Starting phenix.real_space_refine on Thu Mar 5 15:19:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zlt_11273/03_2026/6zlt_11273.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zlt_11273/03_2026/6zlt_11273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zlt_11273/03_2026/6zlt_11273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zlt_11273/03_2026/6zlt_11273.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zlt_11273/03_2026/6zlt_11273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zlt_11273/03_2026/6zlt_11273.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 260 atoms to isotropic. 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 78 5.16 5 C 14766 2.51 5 N 3968 2.21 5 O 4574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 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: 23386 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4358 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 532} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 7335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 7335 Classifications: {'peptide': 933} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 900} Restraints were copied for chains: C, D Time building chain proxies: 9.15, per 1000 atoms: 0.39 Number of scatterers: 23386 At special positions: 0 Unit cell: (155.15, 110.21, 140.17, 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 78 16.00 O 4574 8.00 N 3968 7.00 C 14766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 299 " distance=2.05 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 389 " distance=2.05 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 299 " distance=2.05 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 389 " distance=2.05 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: 1.93 Conformation dependent library (CDL) restraints added in 841.8 milliseconds 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5396 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 28 sheets defined 22.8% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 1 through 5 Processing helix chain 'A' and resid 17 through 21 removed outlier: 3.738A pdb=" N ALA A 20 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 84 through 108 removed outlier: 4.211A pdb=" N ASN A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 118 through 141 Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.625A pdb=" N TYR A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 185 removed outlier: 4.332A pdb=" N ASP A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 213 removed outlier: 3.906A pdb=" N TYR A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.886A pdb=" N MET A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.759A pdb=" N VAL A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.910A pdb=" N HIS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 422 Processing helix chain 'A' and resid 426 through 442 Processing helix chain 'A' and resid 447 through 451 removed outlier: 4.151A pdb=" N LYS A 451 " --> pdb=" O PHE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'A' and resid 501 through 513 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.675A pdb=" N ASN A 521 " --> pdb=" O ILE A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 3.547A pdb=" N ILE A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.635A pdb=" N ASP B 96 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 97 " --> pdb=" O LYS B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 93 through 97' Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.930A pdb=" N GLY B 113 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 249 Processing helix chain 'B' and resid 377 through 384 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 604 through 608 removed outlier: 3.726A pdb=" N LYS B 608 " --> pdb=" O ASN B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 781 through 786 removed outlier: 3.814A pdb=" N GLY B 786 " --> pdb=" O VAL B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 822 Processing helix chain 'B' and resid 890 through 896 removed outlier: 3.948A pdb=" N PHE B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 914 removed outlier: 3.595A pdb=" N ASN B 913 " --> pdb=" O ARG B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 943 Processing helix chain 'B' and resid 961 through 967 Processing helix chain 'C' and resid 1 through 5 Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.738A pdb=" N ALA C 20 " --> pdb=" O ASP C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 69 through 77 Processing helix chain 'C' and resid 84 through 108 removed outlier: 4.211A pdb=" N ASN C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 118 through 141 Processing helix chain 'C' and resid 153 through 157 removed outlier: 3.625A pdb=" N TYR C 157 " --> pdb=" O PRO C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 185 removed outlier: 4.332A pdb=" N ASP C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 213 removed outlier: 3.906A pdb=" N TYR C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 238 through 244 removed outlier: 3.886A pdb=" N MET C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 289 Processing helix chain 'C' and resid 305 through 313 removed outlier: 3.759A pdb=" N VAL C 309 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 344 removed outlier: 3.910A pdb=" N HIS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 422 Processing helix chain 'C' and resid 426 through 442 Processing helix chain 'C' and resid 447 through 451 removed outlier: 4.151A pdb=" N LYS C 451 " --> pdb=" O PHE C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 485 Processing helix chain 'C' and resid 491 through 499 Processing helix chain 'C' and resid 501 through 513 Processing helix chain 'C' and resid 517 through 521 removed outlier: 3.675A pdb=" N ASN C 521 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 542 removed outlier: 3.547A pdb=" N ILE C 539 " --> pdb=" O PRO C 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 97 removed outlier: 3.635A pdb=" N ASP D 96 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU D 97 " --> pdb=" O LYS D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 97' Processing helix chain 'D' and resid 108 through 113 removed outlier: 3.930A pdb=" N GLY D 113 " --> pdb=" O