Starting phenix.real_space_refine on Thu Mar 5 05:15:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o1u_0605/03_2026/6o1u_0605.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o1u_0605/03_2026/6o1u_0605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6o1u_0605/03_2026/6o1u_0605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o1u_0605/03_2026/6o1u_0605.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o1u_0605/03_2026/6o1u_0605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o1u_0605/03_2026/6o1u_0605.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.097 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 12652 2.51 5 N 3324 2.21 5 O 3496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19612 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4903 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 589} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Restraints were copied for chains: B, C, D Time building chain proxies: 4.14, per 1000 atoms: 0.21 Number of scatterers: 19612 At special positions: 0 Unit cell: (130.257, 130.257, 120.726, 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 3496 8.00 N 3324 7.00 C 12652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 889.1 milliseconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 8 sheets defined 64.2% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.726A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 removed outlier: 4.078A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) 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 106 removed outlier: 3.802A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.193A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.578A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 126 " --> pdb=" O HIS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.537A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.666A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.785A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.617A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.748A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.553A pdb=" N LEU A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.878A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.521A pdb=" N VAL A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 411 Proline residue: A 405 - end of helix removed outlier: 3.827A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.648A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 446 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.773A pdb=" N PHE A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 3.600A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 499 through 512 removed outlier: 3.867A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.371A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 525 through 539 removed outlier: 3.559A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.721A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 584 removed outlier: 3.657A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 608 removed outlier: 3.536A pdb=" N ARG A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 47 removed outlier: 3.726A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 removed outlier: 4.079A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) 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 106 removed outlier: 3.803A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.194A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.578A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET B 126 " --> pdb=" O HIS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.537A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.666A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.784A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.618A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.748A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.553A pdb=" N LEU B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.878A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.521A pdb=" N VAL B 331 " --> pdb=" O PRO B 327 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 411 Proline residue: B 405 - end of helix removed outlier: 3.827A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 removed outlier: 3.649A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 446 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.774A pdb=" N PHE B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 removed outlier: 3.600A pdb=" N THR B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.867A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 4.371A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 525 through 539 removed outlier: 3.559A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.721A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 584 removed outlier: 3.656A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 608 removed outlier: 3.537A pdb=" N ARG B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.726A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 removed outlier: 4.078A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) 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 106 removed outlier: 3.802A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.193A pdb=" N VAL C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.577A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.537A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.666A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.785A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.617A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.748A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.553A pdb=" N LEU C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 310 removed outlier: 3.878A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.521A pdb=" N VAL C 331 " --> pdb=" O PRO C 327 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 411 Proline residue: C 405 - end of helix removed outlier: 3.826A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.649A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 446 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.773A pdb=" N PHE