Starting phenix.real_space_refine on Wed Mar 4 14:17:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n5j_48923/03_2026/9n5j_48923_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n5j_48923/03_2026/9n5j_48923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n5j_48923/03_2026/9n5j_48923_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n5j_48923/03_2026/9n5j_48923_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n5j_48923/03_2026/9n5j_48923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n5j_48923/03_2026/9n5j_48923.map" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 7 Type Number sf(0) Gaussians Mg 4 5.21 5 S 84 5.16 5 Be 2 3.05 5 C 8806 2.51 5 N 2212 2.21 5 O 2572 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13686 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 6837 Classifications: {'peptide': 889} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 855} Chain: "C" Number of atoms: 6837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 6837 Classifications: {'peptide': 889} Link IDs: {'PTRANS': 32, 'TRANS': 856} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' MG': 2, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' MG': 2, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.17, per 1000 atoms: 0.23 Number of scatterers: 13686 At special positions: 0 Unit cell: (101.37, 92.07, 226.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 84 16.00 Mg 4 11.99 F 6 9.00 O 2572 8.00 N 2212 7.00 C 8806 6.00 Be 2 4.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 520.7 milliseconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3332 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 56.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.813A pdb=" N ARG A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 42 Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 84 through 102 Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 267 through 299 removed outlier: 3.557A pdb=" N VAL A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 3.736A pdb=" N LYS A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 317 Processing helix chain 'A' and resid 320 through 338 removed outlier: 3.637A pdb=" N LYS A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 354 Processing helix chain 'A' and resid 385 through 397 removed outlier: 3.807A pdb=" N TYR A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 416 Processing helix chain 'A' and resid 454 through 458 removed outlier: 4.298A pdb=" N THR A 457 " --> pdb=" O ASN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 473 removed outlier: 3.575A pdb=" N MET A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 467 through 473' Processing helix chain 'A' and resid 488 through 505 removed outlier: 3.518A pdb=" N LEU A 502 " --> pdb=" O LYS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 569 through 581 Processing helix chain 'A' and resid 590 through 596 removed outlier: 3.573A pdb=" N GLN A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 608 removed outlier: 3.980A pdb=" N VAL A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 629 removed outlier: 3.685A pdb=" N ALA A 620 " --> pdb=" O PRO A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 648 removed outlier: 4.323A pdb=" N ALA A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA A 645 " --> pdb=" O ASN A 641 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 666 Processing helix chain 'A' and resid 676 through 714 removed outlier: 3.577A pdb=" N SER A 709 " --> pdb=" O GLY A 705 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 710 " --> pdb=" O ASN A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 739 Processing helix chain 'A' and resid 740 through 744 Processing helix chain 'A' and resid 747 through 751 removed outlier: 3.595A pdb=" N LEU A 751 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 787 Proline residue: A 771 - end of helix removed outlier: 3.638A pdb=" N SER A 774 " --> pdb=" O GLY A 770 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 775 " --> pdb=" O PRO A 771 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE A 776 " --> pdb=" O THR A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 792 removed outlier: 3.567A pdb=" N ALA A 791 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 803 through 828 Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 845 through 862 Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 877 through 879 No H-bonds generated for 'chain 'A' and resid 877 through 879' Processing helix chain 'A' and resid 880 through 907 Processing helix chain 'C' and resid 25 through 33 Processing helix chain 'C' and resid 34 through 42 Processing helix chain 'C' and resid 51 through 61 removed outlier: 3.843A pdb=" N GLU C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 82 removed outlier: 3.578A pdb=" N TYR C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 102 Processing helix chain 'C' and resid 112 through 134 removed outlier: 3.805A pdb=" N ILE C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 168 removed outlier: 3.664A pdb=" N GLU C 167 " --> pdb=" O PRO C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 251 through 256 removed outlier: 3.759A pdb=" N MET C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 297 removed outlier: 3.711A pdb=" N VAL C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 286 " --> pdb=" O ARG C 282 " (cutoff:3.500A) Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 301 through 317 Processing helix chain 'C' and resid 320 through 338 removed outlier: 3.540A pdb=" N LYS C 338 " --> pdb=" O VAL