ILE D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 Processing helix chain 'D' and resid 377 through 384 Processing helix chain 'D' and resid 409 through 417 Processing helix chain 'D' and resid 604 through 608 removed outlier: 3.726A pdb=" N LYS D 608 " --> pdb=" O ASN D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 729 Processing helix chain 'D' and resid 781 through 786 removed outlier: 3.814A pdb=" N GLY D 786 " --> pdb=" O VAL D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 822 Processing helix chain 'D' and resid 890 through 896 removed outlier: 3.948A pdb=" N PHE D 896 " --> pdb=" O LYS D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 914 removed outlier: 3.595A pdb=" N ASN D 913 " --> pdb=" O ARG D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 943 Processing helix chain 'D' and resid 961 through 967 Processing sheet with id=1, first strand: chain 'A' and resid 269 through 271 removed outlier: 4.076A pdb=" N TRP A 269 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE A 405 " --> pdb=" O TRP A 269 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 271 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE A 403 " --> pdb=" O ILE A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=1 Processing sheet with id=2, first strand: chain 'B' and resid 85 through 87 removed outlier: 4.019A pdb=" N THR B 90 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 101 through 104 removed outlier: 4.363A pdb=" N ILE B 179 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER B 178 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 156 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE B 202 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE B 158 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 157 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 162 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 128 through 132 Processing sheet with id=5, first strand: chain 'B' and resid 338 through 342 removed outlier: 3.671A pdb=" N TYR B 327 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL B 304 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 305 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 218 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B1012 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 220 " --> pdb=" O PHE B1010 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN B 953 " --> pdb=" O PHE B 877 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 873 " --> pdb=" O GLY B 957 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU B 760 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 745 " --> pdb=" O TYR B 711 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 711 " --> pdb=" O GLY B 745 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN B 749 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 706 " --> pdb=" O PHE B 697 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 712 " --> pdb=" O THR B 691 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN B 627 " --> pdb=" O GLU B 686 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 617 " --> pdb=" O ASP B 696 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLY B 626 " --> pdb=" O THR B 591 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N THR B 591 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 574 " --> pdb=" O SER B 594 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 514 " --> pdb=" O TYR B 552 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 554 " --> pdb=" O ASN B 512 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY B 508 " --> pdb=" O PHE B 558 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 506 " --> pdb=" O LYS B 560 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET B 509 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 490 " --> pdb=" O MET B 509 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP B 488 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 221 through 224 Processing sheet with id=7, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.794A pdb=" N ARG B 345 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.702A pdb=" N ARG B 426 " --> pdb=" O ASN B 366 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 452 " --> pdb=" O TRP B 483 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS B 482 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS B 518 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'B' and resid 458 through 460 removed outlier: 3.785A pdb=" N ALA B 475 " --> pdb=" O THR B 460 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.570A pdb=" N ILE B 736 " --> pdb=" O THR B 720 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 879 through 881 Processing sheet with id=12, first strand: chain 'B' and resid 259 through 265 removed outlier: 6.802A pdb=" N GLY B 264 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU B 273 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.606A pdb=" N GLU B 777 " --> pdb=" O ALA B 740 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS B 742 " --> pdb=" O ILE B 775 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE B 775 " --> pdb=" O LYS B 742 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLN B 744 " --> pdb=" O ASN B 773 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN B 773 " --> pdb=" O GLN B 744 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'B' and resid 804 through 806 removed outlier: 3.765A pdb=" N TYR B 853 " --> pdb=" O GLN B 804 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY B 806 " --> pdb=" O TRP B 851 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TRP B 851 " --> pdb=" O GLY B 806 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 269 through 271 removed outlier: 4.076A pdb=" N TRP C 269 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE C 405 " --> pdb=" O TRP C 269 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 271 " --> pdb=" O ILE C 403 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE C 403 " --> pdb=" O ILE C 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=15 Processing sheet with id=16, first strand: chain 'D' and resid 85 through 87 removed outlier: 4.019A pdb=" N THR D 90 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'D' and resid 101 through 104 removed outlier: 4.363A pdb=" N ILE D 179 