Starting phenix.real_space_refine on Fri Sep 19 00:24:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5yx9_6856/09_2025/5yx9_6856_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yx9_6856/09_2025/5yx9_6856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5yx9_6856/09_2025/5yx9_6856_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yx9_6856/09_2025/5yx9_6856_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5yx9_6856/09_2025/5yx9_6856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yx9_6856/09_2025/5yx9_6856.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 13868 2.51 5 N 3536 2.21 5 O 3852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21392 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5348 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 18, 'TRANS': 656} Chain breaks: 6 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 72 Restraints were copied for chains: B, C, D Time building chain proxies: 5.29, per 1000 atoms: 0.25 Number of scatterers: 21392 At special positions: 0 Unit cell: (131.67, 131.67, 167.58, 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 136 16.00 O 3852 8.00 N 3536 7.00 C 13868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 935.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5160 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 0 sheets defined 76.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 96 through 108 Processing helix chain 'A' and resid 110 through 121 removed outlier: 3.618A pdb=" N VAL A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS A 121 " --> pdb=" O MET A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 143 removed outlier: 3.708A pdb=" N ASN A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 160 through 172 Processing helix chain 'A' and resid 173 through 182 removed outlier: 3.518A pdb=" N SER A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.826A pdb=" N ARG A 271 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 4.292A pdb=" N SER A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 311 removed outlier: 4.144A pdb=" N THR A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 335 removed outlier: 3.718A pdb=" N LEU A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.012A pdb=" N VAL A 378 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 379' Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.552A pdb=" N GLU A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 414 removed outlier: 3.717A pdb=" N PHE A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 removed outlier: 4.502A pdb=" N LEU A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 437 removed outlier: 3.548A pdb=" N ARG A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 463 removed outlier: 3.534A pdb=" N LYS A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 443 " --> pdb=" O PRO A 439 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 463 " --> pdb=" O MET A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 516 removed outlier: 4.129A pdb=" N THR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 524 through 558 removed outlier: 4.040A pdb=" N PHE A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 608 removed outlier: 3.778A pdb=" N ILE A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.540A pdb=" N TYR A 612 " --> pdb=" O ARG A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 657 removed outlier: 3.895A pdb=" N GLY A 628 " --> pdb=" O GLN A 624 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 629 " --> pdb=" O ILE A 625 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE A 640 " --> pdb=" O LYS A 636 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 680 removed outlier: 3.815A pdb=" N LYS A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 697 through 733 removed outlier: 3.693A pdb=" N ASN A 721 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 854 through 876 Processing helix chain 'A' and resid 880 through 921 removed outlier: 3.674A pdb=" N LEU A 884 " --> pdb=" O ASN A 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 108 Processing helix chain 'B' and resid 110 through 121 removed outlier: 3.618A pdb=" N VAL B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.708A pdb=" N ASN B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 Processing helix chain 'B' and resid 160 through 172 Processing helix chain 'B' and resid 173 through 182 removed outlier: 3.518A pdb=" N SER B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 256 through 263 Processing helix chain 'B' and resid 267 through 281 removed outlier: 3.826A pdb=" N ARG B 271 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 removed outlier: 4.292A pdb=" N SER B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 311 removed outlier: 4.144A pdb=" N THR B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 335 removed outlier: 3.718A pdb=" N LEU B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 374 through 379 removed outlier: 4.012A pdb=" N VAL B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 374 through 379' Processing helix chain 'B' and resid 380 through 393 removed outlier: 3.552A pdb=" N GLU B 393 " --> pdb=" O SER B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 414 removed outlier: 3.717A pdb=" N PHE B 407 " --> pdb=" O MET B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 427 removed outlier: 4.502A pdb=" N LEU B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 437 removed outlier: 3.548A pdb=" N ARG B 437 " --> pdb=" O GLY B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 463 removed outlier: 3.534A pdb=" N LYS B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 443 " --> pdb=" O PRO B 439 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 463 " --> pdb=" O MET B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 516 removed outlier: 4.129A pdb=" N THR B 515 " --> pdb=" O LYS B 511 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 522 Processing helix chain 'B' and resid 524 through 558 removed outlier: 4.040A pdb=" N PHE B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 608 removed outlier: 3.778A pdb=" N ILE B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE B 601 " --> pdb=" O GLY B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.540A pdb=" N TYR B 612 " --> pdb=" O ARG B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 657 removed outlier: 3.895A pdb=" N GLY B 628 " --> pdb=" O GLN B 624 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 629 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS B 636 " --> pdb=" O LYS B 632 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE B 637 " --> pdb=" O ASP B 633 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 680 removed outlier: 3.815A pdb=" N LYS B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 697 through 733 removed outlier: 3.693A pdb=" N ASN B 721 " --> pdb=" O ILE B 717 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 752 Processing helix chain 'B' and resid 854 through 876 Processing helix chain 'B' and resid 880 through 921 removed outlier: 3.674A pdb=" N LEU B 884 " --> pdb=" O ASN B 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 108 Processing helix chain 'C' and resid 110 through 121 removed outlier: 3.618A pdb=" N VAL C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS C 121 " --> pdb=" O MET C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 143 removed outlier: 3.708A pdb=" N ASN C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 153 Processing helix chain 'C' and resid 160 through 172 Processing helix chain 'C' and resid 173 through 182 removed outlier: 3.518A pdb=" N SER C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 229 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 267 through 281 removed outlier: 3.826A pdb=" N ARG C 271 " --> pdb=" O PHE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 removed outlier: 4.292A pdb=" N SER C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 311 removed outlier: 4.144A pdb=" N THR C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 335 removed outlier: 3.718A pdb=" N LEU C 335 " --> pdb=" O GLY C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 364 through 372 Processing helix chain 'C' and resid 374 through 379 removed outlier: 4.012A pdb=" N VAL C 378 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 374 through 379' Processing helix chain 'C' and resid 380 through 393 removed outlier: 3.552A pdb=" N GLU C 393 " --> pdb=" O SER C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 414 removed outlier: 3.717A pdb=" N PHE C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 removed outlier: 4.502A pdb=" N LEU C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 437 removed outlier: 3.548A pdb=" N ARG C 437 " --> pdb=" O GLY C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 463 removed outlier: 3.534A pdb=" N LYS C 442 " --> pdb=" O GLY C 438 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE C 443 " --> pdb=" O PRO C 439 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 516 removed outlier: 4.129A pdb=" N THR C 515 " --> pdb=" O LYS C 511 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN C 516 " --> pdb=" O GLU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 522 Processing helix chain 'C' and resid 524 through 558 removed outlier: 4.040A pdb=" N PHE C 531 " --> pdb=" O ASN C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 608 removed outlier: 3.778A pdb=" N ILE C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE C 601 " --> pdb=" O GLY C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 removed outlier: 3.540A pdb=" N TYR C 612 " --> pdb=" O ARG C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 657 removed outlier: 3.895A pdb=" N GLY C 628 " --> pdb=" O GLN C 624 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG C 629 " --> pdb=" O ILE C 625 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS C 636 " --> pdb=" O LYS C 632 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE C 637 " --> pdb=" O ASP C 633 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE C 640 " --> pdb=" O LYS C 636 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 