C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 removed outlier: 3.599A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 499 Processing helix chain 'C' and resid 499 through 512 removed outlier: 3.867A pdb=" N ALA C 505 " --> pdb=" O ILE C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 4.372A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 524' Processing helix chain 'C' and resid 525 through 539 removed outlier: 3.559A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.721A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 584 removed outlier: 3.657A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 608 removed outlier: 3.536A pdb=" N ARG C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 47 removed outlier: 3.726A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 removed outlier: 4.078A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) 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 106 removed outlier: 3.802A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 112 through 116 removed outlier: 4.193A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.577A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET D 126 " --> pdb=" O HIS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.537A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 183 removed outlier: 3.666A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.784A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.618A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.748A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 249 " --> pdb=" O LYS D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.553A pdb=" N LEU D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.878A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.521A pdb=" N VAL D 331 " --> pdb=" O PRO D 327 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 411 Proline residue: D 405 - end of helix removed outlier: 3.828A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 418 removed outlier: 3.649A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 446 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.773A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 removed outlier: 3.600A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 499 Processing helix chain 'D' and resid 499 through 512 removed outlier: 3.867A pdb=" N ALA D 505 " --> pdb=" O ILE D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.371A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER D 524 " --> pdb=" O GLY D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 525 through 539 removed outlier: 3.560A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.720A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 584 removed outlier: 3.657A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 608 removed outlier: 3.536A pdb=" N ARG D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.945A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (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: 6.945A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (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: 6.945A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (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: 6.945A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 952 hydrogen bonds defined for protein. 2748 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: 4.02 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3180 1.30 - 1.44: 5433 1.44 - 1.57: 11212 1.57 - 1.71: 7 1.71 - 1.84: 228 Bond restraints: 20060 Sorted by residual: bond pdb=" N TRP B 29 " pdb=" CA TRP B 29 " ideal model delta sigma weight residual 1.459 1.363 0.096 1.17e-02 7.31e+03 6.68e+01 bond pdb=" N TRP C 29 " pdb=" CA TRP C 29 " ideal model delta sigma weight residual 1.459 1.363 0.096 1.18e-02 7.18e+03 6.64e+01 bond pdb=" N TRP A 29 " pdb=" CA TRP A 29 " ideal model delta sigma weight residual 1.459 1.364 0.095 1.17e-02 7.31e+03 6.62e+01 bond pdb=" N TRP D 29 " pdb=" CA TRP D 29 " ideal model delta sigma weight residual 1.459 1.364 0.095 1.17e-02 7.31e+03 6.58e+01 bond pdb=" N MET A 474 " pdb=" CA MET A 474 " ideal model delta sigma weight residual 1.459 1.388 0.071 1.18e-02 7.18e+03 3.63e+01 ... (remaining 20055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 26814 3.55 - 7.09: 370 7.09 - 10.64: 48 10.64 - 14.18: 0 14.18 - 17.73: 4 Bond angle restraints: 27236 Sorted by residual: angle pdb=" CB MET C 440 " pdb=" CG MET C 440 " pdb=" SD MET C 440 " ideal model delta sigma weight residual 112.70 130.43 -17.73 3.00e+00 1.11e-01 3.49e+01 angle pdb=" CB MET D 440 " pdb=" CG MET D 440 " pdb=" SD MET D 440 " ideal model delta sigma weight residual 112.70 130.42 -17.72 3.00e+00 1.11e-01 3.49e+01 angle pdb=" CB MET A 440 " pdb=" CG MET A 440 " pdb=" SD MET A 440 " ideal model delta sigma weight residual 112.70 130.40 -17.70 3.00e+00 1.11e-01 3.48e+01 angle pdb=" CB MET B 440 " pdb=" CG MET B 440 " pdb=" SD MET B 440 " ideal model delta sigma weight residual 112.70 130.40 -17.70 3.00e+00 1.11e-01 3.48e+01 angle pdb=" N TRP A 29 " pdb=" CA TRP A 29 " pdb=" C TRP A 29 " ideal model delta sigma weight residual 110.97 117.21 -6.24 1.09e+00 8.42e-01 3.28e+01 ... (remaining 27231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 10579 17.20 - 34.40: 1066 34.40 - 51.60: 231 51.60 - 68.79: 56 68.79 - 85.99: 16 Dihedral angle restraints: 11948 sinusoidal: 4776 harmonic: 7172 Sorted by residual: dihedral pdb=" CA ASP C 364 " pdb=" C ASP C 364 " pdb=" N ILE C 365 " pdb=" CA ILE C 365 " ideal model delta harmonic sigma weight residual -180.00 -138.19 -41.81 0 5.00e+00 4.00e-02 6.99e+01 dihedral pdb=" CA ASP A 364 " pdb=" C ASP A 364 " pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta harmonic sigma weight residual -180.00 -138.19 -41.81 0 5.00e+00 4.00e-02 6.99e+01 dihedral pdb=" CA ASP D 364 " pdb=" C ASP D 364 " pdb=" N ILE D 365 " pdb=" CA ILE D 365 " ideal model delta harmonic sigma weight residual -180.00 -138.23 -41.77 0 5.00e+00 4.00e-02 6.98e+01 ... (remaining 11945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2697 0.083 - 0.167: 367 0.167 - 0.250: 28 0.250 - 0.333: 8 0.333 - 0.417: 4 Chirality restraints: 3104 Sorted by residual: chirality pdb=" CA TRP B 