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER D 178 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU D 156 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE D 202 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE D 158 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 157 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 162 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 128 through 132 Processing sheet with id=19, first strand: chain 'D' and resid 338 through 342 removed outlier: 3.671A pdb=" N TYR D 327 " --> pdb=" O TYR D 308 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL D 304 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D 305 " --> pdb=" O SER D 221 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 218 " --> pdb=" O LEU D1012 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D1012 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL D 220 " --> pdb=" O PHE D1010 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN D 953 " --> pdb=" O PHE D 877 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP D 873 " --> pdb=" O GLY D 957 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU D 760 " --> pdb=" O THR D 756 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 745 " --> pdb=" O TYR D 711 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR D 711 " --> pdb=" O GLY D 745 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN D 749 " --> pdb=" O SER D 707 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY D 706 " --> pdb=" O PHE D 697 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR D 712 " --> pdb=" O THR D 691 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN D 627 " --> pdb=" O GLU D 686 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 617 " --> pdb=" O ASP D 696 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLY D 626 " --> pdb=" O THR D 591 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N THR D 591 " --> pdb=" O GLY D 626 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 574 " --> pdb=" O SER D 594 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 514 " --> pdb=" O TYR D 552 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 554 " --> pdb=" O ASN D 512 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY D 508 " --> pdb=" O PHE D 558 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET D 506 " --> pdb=" O LYS D 560 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET D 509 " --> pdb=" O ALA D 490 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 490 " --> pdb=" O MET D 509 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP D 488 " --> pdb=" O LEU D 511 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'D' and resid 221 through 224 Processing sheet with id=21, first strand: chain 'D' and resid 311 through 313 removed outlier: 3.794A pdb=" N ARG D 345 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'D' and resid 365 through 368 removed outlier: 3.702A pdb=" N ARG D 426 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA D 452 " --> pdb=" O TRP D 483 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS D 482 " --> pdb=" O SER D 517 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS D 518 " --> pdb=" O ALA D 548 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'D' and resid 458 through 460 removed outlier: 3.785A pdb=" N ALA D 475 " --> pdb=" O THR D 460 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'D' and resid 719 through 722 removed outlier: 3.570A pdb=" N ILE D 736 " --> pdb=" O THR D 720 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'D' and resid 879 through 881 Processing sheet with id=26, first strand: chain 'D' and resid 259 through 265 removed outlier: 6.802A pdb=" N GLY D 264 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU D 273 " --> pdb=" O GLY D 264 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'D' and resid 740 through 744 removed outlier: 3.606A pdb=" N GLU D 777 " --> pdb=" O ALA D 740 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS D 742 " --> pdb=" O ILE D 775 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE D 775 " --> pdb=" O LYS D 742 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLN D 744 " --> pdb=" O ASN D 773 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN D 773 " --> pdb=" O GLN D 744 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'D' and resid 804 through 806 removed outlier: 3.765A pdb=" N TYR D 853 " --> pdb=" O GLN D 804 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY D 806 " --> pdb=" O TRP D 851 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TRP D 851 " --> pdb=" O GLY D 806 " (cutoff:3.500A) 758 hydrogen bonds defined for protein. 2064 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: 4.56 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7760 1.34 - 1.47: 6076 1.47 - 1.59: 9968 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 23942 Sorted by residual: bond pdb=" N ASP C 300 " pdb=" CA ASP C 300 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.06e+00 bond pdb=" N ASP A 300 " pdb=" CA ASP A 300 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.06e+00 bond pdb=" C CYS C 298 " pdb=" N CYS C 299 " ideal model delta sigma weight residual 1.329 1.351 -0.022 1.40e-02 5.10e+03 2.47e+00 bond pdb=" C CYS A 298 " pdb=" N CYS A 299 " ideal model delta sigma weight residual 1.329 1.351 -0.022 1.40e-02 5.10e+03 2.47e+00 bond pdb=" CA LYS B 701 " pdb=" CB LYS B 701 " ideal model delta sigma weight residual 1.530 1.554 -0.023 1.51e-02 4.39e+03 2.41e+00 ... (remaining 23937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 31398 1.92 - 3.84: 942 3.84 - 5.76: 120 5.76 - 7.68: 34 7.68 - 9.60: 16 Bond angle restraints: 32510 Sorted by residual: angle pdb=" C CYS C 298 " pdb=" N CYS C 299 " pdb=" CA CYS C 299 " ideal model delta sigma weight residual 121.70 129.32 -7.62 1.80e+00 3.09e-01 1.79e+01 angle pdb=" C CYS A 298 " pdb=" N CYS A 299 " pdb=" CA CYS A 299 " ideal model delta sigma weight residual 121.70 129.32 -7.62 1.80e+00 3.09e-01 1.79e+01 angle pdb=" C GLY D 167 " pdb=" N MET D 168 " pdb=" CA MET D 168 " ideal model delta sigma weight residual 121.54 129.51 -7.97 1.91e+00 2.74e-01 1.74e+01 angle pdb=" C GLY B 167 " pdb=" N MET B 168 " pdb=" CA MET B 168 " ideal model delta sigma weight residual 121.54 129.51 -7.97 1.91e+00 2.74e-01 1.74e+01 