C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 385 through 397 removed outlier: 3.705A pdb=" N LEU C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 417 removed outlier: 3.579A pdb=" N GLN C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 424 Processing helix chain 'C' and resid 468 through 473 removed outlier: 3.850A pdb=" N ASP C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 505 removed outlier: 3.867A pdb=" N GLU C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 Processing helix chain 'C' and resid 525 through 530 removed outlier: 3.978A pdb=" N GLU C 529 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 530 " --> pdb=" O GLN C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 558 removed outlier: 3.643A pdb=" N ALA C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 581 Processing helix chain 'C' and resid 590 through 595 removed outlier: 3.588A pdb=" N ASP C 594 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 595' Processing helix chain 'C' and resid 597 through 606 Processing helix chain 'C' and resid 615 through 629 removed outlier: 3.551A pdb=" N ALA C 620 " --> pdb=" O PRO C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 648 removed outlier: 4.520A pdb=" N ALA C 645 " --> pdb=" O ASN C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 665 Processing helix chain 'C' and resid 676 through 714 removed outlier: 3.696A pdb=" N LYS C 680 " --> pdb=" O MET C 676 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER C 709 " --> pdb=" O GLY C 705 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL C 710 " --> pdb=" O ASN C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 739 Processing helix chain 'C' and resid 740 through 744 Processing helix chain 'C' and resid 747 through 751 Processing helix chain 'C' and resid 758 through 770 Processing helix chain 'C' and resid 770 through 787 removed outlier: 3.600A pdb=" N SER C 774 " --> pdb=" O GLY C 770 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 775 " --> pdb=" O PRO C 771 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE C 776 " --> pdb=" O THR C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 799 Processing helix chain 'C' and resid 803 through 828 Processing helix chain 'C' and resid 828 through 833 Processing helix chain 'C' and resid 845 through 862 Processing helix chain 'C' and resid 865 through 872 Processing helix chain 'C' and resid 880 through 907 removed outlier: 3.598A pdb=" N THR C 896 " --> pdb=" O MET C 892 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 164 removed outlier: 4.886A pdb=" N ASN A 152 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A 175 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE A 173 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE A 195 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP A 193 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 240 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA A 191 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N GLY A 242 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE A 189 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A 244 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG A 187 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU A 194 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 164 removed outlier: 4.886A pdb=" N ASN A 152 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A 175 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE A 173 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE A 195 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP A 193 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 240 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA A 191 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N GLY A 242 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE A 189 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A 244 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG A 187 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 341 through 343 removed outlier: 6.370A pdb=" N GLY A 652 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU A 670 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER A 654 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL A 633 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ILE A 653 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR A 635 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU A 358 " --> pdb=" O LYS A 563 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU A 565 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N THR A 360 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N PHE A 611 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE A 564 " --> pdb=" O PHE A 611 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 378 removed outlier: 4.694A pdb=" N LEU A 373 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 541 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL A 512 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR A 537 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 510 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA A 539 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ARG A 508 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER A 446 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU A 435 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 378 removed outlier: 4.694A pdb=" N LEU A 373 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 541 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU A 534 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL A 478 