29 " pdb=" N TRP B 29 " pdb=" C TRP B 29 " pdb=" CB TRP B 29 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA TRP A 29 " pdb=" N TRP A 29 " pdb=" C TRP A 29 " pdb=" CB TRP A 29 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CA TRP C 29 " pdb=" N TRP C 29 " pdb=" C TRP C 29 " pdb=" CB TRP C 29 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 3101 not shown) Planarity restraints: 3464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 326 " -0.044 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO C 327 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 327 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 327 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 326 " 0.044 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO B 327 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 327 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 327 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 326 " 0.044 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO A 327 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " 0.037 5.00e-02 4.00e+02 ... (remaining 3461 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1657 2.72 - 3.27: 19207 3.27 - 3.81: 33319 3.81 - 4.36: 42029 4.36 - 4.90: 69678 Nonbonded interactions: 165890 Sorted by model distance: nonbonded pdb=" OG1 THR A 514 " pdb=" O GLN B 370 " model vdw 2.180 3.040 nonbonded pdb=" OD1 ASP B 34 " pdb=" NH1 ARG C 632 " model vdw 2.226 3.120 nonbonded pdb=" O GLN A 370 " pdb=" OG1 THR D 514 " model vdw 2.229 3.040 nonbonded pdb=" O LEU C 92 " pdb=" OG1 THR C 96 " model vdw 2.257 3.040 nonbonded pdb=" O LEU B 92 " pdb=" OG1 THR B 96 " model vdw 2.257 3.040 ... (remaining 165885 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: 0.05 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.760 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.010 0.100 20060 Z= 0.487 Angle : 1.084 17.727 27236 Z= 0.602 Chirality : 0.061 0.417 3104 Planarity : 0.007 0.065 3464 Dihedral : 14.745 85.992 7316 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.65 % Allowed : 8.08 % Favored : 89.27 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.22 (0.12), residues: 2448 helix: -3.92 (0.07), residues: 1392 sheet: -2.40 (0.46), residues: 84 loop : -2.54 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 589 TYR 0.023 0.003 TYR B 377 PHE 0.015 0.002 PHE B 537 TRP 0.015 0.003 TRP A 593 HIS 0.007 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.01049 (20060) covalent geometry : angle 1.08378 (27236) hydrogen bonds : bond 0.28268 ( 952) hydrogen bonds : angle 9.86063 ( 2748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 336 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9215 (mtp) cc_final: 0.8953 (mtm) REVERT: A 213 CYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7903 (m) REVERT: A 306 GLN cc_start: 0.8573 (mt0) cc_final: 0.8340 (mm110) REVERT: A 406 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8171 (t0) REVERT: A 474 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8122 (mtt) REVERT: A 594 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7598 (ttp-110) REVERT: B 306 GLN cc_start: 0.8605 (mt0) cc_final: 0.8300 (mm110) REVERT: B 406 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8222 (t0) REVERT: B 474 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8157 (mtt) REVERT: B 481 MET cc_start: 0.6738 (mtm) cc_final: 0.6486 (mtt) REVERT: B 485 MET cc_start: 0.7677 (mtt) cc_final: 0.7281 (mpp) REVERT: B 569 LEU cc_start: 0.8387 (mp) cc_final: 0.8067 (tp) REVERT: C 29 TRP cc_start: 0.7452 (OUTLIER) cc_final: 0.6511 (t60) REVERT: C 306 GLN cc_start: 0.8620 (mt0) cc_final: 0.8405 (mm110) REVERT: C 324 TYR cc_start: 0.8542 (m-80) cc_final: 0.8208 (m-80) REVERT: C 406 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7908 (t0) REVERT: C 447 MET cc_start: 0.8216 (mtt) cc_final: 0.7963 (mtm) REVERT: C 474 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7373 (mtm) REVERT: C 554 MET cc_start: 0.8522 (tpt) cc_final: 0.8314 (tpt) REVERT: C 594 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7623 (ttp-110) REVERT: D 306 GLN cc_start: 0.8630 (mt0) cc_final: 0.8306 (mm110) REVERT: D 406 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8214 (t0) REVERT: D 447 MET cc_start: 0.8209 (mtt) cc_final: 0.7998 (mtm) REVERT: D 474 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7783 (mtm) outliers start: 56 outliers final: 9 residues processed: 372 average time/residue: 0.6100 time to fit residues: 255.9109 Evaluate side-chains 238 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 479 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0670 chunk 235 optimal weight: 0.7980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 257 GLN A 265 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 HIS A 446 ASN A 519 ASN A 572 ASN A 637 HIS B 37 ASN B 74 GLN B 257 GLN B 265 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN B 519 ASN B 572 ASN B 637 HIS C 31 GLN C 74 GLN C 230 GLN C 257 GLN C 265 HIS C 267 GLN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS C 446 ASN C 519 ASN C 572 ASN C 637 HIS D 37 ASN D 74 GLN D 257 GLN D 261 GLN D 265 HIS D 370 GLN D 380 HIS D 446 ASN D 519 ASN D 572 ASN D 637 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.114374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.091545 restraints weight = 34521.884| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.60 r_work: 0.3157 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20060 Z= 0.138 Angle : 0.630 7.171 27236 Z= 0.331 Chirality : 0.041 0.143 3104 Planarity : 0.006 0.056 3464 Dihedral : 6.165 52.945 2715 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.46 % Allowed : 14.51 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.14), residues: 2448 helix: -1.92 (0.11), residues: 1484 sheet: -1.66 (0.52), residues: 84 loop : -2.10 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 492 TYR 0.009 0.001 TYR C 555 PHE 0.011 0.001 PHE A 537 TRP 0.013 0.002 TRP C 613 HIS 0.007 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00307 (20060) covalent geometry : angle 0.62994 (27236) hydrogen bonds : bond 0.03928 ( 952) hydrogen bonds : angle 4.56156 ( 2748) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 