angle pdb=" C ASP C 388 " pdb=" N CYS C 389 " pdb=" CA CYS C 389 " ideal model delta sigma weight residual 120.28 126.22 -5.94 1.44e+00 4.82e-01 1.70e+01 ... (remaining 32505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 12448 17.84 - 35.68: 1190 35.68 - 53.52: 270 53.52 - 71.36: 52 71.36 - 89.20: 32 Dihedral angle restraints: 13992 sinusoidal: 5446 harmonic: 8546 Sorted by residual: dihedral pdb=" CA CYS A 387 " pdb=" C CYS A 387 " pdb=" N ASP A 388 " pdb=" CA ASP A 388 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA CYS C 387 " pdb=" C CYS C 387 " pdb=" N ASP C 388 " pdb=" CA ASP C 388 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ALA D 566 " pdb=" C ALA D 566 " pdb=" N ASP D 567 " pdb=" CA ASP D 567 " ideal model delta harmonic sigma weight residual 180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 13989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2726 0.063 - 0.126: 570 0.126 - 0.189: 104 0.189 - 0.252: 10 0.252 - 0.315: 4 Chirality restraints: 3414 Sorted by residual: chirality pdb=" CB ILE D 212 " pdb=" CA ILE D 212 " pdb=" CG1 ILE D 212 " pdb=" CG2 ILE D 212 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB ILE B 212 " pdb=" CA ILE B 212 " pdb=" CG1 ILE B 212 " pdb=" CG2 ILE B 212 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB VAL B 668 " pdb=" CA VAL B 668 " pdb=" CG1 VAL B 668 " pdb=" CG2 VAL B 668 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 3411 not shown) Planarity restraints: 4290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 436 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO B 437 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 437 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 437 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 436 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO D 437 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 437 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 437 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 826 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" CD GLU B 826 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU B 826 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 826 " -0.013 2.00e-02 2.50e+03 ... (remaining 4287 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2136 2.74 - 3.28: 21776 3.28 - 3.82: 37984 3.82 - 4.36: 43678 4.36 - 4.90: 77374 Nonbonded interactions: 182948 Sorted by model distance: nonbonded pdb=" O THR A 324 " pdb=" OG1 THR A 324 " model vdw 2.198 3.040 nonbonded pdb=" O THR C 324 " pdb=" OG1 THR C 324 " model vdw 2.198 3.040 nonbonded pdb=" O SER A 55 " pdb=" OG SER A 55 " model vdw 2.215 3.040 nonbonded pdb=" O SER C 55 " pdb=" OG SER C 55 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR C 38 " pdb=" O SER D 653 " model vdw 2.252 3.040 ... (remaining 182943 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' 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 group one per residue 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 24.280 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.005 0.048 23946 Z= 0.243 Angle : 0.818 9.596 32518 Z= 0.459 Chirality : 0.055 0.315 3414 Planarity : 0.006 0.056 4290 Dihedral : 15.478 89.199 8584 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.98 % Allowed : 10.99 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -4.15 (0.13), residues: 2962 helix: -2.67 (0.14), residues: 634 sheet: -2.81 (0.17), residues: 760 loop : -2.74 (0.13), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 588 TYR 0.028 0.002 TYR B 191 PHE 0.025 0.002 PHE B 438 TRP 0.020 0.002 TRP B 599 HIS 0.007 0.001 HIS D 482 Details of bonding type rmsd covalent geometry : bond 0.00521 (23942) covalent geometry : angle 0.81677 (32510) SS BOND : bond 0.01942 ( 4) SS BOND : angle 2.80009 ( 8) hydrogen bonds : bond 0.23642 ( 754) hydrogen bonds : angle 8.15539 ( 2064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 295 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 MET cc_start: 0.8174 (mmm) cc_final: 0.7895 (mmm) REVERT: B 176 ILE cc_start: 0.8706 (mm) cc_final: 0.8203 (tp) REVERT: B 308 TYR cc_start: 0.8389 (m-80) cc_final: 0.8182 (m-80) REVERT: B 450 ASP cc_start: 0.7839 (t70) cc_final: 0.7509 (t0) REVERT: B 607 MET cc_start: 0.6665 (mmm) cc_final: 0.6375 (tpp) REVERT: B 1010 PHE cc_start: 0.7214 (m-80) cc_final: 0.6994 (t80) REVERT: D 168 MET cc_start: 0.8383 (mmm) cc_final: 0.8168 (mmm) REVERT: D 408 ARG cc_start: 0.8475 (ttt90) cc_final: 0.8261 (ttt90) REVERT: D 419 ASP cc_start: 0.7216 (m-30) cc_final: 0.7014 (m-30) REVERT: D 607 MET cc_start: 0.6620 (mmm) cc_final: 0.5662 (tpp) REVERT: D 695 ILE cc_start: 0.9156 (mp) cc_final: 0.8903 (mt) REVERT: D 859 PHE cc_start: 0.7352 (t80) cc_final: 0.6979 (t80) outliers start: 24 outliers final: 5 residues processed: 315 average time/residue: 0.1757 time to fit residues: 83.7516 Evaluate side-chains 183 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 178 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 608 LYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 608 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 0.0470 overall best weight: 2.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 134 HIS A 215 GLN A 263 ASN A 506 ASN B 112 GLN B 115 ASN B 174 ASN B 347 ASN B 587 HIS B 603 GLN B 628 GLN B 754 ASN C 121 GLN C 134 HIS C 215 GLN C 263 ASN C 283 ASN C 506 ASN D 112 GLN D 115 ASN D 347 ASN D 603 GLN D 628 GLN D 754 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.157112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128379 restraints weight = 35636.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125574 restraints weight = 43165.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.122304 restraints weight = 38667.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.122448 restraints weight = 36566.