651 " --> pdb=" O ALA C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 680 removed outlier: 3.815A pdb=" N LYS C 676 " --> pdb=" O GLU C 672 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 692 Processing helix chain 'C' and resid 697 through 733 removed outlier: 3.693A pdb=" N ASN C 721 " --> pdb=" O ILE C 717 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 733 " --> pdb=" O SER C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 854 through 876 Processing helix chain 'C' and resid 880 through 921 removed outlier: 3.674A pdb=" N LEU C 884 " --> pdb=" O ASN C 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 108 Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.618A pdb=" N VAL D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 143 removed outlier: 3.708A pdb=" N ASN D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 153 Processing helix chain 'D' and resid 160 through 172 Processing helix chain 'D' and resid 173 through 182 removed outlier: 3.518A pdb=" N SER D 182 " --> pdb=" O GLU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 256 through 263 Processing helix chain 'D' and resid 267 through 281 removed outlier: 3.826A pdb=" N ARG D 271 " --> pdb=" O PHE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 290 removed outlier: 4.292A pdb=" N SER D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 311 removed outlier: 4.144A pdb=" N THR D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 311 " --> pdb=" O LEU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 335 removed outlier: 3.718A pdb=" N LEU D 335 " --> pdb=" O GLY D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 347 Processing helix chain 'D' and resid 364 through 372 Processing helix chain 'D' and resid 374 through 379 removed outlier: 4.012A pdb=" N VAL D 378 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 379 " --> pdb=" O LYS D 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 374 through 379' Processing helix chain 'D' and resid 380 through 393 removed outlier: 3.552A pdb=" N GLU D 393 " --> pdb=" O SER D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 414 removed outlier: 3.717A pdb=" N PHE D 407 " --> pdb=" O MET D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 427 removed outlier: 4.502A pdb=" N LEU D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 437 removed outlier: 3.548A pdb=" N ARG D 437 " --> pdb=" O GLY D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 463 removed outlier: 3.534A pdb=" N LYS D 442 " --> pdb=" O GLY D 438 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE D 443 " --> pdb=" O PRO D 439 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP D 463 " --> pdb=" O MET D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 516 removed outlier: 4.129A pdb=" N THR D 515 " --> pdb=" O LYS D 511 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 522 Processing helix chain 'D' and resid 524 through 558 removed outlier: 4.040A pdb=" N PHE D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 608 removed outlier: 3.778A pdb=" N ILE D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 3.540A pdb=" N TYR D 612 " --> pdb=" O ARG D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 657 removed outlier: 3.895A pdb=" N GLY D 628 " --> pdb=" O GLN D 624 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG D 629 " --> pdb=" O ILE D 625 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS D 636 " --> pdb=" O LYS D 632 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE D 637 " --> pdb=" O ASP D 633 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE D 640 " --> pdb=" O LYS D 636 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY D 651 " --> pdb=" O ALA D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 680 removed outlier: 3.815A pdb=" N LYS D 676 " --> pdb=" O GLU D 672 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 692 Processing helix chain 'D' and resid 697 through 733 removed outlier: 3.693A pdb=" N ASN D 721 " --> pdb=" O ILE D 717 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 733 " --> pdb=" O SER D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 752 Processing helix chain 'D' and resid 854 through 876 Processing helix chain 'D' and resid 880 through 921 removed outlier: 3.674A pdb=" N LEU D 884 " --> pdb=" O ASN D 880 " (cutoff:3.500A) 1396 hydrogen bonds defined for protein. 4140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.63 Time building geometry restraints manager: 2.54 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: 6764 1.34 - 1.46: 5004 1.46 - 1.58: 9852 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 21848 Sorted by residual: bond pdb=" CZ TYR D 521 " pdb=" OH TYR D 521 " ideal model delta sigma weight residual 1.376 1.420 -0.044 2.10e-02 2.27e+03 4.29e+00 bond pdb=" CZ TYR A 521 " pdb=" OH TYR A 521 " ideal model delta sigma weight residual 1.376 1.420 -0.044 2.10e-02 2.27e+03 4.29e+00 bond pdb=" CZ TYR B 521 " pdb=" OH TYR B 521 " ideal model delta sigma weight residual 1.376 1.420 -0.044 2.10e-02 2.27e+03 4.29e+00 bond pdb=" CZ TYR C 521 " pdb=" OH TYR C 521 " ideal model delta sigma weight residual 1.376 1.420 -0.044 2.10e-02 2.27e+03 4.29e+00 bond pdb=" CA TYR A 521 " pdb=" CB TYR A 521 " ideal model delta sigma weight residual 1.528 1.553 -0.025 1.56e-02 4.11e+03 2.53e+00 ... (remaining 21843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 28904 2.01 - 4.02: 516 4.02 - 6.03: 68 6.03 - 8.04: 20 8.04 - 10.04: 12 Bond angle restraints: 29520 Sorted by residual: angle pdb=" N GLN C 516 " pdb=" CA GLN C 516 " pdb=" C GLN C 516 " ideal model delta sigma weight residual 109.07 119.11 -10.04 1.61e+00 3.86e-01 3.89e+01 angle pdb=" N GLN D 516 " pdb=" CA GLN D 516 " pdb=" C GLN D 516 " ideal model delta sigma weight residual 109.07 119.11 -10.04 1.61e+00 3.86e-01 3.89e+01 angle pdb=" N GLN B 516 " pdb=" CA GLN B 516 " pdb=" C GLN B 516 " ideal model delta sigma weight residual 109.07 119.11 -10.04 1.61e+00 3.86e-01 3.89e+01 angle pdb=" N GLN A 516 " pdb=" CA GLN A 516 " pdb=" C GLN A 516 " ideal model delta sigma weight residual 109.07 119.11 -10.04 1.61e+00 3.86e-01 3.89e+01 angle pdb=" C GLU D 666 " pdb=" N ALA D 667 " pdb=" CA ALA D 667 " ideal model delta sigma weight residual 121.53 130.59 -9.06 2.25e+00 1.98e-01 1.62e+01 ... (remaining 29515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 11816 17.05 - 34.11: 892 34.11 - 51.16: 260 51.16 - 68.22: 60 68.22 - 85.27: 16 Dihedral angle restraints: 13044 sinusoidal: 5104 harmonic: 7940 Sorted by residual: dihedral pdb=" CA GLY B 189 " pdb=" C GLY B 189 " pdb=" N LYS B 190 " pdb=" CA LYS B 190 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA GLY C 189 " pdb=" C GLY C 189 " pdb=" N LYS C 190 " pdb=" CA LYS C 190 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA GLY A 189 " pdb=" C GLY A 189 " pdb=" N LYS A 190 " pdb=" CA LYS A 190 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 13041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2832 0.055 - 0.110: 404 0.110 - 0.166: 56 0.166 - 0.221: 4 0.221 - 0.276: 4 Chirality restraints: 3300 Sorted by residual: chirality pdb=" CA GLN A 516 " pdb=" N GLN A 516 " pdb=" C GLN A 516 " pdb=" CB GLN A 516 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA GLN D 516 " pdb=" N GLN D 516 " pdb=" C GLN D 516 " pdb=" CB GLN D 516 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA GLN C 516 " pdb=" N GLN C 516 " pdb=" C GLN C 516 " pdb=" CB GLN C 516 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 3297 not shown) Planarity restraints: 3712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 521 " -0.027 2.00e-02 2.50e+03 4.27e-02 3.65e+01 pdb=" CG TYR A 521 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 521 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 521 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 521 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR A 521 " 0.056 2.00e-02 2.50e+03 pdb=" CZ TYR A 521 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR A 521 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 521 " -0.027 2.00e-02 2.50e+03 4.27e-02 3.65e+01 pdb=" CG TYR D 521 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR D 521 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR D 521 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 521 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR D 521 " 0.056 2.00e-02 2.50e+03 pdb=" CZ TYR D 521 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR D 521 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 521 " 0.027 2.00e-02 2.50e+03 4.27e-02 3.65e+01 pdb=" CG TYR B 521 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR B 521 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 521 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 521 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR B 521 " -0.056 2.00e-02 2.50e+03 pdb=" CZ TYR B 521 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR B 521 " 0.083 2.00e-02 2.50e+03 ... (remaining 3709 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4140 2.77 - 3.31: 21196 3.31 - 3.84: 33704 3.84 - 4.37: 37856 4.37 - 4.90: 64160 Nonbonded interactions: 161056 Sorted by model distance: nonbonded pdb=" O SER C 552 " pdb=" OG SER C 556 " model vdw 2.243 3.040 nonbonded pdb=" O SER D 552 " pdb=" OG SER D 556 " model vdw 2.243 3.040 nonbonded pdb=" O SER B 552 " pdb=" OG SER B 556 " model vdw 2.243 3.040 nonbonded pdb=" O SER A 552 " pdb=" OG SER A 556 " model vdw 2.243 3.040 nonbonded pdb=" CG2 ILE C 513 " pdb=" CE1 TYR C 521 " model vdw 2.244 3.760 ... (remaining 161051 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.280 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21848 Z= 0.172 Angle : 0.684 10.044 29520 Z= 0.381 Chirality : 0.041 0.276 3300 Planarity : 0.004 0.054 3712 Dihedral : 14.253 85.272 7884 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.60 % Favored : 94.25 % Rotamer: Outliers : 2.14 % Allowed : 11.94 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.27 (0.13), residues: 2644 helix: -1.80 (0.10), residues: 1916 sheet: None (None), residues: 0 loop : -2.69 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 