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N GLY A 536 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AA7, first strand: chain 'C' and resid 173 through 176 removed outlier: 3.853A pdb=" N GLN C 190 " --> pdb=" O TYR C 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 208 through 210 removed outlier: 4.434A pdb=" N LEU C 194 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE C 195 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 341 through 343 removed outlier: 6.387A pdb=" N GLY C 652 " --> pdb=" O VAL C 668 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU C 670 " --> pdb=" O GLY C 652 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER C 654 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL C 633 " --> pdb=" O VAL C 651 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ILE C 653 " --> pdb=" O VAL C 633 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR C 635 " --> pdb=" O ILE C 653 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU C 358 " --> pdb=" O LYS C 563 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU C 565 " --> pdb=" O LEU C 358 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N THR C 360 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N PHE C 611 " --> pdb=" O VAL C 562 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE C 564 " --> pdb=" O PHE C 611 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 372 through 375 removed outlier: 5.905A pdb=" N LEU C 373 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU C 541 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N SER C 446 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLU C 435 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 448 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 460 through 461 removed outlier: 3.531A pdb=" N THR C 460 " --> pdb=" O ASN C 517 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 477 through 478 removed outlier: 7.647A pdb=" N LEU C 477 " --> pdb=" O LEU C 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 740 hydrogen bonds defined for protein. 2112 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: 2.35 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4341 1.35 - 1.46: 2993 1.46 - 1.58: 6422 1.58 - 1.70: 0 1.70 - 1.82: 162 Bond restraints: 13918 Sorted by residual: bond pdb=" F2 BEF A1003 " pdb="BE BEF A1003 " ideal model delta sigma weight residual 1.476 1.766 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" F3 BEF C1003 " pdb="BE BEF C1003 " ideal model delta sigma weight residual 1.476 1.766 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" F1 BEF C1003 " pdb="BE BEF C1003 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" F1 BEF A1003 " pdb="BE BEF A1003 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" F2 BEF C1003 " pdb="BE BEF C1003 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.09e+02 ... (remaining 13913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 18620 2.41 - 4.81: 197 4.81 - 7.22: 25 7.22 - 9.63: 12 9.63 - 12.04: 4 Bond angle restraints: 18858 Sorted by residual: angle pdb=" N PHE C 253 " pdb=" CA PHE C 253 " pdb=" C PHE C 253 " ideal model delta sigma weight residual 111.81 103.90 7.91 1.44e+00 4.82e-01 3.02e+01 angle pdb=" CA LYS A 192 " pdb=" CB LYS A 192 " pdb=" CG LYS A 192 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 angle pdb=" C ASN C 452 " pdb=" CA ASN C 452 " pdb=" CB ASN C 452 " ideal model delta sigma weight residual 115.79 110.56 5.23 1.19e+00 7.06e-01 1.94e+01 angle pdb=" CB MET A 532 " pdb=" CG MET A 532 " pdb=" SD MET A 532 " ideal model delta sigma weight residual 112.70 124.74 -12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C PRO A 518 " pdb=" N SER A 519 " pdb=" CA SER A 519 " ideal model delta sigma weight residual 121.80 131.51 -9.71 2.44e+00 1.68e-01 1.58e+01 ... (remaining 18853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 7195 17.63 - 35.27: 907 35.27 - 52.90: 266 52.90 - 70.54: 53 70.54 - 88.17: 11 Dihedral angle restraints: 8432 sinusoidal: 3288 harmonic: 5144 Sorted by residual: dihedral pdb=" CA THR A 120 " pdb=" C THR A 120 " pdb=" N MET A 121 " pdb=" CA MET A 121 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA SER C 530 " pdb=" C SER C 530 " pdb=" N GLU C 531 " pdb=" CA GLU C 531 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA TYR C 695 " pdb=" C TYR C 695 " pdb=" N ILE C 696 " pdb=" CA ILE C 696 " ideal model delta harmonic sigma weight residual 180.00 -161.82 -18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 8429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1587 0.039 - 0.079: 525 0.079 - 0.118: 144 0.118 - 0.157: 23 0.157 - 0.196: 3 Chirality restraints: 2282 Sorted by residual: chirality pdb=" CA GLU C 531 " pdb=" N GLU C 531 " pdb=" C GLU C 531 " pdb=" CB GLU C 531 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA MET C 374 " pdb=" N MET C 374 " pdb=" C MET C 374 " pdb=" CB MET C 374 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CB ILE A 147 " pdb=" CA ILE A 147 " pdb=" CG1 ILE A 147 " pdb=" CG2 ILE A 147 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 2279 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 120 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C THR A 120 " -0.048 2.00e-02 2.50e+03 pdb=" O THR A 120 " 0.018 2.00e-02 2.50e+03 pdb=" N MET A 121 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 688 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C THR C 688 " 0.032 2.00e-02 2.50e+03 pdb=" O THR C 688 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR C 689 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 690 