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121818 restraints weight = 29180.031| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 23946 Z= 0.184 Angle : 0.608 12.573 32518 Z= 0.327 Chirality : 0.044 0.161 3414 Planarity : 0.004 0.053 4290 Dihedral : 5.486 56.582 3291 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.40 % Allowed : 15.35 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.94 (0.14), residues: 2962 helix: -0.90 (0.19), residues: 648 sheet: -2.20 (0.18), residues: 764 loop : -2.27 (0.14), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 421 TYR 0.021 0.001 TYR D 191 PHE 0.017 0.001 PHE C 135 TRP 0.039 0.001 TRP B 599 HIS 0.004 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00416 (23942) covalent geometry : angle 0.60418 (32510) SS BOND : bond 0.01364 ( 4) SS BOND : angle 4.20187 ( 8) hydrogen bonds : bond 0.04483 ( 754) hydrogen bonds : angle 5.18326 ( 2064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 191 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6614 (t80) REVERT: D 408 ARG cc_start: 0.8486 (ttt90) cc_final: 0.8136 (ttt90) REVERT: D 607 MET cc_start: 0.7498 (mmm) cc_final: 0.6637 (tpp) outliers start: 59 outliers final: 33 residues processed: 245 average time/residue: 0.1549 time to fit residues: 60.7573 Evaluate side-chains 206 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 876 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 256 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 245 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 220 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 chunk 160 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 139 GLN A 226 ASN A 283 ASN B 174 ASN B 243 GLN B 603 GLN B 628 GLN B 743 ASN C 134 HIS C 226 ASN D 174 ASN D 628 GLN D 743 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.158984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.131420 restraints weight = 35404.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.128397 restraints weight = 41972.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125797 restraints weight = 36008.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124782 restraints weight = 36366.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.124271 restraints weight = 32894.940| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 23946 Z= 0.109 Angle : 0.533 12.497 32518 Z= 0.287 Chirality : 0.042 0.139 3414 Planarity : 0.004 0.045 4290 Dihedral : 4.846 53.627 3283 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.40 % Allowed : 16.90 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.34 (0.15), residues: 2962 helix: -0.32 (0.21), residues: 652 sheet: -1.70 (0.19), residues: 770 loop : -2.02 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 832 TYR 0.015 0.001 TYR D 191 PHE 0.025 0.001 PHE A 312 TRP 0.033 0.001 TRP B 599 HIS 0.008 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00240 (23942) covalent geometry : angle 0.53098 (32510) SS BOND : bond 0.00678 ( 4) SS BOND : angle 2.62193 ( 8) hydrogen bonds : bond 0.03511 ( 754) hydrogen bonds : angle 4.65237 ( 2064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: B 168 MET cc_start: 0.8521 (mmm) cc_final: 0.8186 (mmm) REVERT: B 628 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8352 (pp30) REVERT: B 771 TYR cc_start: 0.7605 (t80) cc_final: 0.7399 (t80) REVERT: D 168 MET cc_start: 0.8577 (mmm) cc_final: 0.8328 (mmm) REVERT: D 408 ARG cc_start: 0.8483 (ttt90) cc_final: 0.8124 (ttt90) REVERT: D 419 ASP cc_start: 0.8383 (p0) cc_final: 0.8004 (p0) REVERT: D 607 MET cc_start: 0.7435 (mmm) cc_final: 0.6657 (tpp) REVERT: D 750 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8356 (tt) outliers start: 59 outliers final: 31 residues processed: 242 average time/residue: 0.1432 time to fit residues: 55.7406 Evaluate side-chains 209 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 599 TRP Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 628 GLN Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 750 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 42 optimal weight: 20.0000 chunk 257 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 256 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 280 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 283 ASN A 294 GLN B 180 GLN B 743 ASN C 134 HIS C 283 ASN C 294 GLN D 174 ASN D 266 ASN ** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 743 ASN ** D 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.153948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125470 restraints weight = 35956.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123560 restraints weight = 44065.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121345 restraints weight = 36690.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120651 restraints weight = 38627.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120159 restraints weight = 34631.021| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 23946 Z= 0.274 Angle : 0.625 11.866 32518 Z= 0.338 Chirality : 0.045 0.163 3414 Planarity : 0.004 0.048 4290 Dihedral : 5.150 50.740 3279 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.87 % Allowed : 16.53 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.25 (0.15), residues: 2962 helix: -0.08 (0.21), residues: 650 sheet: -1.76 (0.19), residues: 774 loop : -1.97 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 832 TYR 0.028 0.002 TYR D 191 PHE 0.018 0.002 PHE A 312 TRP 0.035 0.002 TRP B 599 HIS 0.011 0.002 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00624 (23942) covalent geometry : angle 0.62369 (32510) SS BOND : bond 0.01352 ( 4) SS BOND : angle 2.58071 ( 8) hydrogen bonds : bond 0.04237 ( 754) hydrogen bonds : angle 4.78571 ( 2064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 185 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 ILE cc_start: 0.8881 (mm) cc_final: 0.8627 (mm) REVERT: B 168 MET cc_start: 0.8446 (mmm) cc_final: 0.8241 (mmm) REVERT: B 191 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.7130 (t80) REVERT: C 347 MET cc_start: 0.6389 (mmp) cc_final: 0.6070 (mmm) REVERT: D 109 ILE cc_start: 0.8868 (mm) cc_final: 0.8626 (mm) REVERT: D 110 GLN cc_start: 0.8310 (pm20) cc_final: 0.8016 (pp30) REVERT: D 191 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.6992 (t80) REVERT: D 203 THR cc_start: 0.8917 (t) cc_final: 0.8700 (p) REVERT: D 408 ARG cc_start: 0.8506 (ttt90) cc_final: 0.8065 (ttt90) REVERT: D 750 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8382 (tt) outliers start: 95 outliers final: 69 residues processed: 256 average time/residue: 0.1432 time to fit residues: 60.0316 Evaluate side-chains 248 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 176 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 822 HIS