895 TYR 0.083 0.003 TYR A 521 PHE 0.014 0.001 PHE D 731 TRP 0.019 0.001 TRP C 750 HIS 0.008 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00331 (21848) covalent geometry : angle 0.68421 (29520) hydrogen bonds : bond 0.11891 ( 1396) hydrogen bonds : angle 7.37667 ( 4140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 600 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8046 (tppt) REVERT: A 295 MET cc_start: 0.9251 (tpt) cc_final: 0.8397 (tpp) REVERT: A 307 LEU cc_start: 0.9513 (mp) cc_final: 0.8813 (tt) REVERT: A 309 ASN cc_start: 0.9451 (m-40) cc_final: 0.8775 (p0) REVERT: A 311 GLU cc_start: 0.8575 (tt0) cc_final: 0.8008 (tt0) REVERT: A 315 LYS cc_start: 0.8795 (tttt) cc_final: 0.8400 (pttp) REVERT: A 327 ASP cc_start: 0.9519 (t70) cc_final: 0.9271 (t0) REVERT: A 336 CYS cc_start: 0.8927 (p) cc_final: 0.8719 (p) REVERT: A 432 MET cc_start: 0.9194 (mmm) cc_final: 0.8852 (mmt) REVERT: A 456 LEU cc_start: 0.9304 (mt) cc_final: 0.9066 (tt) REVERT: A 507 TRP cc_start: 0.8983 (t-100) cc_final: 0.8705 (t-100) REVERT: A 521 TYR cc_start: 0.7924 (t80) cc_final: 0.7410 (t80) REVERT: A 599 TYR cc_start: 0.9433 (t80) cc_final: 0.9032 (t80) REVERT: A 633 ASP cc_start: 0.9071 (m-30) cc_final: 0.8531 (m-30) REVERT: A 649 MET cc_start: 0.9452 (tmm) cc_final: 0.9136 (ppp) REVERT: A 687 GLU cc_start: 0.9318 (mt-10) cc_final: 0.9112 (tp30) REVERT: A 715 MET cc_start: 0.9203 (ppp) cc_final: 0.9002 (tmm) REVERT: A 722 MET cc_start: 0.9406 (mmm) cc_final: 0.9125 (tpp) REVERT: A 897 GLU cc_start: 0.9189 (tt0) cc_final: 0.8453 (tp30) REVERT: A 900 GLU cc_start: 0.8874 (tp30) cc_final: 0.8341 (tm-30) REVERT: B 190 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8047 (tppt) REVERT: B 295 MET cc_start: 0.9250 (tpt) cc_final: 0.8399 (tpp) REVERT: B 307 LEU cc_start: 0.9513 (mp) cc_final: 0.8813 (tt) REVERT: B 309 ASN cc_start: 0.9451 (m-40) cc_final: 0.8774 (p0) REVERT: B 311 GLU cc_start: 0.8571 (tt0) cc_final: 0.8009 (tt0) REVERT: B 315 LYS cc_start: 0.8796 (tttt) cc_final: 0.8401 (pttp) REVERT: B 327 ASP cc_start: 0.9519 (t70) cc_final: 0.9272 (t0) REVERT: B 336 CYS cc_start: 0.8927 (p) cc_final: 0.8718 (p) REVERT: B 432 MET cc_start: 0.9193 (mmm) cc_final: 0.8849 (mmt) REVERT: B 456 LEU cc_start: 0.9304 (mt) cc_final: 0.9066 (tt) REVERT: B 507 TRP cc_start: 0.8982 (t-100) cc_final: 0.8705 (t-100) REVERT: B 521 TYR cc_start: 0.7922 (t80) cc_final: 0.7405 (t80) REVERT: B 599 TYR cc_start: 0.9432 (t80) cc_final: 0.9032 (t80) REVERT: B 633 ASP cc_start: 0.9072 (m-30) cc_final: 0.8530 (m-30) REVERT: B 649 MET cc_start: 0.9453 (tmm) cc_final: 0.9137 (ppp) REVERT: B 687 GLU cc_start: 0.9318 (mt-10) cc_final: 0.9112 (tp30) REVERT: B 715 MET cc_start: 0.9203 (ppp) cc_final: 0.9001 (tmm) REVERT: B 722 MET cc_start: 0.9403 (mmm) cc_final: 0.9122 (tpp) REVERT: B 897 GLU cc_start: 0.9188 (tt0) cc_final: 0.8448 (tp30) REVERT: B 900 GLU cc_start: 0.8874 (tp30) cc_final: 0.8339 (tm-30) REVERT: C 190 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8049 (tppt) REVERT: C 295 MET cc_start: 0.9250 (tpt) cc_final: 0.8398 (tpp) REVERT: C 307 LEU cc_start: 0.9513 (mp) cc_final: 0.8811 (tt) REVERT: C 309 ASN cc_start: 0.9451 (m-40) cc_final: 0.8774 (p0) REVERT: C 311 GLU cc_start: 0.8571 (tt0) cc_final: 0.8007 (tt0) REVERT: C 315 LYS cc_start: 0.8794 (tttt) cc_final: 0.8399 (pttp) REVERT: C 327 ASP cc_start: 0.9519 (t70) cc_final: 0.9272 (t0) REVERT: C 336 CYS cc_start: 0.8931 (p) cc_final: 0.8723 (p) REVERT: C 432 MET cc_start: 0.9193 (mmm) cc_final: 0.8849 (mmt) REVERT: C 456 LEU cc_start: 0.9304 (mt) cc_final: 0.9066 (tt) REVERT: C 507 TRP cc_start: 0.8982 (t-100) cc_final: 0.8704 (t-100) REVERT: C 521 TYR cc_start: 0.7922 (t80) cc_final: 0.7407 (t80) REVERT: C 599 TYR cc_start: 0.9432 (t80) cc_final: 0.9031 (t80) REVERT: C 633 ASP cc_start: 0.9073 (m-30) cc_final: 0.8533 (m-30) REVERT: C 649 MET cc_start: 0.9453 (tmm) cc_final: 0.9136 (ppp) REVERT: C 687 GLU cc_start: 0.9317 (mt-10) cc_final: 0.9113 (tp30) REVERT: C 715 MET cc_start: 0.9200 (ppp) cc_final: 0.8999 (tmm) REVERT: C 722 MET cc_start: 0.9405 (mmm) cc_final: 0.9121 (tpp) REVERT: C 897 GLU cc_start: 0.9189 (tt0) cc_final: 0.8450 (tp30) REVERT: C 900 GLU cc_start: 0.8874 (tp30) cc_final: 0.8340 (tm-30) REVERT: D 190 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8048 (tppt) REVERT: D 295 MET cc_start: 0.9250 (tpt) cc_final: 0.8396 (tpp) REVERT: D 307 LEU cc_start: 0.9513 (mp) cc_final: 0.8813 (tt) REVERT: D 309 ASN cc_start: 0.9451 (m-40) cc_final: 0.8776 (p0) REVERT: D 311 GLU cc_start: 0.8573 (tt0) cc_final: 0.8007 (tt0) REVERT: D 315 LYS cc_start: 0.8795 (tttt) cc_final: 0.8401 (pttp) REVERT: D 327 ASP cc_start: 0.9517 (t70) cc_final: 0.9271 (t0) REVERT: D 336 CYS cc_start: 0.8925 (p) cc_final: 0.8721 (p) REVERT: D 432 MET cc_start: 0.9193 (mmm) cc_final: 0.8851 (mmt) REVERT: D 456 LEU cc_start: 0.9304 (mt) cc_final: 0.9067 (tt) REVERT: D 507 TRP cc_start: 0.8982 (t-100) cc_final: 0.8704 (t-100) REVERT: D 521 TYR cc_start: 0.7923 (t80) cc_final: 0.7408 (t80) REVERT: D 599 TYR cc_start: 0.9431 (t80) cc_final: 0.9031 (t80) REVERT: D 633 ASP cc_start: 0.9072 (m-30) cc_final: 0.8532 (m-30) REVERT: D 649 MET cc_start: 0.9453 (tmm) cc_final: 0.9135 (ppp) REVERT: D 687 GLU cc_start: 0.9319 (mt-10) cc_final: 0.9113 (tp30) REVERT: D 715 MET cc_start: 0.9202 (ppp) cc_final: 0.9001 (tmm) REVERT: D 722 MET cc_start: 0.9405 (mmm) cc_final: 0.9122 (tpp) REVERT: D 897 GLU cc_start: 0.9191 (tt0) cc_final: 0.8445 (tp30) REVERT: D 900 GLU cc_start: 0.8873 (tp30) cc_final: 0.8341 (tm-30) outliers start: 48 outliers final: 17 residues processed: 624 average time/residue: 0.1563 time to fit residues: 148.7415 Evaluate side-chains 373 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 352 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 264 HIS Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 608 SER Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 264 HIS Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 264 HIS Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 608 SER Chi-restraints excluded: chain D residue 901 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 732 GLN B 230 GLN B 732 GLN C 230 GLN C 732 GLN D 230 GLN D 732 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.081881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.066766 restraints weight = 68845.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.068947 restraints weight = 36422.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.070436 restraints weight = 23956.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.071470 restraints weight = 17819.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.072178 restraints weight = 14485.277| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21848 Z= 0.144 Angle : 0.644 8.613 29520 Z= 0.328 Chirality : 0.040 0.178 3300 Planarity : 0.004 0.042 3712 Dihedral : 5.916 48.912 2931 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.94 % Allowed : 17.34 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.16), residues: 2644 helix: 0.67 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : -3.03 (0.18), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 853 TYR 0.014 0.002 TYR B 658 PHE 0.017 0.001 PHE A 731 TRP 0.020 0.001 TRP D 750 HIS 0.010 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00312 (21848) covalent geometry : angle 0.64382 (29520) hydrogen bonds : bond 0.04450 ( 1396) hydrogen bonds : angle 4.30239 ( 4140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 408 time to evaluate : 0.891 Fit side-chains REVERT: A 87 MET cc_start: 0.8085 (tmm) cc_final: 0.7614 (tmm) REVERT: A 309 ASN cc_start: 0.9062 (t0) cc_final: 0.8643 (p0) REVERT: A 311 GLU cc_start: 0.7983 (tt0) cc_final: 0.7515 (tt0) REVERT: A 327 ASP cc_start: 0.9057 (t70) cc_final: 0.8765 (t0) REVERT: A 403 MET cc_start: 0.7748 (tpp) cc_final: 0.7508 (tpp) REVERT: A 494 MET cc_start: 0.8828 (mmp) cc_final: 0.8147 (mtm) REVERT: A 510 CYS cc_start: 0.8524 (m) cc_final: 0.8205 (t) REVERT: A 533 MET cc_start: 0.9075 (tmm) cc_final: 0.8447 (tmm) REVERT: A 607 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8640 (t80) REVERT: A 633 ASP cc_start: 0.8714 (m-30) cc_final: 0.8202 (m-30) REVERT: A 649 MET cc_start: 0.9009 (tmm) cc_final: 0.8780 (ppp) REVERT: A 670 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8716 (p) REVERT: A 687 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8085 (pt0) REVERT: A 701 GLU cc_start: 0.8864 (tt0) cc_final: 0.8434 (pt0) REVERT: A 897 GLU cc_start: 0.8683 (tt0) cc_final: 0.8466 (mt-10) REVERT: B 87 MET cc_start: 0.8081 (tmm) cc_final: 0.7606 (tmm) REVERT: B 309 ASN cc_start: 0.9064 (t0) cc_final: 0.8644 (p0) REVERT: B 311 GLU cc_start: 0.7982 (tt0) cc_final: 0.7514 (tt0) REVERT: B 327 ASP cc_start: 0.9064 (t70) cc_final: 0.8776 (t0) REVERT: B 403 MET cc_start: 0.7750 (tpp) cc_final: 0.7507 (tpp) REVERT: B 494 MET cc_start: 0.8827 (mmp) cc_final: 0.8146 (mtm) REVERT: B 510 CYS cc_start: 0.8532 (m) cc_final: 0.8210 (t) REVERT: B 533 MET cc_start: 0.9081 (tmm) cc_final: 0.8451 (tmm) REVERT: B 607 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8640 (t80) REVERT: B 633 ASP cc_start: 0.8718 (m-30) cc_final: 0.8205 (m-30) REVERT: B 649 MET cc_start: 0.9011 (tmm) cc_final: 0.8780 (ppp) REVERT: B 670 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8710 (p) REVERT: B 687 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8093 (pt0) REVERT: B 701 GLU cc_start: 0.8863 (tt0) cc_final: 0.8436 (pt0) REVERT: B 897 GLU cc_start: 0.8675 (tt0) cc_final: 0.8461 (mt-10) REVERT: C 87 MET cc_start: 0.8084 (tmm) cc_final: 0.7612 (tmm) REVERT: C 309 ASN cc_start: 0.9062 (t0) cc_final: 0.8641 (p0) REVERT: C 311 GLU cc_start: 0.7976 (tt0) cc_final: 0.7510 (tt0) REVERT: C 327 ASP cc_start: 0.9054 (t70) cc_final: 0.8764 (t0) REVERT: C 403 MET cc_start: 0.7752 (tpp) cc_final: 0.7510 (tpp) REVERT: C 494 MET cc_start: 0.8828 (mmp) cc_final: 0.8148 (mtm) REVERT: C 510 CYS cc_start: 0.8542 (m) cc_final: 0.8219 (t) REVERT: C 533 MET cc_start: 0.9075 (tmm) cc_final: 0.8446 (tmm) REVERT: C 607 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8636 (t80) REVERT: C 633 ASP cc_start: 0.8716 (m-30) cc_final: 0.8203 (m-30) REVERT: C 649 MET cc_start: 0.9013 (tmm) cc_final: 0.8782 (ppp) REVERT: C 670 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8711 (p) REVERT: C 687 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8096 (pt0) REVERT: C 701 GLU cc_start: 0.8865 (tt0) cc_final: 0.8438 (pt0) REVERT: C 897 GLU cc_start: 0.8680 (tt0) cc_final: 0.8463 (mt-10) REVERT: D 87 MET cc_start: 0.8090 (tmm) cc_final: 0.7615 (tmm) REVERT: D 309 ASN cc_start: 0.9062 (t0) cc_final: 0.8642 (p0) REVERT: D 311 GLU cc_start: 0.7972 (tt0) cc_final: 0.7504 (tt0) REVERT: D 327 ASP cc_start: 0.9056 (t70) cc_final: 0.8765 (t0) REVERT: D 403 MET cc_start: 0.7750 (tpp) cc_final: 0.7508 (tpp) REVERT: D 494 MET cc_start: 0.8823 (mmp) cc_final: 0.8145 (mtm) REVERT: D 510 CYS cc_start: 0.8534 (m) cc_final: 0.8214 (t) REVERT: D 533 MET cc_start: 0.9072 (tmm) cc_final: 0.8444 (tmm) REVERT: D 607 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8641 (t80) REVERT: D 633 ASP cc_start: 0.8716 (m-30) cc_final: 0.8204 (m-30) REVERT: D 649 MET cc_start: 0.9017 (tmm) cc_final: 0.8786 (ppp) REVERT: D 670 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8712 (p) REVERT: D 687 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8085 (pt0) REVERT: D 701 GLU cc_start: 0.8867 (tt0) cc_final: 0.8438 (pt0) REVERT: D 897 GLU cc_start: 0.8690 (tt0) cc_final: 0.8478 (mt-10) REVERT: D 900 GLU cc_start: 0.8407 (tp30) cc_final: 0.8203 (tm-30) outliers start: 66 outliers final: 20 residues processed: 445 average time/residue: 0.1429 time to fit residues: 103.1050 Evaluate side-chains 366 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 338 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 264 HIS Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 264 HIS Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 264 HIS Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 607 PHE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 677 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 187 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.081508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.066447 restraints weight = 70324.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.068628 restraints weight = 37091.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.070106 restraints weight = 24337.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.071104 restraints weight = 18173.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.071852 restraints weight = 14792.539| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21848 Z= 0.148 Angle : 0.637 9.589 29520 Z= 0.319 Chirality : 0.040 0.176 3300 Planarity : 0.004 0.040 3712 Dihedral : 4.873 38.136 2900 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.58 % Allowed : 20.94 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.16), residues: 2644 helix: 1.47 (0.12), residues: 1996 sheet: None (None), residues: 0 loop : -3.23 (0.18), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 437 TYR 0.016 0.001 TYR D 521 PHE 0.014 0.001 PHE A 731 TRP 0.020 0.001 TRP D 750 HIS 0.009 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00326 (21848) covalent geometry : angle 0.63659 (29520) hydrogen bonds : bond 0.04061 ( 1396) hydrogen bonds : angle 3.97126 ( 4140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 341 time to evaluate : 1.195 Fit side-chains REVERT: A 87 MET cc_start: 0.8201 (tmm) cc_final: 0.7822 (tmm) REVERT: A 299 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8029 (mt-10) REVERT: A 309 ASN cc_start: 0.8925 (t0) cc_final: 0.8639 (p0) REVERT: A 311 GLU cc_start: 0.8109 (tt0) cc_final: 0.7644 (tt0) REVERT: A 327 ASP cc_start: 0.8891 (t70) cc_final: 0.8586 (t0) REVERT: A 436 MET cc_start: 0.9021 (mmm) cc_final: 0.8701 (mmm) REVERT: A 494 MET cc_start: 0.8685 (mmp) cc_final: 0.8210 (mtm) REVERT: A 496 MET cc_start: 0.9296 (mmm) cc_final: 0.8705 (mpp) REVERT: A 510 CYS cc_start: 0.8217 (m) cc_final: 0.7970 (t) REVERT: A 607 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8845 (t80) REVERT: A 633 ASP cc_start: 0.8736 (m-30) cc_final: 0.8184 (m-30) REVERT: A 642 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8672 (tp) REVERT: A 649 MET cc_start: 0.9018 (tmm) cc_final: 0.8786 (ppp) REVERT: A 670 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8578 (p) REVERT: A 701 GLU cc_start: 0.8841 (tt0) cc_final: 0.8485 (pt0) REVERT: B 87 MET cc_start: 0.8194 (tmm) cc_final: 0.7814 (tmm) REVERT: B 299 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8038 (mt-10) REVERT: B 309 ASN cc_start: 0.8936 (t0) cc_final: 0.8642 (p0) REVERT: B 311 GLU cc_start: 0.8132 (tt0) cc_final: 0.7660 (tt0) REVERT: B 327 ASP cc_start: 0.8893 (t70) cc_final: 0.8589 (t0) REVERT: B 436 MET cc_start: 0.9023 (mmm) cc_final: 0.8698 (mmm) REVERT: B 494 MET cc_start: 0.8679 (mmp) cc_final: 0.8208 (mtm) REVERT: B 496 MET cc_start: 0.9297 (mmm) cc_final: 0.8703 (mpp) REVERT: B 510 CYS cc_start: 0.8218 (m) cc_final: 0.7967 (t) REVERT: B 607 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8846 (t80) REVERT: B 633 ASP cc_start: 0.8736 (m-30) cc_final: 0.8184 (m-30) REVERT: B 642 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8668 (tp) REVERT: B 649 MET cc_start: 0.9023 (tmm) cc_final: 0.8787 (ppp) REVERT: B 670 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8573 (p) REVERT: B 701 GLU cc_start: 0.8846 (tt0) cc_final: 0.8485 (pt0) REVERT: C 87 MET cc_start: 0.8196 (tmm) cc_final: 0.7819 (tmm) REVERT: C 299 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8031 (mt-10) REVERT: C 309 ASN cc_start: 0.8938 (t0) cc_final: 0.8644 (p0) REVERT: C 311 GLU cc_start: 0.8121 (tt0) cc_final: 0.7650 (tt0) REVERT: C 327 ASP cc_start: 0.8899 (t70) cc_final: 0.8595 (t0) REVERT: C 436 MET cc_start: 0.9017 (mmm) cc_final: 0.8694 (mmm) REVERT: C 494 MET cc_start: 0.8678 (mmp) cc_final: 0.8207 (mtm) REVERT: C 496 MET cc_start: 0.9297 (mmm) cc_final: 0.8709 (mpp) REVERT: C 510 CYS cc_start: 0.8221 (m) cc_final: 0.7968 (t) REVERT: C 607 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8843 (t80) REVERT: C 633 ASP cc_start: 0.8735 (m-30) cc_final: 0.8182 (m-30) REVERT: C 642 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8664 (tp) REVERT: C 649 MET cc_start: 0.9018 (tmm) cc_final: 0.8785 (ppp) REVERT: C 670 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8573 (p) REVERT: C 701 GLU cc_start: 0.8843 (tt0) cc_final: 0.8485 (pt0) REVERT: D 87 MET cc_start: 0.8206 (tmm) cc_final: 0.7826 (tmm) REVERT: D 299 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8035 (mt-10) REVERT: D 309 ASN cc_start: 0.8928 (t0) cc_final: 0.8639 (p0) REVERT: D 311 GLU cc_start: 0.8116 (tt0) cc_final: 0.7647 (tt0) REVERT: D 327 ASP cc_start: 0.8895 (t70) cc_final: 0.8590 (t0) REVERT: D 436 MET cc_start: 0.9012 (mmm) cc_final: 0.8693 (mmm) REVERT: D 494 MET cc_start: 0.8675 (mmp) cc_final: 0.8209 (mtm) REVERT: D 496 MET cc_start: 0.9292 (mmm) cc_final: 0.8703 (mpp) REVERT: D 510 CYS cc_start: 0.8221 (m) cc_final: 0.7972 (t) REVERT: D 607 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8841 (t80) REVERT: D 633 ASP cc_start: 0.8733 (m-30) cc_final: 0.8181 (m-30) REVERT: D 642 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8668 (tp) REVERT: D 649 MET cc_start: 0.9015 (tmm) cc_final: 0.8786 (ppp) REVERT: D 670 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8575 (p) REVERT: D 701 GLU cc_start: 0.8846 (tt0) cc_final: 0.8485 (pt0) REVERT: D 897 GLU cc_start: 0.8682 (tt0) cc_final: 0.8461 (mt-10) outliers start: 58 outliers final: 28 residues processed: 367 average time/residue: 0.1403 time to fit residues: 85.0761 Evaluate side-chains 317 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 705 TYR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 705 TYR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 607 PHE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 677 THR Chi-restraints excluded: chain D residue 705 TYR Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 148 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 138 optimal weight: 0.0980 chunk 41 optimal weight: 7.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 460 ASN A 856 GLN B 249 HIS B 460 ASN B 856 GLN C 249 HIS C 460 ASN C 856 GLN D 249 HIS D 460 ASN D 856 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.080337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.065236 restraints weight = 70894.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.067352 restraints weight = 37669.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.068797 restraints weight = 24870.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.069771 restraints weight = 18717.