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C ALA C 690 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA C 690 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN C 691 " 0.011 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 48 2.38 - 3.01: 8007 3.01 - 3.64: 21421 3.64 - 4.27: 31512 4.27 - 4.90: 53254 Nonbonded interactions: 114242 Sorted by model distance: nonbonded pdb="MG MG A1002 " pdb=" F1 BEF A1003 " model vdw 1.754 2.120 nonbonded pdb=" OD2 ASP A 361 " pdb=" F1 BEF A1003 " model vdw 1.812 2.990 nonbonded pdb=" OD1 ASP C 638 " pdb="MG MG C1001 " model vdw 1.951 2.170 nonbonded pdb=" OD1 ASP A 638 " pdb="MG MG A1002 " model vdw 1.963 2.170 nonbonded pdb=" OD1 ASN A 706 " pdb="MG MG A1001 " model vdw 2.005 2.170 ... (remaining 114237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.510 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:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 : 0.009 0.531 13920 Z= 0.699 Angle : 0.652 12.037 18858 Z= 0.341 Chirality : 0.042 0.196 2282 Planarity : 0.004 0.050 2352 Dihedral : 17.205 88.172 5100 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.52 % Favored : 94.02 % Rotamer: Outliers : 2.16 % Allowed : 32.66 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.20), residues: 1774 helix: 1.03 (0.18), residues: 910 sheet: -0.49 (0.37), residues: 173 loop : -1.68 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 58 TYR 0.013 0.001 TYR C 494 PHE 0.019 0.001 PHE A 818 TRP 0.009 0.001 TRP C 278 HIS 0.006 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00662 (13918) covalent geometry : angle 0.65188 (18858) hydrogen bonds : bond 0.14562 ( 723) hydrogen bonds : angle 6.04548 ( 2112) Misc. bond : bond 0.51524 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8927 (tppt) cc_final: 0.8523 (tptp) REVERT: A 74 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8440 (tm) REVERT: A 445 MET cc_start: 0.8579 (tmm) cc_final: 0.8296 (tmm) REVERT: A 462 MET cc_start: 0.8015 (ttt) cc_final: 0.7720 (tmt) REVERT: A 507 MET cc_start: 0.8339 (mtm) cc_final: 0.8082 (mtm) REVERT: C 47 LYS cc_start: 0.8798 (mmmm) cc_final: 0.8528 (tptp) REVERT: C 405 MET cc_start: 0.9109 (mpp) cc_final: 0.8811 (mpp) REVERT: C 432 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7272 (tmtt) REVERT: C 445 MET cc_start: 0.6960 (mmp) cc_final: 0.6585 (mmp) REVERT: C 507 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6535 (tpp) REVERT: C 545 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.6801 (pptt) REVERT: C 660 ASP cc_start: 0.8201 (m-30) cc_final: 0.7659 (t0) REVERT: C 892 MET cc_start: 0.8562 (mtm) cc_final: 0.8200 (mmm) REVERT: C 893 MET cc_start: 0.8738 (mtt) cc_final: 0.8479 (mtp) outliers start: 33 outliers final: 27 residues processed: 152 average time/residue: 0.5392 time to fit residues: 90.6995 Evaluate side-chains 154 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 376 HIS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 792 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.133559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.069384 restraints weight = 22169.335| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.36 r_work: 0.2717 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13920 Z= 0.162 Angle : 0.610 9.717 18858 Z= 0.317 Chirality : 0.043 0.185 2282 Planarity : 0.004 0.044 2352 Dihedral : 5.974 59.773 1910 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.09 % Favored : 93.46 % Rotamer: Outliers : 3.40 % Allowed : 29.78 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.20), residues: 1774 helix: 1.26 (0.17), residues: 921 sheet: -0.58 (0.36), residues: 183 loop : -1.65 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 386 TYR 0.015 0.002 TYR A 396 PHE 0.019 0.001 PHE C 776 TRP 0.009 0.001 TRP A 278 HIS 0.006 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00376 (13918) covalent geometry : angle 0.61041 (18858) hydrogen bonds : bond 0.04820 ( 723) hydrogen bonds : angle 4.69539 ( 2112) Misc. bond : bond 0.00127 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 123 time to evaluate : 0.421 Fit side-chains REVERT: A 74 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8321 (tm) REVERT: A 303 MET cc_start: 0.8477 (mmm) cc_final: 0.8273 (tpp) REVERT: A 445 MET cc_start: 0.8596 (tmm) cc_final: 0.8309 (tmm) REVERT: A 462 MET cc_start: 0.7911 (ttt) cc_final: 0.7519 (tmt) REVERT: A 507 MET cc_start: 0.8361 (mtm) cc_final: 0.8056 (mtm) REVERT: A 755 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8731 (mtt180) REVERT: C 445 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6557 (mmp) REVERT: C 479 GLU cc_start: 0.5295 (OUTLIER) cc_final: 0.4576 (tm-30) REVERT: C 507 MET cc_start: 0.7049 (ttp) cc_final: 0.6542 (tpp) REVERT: C 540 PHE cc_start: 0.7536 (m-10) cc_final: 0.7163 (m-10) REVERT: C 545 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7826 (mptt) REVERT: C 660 ASP cc_start: 0.8044 (m-30) cc_final: 0.7503 (t0) REVERT: C 892 MET cc_start: 0.8676 (mtm) cc_final: 0.8252 (mmm) outliers start: 52 outliers final: 19 residues processed: 166 average time/residue: 0.5248 time to fit residues: 96.4821 Evaluate side-chains 141 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 376 HIS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 871 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 151 optimal weight: 0.0470 chunk 140 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 162 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 156 optimal weight: 0.5980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.134079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.069989 