8116 (ttm) REVERT: A 615 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8308 (ttt180) REVERT: B 55 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6886 (mm-30) REVERT: B 80 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7586 (pt0) REVERT: B 273 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8122 (pp) REVERT: B 366 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8751 (m) REVERT: B 466 MET cc_start: 0.8737 (mtm) cc_final: 0.8488 (mtt) REVERT: B 474 MET cc_start: 0.8040 (ptm) cc_final: 0.7665 (ptm) REVERT: B 497 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8084 (ttm) REVERT: B 615 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8247 (ttt180) REVERT: C 35 ARG cc_start: 0.8065 (ttt90) cc_final: 0.7726 (ttt180) REVERT: C 55 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6881 (mm-30) REVERT: C 80 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7565 (pt0) REVERT: C 273 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8139 (pp) REVERT: C 366 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8747 (m) REVERT: C 474 MET cc_start: 0.8042 (ptm) cc_final: 0.7684 (ptm) REVERT: C 615 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8275 (ttt180) REVERT: D 35 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7481 (ttt90) REVERT: D 80 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7604 (pt0) REVERT: D 273 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8116 (pp) REVERT: D 366 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8740 (m) REVERT: D 466 MET cc_start: 0.8675 (mtm) cc_final: 0.8402 (mtt) REVERT: D 474 MET cc_start: 0.7992 (ptm) cc_final: 0.7672 (ptt) REVERT: D 497 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8115 (ttm) REVERT: D 615 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8293 (ttt180) outliers start: 55 outliers final: 21 residues processed: 261 average time/residue: 1.2686 time to fit residues: 374.9784 Evaluate side-chains 261 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 2.128 ------------------------------------------------------------------------------- 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 366 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 497 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 366 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 497 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 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 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 486 ILE Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 592 LEU 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 148 optimal weight: 0.9980 chunk 140 optimal weight: 0.1980 chunk 154 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 228 optimal weight: 0.0050 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 51 GLN D 637 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.152502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129087 restraints weight = 21835.435| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.13 r_work: 0.3324 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2822 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= 0.115 Angle : 0.529 6.647 26964 Z= 0.273 Chirality : 0.038 0.172 3072 Planarity : 0.004 0.035 3416 Dihedral : 3.617 20.247 2644 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.00 % Allowed : 14.93 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.18), residues: 2408 helix: 2.02 (0.13), residues: 1504 sheet: -2.33 (0.44), residues: 132 loop : -0.28 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 29 HIS 0.003 0.001 HIS D 201 PHE 0.014 0.001 PHE A 456 TYR 0.007 0.001 TYR A 336 ARG 0.007 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 1128) hydrogen bonds : angle 3.70543 ( 3228) covalent geometry : bond 0.00254 (19860) covalent geometry : angle 0.52909 (26964) *********************** 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 269 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 2.054 Fit side-chains REVERT: A 55 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6884 (mm-30) REVERT: A 80 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7613 (pt0) REVERT: A 273 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8112 (pp) REVERT: A 366 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8780 (m) REVERT: A 474 MET cc_start: 0.8036 (ptm) cc_final: 0.7692 (ptt) REVERT: A 497 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8172 (ttm) REVERT: A 615 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8381 (ttt180) REVERT: B 55 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6955 (mm-30) REVERT: B 80 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7625 (pt0) REVERT: B 273 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8130 (pp) REVERT: B 366 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8777 (m) REVERT: B 466 MET cc_start: 0.8835 (mtm) cc_final: 0.8572 (mtt) REVERT: B 474 MET cc_start: 0.8087 (ptm) cc_final: 0.7763 (ptt) REVERT: B 497 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8154 (ttm) REVERT: B 615 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8271 (ttm170) REVERT: C 35 ARG cc_start: 0.8170 (ttt90) cc_final: 0.7826 (ttt180) REVERT: C 55 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6914 (mm-30) REVERT: C 80 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: C 273 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8139 (pp) REVERT: C 366 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8780 (m) REVERT: C 615 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8356 (ttt180) REVERT: D 35 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7571 (ttt90) REVERT: D 80 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7612 (pt0) REVERT: D 273 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8123 (pp) REVERT: D 366 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8766 (m) REVERT: D 466 MET cc_start: 0.8832 (mtm) cc_final: 0.8574 (mtt) REVERT: D 497 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8165 (ttm) REVERT: D 615 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8364 (ttt180) outliers start: 42 outliers final: 16 residues processed: 251 average time/residue: 1.3633 time to fit residues: 384.2746 Evaluate side-chains 256 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 2.165 ------------------------------------------------------------------------------- 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 497 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 497 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 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 366 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 577 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 44 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 112 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 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 637 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.151777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130777 restraints weight = 21688.190| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 0.89 r_work: 0.3337 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2896 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 : 0.542 6.779 26964 Z= 0.280 Chirality : 0.039 0.173 3072 Planarity : 0.004 0.035 3416 Dihedral : 3.667 22.777 2644 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.86 % Allowed : 15.55 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2408 helix: 1.97 (0.13), residues: 1500 sheet: -2.37 (0.44), residues: 132 loop : -0.30 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 29 HIS 0.004 0.001 HIS D 201 PHE 0.016 0.001 PHE C 456 TYR 0.008 0.001 TYR A 559 ARG 0.007 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 1128) hydrogen bonds : angle 3.74005 ( 3228) covalent geometry : bond 0.00284 (19860) covalent geometry : angle 0.54185 (26964) ********************** 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 265 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 1.860 Fit side-chains REVERT: A 35 ARG cc_start: 0.8077 (ttt90) cc_final: 0.7746 (ttt180) REVERT: A 80 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7532 (pt0) REVERT: A 273 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8110 (pp) REVERT: A 366 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8760 (m) REVERT: A 474 MET cc_start: 0.7952 (ptm) cc_final: 0.7627 (ptt) REVERT: A 497 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8152 (ttm) REVERT: A 615 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8280 (ttt180) REVERT: B 55 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6877 (mm-30) REVERT: B 80 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7578 (pt0) REVERT: B 273 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8154 (pp) REVERT: B 366 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8762 (m) REVERT: B 466 MET cc_start: 0.8787 (mtm) cc_final: 0.8523 (mtt) REVERT: B 497 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8133 (ttm) REVERT: B 615 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8243 (ttt180) REVERT: C 35 ARG cc_start: 0.8090 (ttt90) cc_final: 0.7750 (ttt180) REVERT: C 80 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7517 (pt0) REVERT: C 273 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8072 (pp) REVERT: C 366 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8758 (m) REVERT: C 474 MET cc_start: 0.8016 (ptm) cc_final: 0.7664 (ptm) REVERT: C 615 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8281 (ttt180) REVERT: D 35 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7520 (ttt90) REVERT: D 80 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7483 (pt0) REVERT: D 273 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8153 (pp) REVERT: D 366 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8751 (m) REVERT: D 466 MET cc_start: 0.8788 (mtm) cc_final: 0.8523 (mtt) REVERT: D 497 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8131 (ttm) REVERT: D 615 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8250 (ttt180) outliers start: 39 outliers final: 20 residues processed: 248 average time/residue: 1.5214 time to fit residues: 426.8701 Evaluate side-chains 263 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 2.188 ------------------------------------------------------------------------------- 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 366 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 497 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 366 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 497 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 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 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 497 MET Chi-restraints excluded: chain D residue 577 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 18 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 637 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.136848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.106883 restraints weight = 23020.054| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.60 r_work: 0.3010 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19860 Z= 0.152 Angle : 0.570 7.106 26964 Z= 0.294 Chirality : 0.040 0.186 3072 Planarity : 0.004 0.035 3416 Dihedral : 3.776 26.226 2644 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.24 % Allowed : 15.51 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.17), residues: 2408 helix: 1.86 (0.13), residues: 1500 sheet: -2.37 (0.45), residues: 132 loop : -0.32 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 29 HIS 0.005 0.001 HIS D 201 PHE 0.017 0.001 PHE C 456 TYR 0.011 0.001 TYR A 559 ARG 0.007 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 1128) hydrogen bonds : angle 3.83654 ( 3228) covalent geometry : bond 0.00363 (19860) covalent geometry : angle 0.56969 (26964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15088.78 seconds wall clock time: 268 minutes 29.07 seconds (16109.07 seconds total)