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.070453 restraints weight = 15349.855| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21848 Z= 0.192 Angle : 0.637 7.907 29520 Z= 0.329 Chirality : 0.040 0.179 3300 Planarity : 0.004 0.040 3712 Dihedral : 4.737 35.822 2892 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.21 % Allowed : 21.35 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.16), residues: 2644 helix: 1.70 (0.12), residues: 1996 sheet: None (None), residues: 0 loop : -3.16 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 91 TYR 0.012 0.001 TYR B 658 PHE 0.012 0.001 PHE A 731 TRP 0.023 0.002 TRP D 750 HIS 0.009 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00422 (21848) covalent geometry : angle 0.63747 (29520) hydrogen bonds : bond 0.04141 ( 1396) hydrogen bonds : angle 3.94030 ( 4140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 317 time to evaluate : 0.855 Fit side-chains REVERT: A 87 MET cc_start: 0.8337 (tmm) cc_final: 0.7977 (tmm) REVERT: A 295 MET cc_start: 0.8197 (tpp) cc_final: 0.7979 (tpp) REVERT: A 311 GLU cc_start: 0.8127 (tt0) cc_final: 0.7672 (tt0) REVERT: A 327 ASP cc_start: 0.8904 (t70) cc_final: 0.8617 (t0) REVERT: A 419 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8345 (m-80) REVERT: A 496 MET cc_start: 0.9259 (mmm) cc_final: 0.8676 (mpp) REVERT: A 607 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8845 (t80) REVERT: A 633 ASP cc_start: 0.8683 (m-30) cc_final: 0.8318 (m-30) REVERT: A 642 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8561 (tp) REVERT: A 649 MET cc_start: 0.9004 (tmm) cc_final: 0.8715 (ppp) REVERT: A 670 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8685 (p) REVERT: A 701 GLU cc_start: 0.8853 (tt0) cc_final: 0.8540 (pt0) REVERT: B 87 MET cc_start: 0.8331 (tmm) cc_final: 0.7971 (tmm) REVERT: B 295 MET cc_start: 0.8204 (tpp) cc_final: 0.7987 (tpp) REVERT: B 311 GLU cc_start: 0.8129 (tt0) cc_final: 0.7672 (tt0) REVERT: B 327 ASP cc_start: 0.8912 (t70) cc_final: 0.8622 (t0) REVERT: B 419 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: B 496 MET cc_start: 0.9260 (mmm) cc_final: 0.8676 (mpp) REVERT: B 607 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8843 (t80) REVERT: B 633 ASP cc_start: 0.8688 (m-30) cc_final: 0.8319 (m-30) REVERT: B 642 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8552 (tp) REVERT: B 649 MET cc_start: 0.9009 (tmm) cc_final: 0.8719 (ppp) REVERT: B 670 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8682 (p) REVERT: B 701 GLU cc_start: 0.8857 (tt0) cc_final: 0.8542 (pt0) REVERT: C 87 MET cc_start: 0.8336 (tmm) cc_final: 0.7977 (tmm) REVERT: C 295 MET cc_start: 0.8191 (tpp) cc_final: 0.7977 (tpp) REVERT: C 311 GLU cc_start: 0.8121 (tt0) cc_final: 0.7671 (tt0) REVERT: C 327 ASP cc_start: 0.8913 (t70) cc_final: 0.8625 (t0) REVERT: C 419 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: C 496 MET cc_start: 0.9254 (mmm) cc_final: 0.8676 (mpp) REVERT: C 607 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8841 (t80) REVERT: C 633 ASP cc_start: 0.8690 (m-30) cc_final: 0.8319 (m-30) REVERT: C 642 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8554 (tp) REVERT: C 649 MET cc_start: 0.9000 (tmm) cc_final: 0.8712 (ppp) REVERT: C 670 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8684 (p) REVERT: C 701 GLU cc_start: 0.8851 (tt0) cc_final: 0.8540 (pt0) REVERT: D 87 MET cc_start: 0.8340 (tmm) cc_final: 0.7982 (tmm) REVERT: D 295 MET cc_start: 0.8186 (tpp) cc_final: 0.7969 (tpp) REVERT: D 311 GLU cc_start: 0.8126 (tt0) cc_final: 0.7673 (tt0) REVERT: D 327 ASP cc_start: 0.8904 (t70) cc_final: 0.8614 (t0) REVERT: D 419 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: D 496 MET cc_start: 0.9254 (mmm) cc_final: 0.8674 (mpp) REVERT: D 607 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8843 (t80) REVERT: D 633 ASP cc_start: 0.8683 (m-30) cc_final: 0.8314 (m-30) REVERT: D 642 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8554 (tp) REVERT: D 649 MET cc_start: 0.8998 (tmm) cc_final: 0.8712 (ppp) REVERT: D 670 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8686 (p) REVERT: D 701 GLU cc_start: 0.8857 (tt0) cc_final: 0.8542 (pt0) outliers start: 72 outliers final: 32 residues processed: 361 average time/residue: 0.1396 time to fit residues: 83.2453 Evaluate side-chains 336 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 288 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 419 PHE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 607 PHE Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 677 THR Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 14 optimal weight: 0.0670 chunk 148 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 136 optimal weight: 0.0980 chunk 266 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN B 460 ASN C 460 ASN D 460 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.084399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.069291 restraints weight = 69359.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.071517 restraints weight = 36707.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073048 restraints weight = 23969.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.074030 restraints weight = 17812.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.074785 restraints weight = 14487.517| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21848 Z= 0.118 Angle : 0.607 8.193 29520 Z= 0.297 Chirality : 0.038 0.180 3300 Planarity : 0.004 0.041 3712 Dihedral : 4.409 36.799 2892 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.85 % Allowed : 22.37 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.17), residues: 2644 helix: 2.00 (0.12), residues: 2000 sheet: None (None), residues: 0 loop : -3.25 (0.19), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 853 TYR 0.009 0.001 TYR B 659 PHE 0.011 0.001 PHE D 731 TRP 0.019 0.001 TRP A 750 HIS 0.009 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00246 (21848) covalent geometry : angle 0.60655 (29520) hydrogen bonds : bond 0.03446 ( 1396) hydrogen bonds : angle 3.51490 ( 4140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 299 time to evaluate : 0.893 Fit side-chains REVERT: A 87 MET cc_start: 0.8259 (tmm) cc_final: 0.7932 (tmm) REVERT: A 186 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8308 (t80) REVERT: A 311 GLU cc_start: 0.8040 (tt0) cc_final: 0.7545 (tt0) REVERT: A 327 ASP cc_start: 0.8902 (t70) cc_final: 0.8572 (t0) REVERT: A 419 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: A 494 MET cc_start: 0.8853 (mmp) cc_final: 0.8111 (mtm) REVERT: A 496 MET cc_start: 0.9220 (mmm) cc_final: 0.8710 (mpp) REVERT: A 607 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8834 (t80) REVERT: A 633 ASP cc_start: 0.8677 (m-30) cc_final: 0.8270 (m-30) REVERT: A 649 MET cc_start: 0.8932 (tmm) cc_final: 0.8595 (ppp) REVERT: A 670 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8618 (p) REVERT: A 701 GLU cc_start: 0.8761 (tt0) cc_final: 0.8508 (pt0) REVERT: A 859 MET cc_start: 0.9071 (mmp) cc_final: 0.8758 (mmt) REVERT: B 87 MET cc_start: 0.8262 (tmm) cc_final: 0.7935 (tmm) REVERT: B 186 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8312 (t80) REVERT: B 311 GLU cc_start: 0.8040 (tt0) cc_final: 0.7546 (tt0) REVERT: B 327 ASP cc_start: 0.8907 (t70) cc_final: 0.8575 (t0) REVERT: B 419 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: B 494 MET cc_start: 0.8847 (mmp) cc_final: 0.8113 (mtm) REVERT: B 496 MET cc_start: 0.9219 (mmm) cc_final: 0.8709 (mpp) REVERT: B 607 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8737 (t80) REVERT: B 633 ASP cc_start: 0.8674 (m-30) cc_final: 0.8266 (m-30) REVERT: B 649 MET cc_start: 0.8934 (tmm) cc_final: 0.8597 (ppp) REVERT: B 670 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8617 (p) REVERT: B 701 GLU cc_start: 0.8762 (tt0) cc_final: 0.8505 (pt0) REVERT: B 859 MET cc_start: 0.9068 (mmp) cc_final: 0.8757 (mmt) REVERT: C 87 MET cc_start: 0.8264 (tmm) cc_final: 0.7935 (tmm) REVERT: C 186 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8318 (t80) REVERT: C 311 GLU cc_start: 0.8023 (tt0) cc_final: 0.7536 (tt0) REVERT: C 327 ASP cc_start: 0.8899 (t70) cc_final: 0.8569 (t0) REVERT: C 419 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: C 494 MET cc_start: 0.8848 (mmp) cc_final: 0.8108 (mtm) REVERT: C 496 MET cc_start: 0.9216 (mmm) cc_final: 0.8709 (mpp) REVERT: C 607 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8732 (t80) REVERT: C 633 ASP cc_start: 0.8677 (m-30) cc_final: 0.8269 (m-30) REVERT: C 649 MET cc_start: 0.8924 (tmm) cc_final: 0.8592 (ppp) REVERT: C 670 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8619 (p) REVERT: C 701 GLU cc_start: 0.8755 (tt0) cc_final: 0.8502 (pt0) REVERT: C 859 MET cc_start: 0.9064 (mmp) cc_final: 0.8749 (mmt) REVERT: D 87 MET cc_start: 0.8269 (tmm) cc_final: 0.7942 (tmm) REVERT: D 186 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8315 (t80) REVERT: D 311 GLU cc_start: 0.8018 (tt0) cc_final: 0.7528 (tt0) REVERT: D 327 ASP cc_start: 0.8898 (t70) cc_final: 0.8569 (t0) REVERT: D 419 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: D 494 MET cc_start: 0.8849 (mmp) cc_final: 0.8105 (mtm) REVERT: D 496 MET cc_start: 0.9215 (mmm) cc_final: 0.8710 (mpp) REVERT: D 607 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8738 (t80) REVERT: D 633 ASP cc_start: 0.8674 (m-30) cc_final: 0.8266 (m-30) REVERT: D 649 MET cc_start: 0.8933 (tmm) cc_final: 0.8598 (ppp) REVERT: D 670 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8616 (p) REVERT: D 701 GLU cc_start: 0.8755 (tt0) cc_final: 0.8502 (pt0) REVERT: D 859 MET cc_start: 0.9061 (mmp) cc_final: 0.8745 (mmt) outliers start: 64 outliers final: 24 residues processed: 343 average time/residue: 0.1375 time to fit residues: 77.6214 Evaluate side-chains 333 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 293 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 419 PHE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 607 PHE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 677 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 138 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS B 249 HIS C 249 HIS D 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.081750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.066740 restraints weight = 70058.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.068880 restraints weight = 37186.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.070339 restraints weight = 24460.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.071338 restraints weight = 18293.