Chi-restraints excluded: chain B residue 859 PHE Chi-restraints excluded: chain B residue 865 ILE Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 599 TRP Chi-restraints excluded: chain D residue 638 ILE Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 822 HIS Chi-restraints excluded: chain D residue 859 PHE Chi-restraints excluded: chain D residue 876 MET Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 970 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 201 optimal weight: 3.9990 chunk 284 optimal weight: 0.8980 chunk 288 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 264 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 263 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN B 628 GLN ** B 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS D 129 ASN D 243 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.155290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126564 restraints weight = 35501.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124855 restraints weight = 44547.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123368 restraints weight = 35694.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122767 restraints weight = 35156.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122356 restraints weight = 31427.380| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 23946 Z= 0.204 Angle : 0.594 16.099 32518 Z= 0.318 Chirality : 0.044 0.154 3414 Planarity : 0.004 0.047 4290 Dihedral : 5.007 45.728 3279 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.11 % Allowed : 17.71 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.09 (0.15), residues: 2962 helix: 0.15 (0.22), residues: 638 sheet: -1.66 (0.19), residues: 774 loop : -1.91 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 832 TYR 0.024 0.001 TYR D 191 PHE 0.015 0.001 PHE B 342 TRP 0.034 0.001 TRP B 599 HIS 0.007 0.002 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00466 (23942) covalent geometry : angle 0.58992 (32510) SS BOND : bond 0.01099 ( 4) SS BOND : angle 4.34907 ( 8) hydrogen bonds : bond 0.03868 ( 754) hydrogen bonds : angle 4.64332 ( 2064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 178 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 ILE cc_start: 0.8902 (mm) cc_final: 0.8653 (mm) REVERT: B 191 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.6932 (t80) REVERT: C 347 MET cc_start: 0.6555 (mmp) cc_final: 0.6034 (mmm) REVERT: D 109 ILE cc_start: 0.8896 (mm) cc_final: 0.8671 (mm) REVERT: D 191 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6816 (t80) REVERT: D 408 ARG cc_start: 0.8535 (ttt90) cc_final: 0.8095 (ttt90) REVERT: D 607 MET cc_start: 0.7487 (mmm) cc_final: 0.7132 (tpp) REVERT: D 750 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8314 (tt) outliers start: 101 outliers final: 73 residues processed: 255 average time/residue: 0.1313 time to fit residues: 55.2491 Evaluate side-chains 243 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 167 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 599 TRP Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 822 HIS Chi-restraints excluded: chain B residue 859 PHE Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 599 TRP Chi-restraints excluded: chain D residue 638 ILE Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 859 PHE Chi-restraints excluded: chain D residue 876 MET Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 970 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 88 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 234 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 196 optimal weight: 9.9990 chunk 213 optimal weight: 0.3980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** B 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS D 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126464 restraints weight = 35566.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124619 restraints weight = 46946.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122626 restraints weight = 37660.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122631 restraints weight = 35415.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122003 restraints weight = 30296.325| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23946 Z= 0.148 Angle : 0.543 11.866 32518 Z= 0.291 Chirality : 0.043 0.144 3414 Planarity : 0.003 0.046 4290 Dihedral : 4.734 38.682 3279 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.46 % Allowed : 19.30 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.15), residues: 2962 helix: 0.37 (0.22), residues: 624 sheet: -1.48 (0.19), residues: 754 loop : -1.81 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 576 TYR 0.020 0.001 TYR D 191 PHE 0.013 0.001 PHE B 342 TRP 0.034 0.001 TRP B 599 HIS 0.006 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00336 (23942) covalent geometry : angle 0.54093 (32510) SS BOND : bond 0.00918 ( 4) SS BOND : angle 2.91437 ( 8) hydrogen bonds : bond 0.03506 ( 754) hydrogen bonds : angle 4.47853 ( 2064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 184 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.8899 (mmt) cc_final: 0.8616 (mpp) REVERT: B 109 ILE cc_start: 0.8881 (mm) cc_final: 0.8640 (mm) REVERT: B 191 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.6992 (t80) REVERT: C 347 MET cc_start: 0.6630 (mmp) cc_final: 0.6072 (mmm) REVERT: C 488 GLU cc_start: 0.7570 (mt-10) cc_final: 0.6557 (tm-30) REVERT: D 170 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8150 (pm20) REVERT: D 191 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.6614 (t80) REVERT: D 408 ARG cc_start: 0.8565 (ttt90) cc_final: 0.8120 (ttt90) REVERT: D 607 MET cc_start: 0.7553 (mmm) cc_final: 0.7265 (tpp) REVERT: D 750 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8393 (tt) outliers start: 85 outliers final: 67 residues processed: 248 average time/residue: 0.1439 time to fit residues: 58.6617 Evaluate side-chains 245 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 174 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 599 TRP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 859 PHE Chi-restraints excluded: chain B residue 865 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 859 PHE Chi-restraints excluded: chain D residue 876 MET Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 970 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 31 optimal weight: 8.9990 chunk 206 optimal weight: 0.9990 chunk 291 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 204 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** D 822 HIS ** 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 = 0.3855 r_free = 0.3855 target = 0.158032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127959 restraints weight = 35351.