267 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8535 (tm) REVERT: A 229 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7412 (tm) REVERT: A 306 GLN cc_start: 0.8709 (mt0) cc_final: 0.8303 (mm110) REVERT: A 406 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8008 (t0) REVERT: A 440 MET cc_start: 0.6527 (mmp) cc_final: 0.5971 (tpt) REVERT: A 474 MET cc_start: 0.8806 (mtp) cc_final: 0.8356 (mtm) REVERT: A 485 MET cc_start: 0.7738 (mtt) cc_final: 0.7514 (mtm) REVERT: A 580 ASP cc_start: 0.8360 (m-30) cc_final: 0.8135 (m-30) REVERT: A 594 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.7982 (ttp-110) REVERT: A 612 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7598 (mp) REVERT: B 229 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7450 (tm) REVERT: B 306 GLN cc_start: 0.8765 (mt0) cc_final: 0.8306 (mm110) REVERT: B 338 LEU cc_start: 0.8896 (tt) cc_final: 0.8677 (mt) REVERT: B 406 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8076 (t0) REVERT: B 474 MET cc_start: 0.8783 (mtp) cc_final: 0.8282 (mtm) REVERT: B 481 MET cc_start: 0.7375 (mtm) cc_final: 0.6905 (mtt) REVERT: B 485 MET cc_start: 0.7762 (mtt) cc_final: 0.7398 (mpp) REVERT: B 594 ARG cc_start: 0.8453 (ttp-110) cc_final: 0.8252 (ttp-110) REVERT: B 612 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7539 (mp) REVERT: C 80 GLU cc_start: 0.7953 (pt0) cc_final: 0.7397 (pm20) REVERT: C 113 GLU cc_start: 0.7428 (tt0) cc_final: 0.7228 (tp30) REVERT: C 213 CYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7473 (m) REVERT: C 229 LEU cc_start: 0.7845 (mm) cc_final: 0.7198 (tm) REVERT: C 302 ARG cc_start: 0.8357 (mtp-110) cc_final: 0.8057 (mtp85) REVERT: C 306 GLN cc_start: 0.8792 (mt0) cc_final: 0.8380 (mm110) REVERT: C 324 TYR cc_start: 0.8722 (m-80) cc_final: 0.8491 (m-80) REVERT: C 406 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8066 (t0) REVERT: C 447 MET cc_start: 0.8508 (mtt) cc_final: 0.8303 (mtm) REVERT: C 474 MET cc_start: 0.8514 (mtp) cc_final: 0.8025 (mtm) REVERT: C 594 ARG cc_start: 0.8393 (mtm-85) cc_final: 0.7982 (ttp-110) REVERT: D 80 GLU cc_start: 0.8009 (pt0) cc_final: 0.7602 (pm20) REVERT: D 229 LEU cc_start: 0.8028 (mm) cc_final: 0.7400 (tm) REVERT: D 306 GLN cc_start: 0.8780 (mt0) cc_final: 0.8294 (mm110) REVERT: D 406 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8091 (t0) REVERT: D 474 MET cc_start: 0.8758 (mtp) cc_final: 0.8307 (mtm) outliers start: 52 outliers final: 15 residues processed: 298 average time/residue: 0.5601 time to fit residues: 190.0958 Evaluate side-chains 232 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 139 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN A 446 ASN B 261 GLN B 370 GLN C 261 GLN ** C 370 GLN ** 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 = 0.3610 r_free = 0.3610 target = 0.115491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.092860 restraints weight = 35068.832| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.61 r_work: 0.3165 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20060 Z= 0.118 Angle : 0.570 8.493 27236 Z= 0.296 Chirality : 0.039 0.143 3104 Planarity : 0.004 0.056 3464 Dihedral : 5.302 52.080 2690 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.79 % Allowed : 16.02 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.15), residues: 2448 helix: -0.49 (0.12), residues: 1468 sheet: -1.13 (0.51), residues: 84 loop : -1.87 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 492 TYR 0.012 0.001 TYR C 621 PHE 0.009 0.001 PHE D 611 TRP 0.010 0.001 TRP D 29 HIS 0.006 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00267 (20060) covalent geometry : angle 0.57015 (27236) hydrogen bonds : bond 0.03372 ( 952) hydrogen bonds : angle 3.99874 ( 2748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 242 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7916 (pt0) cc_final: 0.7589 (pm20) REVERT: A 229 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7436 (tm) REVERT: A 306 GLN cc_start: 0.8697 (mt0) cc_final: 0.8297 (mm110) REVERT: A 315 GLU cc_start: 0.8524 (mp0) cc_final: 0.8053 (mp0) REVERT: A 406 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7830 (t0) REVERT: A 474 MET cc_start: 0.8745 (mtp) cc_final: 0.8258 (mtm) REVERT: A 513 GLN cc_start: 0.8509 (tt0) cc_final: 0.8167 (tt0) REVERT: A 594 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.7953 (ttp-110) REVERT: B 80 GLU cc_start: 0.7951 (pt0) cc_final: 0.7640 (pm20) REVERT: B 229 LEU cc_start: 0.8043 (mm) cc_final: 0.7456 (tm) REVERT: B 306 GLN cc_start: 0.8752 (mt0) cc_final: 0.8266 (mm110) REVERT: B 315 GLU cc_start: 0.8528 (mp0) cc_final: 0.8077 (mp0) REVERT: B 474 MET cc_start: 0.8807 (mtp) cc_final: 0.8264 (mtm) REVERT: B 481 MET cc_start: 0.7512 (mtm) cc_final: 0.7205 (mtt) REVERT: B 581 THR cc_start: 0.6821 (OUTLIER) cc_final: 0.6550 (p) REVERT: B 594 ARG cc_start: 0.8460 (ttp-110) cc_final: 0.8171 (ttp-110) REVERT: C 31 GLN cc_start: 0.8584 (mt0) cc_final: 0.8352 (mt0) REVERT: C 80 GLU cc_start: 0.7948 (pt0) cc_final: 0.7471 (pm20) REVERT: C 229 LEU cc_start: 0.7801 (mm) cc_final: 0.7183 (tm) REVERT: C 300 LYS cc_start: 0.9038 (mttt) cc_final: 0.8835 (mmtp) REVERT: C 302 ARG cc_start: 0.8348 (mtp-110) cc_final: 0.8096 (mtp85) REVERT: C 306 GLN cc_start: 0.8705 (mt0) cc_final: 0.8229 (mm110) REVERT: C 315 GLU cc_start: 0.8528 (mp0) cc_final: 0.8114 (mp0) REVERT: C 447 MET cc_start: 0.8422 (mtt) cc_final: 0.8205 (mtm) REVERT: C 474 MET cc_start: 0.8613 (mtp) cc_final: 0.8127 (mtm) REVERT: C 577 MET cc_start: 0.8291 (ptm) cc_final: 0.8041 (ptm) REVERT: C 581 THR cc_start: 0.7008 (OUTLIER) cc_final: 0.6792 (p) REVERT: C 594 ARG cc_start: 0.8390 (mtm-85) cc_final: 0.7974 (ttp-110) REVERT: D 66 LEU cc_start: 0.8373 (tt) cc_final: 0.8113 (tp) REVERT: D 80 GLU cc_start: 0.7958 (pt0) cc_final: 0.7651 (pm20) REVERT: D 229 LEU cc_start: 0.8044 (mm) cc_final: 0.7429 (tm) REVERT: D 302 ARG cc_start: 0.8314 (mtp-110) cc_final: 0.8086 (mtp85) REVERT: D 306 GLN cc_start: 0.8730 (mt0) cc_final: 0.8214 (mm110) REVERT: D 315 GLU cc_start: 0.8563 (mp0) cc_final: 0.8103 (mp0) REVERT: D 474 MET cc_start: 0.8731 (mtp) cc_final: 0.8270 (mtm) REVERT: D 569 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7828 (tt) REVERT: D 594 