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072000 restraints weight = 14875.786| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21848 Z= 0.164 Angle : 0.625 9.042 29520 Z= 0.314 Chirality : 0.039 0.185 3300 Planarity : 0.004 0.040 3712 Dihedral : 4.403 34.718 2892 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.72 % Allowed : 23.13 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.17), residues: 2644 helix: 2.09 (0.12), residues: 2000 sheet: None (None), residues: 0 loop : -3.18 (0.19), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 337 TYR 0.009 0.001 TYR B 285 PHE 0.012 0.001 PHE C 607 TRP 0.019 0.001 TRP A 750 HIS 0.009 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00366 (21848) covalent geometry : angle 0.62473 (29520) hydrogen bonds : bond 0.03718 ( 1396) hydrogen bonds : angle 3.62786 ( 4140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 278 time to evaluate : 0.932 Fit side-chains REVERT: A 87 MET cc_start: 0.8281 (tmm) cc_final: 0.7954 (tmm) REVERT: A 186 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8231 (t80) REVERT: A 311 GLU cc_start: 0.8077 (tt0) cc_final: 0.7602 (tt0) REVERT: A 327 ASP cc_start: 0.8909 (t70) cc_final: 0.8599 (t0) REVERT: A 419 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: A 436 MET cc_start: 0.8990 (mmm) cc_final: 0.8548 (mmm) REVERT: A 496 MET cc_start: 0.9226 (mmm) cc_final: 0.8675 (mpp) REVERT: A 607 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8917 (t80) REVERT: A 633 ASP cc_start: 0.8689 (m-30) cc_final: 0.8351 (m-30) REVERT: A 649 MET cc_start: 0.8985 (tmm) cc_final: 0.8651 (ppp) REVERT: A 670 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8735 (p) REVERT: A 701 GLU cc_start: 0.8753 (tt0) cc_final: 0.8438 (pt0) REVERT: A 715 MET cc_start: 0.8575 (tmm) cc_final: 0.8369 (tmm) REVERT: A 726 MET cc_start: 0.8245 (mmm) cc_final: 0.8020 (mmm) REVERT: B 87 MET cc_start: 0.8283 (tmm) cc_final: 0.7956 (tmm) REVERT: B 186 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8233 (t80) REVERT: B 311 GLU cc_start: 0.8071 (tt0) cc_final: 0.7601 (tt0) REVERT: B 327 ASP cc_start: 0.8910 (t70) cc_final: 0.8599 (t0) REVERT: B 419 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: B 436 MET cc_start: 0.8998 (mmm) cc_final: 0.8552 (mmm) REVERT: B 496 MET cc_start: 0.9220 (mmm) cc_final: 0.8673 (mpp) REVERT: B 607 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8479 (t80) REVERT: B 633 ASP cc_start: 0.8688 (m-30) cc_final: 0.8349 (m-30) REVERT: B 649 MET cc_start: 0.8976 (tmm) cc_final: 0.8642 (ppp) REVERT: B 670 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8726 (p) REVERT: B 701 GLU cc_start: 0.8758 (tt0) cc_final: 0.8437 (pt0) REVERT: B 715 MET cc_start: 0.8573 (tmm) cc_final: 0.8367 (tmm) REVERT: B 726 MET cc_start: 0.8233 (mmm) cc_final: 0.8010 (mmm) REVERT: C 87 MET cc_start: 0.8284 (tmm) cc_final: 0.7956 (tmm) REVERT: C 186 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8238 (t80) REVERT: C 311 GLU cc_start: 0.8066 (tt0) cc_final: 0.7597 (tt0) REVERT: C 327 ASP cc_start: 0.8908 (t70) cc_final: 0.8598 (t0) REVERT: C 419 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8184 (m-80) REVERT: C 436 MET cc_start: 0.8993 (mmm) cc_final: 0.8549 (mmm) REVERT: C 496 MET cc_start: 0.9220 (mmm) cc_final: 0.8676 (mpp) REVERT: C 607 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8476 (t80) REVERT: C 633 ASP cc_start: 0.8688 (m-30) cc_final: 0.8350 (m-30) REVERT: C 649 MET cc_start: 0.8977 (tmm) cc_final: 0.8647 (ppp) REVERT: C 670 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8739 (p) REVERT: C 701 GLU cc_start: 0.8753 (tt0) cc_final: 0.8437 (pt0) REVERT: C 715 MET cc_start: 0.8570 (tmm) cc_final: 0.8365 (tmm) REVERT: C 726 MET cc_start: 0.8225 (mmm) cc_final: 0.8001 (mmm) REVERT: D 87 MET cc_start: 0.8285 (tmm) cc_final: 0.7958 (tmm) REVERT: D 186 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8232 (t80) REVERT: D 311 GLU cc_start: 0.8064 (tt0) cc_final: 0.7586 (tt0) REVERT: D 327 ASP cc_start: 0.8900 (t70) cc_final: 0.8590 (t0) REVERT: D 419 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8186 (m-80) REVERT: D 436 MET cc_start: 0.8992 (mmm) cc_final: 0.8550 (mmm) REVERT: D 496 MET cc_start: 0.9216 (mmm) cc_final: 0.8672 (mpp) REVERT: D 607 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8481 (t80) REVERT: D 633 ASP cc_start: 0.8687 (m-30) cc_final: 0.8346 (m-30) REVERT: D 649 MET cc_start: 0.8983 (tmm) cc_final: 0.8650 (ppp) REVERT: D 670 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8734 (p) REVERT: D 701 GLU cc_start: 0.8756 (tt0) cc_final: 0.8438 (pt0) REVERT: D 715 MET cc_start: 0.8573 (tmm) cc_final: 0.8367 (tmm) REVERT: D 726 MET cc_start: 0.8238 (mmm) cc_final: 0.8009 (mmm) outliers start: 61 outliers final: 24 residues processed: 319 average time/residue: 0.1354 time to fit residues: 72.0601 Evaluate side-chains 309 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 269 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 419 PHE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 607 PHE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 677 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 5 optimal weight: 8.9990 chunk 212 optimal weight: 0.0270 chunk 241 optimal weight: 10.0000 chunk 236 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 190 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS B 249 HIS C 249 HIS D 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.083636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.068403 restraints weight = 70145.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.070609 restraints weight = 37438.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.072063 restraints weight = 24641.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.073094 restraints weight = 18450.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.073773 restraints weight = 15020.466| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21848 Z= 0.122 Angle : 0.617 9.808 29520 Z= 0.301 Chirality : 0.038 0.199 3300 Planarity : 0.003 0.039 3712 Dihedral : 4.293 33.502 2892 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.07 % Allowed : 23.80 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.17), residues: 2644 helix: 2.11 (0.12), residues: 2012 sheet: None (None), residues: 0 loop : -3.05 (0.20), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 609 TYR 0.008 0.001 TYR D 659 PHE 0.011 0.001 PHE D 607 TRP 0.017 0.001 TRP C 750 HIS 0.009 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00271 (21848) covalent geometry : angle 0.61717 (29520) hydrogen bonds : bond 0.03467 ( 1396) hydrogen bonds : angle 3.49517 ( 4140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 280 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8264 (tmm) cc_final: 0.7942 (tmm) REVERT: A 186 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8247 (t80) REVERT: A 311 GLU cc_start: 0.8025 (tt0) cc_final: 0.7558 (tt0) REVERT: A 327 ASP cc_start: 0.8905 (t70) cc_final: 0.8603 (t0) REVERT: A 419 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: A 436 MET cc_start: 0.8983 (mmm) cc_final: 0.8572 (mmm) REVERT: A 496 MET cc_start: 0.9197 (mmm) cc_final: 0.8681 (mpp) REVERT: A 607 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8547 (t80) REVERT: A 633 ASP cc_start: 0.8679 (m-30) cc_final: 0.8342 (m-30) REVERT: A 649 MET cc_start: 0.8964 (tmm) cc_final: 0.8638 (ppp) REVERT: A 652 MET cc_start: 0.9325 (mmt) cc_final: 0.9073 (mmm) REVERT: A 670 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8737 (p) REVERT: A 701 GLU cc_start: 0.8716 (tt0) cc_final: 0.8472 (pt0) REVERT: A 715 MET cc_start: 0.8524 (tmm) cc_final: 0.8309 (tmm) REVERT: A 859 MET cc_start: 0.8917 (mmp) cc_final: 0.8497 (mmt) REVERT: B 87 MET cc_start: 0.8263 (tmm) cc_final: 0.7940 (tmm) REVERT: B 186 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8249 (t80) REVERT: B 311 GLU cc_start: 0.8022 (tt0) cc_final: 0.7560 (tt0) REVERT: B 327 ASP cc_start: 0.8904 (t70) cc_final: 0.8602 (t0) REVERT: B 419 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8095 (m-80) REVERT: B 436 MET cc_start: 0.8992 (mmm) cc_final: 0.8576 (mmm) REVERT: B 496 MET cc_start: 0.9026 (mmm) cc_final: 0.8572 (mpp) REVERT: B 599 TYR cc_start: 0.8794 (t80) cc_final: 0.8557 (t80) REVERT: B 633 ASP cc_start: 0.8681 (m-30) cc_final: 0.8347 (m-30) REVERT: B 649 MET cc_start: 0.8973 (tmm) cc_final: 0.8636 (ppp) REVERT: B 670 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8740 (p) REVERT: B 701 GLU cc_start: 0.8716 (tt0) cc_final: 0.8473 (pt0) REVERT: B 715 MET cc_start: 0.8518 (tmm) cc_final: 0.8314 (tmm) REVERT: B 859 MET cc_start: 0.8915 (mmp) cc_final: 0.8494 (mmt) REVERT: C 87 MET cc_start: 0.8267 (tmm) cc_final: 0.7944 (tmm) REVERT: C 186 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8252 (t80) REVERT: C 311 GLU cc_start: 0.8012 (tt0) cc_final: 0.7552 (tt0) REVERT: C 327 ASP cc_start: 0.8899 (t70) cc_final: 0.8596 (t0) REVERT: C 419 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: C 436 MET cc_start: 0.8985 (mmm) cc_final: 0.8573 (mmm) REVERT: C 496 MET cc_start: 0.9022 (mmm) cc_final: 0.8571 (mpp) REVERT: C 599 TYR cc_start: 0.8796 (t80) cc_final: 0.8561 (t80) REVERT: C 633 ASP cc_start: 0.8684 (m-30) cc_final: 0.8345 (m-30) REVERT: C 649 MET cc_start: 0.8961 (tmm) cc_final: 0.8635 (ppp) REVERT: C 652 MET cc_start: 0.9323 (mmt) cc_final: 0.9075 (mmm) REVERT: C 670 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8738 (p) REVERT: C 701 GLU cc_start: 0.8713 (tt0) cc_final: 0.8465 (pt0) REVERT: C 715 MET cc_start: 0.8518 (tmm) cc_final: 0.8305 (tmm) REVERT: C 859 MET cc_start: 0.8906 (mmp) cc_final: 0.8485 (mmt) REVERT: D 87 MET cc_start: 0.8269 (tmm) cc_final: 0.7948 (tmm) REVERT: D 186 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8252 (t80) REVERT: D 311 GLU cc_start: 0.8010 (tt0) cc_final: 0.7545 (tt0) REVERT: D 327 ASP cc_start: 0.8894 (t70) cc_final: 0.8593 (t0) REVERT: D 419 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: D 436 MET cc_start: 0.8979 (mmm) cc_final: 0.8568 (mmm) REVERT: D 496 MET cc_start: 0.9011 (mmm) cc_final: 0.8566 (mpp) REVERT: D 599 TYR cc_start: 0.8790 (t80) cc_final: 0.8554 (t80) REVERT: D 633 ASP cc_start: 0.8680 (m-30) cc_final: 0.8342 (m-30) REVERT: D 649 MET cc_start: 0.8962 (tmm) cc_final: 0.8636 (ppp) REVERT: D 652 MET cc_start: 0.9328 (mmt) cc_final: 0.9080 (mmm) REVERT: D 670 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8739 (p) REVERT: D 701 GLU cc_start: 0.8717 (tt0) cc_final: 0.8468 (pt0) REVERT: D 715 MET cc_start: 0.8518 (tmm) cc_final: 0.8310 (tmm) REVERT: D 859 MET cc_start: 0.8906 (mmp) cc_final: 0.8489 (mmt) outliers start: 69 outliers final: 31 residues processed: 327 average time/residue: 0.1327 time to fit residues: 72.4982 Evaluate side-chains 314 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 270 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 705 TYR Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 419 PHE Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 510 CYS Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 677 THR Chi-restraints excluded: chain D residue 705 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 0.4980 chunk 57 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS B 249 HIS C 249 HIS D 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.082834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.067607 restraints weight = 69827.