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126168 restraints weight = 47435.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124539 restraints weight = 39017.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.124435 restraints weight = 34754.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123965 restraints weight = 28961.540| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23946 Z= 0.126 Angle : 0.522 11.928 32518 Z= 0.279 Chirality : 0.042 0.136 3414 Planarity : 0.003 0.044 4290 Dihedral : 4.526 26.169 3279 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.62 % Allowed : 19.99 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.15), residues: 2962 helix: 0.38 (0.22), residues: 636 sheet: -1.28 (0.19), residues: 752 loop : -1.67 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 421 TYR 0.018 0.001 TYR D 191 PHE 0.020 0.001 PHE B 606 TRP 0.033 0.001 TRP B 599 HIS 0.005 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00282 (23942) covalent geometry : angle 0.52073 (32510) SS BOND : bond 0.00854 ( 4) SS BOND : angle 2.41773 ( 8) hydrogen bonds : bond 0.03236 ( 754) hydrogen bonds : angle 4.32055 ( 2064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 188 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 488 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6479 (tm-30) REVERT: B 109 ILE cc_start: 0.8876 (mm) cc_final: 0.8642 (mm) REVERT: C 347 MET cc_start: 0.6598 (mmp) cc_final: 0.6000 (mmm) REVERT: C 488 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6457 (tm-30) REVERT: D 191 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6474 (t80) REVERT: D 408 ARG cc_start: 0.8539 (ttt90) cc_final: 0.8084 (ttt90) REVERT: D 607 MET cc_start: 0.7540 (mmm) cc_final: 0.7268 (tpp) outliers start: 89 outliers final: 63 residues processed: 256 average time/residue: 0.1439 time to fit residues: 60.5719 Evaluate side-chains 240 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 176 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 599 TRP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 859 PHE Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 638 ILE Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 859 PHE Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain D residue 973 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 48 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 278 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 628 GLN ** B 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** D 822 HIS ** 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 = 0.3823 r_free = 0.3823 target = 0.154891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126670 restraints weight = 35595.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.123742 restraints weight = 44829.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121408 restraints weight = 40433.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.120909 restraints weight = 37819.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120180 restraints weight = 33258.325| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 23946 Z= 0.219 Angle : 0.605 19.820 32518 Z= 0.322 Chirality : 0.044 0.155 3414 Planarity : 0.004 0.046 4290 Dihedral : 4.857 59.967 3278 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.71 % Allowed : 19.91 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.75 (0.15), residues: 2962 helix: 0.33 (0.22), residues: 636 sheet: -1.37 (0.19), residues: 754 loop : -1.69 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 426 TYR 0.036 0.001 TYR B 771 PHE 0.017 0.001 PHE B 342 TRP 0.035 0.001 TRP B 599 HIS 0.006 0.001 HIS B 518 Details of bonding type rmsd covalent geometry : bond 0.00507 (23942) covalent geometry : angle 0.59836 (32510) SS BOND : bond 0.00926 ( 4) SS BOND : angle 5.75263 ( 8) hydrogen bonds : bond 0.03751 ( 754) hydrogen bonds : angle 4.55028 ( 2064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 177 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 488 GLU cc_start: 0.7555 (mt-10) cc_final: 0.6575 (tm-30) REVERT: B 109 ILE cc_start: 0.8890 (mm) cc_final: 0.8648 (mm) REVERT: B 449 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8796 (tp) REVERT: C 347 MET cc_start: 0.6655 (mmp) cc_final: 0.5984 (mmm) REVERT: C 488 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6512 (tm-30) REVERT: D 191 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7248 (t80) outliers start: 91 outliers final: 71 residues processed: 249 average time/residue: 0.1429 time to fit residues: 59.1993 Evaluate side-chains 246 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 173 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 599 TRP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 822 HIS Chi-restraints excluded: chain B residue 859 PHE Chi-restraints excluded: chain B residue 865 ILE Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 599 TRP Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 822 HIS Chi-restraints excluded: chain D residue 859 PHE Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 954 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 230 optimal weight: 5.9990 chunk 264 optimal weight: 9.9990 chunk 259 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 628 GLN ** B 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS C 422 ASN ** D 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126533 restraints weight = 35751.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124581 restraints weight = 45597.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122975 restraints weight = 38030.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122897 restraints weight = 32777.