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.8135 (ttp-110) outliers start: 59 outliers final: 8 residues processed: 273 average time/residue: 0.5789 time to fit residues: 179.0070 Evaluate side-chains 215 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 33 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 222 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN C 267 GLN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.110511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.087361 restraints weight = 35290.594| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.63 r_work: 0.3093 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20060 Z= 0.197 Angle : 0.633 8.887 27236 Z= 0.320 Chirality : 0.043 0.170 3104 Planarity : 0.004 0.060 3464 Dihedral : 5.057 50.165 2682 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.32 % Allowed : 17.91 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.16), residues: 2448 helix: -0.02 (0.13), residues: 1472 sheet: -1.05 (0.52), residues: 84 loop : -1.73 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 492 TYR 0.014 0.002 TYR C 555 PHE 0.023 0.001 PHE C 611 TRP 0.013 0.001 TRP A 29 HIS 0.004 0.001 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00461 (20060) covalent geometry : angle 0.63259 (27236) hydrogen bonds : bond 0.03615 ( 952) hydrogen bonds : angle 4.07059 ( 2748) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 235 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8013 (pt0) cc_final: 0.7633 (pm20) REVERT: A 306 GLN cc_start: 0.8723 (mt0) cc_final: 0.8270 (mm110) REVERT: A 315 GLU cc_start: 0.8560 (mp0) cc_final: 0.8092 (mp0) REVERT: A 445 THR cc_start: 0.8973 (m) cc_final: 0.8697 (p) REVERT: A 447 MET cc_start: 0.8184 (mtp) cc_final: 0.7852 (mtp) REVERT: A 474 MET cc_start: 0.8633 (mtp) cc_final: 0.8120 (mtm) REVERT: A 594 ARG cc_start: 0.8487 (mtm-85) cc_final: 0.8054 (ttp-110) REVERT: B 80 GLU cc_start: 0.8042 (pt0) cc_final: 0.7692 (pm20) REVERT: B 306 GLN cc_start: 0.8777 (mt0) cc_final: 0.8343 (mm110) REVERT: B 315 GLU cc_start: 0.8566 (mp0) cc_final: 0.8110 (mp0) REVERT: B 445 THR cc_start: 0.8961 (m) cc_final: 0.8660 (p) REVERT: B 474 MET cc_start: 0.8816 (mtp) cc_final: 0.8307 (mtm) REVERT: B 481 MET cc_start: 0.7420 (mtm) cc_final: 0.7197 (mtt) REVERT: B 569 LEU cc_start: 0.8322 (mp) cc_final: 0.7885 (tt) REVERT: B 581 THR cc_start: 0.6847 (OUTLIER) cc_final: 0.6636 (p) REVERT: B 594 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.8148 (ttp-110) REVERT: C 31 GLN cc_start: 0.8631 (mt0) cc_final: 0.8350 (mt0) REVERT: C 80 GLU cc_start: 0.8040 (pt0) cc_final: 0.7760 (pm20) REVERT: C 229 LEU cc_start: 0.7903 (mm) cc_final: 0.7237 (tm) REVERT: C 306 GLN cc_start: 0.8784 (mt0) cc_final: 0.8347 (mm110) REVERT: C 315 GLU cc_start: 0.8636 (mp0) cc_final: 0.8184 (mp0) REVERT: C 445 THR cc_start: 0.8764 (m) cc_final: 0.8478 (p) REVERT: C 474 MET cc_start: 0.8603 (mtp) cc_final: 0.8072 (mtm) REVERT: C 569 LEU cc_start: 0.8266 (mp) cc_final: 0.7868 (tt) REVERT: C 577 MET cc_start: 0.8368 (ptm) cc_final: 0.8113 (ptm) REVERT: C 581 THR cc_start: 0.7134 (OUTLIER) cc_final: 0.6926 (p) REVERT: C 594 ARG cc_start: 0.8439 (mtm-85) cc_final: 0.8025 (ttp-110) REVERT: D 80 GLU cc_start: 0.8127 (pt0) cc_final: 0.7729 (pm20) REVERT: D 306 GLN cc_start: 0.8773 (mt0) cc_final: 0.8302 (mm110) REVERT: D 315 GLU cc_start: 0.8616 (mp0) cc_final: 0.8126 (mp0) REVERT: D 380 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.7534 (t-90) REVERT: D 474 MET cc_start: 0.8684 (mtp) cc_final: 0.8176 (mtm) outliers start: 49 outliers final: 16 residues processed: 266 average time/residue: 0.6084 time to fit residues: 182.2907 Evaluate side-chains 220 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 199 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN C 230 GLN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.110617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.087561 restraints weight = 35108.074| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.62 r_work: 0.3069 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20060 Z= 0.197 Angle : 0.624 9.624 27236 Z= 0.318 Chirality : 0.043 0.183 3104 Planarity : 0.004 0.063 3464 Dihedral : 4.877 30.528 2680 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.79 % Allowed : 17.77 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.16), residues: 2448 helix: 0.26 (0.13), residues: 1476 sheet: -1.00 (0.54), residues: 84 loop : -1.64 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 594 TYR 0.013 0.002 TYR B 555 PHE 0.018 0.001 PHE C 611 TRP 0.017 0.001 TRP A 29 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00465 (20060) covalent geometry : angle 0.62383 (27236) hydrogen bonds : bond 0.03515 ( 952) hydrogen bonds : angle 4.05726 ( 2748) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8141 (pt0) cc_final: 0.7781 (pm20) REVERT: A 306 GLN cc_start: 0.8731 (mt0) cc_final: 0.8318 (mm110) REVERT: A 315 GLU cc_start: 0.8520 (mp0) cc_final: 0.8066 (mp0) REVERT: A 474 MET cc_start: 0.8646 (mtp) cc_final: 0.8104 (mtm) REVERT: A 594 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.8058 (ttp-110) REVERT: B 80 GLU cc_start: 0.8148 (pt0) cc_final: 0.7779 (pm20) REVERT: B 306 GLN cc_start: 0.8751 (mt0) cc_final: 0.8306 (mm110) REVERT: B 315 GLU cc_start: 0.8520 (mp0) cc_final: 0.8088 (mp0) REVERT: B 445 THR cc_start: 0.8838 (m) cc_final: 0.8600 (p) REVERT: B 474 MET cc_start: 0.8733 (mtp) cc_final: 0.8249 (mtm) REVERT: B 481 MET cc_start: 0.7440 (mtm) cc_final: 0.7200 (mtt) REVERT: B 569 LEU cc_start: 0.8317 (mp) cc_final: 0.7894 (tt) REVERT: B 581 THR cc_start: 0.6859 (OUTLIER) cc_final: 0.6615 (p) REVERT: B 594 ARG cc_start: 0.8458 (ttp-110) cc_final: 0.8098 (ttp-110) REVERT: C 31 GLN cc_start: 0.8653 (mt0) cc_final: 0.8380 (mt0) REVERT: C 80 GLU cc_start: 0.8123 (pt0) cc_final: 0.7832 (pm20) REVERT: C 229 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7402 (tm) REVERT: C 306 GLN cc_start: 0.8737 (mt0) cc_final: 0.8295 (mm110) REVERT: C 315 GLU cc_start: 0.8547 (mp0) cc_final: 0.8174 (mp0) REVERT: C 445 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8553 (p) REVERT: C 474 MET cc_start: 0.8600 (mtp) cc_final: 0.8095 (mtm) REVERT: C 569 LEU cc_start: 0.8203 (mp) cc_final: 0.7864 (tt) REVERT: C 577 MET cc_start: 0.8343 (ptm) cc_final: 0.8090 (ptm) REVERT: C 594 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.8029 (ttp-110) REVERT: D 80 GLU cc_start: 0.8163 (pt0) cc_final: 0.7847 (pm20) REVERT: D 306 GLN cc_start: 0.8754 (mt0) cc_final: 0.8288 (mm110) REVERT: D 315 GLU cc_start: 0.8588 (mp0) cc_final: 0.8140 (mp0) REVERT: D 474 MET cc_start: 0.8644 (mtp) cc_final: 0.8137 (mtm) REVERT: D 594 ARG cc_start: 0.8516 (ttp-110) cc_final: 0.8194 (ttp-110) outliers start: 59 outliers final: 21 residues processed: 263 average time/residue: 0.6394 time to fit residues: 189.2490 Evaluate side-chains 229 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 193 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 232 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.111402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.088347 restraints weight = 34949.737| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.62 r_work: 0.3084 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20060 Z= 0.169 Angle : 0.612 9.590 27236 Z= 0.310 Chirality : 0.042 0.185 3104 Planarity : 0.004 0.064 3464 Dihedral : 4.790 31.910 2680 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.07 % Allowed : 17.96 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.17), residues: 2448 helix: 0.49 (0.13), residues: 1472 sheet: -0.87 (0.55), residues: 84 loop : -1.58 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 589 TYR 0.011 0.001 TYR C 555 PHE 0.017 0.001 PHE C 611 TRP 0.018 0.001 TRP B 29 HIS 0.006 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00400 (20060) covalent geometry : angle 0.61166 (27236) hydrogen bonds : bond 0.03333 ( 952) hydrogen bonds : angle 3.98976 ( 2748) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 218 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8218 (pt0) cc_final: 0.7877 (pm20) REVERT: A 139 ARG cc_start: 0.8574 (mmt180) cc_final: 0.8347 (mpt180) REVERT: A 306 GLN cc_start: 0.8705 (mt0) cc_final: 0.8249 (mp10) REVERT: A 315 GLU cc_start: 0.8540 (mp0) cc_final: 0.8111 (mp0) REVERT: A 445 THR cc_start: 0.8949 (m) cc_final: 0.8695 (p) REVERT: A 474 MET cc_start: 0.8634 (mtp) cc_final: 0.8082 (mtm) REVERT: A 485 MET cc_start: 0.7617 (mtt) cc_final: 0.7348 (mpp) REVERT: A 594 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.8057 (ttp-110) REVERT: B 31 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8263 (mt0) REVERT: B 80 GLU cc_start: 0.8194 (pt0) cc_final: 0.7914 (pm20) REVERT: B 306 GLN cc_start: 0.8742 (mt0) cc_final: 0.8304 (mm110) REVERT: B 315 GLU cc_start: 0.8534 (mp0) cc_final: 0.8120 (mp0) REVERT: B 445 THR cc_start: 0.8822 (m) cc_final: 0.8599 (p) REVERT: B 474 MET cc_start: 0.8673 (mtp) cc_final: 0.8178 (mtm) REVERT: B 481 MET cc_start: 0.7412 (mtm) cc_final: 0.7146 (mtt) REVERT: B 569 LEU cc_start: 0.8260 (mp) cc_final: 0.7838 (tt) REVERT: B 577 MET cc_start: 0.8655 (ptt) cc_final: 0.8362 (ptm) REVERT: B 581 THR cc_start: 0.6806 (OUTLIER) cc_final: 0.6589 (p) REVERT: C 31 GLN cc_start: 0.8671 (mt0) cc_final: 0.8417 (mt0) REVERT: C 80 GLU cc_start: 0.8114 (pt0) cc_final: 0.7841 (pm20) REVERT: C 306 GLN cc_start: 0.8732 (mt0) cc_final: 0.8277 (mm110) REVERT: C 315 GLU cc_start: 0.8548 (mp0) cc_final: 0.8182 (mp0) REVERT: C 445 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8577 (p) REVERT: C 474 MET cc_start: 0.8542 (mtp) cc_final: 0.8053 (mtm) REVERT: C 569 LEU cc_start: 0.8242 (mp) cc_final: 0.7838 (tt) REVERT: C 594 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.8051 (ttp-110) REVERT: D 80 GLU cc_start: 0.8145 (pt0) cc_final: 0.7856 (pm20) REVERT: D 306 GLN cc_start: 0.8750 (mt0) cc_final: 0.8282 (mm110) REVERT: D 315 GLU cc_start: 0.8577 (mp0) cc_final: 0.8143 (mp0) REVERT: D 474 MET cc_start: 0.8576 (mtp) cc_final: 0.8068 (mtm) REVERT: D 594 ARG cc_start: 0.8483 (ttp-110) cc_final: 0.8183 (ttp-110) outliers start: 65 outliers final: 30 residues processed: 261 average time/residue: 0.6169 time to fit residues: 180.7208 Evaluate side-chains 234 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 221 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 226 optimal weight: 0.5980 chunk 168 optimal weight: 0.4980 chunk 217 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.115340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.092486 restraints weight = 35017.007| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.63 r_work: 0.3161 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20060 Z= 0.113 Angle : 0.567 10.510 27236 Z= 0.287 Chirality : 0.040 0.152 3104 Planarity : 0.004 0.067 3464 Dihedral : 4.485 31.056 2680 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.22 % Allowed : 18.76 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2448 helix: 0.88 (0.14), residues: 1472 sheet: -0.95 (0.54), residues: 92 loop : -1.45 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 594 TYR 0.011 0.001 TYR B 555 PHE 0.018 0.001 PHE C 611 TRP 0.018 0.001 TRP B 29 HIS 0.005 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00261 (20060) covalent geometry : angle 0.56667 (27236) hydrogen bonds : bond 0.02855 ( 952) hydrogen bonds : angle 3.75517 ( 2748) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8121 (pt0) cc_final: 0.7866 (pm20) REVERT: A 302 ARG cc_start: 0.8298 (mtp85) cc_final: 0.7832 (ttm-80) REVERT: A 306 GLN cc_start: 0.8694 (mt0) cc_final: 0.8269 (mp10) REVERT: A 315 GLU cc_start: 0.8443 (mp0) cc_final: 0.8039 (mp0) REVERT: A 445 THR cc_start: 0.8834 (m) cc_final: 0.8622 (p) REVERT: A 474 MET cc_start: 0.8411 (mtp) cc_final: 0.7957 (mtm) REVERT: A 485 MET cc_start: 0.7574 (mtt) cc_final: 0.7346 (mpp) REVERT: A 594 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8051 (ttp-110) REVERT: B 31 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8292 (mt0) REVERT: B 80 GLU cc_start: 0.8070 (pt0) cc_final: 0.7845 (pm20) REVERT: B 306 GLN cc_start: 0.8677 (mt0) cc_final: 0.8219 (mm110) REVERT: B 315 GLU cc_start: 0.8460 (mp0) cc_final: 0.8055 (mp0) REVERT: B 474 MET cc_start: 0.8519 (mtp) cc_final: 0.8084 (mtm) REVERT: B 513 GLN cc_start: 0.8694 (tt0) cc_final: 0.8344 (tt0) REVERT: B 569 LEU cc_start: 0.8184 (mp) cc_final: 0.7742 (tt) REVERT: B 577 MET cc_start: 0.8472 (ptt) cc_final: 0.8221 (ptm) REVERT: B 594 ARG cc_start: 