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069775 restraints weight = 37387.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.071230 restraints weight = 24654.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.072187 restraints weight = 18513.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.072915 restraints weight = 15183.553| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21848 Z= 0.141 Angle : 0.622 9.714 29520 Z= 0.308 Chirality : 0.038 0.196 3300 Planarity : 0.004 0.039 3712 Dihedral : 4.087 21.093 2884 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.54 % Allowed : 25.04 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.17), residues: 2644 helix: 2.16 (0.12), residues: 2000 sheet: None (None), residues: 0 loop : -3.05 (0.20), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 609 TYR 0.008 0.001 TYR B 285 PHE 0.016 0.001 PHE C 607 TRP 0.017 0.001 TRP C 750 HIS 0.009 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00318 (21848) covalent geometry : angle 0.62196 (29520) hydrogen bonds : bond 0.03547 ( 1396) hydrogen bonds : angle 3.54932 ( 4140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 276 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8266 (tmm) cc_final: 0.7950 (tmm) REVERT: A 186 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8257 (t80) REVERT: A 311 GLU cc_start: 0.8044 (tt0) cc_final: 0.7583 (tt0) REVERT: A 327 ASP cc_start: 0.8919 (t70) cc_final: 0.8616 (t0) REVERT: A 419 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: A 436 MET cc_start: 0.8978 (mmm) cc_final: 0.8639 (mmm) REVERT: A 496 MET cc_start: 0.9204 (mmm) cc_final: 0.8683 (mpp) REVERT: A 505 MET cc_start: 0.8642 (mtt) cc_final: 0.8360 (mmm) REVERT: A 633 ASP cc_start: 0.8682 (m-30) cc_final: 0.8355 (m-30) REVERT: A 649 MET cc_start: 0.8919 (tmm) cc_final: 0.8547 (ppp) REVERT: A 652 MET cc_start: 0.9307 (mmt) cc_final: 0.9057 (mmm) REVERT: A 670 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8754 (p) REVERT: A 701 GLU cc_start: 0.8736 (tt0) cc_final: 0.8494 (pt0) REVERT: A 726 MET cc_start: 0.8055 (mmm) cc_final: 0.7853 (mmm) REVERT: B 87 MET cc_start: 0.8271 (tmm) cc_final: 0.7955 (tmm) REVERT: B 186 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8252 (t80) REVERT: B 311 GLU cc_start: 0.8031 (tt0) cc_final: 0.7580 (tt0) REVERT: B 327 ASP cc_start: 0.8923 (t70) cc_final: 0.8621 (t0) REVERT: B 419 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: B 436 MET cc_start: 0.8985 (mmm) cc_final: 0.8641 (mmm) REVERT: B 456 LEU cc_start: 0.8416 (tt) cc_final: 0.7529 (mm) REVERT: B 496 MET cc_start: 0.9244 (mmm) cc_final: 0.8712 (mpp) REVERT: B 505 MET cc_start: 0.8647 (mtt) cc_final: 0.8381 (mmm) REVERT: B 599 TYR cc_start: 0.8799 (t80) cc_final: 0.8557 (t80) REVERT: B 633 ASP cc_start: 0.8682 (m-30) cc_final: 0.8356 (m-30) REVERT: B 649 MET cc_start: 0.8941 (tmm) cc_final: 0.8570 (ppp) REVERT: B 701 GLU cc_start: 0.8721 (tt0) cc_final: 0.8483 (pt0) REVERT: B 726 MET cc_start: 0.8051 (mmm) cc_final: 0.7844 (mmm) REVERT: C 87 MET cc_start: 0.8273 (tmm) cc_final: 0.7957 (tmm) REVERT: C 186 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8256 (t80) REVERT: C 311 GLU cc_start: 0.8019 (tt0) cc_final: 0.7570 (tt0) REVERT: C 327 ASP cc_start: 0.8922 (t70) cc_final: 0.8620 (t0) REVERT: C 419 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: C 436 MET cc_start: 0.8982 (mmm) cc_final: 0.8643 (mmm) REVERT: C 496 MET cc_start: 0.9236 (mmm) cc_final: 0.8696 (mpp) REVERT: C 599 TYR cc_start: 0.8798 (t80) cc_final: 0.8560 (t80) REVERT: C 633 ASP cc_start: 0.8681 (m-30) cc_final: 0.8349 (m-30) REVERT: C 649 MET cc_start: 0.8915 (tmm) cc_final: 0.8541 (ppp) REVERT: C 652 MET cc_start: 0.9309 (mmt) cc_final: 0.9057 (mmm) REVERT: C 670 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8752 (p) REVERT: C 701 GLU cc_start: 0.8733 (tt0) cc_final: 0.8489 (pt0) REVERT: C 726 MET cc_start: 0.8041 (mmm) cc_final: 0.7837 (mmm) REVERT: D 87 MET cc_start: 0.8270 (tmm) cc_final: 0.7957 (tmm) REVERT: D 186 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8259 (t80) REVERT: D 311 GLU cc_start: 0.8023 (tt0) cc_final: 0.7568 (tt0) REVERT: D 327 ASP cc_start: 0.8913 (t70) cc_final: 0.8613 (t0) REVERT: D 419 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: D 436 MET cc_start: 0.8974 (mmm) cc_final: 0.8634 (mmm) REVERT: D 456 LEU cc_start: 0.8407 (tt) cc_final: 0.7522 (mm) REVERT: D 496 MET cc_start: 0.9239 (mmm) cc_final: 0.8709 (mpp) REVERT: D 505 MET cc_start: 0.8644 (mtt) cc_final: 0.8381 (mmm) REVERT: D 599 TYR cc_start: 0.8796 (t80) cc_final: 0.8556 (t80) REVERT: D 633 ASP cc_start: 0.8680 (m-30) cc_final: 0.8354 (m-30) REVERT: D 649 MET cc_start: 0.8918 (tmm) cc_final: 0.8542 (ppp) REVERT: D 652 MET cc_start: 0.9310 (mmt) cc_final: 0.9061 (mmm) REVERT: D 670 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8752 (p) REVERT: D 701 GLU cc_start: 0.8736 (tt0) cc_final: 0.8492 (pt0) REVERT: D 726 MET cc_start: 0.8048 (mmm) cc_final: 0.7846 (mmm) outliers start: 57 outliers final: 29 residues processed: 314 average time/residue: 0.1309 time to fit residues: 68.6946 Evaluate side-chains 301 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 705 TYR Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 419 PHE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 677 THR Chi-restraints excluded: chain D residue 705 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 42 optimal weight: 0.4980 chunk 199 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 187 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 721 ASN A 732 GLN B 249 HIS B 721 ASN B 732 GLN C 249 HIS C 721 ASN C 732 GLN D 249 HIS D 721 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.083825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.068512 restraints weight = 70047.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.070706 restraints weight = 37392.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072158 restraints weight = 24610.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.073141 restraints weight = 18480.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.073832 restraints weight = 15134.165| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21848 Z= 0.125 Angle : 0.627 10.283 29520 Z= 0.308 Chirality : 0.039 0.201 3300 Planarity : 0.004 0.039 3712 Dihedral : 4.062 20.890 2884 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.99 % Allowed : 25.22 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.17), residues: 2644 helix: 2.16 (0.12), residues: 2016 sheet: None (None), residues: 0 loop : -2.92 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 609 TYR 0.007 0.001 TYR C 285 PHE 0.019 0.001 PHE A 607 TRP 0.016 0.001 TRP C 750 HIS 0.008 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00280 (21848) covalent geometry : angle 0.62682 (29520) hydrogen bonds : bond 0.03451 ( 1396) hydrogen bonds : angle 3.51398 ( 4140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 264 time to evaluate : 0.873 Fit side-chains REVERT: A 87 MET cc_start: 0.8280 (tmm) cc_final: 0.7953 (tmm) REVERT: A 186 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8281 (t80) REVERT: A 311 GLU cc_start: 0.8038 (tt0) cc_final: 0.7602 (tt0) REVERT: A 327 ASP cc_start: 0.8907 (t70) cc_final: 0.8605 (t0) REVERT: A 419 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: A 436 MET cc_start: 0.8864 (mmm) cc_final: 0.8561 (mmm) REVERT: A 496 MET cc_start: 0.9222 (mmm) cc_final: 0.8689 (mpp) REVERT: A 505 MET cc_start: 0.8649 (mtt) cc_final: 0.8377 (mmm) REVERT: A 533 MET cc_start: 0.9240 (ppp) cc_final: 0.8974 (ppp) REVERT: A 633 ASP cc_start: 0.8720 (m-30) cc_final: 0.8454 (m-30) REVERT: A 649 MET cc_start: 0.8915 (tmm) cc_final: 0.8518 (ppp) REVERT: A 652 MET cc_start: 0.9303 (mmt) cc_final: 0.9046 (mmm) REVERT: A 670 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8755 (p) REVERT: A 701 GLU cc_start: 0.8719 (tt0) cc_final: 0.8494 (pt0) REVERT: A 726 MET cc_start: 0.8074 (mmm) cc_final: 0.7866 (mmm) REVERT: A 859 MET cc_start: 0.8917 (mmp) cc_final: 0.8478 (mmt) REVERT: B 87 MET cc_start: 0.8265 (tmm) cc_final: 0.7912 (tmm) REVERT: B 186 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8277 (t80) REVERT: B 311 GLU cc_start: 0.8023 (tt0) cc_final: 0.7599 (tt0) REVERT: B 327 ASP cc_start: 0.8911 (t70) cc_final: 0.8609 (t0) REVERT: B 419 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: B 436 MET cc_start: 0.8868 (mmm) cc_final: 0.8563 (mmm) REVERT: B 456 LEU cc_start: 0.8366 (tt) cc_final: 0.7435 (mm) REVERT: B 496 MET cc_start: 0.9046 (mmm) cc_final: 0.8608 (mpp) REVERT: B 505 MET cc_start: 0.8689 (mtt) cc_final: 0.8444 (mmm) REVERT: B 599 TYR cc_start: 0.8822 (t80) cc_final: 0.8554 (t80) REVERT: B 633 ASP cc_start: 0.8725 (m-30) cc_final: 0.8462 (m-30) REVERT: B 649 MET cc_start: 0.8991 (tmm) cc_final: 0.8566 (ppp) REVERT: B 701 GLU cc_start: 0.8710 (tt0) cc_final: 0.8489 (pt0) REVERT: B 726 MET cc_start: 0.8066 (mmm) cc_final: 0.7853 (mmm) REVERT: B 859 MET cc_start: 0.8907 (mmp) cc_final: 0.8471 (mmt) REVERT: C 87 MET cc_start: 0.8264 (tmm) cc_final: 0.7915 (tmm) REVERT: C 186 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8281 (t80) REVERT: C 311 GLU cc_start: 0.8020 (tt0) cc_final: 0.7593 (tt0) REVERT: C 327 ASP cc_start: 0.8909 (t70) cc_final: 0.8608 (t0) REVERT: C 419 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: C 436 MET cc_start: 0.8856 (mmm) cc_final: 0.8559 (mmm) REVERT: C 456 LEU cc_start: 0.8354 (tt) cc_final: 0.7396 (mm) REVERT: C 496 MET cc_start: 0.9044 (mmm) cc_final: 0.8606 (mpp) REVERT: C 505 MET cc_start: 0.8755 (mtt) cc_final: 0.8476 (mmm) REVERT: C 599 TYR cc_start: 0.8822 (t80) cc_final: 0.8565 (t80) REVERT: C 633 ASP cc_start: 0.8725 (m-30) cc_final: 0.8459 (m-30) REVERT: C 649 MET cc_start: 0.8912 (tmm) cc_final: 0.8512 (ppp) REVERT: C 652 MET cc_start: 0.9304 (mmt) cc_final: 0.9046 (mmm) REVERT: C 670 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8753 (p) REVERT: C 701 GLU cc_start: 0.8718 (tt0) cc_final: 0.8485 (pt0) REVERT: C 726 MET cc_start: 0.8065 (mmm) cc_final: 0.7851 (mmm) REVERT: C 859 MET cc_start: 0.8909 (mmp) cc_final: 0.8472 (mmt) REVERT: D 87 MET cc_start: 0.8268 (tmm) cc_final: 0.7920 (tmm) REVERT: D 186 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8283 (t80) REVERT: D 311 GLU cc_start: 0.8027 (tt0) cc_final: 0.7594 (tt0) REVERT: D 327 ASP cc_start: 0.8903 (t70) cc_final: 0.8603 (t0) REVERT: D 419 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: D 436 MET cc_start: 0.8850 (mmm) cc_final: 0.8552 (mmm) REVERT: D 456 LEU cc_start: 0.8361 (tt) cc_final: 0.7432 (mm) REVERT: D 496 MET cc_start: 0.9039 (mmm) cc_final: 0.8607 (mpp) REVERT: D 505 MET cc_start: 0.8687 (mtt) cc_final: 0.8442 (mmm) REVERT: D 599 TYR cc_start: 0.8819 (t80) cc_final: 0.8549 (t80) REVERT: D 607 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8597 (m-80) REVERT: D 633 ASP cc_start: 0.8720 (m-30) cc_final: 0.8454 (m-30) REVERT: D 649 MET cc_start: 0.8913 (tmm) cc_final: 0.8509 (ppp) REVERT: D 652 MET cc_start: 0.9307 (mmt) cc_final: 0.9050 (mmm) REVERT: D 670 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8752 (p) REVERT: D 701 GLU cc_start: 0.8720 (tt0) cc_final: 0.8490 (pt0) REVERT: D 726 MET cc_start: 0.8069 (mmm) cc_final: 0.7859 (mmm) REVERT: D 859 MET cc_start: 0.8904 (mmp) cc_final: 0.8470 (mmt) outliers start: 67 outliers final: 34 residues processed: 312 average time/residue: 0.1263 time to fit residues: 66.0643 Evaluate side-chains 306 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 260 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 705 TYR Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 419 PHE Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 510 CYS Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 607 PHE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 677 THR Chi-restraints excluded: chain D residue 705 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 81 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN D 732 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.084168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.069059 restraints weight = 69741.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.071221 restraints weight = 37069.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.072686 restraints weight = 24542.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.073715 restraints weight = 18289.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.074321 restraints weight = 14823.007| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21848 Z= 0.118 Angle : 0.639 11.960 29520 Z= 0.306 Chirality : 0.038 0.294 3300 Planarity : 0.004 0.040 3712 Dihedral : 3.960 20.485 2884 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.83 % Allowed : 25.94 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.17), residues: 2644 helix: 2.22 (0.12), residues: 2008 sheet: None (None), residues: 0 loop : -2.97 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 609 TYR 0.006 0.001 TYR B 659 PHE 0.024 0.001 PHE C 607 TRP 0.015 0.001 TRP C 391 HIS 0.008 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00265 (21848) covalent geometry : angle 0.63918 (29520) hydrogen bonds : bond 0.03293 ( 1396) hydrogen bonds : angle 3.45971 ( 4140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 0.909 Fit side-chains REVERT: A 87 MET cc_start: 0.8183 (tmm) cc_final: 0.7838 (tmm) REVERT: A 186 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8376 (t80) REVERT: A 311 GLU cc_start: 0.8045 (tt0) cc_final: 0.7626 (tt0) REVERT: A 327 ASP cc_start: 0.8904 (t70) cc_final: 0.8584 (t0) REVERT: A 419 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: A 441 MET cc_start: 0.8776 (mmm) cc_final: 0.8507 (mmm) REVERT: A 496 MET cc_start: 0.9039 (mmm) cc_final: 0.8589 (mpp) REVERT: A 505 MET cc_start: 0.8631 (mtt) cc_final: 0.8405 (mmm) REVERT: A 533 MET cc_start: 0.9223 (ppp) cc_final: 0.8860 (ppp) REVERT: A 633 ASP cc_start: 0.8729 (m-30) cc_final: 0.8459 (m-30) REVERT: A 649 MET cc_start: 0.8960 (tmm) cc_final: 0.8570 (ppp) REVERT: A 652 MET cc_start: 0.9303 (mmt) cc_final: 0.9038 (mmm) REVERT: A 670 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8752 (p) REVERT: A 701 GLU cc_start: 0.8746 (tt0) cc_final: 0.8528 (pt0) REVERT: A 859 MET cc_start: 0.8923 (mmp) cc_final: 0.8493 (mmt) REVERT: B 87 MET cc_start: 0.8190 (tmm) cc_final: 0.7844 (tmm) REVERT: B 186 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8374 (t80) REVERT: B 311 GLU cc_start: 0.8044 (tt0) cc_final: 0.7634 (tt0) REVERT: B 327 ASP cc_start: 0.8910 (t70) cc_final: 0.8592 (t0) REVERT: B 419 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: B 441 MET cc_start: 0.8780 (mmm) cc_final: 0.8502 (mmm) REVERT: B 456 LEU cc_start: 0.8346 (tt) cc_final: 0.7166 (mm) REVERT: B 494 MET cc_start: 0.8719 (mmp) cc_final: 0.8091 (mtp) REVERT: B 496 MET cc_start: 0.9045 (mmm) cc_final: 0.8620 (mpp) REVERT: B 505 MET cc_start: 0.8709 (mtt) cc_final: 0.8474 (mmm) REVERT: B 534 LEU cc_start: 0.9381 (mt) cc_final: 0.9058 (mm) REVERT: B 599 TYR cc_start: 0.8788 (t80) cc_final: 0.8515 (t80) REVERT: B 633 ASP cc_start: 0.8722 (m-30) cc_final: 0.8451 (m-30) REVERT: B 649 MET cc_start: 0.8999 (tmm) cc_final: 0.8607 (ppp) REVERT: B 701 GLU cc_start: 0.8747 (tt0) cc_final: 0.8522 (pt0) REVERT: B 859 MET cc_start: 0.8927 (mmp) cc_final: 0.8496 (mmt) REVERT: C 87 MET cc_start: 0.8188 (tmm) cc_final: 0.7842 (tmm) REVERT: C 186 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8372 (t80) REVERT: C 311 GLU cc_start: 0.8041 (tt0) cc_final: 0.7627 (tt0) REVERT: C 327 ASP cc_start: 0.8911 (t70) cc_final: 0.8593 (t0) REVERT: C 419 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: C 441 MET cc_start: 0.8768 (mmm) cc_final: 0.8494 (mmm) REVERT: C 456 LEU cc_start: 0.8295 (tt) cc_final: 0.7035 (mm) REVERT: C 494 MET cc_start: 0.8726 (mmp) cc_final: 0.8088 (mtp) REVERT: C 496 MET cc_start: 0.9037 (mmm) cc_final: 0.8628 (mpp) REVERT: C 505 MET cc_start: 0.8716 (mtt) cc_final: 0.8452 (mmm) REVERT: C 599 TYR cc_start: 0.8757 (t80) cc_final: 0.8483 (t80) REVERT: C 633 ASP cc_start: 0.8715 (m-30) cc_final: 0.8450 (m-30) REVERT: C 649 MET cc_start: 0.8946 (tmm) cc_final: 0.8525 (ppp) REVERT: C 652 MET cc_start: 0.9287 (mmt) cc_final: 0.9027 (mmm) REVERT: C 670 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8751 (p) REVERT: C 701 GLU cc_start: 0.8748 (tt0) cc_final: 0.8522 (pt0) REVERT: C 859 MET cc_start: 0.8917 (mmp) cc_final: 0.8483 (mmt) REVERT: D 87 MET cc_start: 0.8192 (tmm) cc_final: 0.7845 (tmm) REVERT: D 186 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8374 (t80) REVERT: D 311 GLU cc_start: 0.8042 (tt0) cc_final: 0.7624 (tt0) REVERT: D 327 ASP cc_start: 0.8904 (t70) cc_final: 0.8585 (t0) REVERT: D 419 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.8113 (m-80) REVERT: D 441 MET cc_start: 0.8763 (mmm) cc_final: 0.8492 (mmm) REVERT: D 456 LEU cc_start: 0.8296 (tt) cc_final: 0.7124 (mm) REVERT: D 494 MET cc_start: 0.8729 (mmp) cc_final: 0.8095 (mtp) REVERT: D 496 MET cc_start: 0.9040 (mmm) cc_final: 0.8617 (mpp) REVERT: D 505 MET cc_start: 0.8702 (mtt) cc_final: 0.8469 (mmm) REVERT: D 534 LEU cc_start: 0.9382 (mt) cc_final: 0.9060 (mm) REVERT: D 599 TYR cc_start: 0.8796 (t80) cc_final: 0.8521 (t80) REVERT: D 633 ASP cc_start: 0.8717 (m-30) cc_final: 0.8460 (m-30) REVERT: D 649 MET cc_start: 0.8952 (tmm) cc_final: 0.8523 (ppp) REVERT: D 652 MET cc_start: 0.9292 (mmt) cc_final: 0.9032 (mmm) REVERT: D 670 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8749 (p) REVERT: D 701 GLU cc_start: 0.8747 (tt0) cc_final: 0.8524 (pt0) REVERT: D 859 MET cc_start: 0.8917 (mmp) cc_final: 0.8488 (mmt) outliers start: 41 outliers final: 28 residues processed: 299 average time/residue: 0.1339 time to fit residues: 66.4178 Evaluate side-chains 305 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 266 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 510 CYS Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 705 TYR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 264 HIS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 419 PHE Chi-restraints excluded: chain B residue 510 CYS Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 264 HIS Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 510 CYS Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 264 HIS Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 510 CYS Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 705 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 230 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 265 optimal weight: 0.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 721 ASN B 249 HIS B 721 ASN C 249 HIS C 721 ASN D 249 HIS D 721 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.083471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.068400 restraints weight = 69967.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.070585 restraints weight = 37215.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.072047 restraints weight = 24390.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.073003 restraints weight = 18205.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.073738 restraints weight = 14875.848| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21848 Z= 0.139 Angle : 0.645 11.532 29520 Z= 0.314 Chirality : 0.039 0.323 3300 Planarity : 0.004 0.039 3712 Dihedral : 3.995 20.838 2884 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.60 % Allowed : 26.38 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.17), residues: 2644 helix: 2.17 (0.12), residues: 2016 sheet: None (None), residues: 0 loop : -2.85 (0.21), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 853 TYR 0.009 0.001 TYR C 285 PHE 0.028 0.001 PHE C 607 TRP 0.016 0.001 TRP A 391 HIS 0.008 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00313 (21848) covalent geometry : angle 0.64501 (29520) hydrogen bonds : bond 0.03408 ( 1396) hydrogen bonds : angle 3.53383 ( 4140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3174.07 seconds wall clock time: 55 minutes 59.55 seconds (3359.55 seconds total)