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122125 restraints weight = 28792.168| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 23946 Z= 0.191 Angle : 0.579 12.019 32518 Z= 0.309 Chirality : 0.044 0.174 3414 Planarity : 0.004 0.045 4290 Dihedral : 4.822 57.759 3278 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.30 % Allowed : 20.81 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.68 (0.15), residues: 2962 helix: 0.39 (0.22), residues: 636 sheet: -1.33 (0.19), residues: 754 loop : -1.64 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 421 TYR 0.024 0.001 TYR D 191 PHE 0.039 0.001 PHE B 606 TRP 0.034 0.001 TRP B 599 HIS 0.006 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00441 (23942) covalent geometry : angle 0.57434 (32510) SS BOND : bond 0.01000 ( 4) SS BOND : angle 4.92570 ( 8) hydrogen bonds : bond 0.03640 ( 754) hydrogen bonds : angle 4.48842 ( 2064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 178 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 488 GLU cc_start: 0.7600 (mt-10) cc_final: 0.6611 (tm-30) REVERT: B 109 ILE cc_start: 0.8899 (mm) cc_final: 0.8648 (mm) REVERT: B 449 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8841 (tp) REVERT: C 488 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6515 (tm-30) REVERT: D 191 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7086 (t80) outliers start: 81 outliers final: 70 residues processed: 240 average time/residue: 0.1396 time to fit residues: 55.7224 Evaluate side-chains 244 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 172 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 599 TRP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 822 HIS Chi-restraints excluded: chain B residue 859 PHE Chi-restraints excluded: chain B residue 865 ILE Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 822 HIS Chi-restraints excluded: chain D residue 859 PHE Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 954 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 283 optimal weight: 7.9990 chunk 213 optimal weight: 0.0970 chunk 143 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 159 optimal weight: 0.0060 chunk 96 optimal weight: 3.9990 chunk 295 optimal weight: 4.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 743 ASN ** B 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** D 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 HIS ** 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 = 0.3857 r_free = 0.3857 target = 0.158391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127870 restraints weight = 35442.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126369 restraints weight = 48942.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.124328 restraints weight = 39944.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123945 restraints weight = 36785.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.122944 restraints weight = 33890.463| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 23946 Z= 0.127 Angle : 0.581 20.669 32518 Z= 0.304 Chirality : 0.043 0.192 3414 Planarity : 0.003 0.044 4290 Dihedral : 4.684 60.053 3278 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.81 % Allowed : 21.25 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.50 (0.15), residues: 2962 helix: 0.45 (0.22), residues: 638 sheet: -1.14 (0.19), residues: 750 loop : -1.53 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 421 TYR 0.017 0.001 TYR D 191 PHE 0.012 0.001 PHE B 342 TRP 0.032 0.001 TRP B 599 HIS 0.011 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00296 (23942) covalent geometry : angle 0.56851 (32510) SS BOND : bond 0.00778 ( 4) SS BOND : angle 7.68624 ( 8) hydrogen bonds : bond 0.03229 ( 754) hydrogen bonds : angle 4.30699 ( 2064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 177 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 488 GLU cc_start: 0.7586 (mt-10) cc_final: 0.6932 (tm-30) REVERT: B 109 ILE cc_start: 0.8851 (mm) cc_final: 0.8610 (mm) REVERT: B 427 MET cc_start: 0.8349 (mtm) cc_final: 0.8050 (mtt) REVERT: C 488 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6443 (tm-30) REVERT: D 191 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.6625 (t80) REVERT: D 408 ARG cc_start: 0.8537 (ttt90) cc_final: 0.8090 (ttt90) outliers start: 69 outliers final: 63 residues processed: 232 average time/residue: 0.1468 time to fit residues: 55.9599 Evaluate side-chains 236 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 172 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 599 TRP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 859 PHE Chi-restraints excluded: chain B residue 865 ILE Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 859 PHE Chi-restraints excluded: chain D residue 900 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 46 optimal weight: 8.9990 chunk 269 optimal weight: 5.9990 chunk 28 optimal weight: 0.0980 chunk 180 optimal weight: 0.3980 chunk 72 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** D 822 HIS ** 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 = 0.3861 r_free = 0.3861 target = 0.158697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129555 restraints weight = 35491.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126471 restraints weight = 44353.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124656 restraints weight = 37664.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124761 restraints weight = 35626.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124659 restraints weight = 27982.052| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 23946 Z= 0.122 Angle : 0.560 12.341 32518 Z= 0.295 Chirality : 0.043 0.174 3414 Planarity : 0.003 0.044 4290 Dihedral : 4.568 58.782 3278 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.85 % Allowed : 21.54 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.41 (0.15), residues: 2962 helix: 0.47 (0.22), residues: 636 sheet: -1.05 (0.19), residues: 752 loop : -1.45 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 421 TYR 0.017 0.001 TYR D 191 PHE 0.048 0.001 PHE B 606 TRP 0.032 0.001 TRP B 599 HIS 0.006 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00282 (23942) covalent geometry : angle 0.55134 (32510) SS BOND : bond 0.00805 ( 4) SS BOND : angle 6.42631 ( 8) hydrogen bonds : bond 0.03161 ( 754) hydrogen bonds : angle 4.25836 ( 2064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2902.57 seconds wall clock time: 51 minutes 27.70 seconds (3087.70 seconds total)