0.8490 (ttp-110) cc_final: 0.7932 (mpp-170) REVERT: C 31 GLN cc_start: 0.8664 (mt0) cc_final: 0.8444 (mt0) REVERT: C 80 GLU cc_start: 0.8146 (pt0) cc_final: 0.7822 (pm20) REVERT: C 306 GLN cc_start: 0.8653 (mt0) cc_final: 0.8164 (mp10) REVERT: C 315 GLU cc_start: 0.8566 (mp0) cc_final: 0.8089 (mp0) REVERT: C 440 MET cc_start: 0.6454 (mmp) cc_final: 0.6194 (tpt) REVERT: C 474 MET cc_start: 0.8168 (mtp) cc_final: 0.7846 (mtm) REVERT: C 485 MET cc_start: 0.7734 (mtt) cc_final: 0.7529 (mpp) REVERT: C 594 ARG cc_start: 0.8410 (mtm-85) cc_final: 0.8063 (ttp-110) REVERT: D 80 GLU cc_start: 0.8040 (pt0) cc_final: 0.7822 (pm20) REVERT: D 306 GLN cc_start: 0.8649 (mt0) cc_final: 0.8146 (mp10) REVERT: D 315 GLU cc_start: 0.8517 (mp0) cc_final: 0.8103 (mp0) REVERT: D 474 MET cc_start: 0.8402 (mtp) cc_final: 0.7996 (mtm) REVERT: D 513 GLN cc_start: 0.8686 (tt0) cc_final: 0.8441 (tt0) REVERT: D 588 GLU cc_start: 0.7411 (tp30) cc_final: 0.6984 (mt-10) outliers start: 47 outliers final: 21 residues processed: 250 average time/residue: 0.6417 time to fit residues: 180.5833 Evaluate side-chains 213 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 74 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN C 230 GLN ** C 370 GLN ** 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 = 0.3608 r_free = 0.3608 target = 0.114899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.091942 restraints weight = 34887.529| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.62 r_work: 0.3159 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20060 Z= 0.122 Angle : 0.586 10.155 27236 Z= 0.295 Chirality : 0.041 0.252 3104 Planarity : 0.004 0.070 3464 Dihedral : 4.432 29.965 2680 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.89 % Allowed : 18.86 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2448 helix: 1.06 (0.14), residues: 1472 sheet: -0.56 (0.58), residues: 84 loop : -1.44 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 594 TYR 0.010 0.001 TYR B 328 PHE 0.017 0.001 PHE C 611 TRP 0.020 0.001 TRP B 29 HIS 0.004 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00283 (20060) covalent geometry : angle 0.58602 (27236) hydrogen bonds : bond 0.02948 ( 952) hydrogen bonds : angle 3.74233 ( 2748) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7808 (mm-30) REVERT: A 80 GLU cc_start: 0.8144 (pt0) cc_final: 0.7865 (pm20) REVERT: A 302 ARG cc_start: 0.8286 (mtp85) cc_final: 0.7829 (ttm-80) REVERT: A 306 GLN cc_start: 0.8661 (mt0) cc_final: 0.8208 (mp10) REVERT: A 315 GLU cc_start: 0.8475 (mp0) cc_final: 0.8029 (mp0) REVERT: A 474 MET cc_start: 0.8436 (mtp) cc_final: 0.7999 (mtm) REVERT: A 485 MET cc_start: 0.7692 (mtt) cc_final: 0.7419 (mpp) REVERT: A 594 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.8050 (ttp-110) REVERT: B 31 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8268 (mt0) REVERT: B 80 GLU cc_start: 0.8089 (pt0) cc_final: 0.7847 (pm20) REVERT: B 306 GLN cc_start: 0.8710 (mt0) cc_final: 0.8272 (mm110) REVERT: B 315 GLU cc_start: 0.8479 (mp0) cc_final: 0.8050 (mp0) REVERT: B 474 MET cc_start: 0.8550 (mtp) cc_final: 0.8112 (mtm) REVERT: B 513 GLN cc_start: 0.8714 (tt0) cc_final: 0.8426 (tt0) REVERT: B 569 LEU cc_start: 0.8212 (mp) cc_final: 0.7723 (tt) REVERT: B 594 ARG cc_start: 0.8470 (ttp-110) cc_final: 0.7919 (mpp-170) REVERT: C 31 GLN cc_start: 0.8639 (mt0) cc_final: 0.8379 (mt0) REVERT: C 80 GLU cc_start: 0.8179 (pt0) cc_final: 0.7788 (pm20) REVERT: C 306 GLN cc_start: 0.8648 (mt0) cc_final: 0.8177 (mp10) REVERT: C 315 GLU cc_start: 0.8573 (mp0) cc_final: 0.8065 (mp0) REVERT: C 440 MET cc_start: 0.6461 (mmp) cc_final: 0.6196 (tpt) REVERT: C 474 MET cc_start: 0.8295 (mtp) cc_final: 0.7897 (mtm) REVERT: C 594 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8062 (ttp-110) REVERT: D 306 GLN cc_start: 0.8705 (mt0) cc_final: 0.8250 (mm110) REVERT: D 315 GLU cc_start: 0.8559 (mp0) cc_final: 0.8106 (mp0) REVERT: D 474 MET cc_start: 0.8425 (mtp) cc_final: 0.8034 (mtm) REVERT: D 588 GLU cc_start: 0.7426 (tp30) cc_final: 0.6984 (mt-10) REVERT: D 594 ARG cc_start: 0.8450 (ttp-110) cc_final: 0.7901 (mpp-170) outliers start: 40 outliers final: 24 residues processed: 228 average time/residue: 0.6701 time to fit residues: 171.3527 Evaluate side-chains 223 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 197 optimal weight: 0.0970 chunk 170 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 69 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.114400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.091496 restraints weight = 34669.217| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.61 r_work: 0.3151 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20060 Z= 0.134 Angle : 0.621 12.011 27236 Z= 0.310 Chirality : 0.042 0.251 3104 Planarity : 0.004 0.073 3464 Dihedral : 4.457 29.217 2680 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.47 % Allowed : 19.75 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.17), residues: 2448 helix: 1.14 (0.14), residues: 1460 sheet: -0.83 (0.55), residues: 92 loop : -1.29 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 594 TYR 0.012 0.001 TYR B 328 PHE 0.017 0.001 PHE C 611 TRP 0.022 0.001 TRP B 29 HIS 0.004 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00315 (20060) covalent geometry : angle 0.62083 (27236) hydrogen bonds : bond 0.02982 ( 952) hydrogen bonds : angle 3.77558 ( 2748) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.7513 (p-90) cc_final: 0.7090 (p-90) REVERT: A 30 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7787 (mm-30) REVERT: A 80 GLU cc_start: 0.8052 (pt0) cc_final: 0.7826 (pm20) REVERT: A 302 ARG cc_start: 0.8300 (mtp85) cc_final: 0.7858 (ttm-80) REVERT: A 306 GLN cc_start: 0.8675 (mt0) cc_final: 0.8228 (mp10) REVERT: A 315 GLU cc_start: 0.8480 (mp0) cc_final: 0.8032 (mp0) REVERT: A 474 MET cc_start: 0.8461 (mtp) cc_final: 0.8028 (mtm) REVERT: A 485 MET cc_start: 0.7578 (mtt) cc_final: 0.7352 (mpp) REVERT: A 594 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.8062 (ttp-110) REVERT: B 31 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: B 80 GLU cc_start: 0.8011 (pt0) cc_final: 0.7805 (pm20) REVERT: B 306 GLN cc_start: 0.8711 (mt0) cc_final: 0.8278 (mm110) REVERT: B 315 GLU cc_start: 0.8492 (mp0) cc_final: 0.8063 (mp0) REVERT: B 474 MET cc_start: 0.8564 (mtp) cc_final: 0.8125 (mtm) REVERT: B 569 LEU cc_start: 0.8167 (mp) cc_final: 0.7708 (tt) REVERT: B 594 ARG cc_start: 0.8462 (ttp-110) cc_final: 0.7925 (mpp-170) REVERT: C 31 GLN cc_start: 0.8632 (mt0) cc_final: 0.8385 (mt0) REVERT: C 80 GLU cc_start: 0.8189 (pt0) cc_final: 0.7791 (pm20) REVERT: C 306 GLN cc_start: 0.8658 (mt0) cc_final: 0.8189 (mp10) REVERT: C 315 GLU cc_start: 0.8572 (mp0) cc_final: 0.8063 (mp0) REVERT: C 440 MET cc_start: 0.6548 (mmp) cc_final: 0.6294 (tpt) REVERT: C 474 MET cc_start: 0.8195 (mtp) cc_final: 0.7889 (mtm) REVERT: C 594 ARG cc_start: 0.8433 (mtm-85) cc_final: 0.8066 (ttp-110) REVERT: D 306 GLN cc_start: 0.8711 (mt0) cc_final: 0.8249 (mp10) REVERT: D 315 GLU cc_start: 0.8558 (mp0) cc_final: 0.8102 (mp0) REVERT: D 474 MET cc_start: 0.8387 (mtp) cc_final: 0.7970 (mtm) REVERT: D 588 GLU cc_start: 0.7421 (tp30) cc_final: 0.7034 (mt-10) REVERT: D 594 ARG cc_start: 0.8426 (ttp-110) cc_final: 0.7865 (mtp180) outliers start: 31 outliers final: 19 residues processed: 218 average time/residue: 0.6774 time to fit residues: 165.2658 Evaluate side-chains 213 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 573 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 239 optimal weight: 0.5980 chunk 145 optimal weight: 0.2980 chunk 50 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 211 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 237 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 chunk 59 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS C 265 HIS ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.117150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.094451 restraints weight = 34841.196| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.63 r_work: 0.3175 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20060 Z= 0.110 Angle : 0.594 10.807 27236 Z= 0.297 Chirality : 0.041 0.243 3104 Planarity : 0.004 0.074 3464 Dihedral : 4.313 28.655 2680 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.09 % Allowed : 20.23 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.17), residues: 2448 helix: 1.32 (0.14), residues: 1456 sheet: -0.75 (0.56), residues: 92 loop : -1.23 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 594 TYR 0.012 0.001 TYR B 555 PHE 0.029 0.001 PHE D 611 TRP 0.022 0.001 TRP B 29 HIS 0.004 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00251 (20060) covalent geometry : angle 0.59373 (27236) hydrogen bonds : bond 0.02685 ( 952) hydrogen bonds : angle 3.68761 ( 2748) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 TRP cc_start: 0.7468 (p-90) cc_final: 0.7156 (p-90) REVERT: A 30 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7816 (mm-30) REVERT: A 302 ARG cc_start: 0.8411 (mtp85) cc_final: 0.7906 (ttm-80) REVERT: A 306 GLN cc_start: 0.8686 (mt0) cc_final: 0.8279 (mp10) REVERT: A 315 GLU cc_start: 0.8435 (mp0) cc_final: 0.8046 (mp0) REVERT: A 474 MET cc_start: 0.8381 (mtp) cc_final: 0.8003 (mtm) REVERT: A 485 MET cc_start: 0.7702 (mtt) cc_final: 0.7443 (mpp) REVERT: A 513 GLN cc_start: 0.8569 (tt0) cc_final: 0.8282 (tt0) REVERT: A 594 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8021 (ttp-110) REVERT: B 31 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8324 (mt0) REVERT: B 306 GLN cc_start: 0.8701 (mt0) cc_final: 0.8269 (mm110) REVERT: B 315 GLU cc_start: 0.8522 (mp0) cc_final: 0.8067 (mp0) REVERT: B 474 MET cc_start: 0.8501 (mtp) cc_final: 0.8074 (mtm) REVERT: B 513 GLN cc_start: 0.8604 (tt0) cc_final: 0.8367 (tt0) REVERT: B 594 ARG cc_start: 0.8439 (ttp-110) cc_final: 0.7836 (mtp180) REVERT: C 31 GLN cc_start: 0.8627 (mt0) cc_final: 0.8386 (mt0) REVERT: C 80 GLU cc_start: 0.8127 (pt0) cc_final: 0.7778 (pm20) REVERT: C 306 GLN cc_start: 0.8653 (mt0) cc_final: 0.8187 (mp10) REVERT: C 315 GLU cc_start: 0.8575 (mp0) cc_final: 0.8227 (mp0) REVERT: C 474 MET cc_start: 0.7899 (mtp) cc_final: 0.7506 (mtm) REVERT: C 485 MET cc_start: 0.7758 (mtp) cc_final: 0.7011 (mpp) REVERT: C 513 GLN cc_start: 0.8577 (tt0) cc_final: 0.8339 (tt0) REVERT: C 594 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.8075 (ttp-110) REVERT: D 306 GLN cc_start: 0.8646 (mt0) cc_final: 0.8174 (mp10) REVERT: D 315 GLU cc_start: 0.8529 (mp0) cc_final: 0.8138 (mp0) REVERT: D 474 MET cc_start: 0.8334 (mtp) cc_final: 0.8006 (mtm) REVERT: D 588 GLU cc_start: 0.7400 (tp30) cc_final: 0.6988 (mt-10) REVERT: D 594 ARG cc_start: 0.8433 (ttp-110) cc_final: 0.7862 (mpp-170) outliers start: 23 outliers final: 12 residues processed: 235 average time/residue: 0.6533 time to fit residues: 172.2022 Evaluate side-chains 220 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 207 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 573 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 49 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 222 optimal weight: 0.0970 chunk 153 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 85 optimal weight: 0.0980 chunk 170 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS C 265 HIS ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 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 = 0.3639 r_free = 0.3639 target = 0.117885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.094837 restraints weight = 34662.490| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.60 r_work: 0.3182 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20060 Z= 0.113 Angle : 0.610 10.516 27236 Z= 0.303 Chirality : 0.041 0.237 3104 Planarity : 0.004 0.072 3464 Dihedral : 4.325 27.886 2680 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.99 % Allowed : 20.89 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.17), residues: 2448 helix: 1.31 (0.14), residues: 1488 sheet: -0.78 (0.57), residues: 92 loop : -1.09 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 589 TYR 0.014 0.001 TYR D 623 PHE 0.031 0.001 PHE A 611 TRP 0.023 0.001 TRP D 29 HIS 0.005 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00259 (20060) covalent geometry : angle 0.60968 (27236) hydrogen bonds : bond 0.02641 ( 952) hydrogen bonds : angle 3.66727 ( 2748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5333.45 seconds wall clock time: 92 minutes 2.38 seconds (5522.38 seconds total)