restraints weight = 22235.947| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.35 r_work: 0.2734 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13920 Z= 0.139 Angle : 0.581 9.685 18858 Z= 0.303 Chirality : 0.042 0.179 2282 Planarity : 0.004 0.043 2352 Dihedral : 5.376 59.888 1884 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.81 % Favored : 93.74 % Rotamer: Outliers : 4.19 % Allowed : 28.99 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1774 helix: 1.37 (0.17), residues: 920 sheet: -0.57 (0.36), residues: 188 loop : -1.58 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 58 TYR 0.012 0.001 TYR A 806 PHE 0.018 0.001 PHE A 818 TRP 0.009 0.001 TRP A 278 HIS 0.005 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00320 (13918) covalent geometry : angle 0.58141 (18858) hydrogen bonds : bond 0.04382 ( 723) hydrogen bonds : angle 4.48994 ( 2112) Misc. bond : bond 0.00078 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 124 time to evaluate : 0.545 Fit side-chains REVERT: A 74 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8331 (tm) REVERT: A 303 MET cc_start: 0.8421 (mmm) cc_final: 0.8220 (tpp) REVERT: A 411 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: A 445 MET cc_start: 0.8614 (tmm) cc_final: 0.8322 (tmm) REVERT: A 462 MET cc_start: 0.7894 (ttt) cc_final: 0.7519 (tmt) REVERT: A 507 MET cc_start: 0.8348 (mtm) cc_final: 0.8121 (mtm) REVERT: A 532 MET cc_start: 0.8708 (mmm) cc_final: 0.8356 (mmm) REVERT: A 749 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.9054 (pm20) REVERT: A 755 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8736 (mtt180) REVERT: C 47 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8478 (tptp) REVERT: C 445 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.6373 (mmp) REVERT: C 507 MET cc_start: 0.7217 (ttp) cc_final: 0.6641 (tpp) REVERT: C 545 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7808 (mptt) REVERT: C 660 ASP cc_start: 0.8058 (m-30) cc_final: 0.7563 (t0) REVERT: C 745 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7859 (p0) REVERT: C 892 MET cc_start: 0.8629 (mtm) cc_final: 0.8230 (mmm) REVERT: C 893 MET cc_start: 0.8850 (mtt) cc_final: 0.8564 (mtp) outliers start: 64 outliers final: 28 residues processed: 179 average time/residue: 0.5309 time to fit residues: 105.2440 Evaluate side-chains 152 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 376 HIS Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 871 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 71 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 GLN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.133393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.069551 restraints weight = 22016.450| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.27 r_work: 0.2710 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13920 Z= 0.162 Angle : 0.612 13.410 18858 Z= 0.313 Chirality : 0.043 0.174 2282 Planarity : 0.004 0.043 2352 Dihedral : 5.422 58.924 1884 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.37 % Favored : 93.18 % Rotamer: Outliers : 4.25 % Allowed : 29.19 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1774 helix: 1.36 (0.17), residues: 920 sheet: -0.55 (0.36), residues: 183 loop : -1.55 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 443 TYR 0.012 0.001 TYR A 806 PHE 0.018 0.001 PHE C 776 TRP 0.010 0.001 TRP A 302 HIS 0.005 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00384 (13918) covalent geometry : angle 0.61165 (18858) hydrogen bonds : bond 0.04504 ( 723) hydrogen bonds : angle 4.41250 ( 2112) Misc. bond : bond 0.00097 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 124 time to evaluate : 0.449 Fit side-chains REVERT: A 74 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8357 (tm) REVERT: A 411 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8451 (mp0) REVERT: A 432 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8719 (tppt) REVERT: A 445 MET cc_start: 0.8615 (tmm) cc_final: 0.8341 (tmm) REVERT: A 477 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8016 (mm) REVERT: A 755 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8783 (mtt180) REVERT: C 47 LYS cc_start: 0.8791 (mmmm) cc_final: 0.8504 (tptp) REVERT: C 432 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7127 (tptp) REVERT: C 445 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6502 (mmp) REVERT: C 475 CYS cc_start: 0.7454 (m) cc_final: 0.7232 (t) REVERT: C 507 MET cc_start: 0.7304 (ttp) cc_final: 0.6750 (tpp) REVERT: C 545 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7809 (mptt) REVERT: C 660 ASP cc_start: 0.8062 (m-30) cc_final: 0.7607 (t0) REVERT: C 745 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7865 (p0) REVERT: C 892 MET cc_start: 0.8689 (mtm) cc_final: 0.8312 (mmm) outliers start: 65 outliers final: 30 residues processed: 179 average time/residue: 0.5195 time to fit residues: 102.9062 Evaluate side-chains 158 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 376 HIS Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 871 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 152 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 103 optimal weight: 9.9990 chunk 35 optimal weight: 0.0060 chunk 150 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.134713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.070775 restraints weight = 22125.428| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.37 r_work: 0.2749 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13920 Z= 0.121 Angle : 0.589 10.957 18858 Z= 0.301 Chirality : 0.042 0.168 2282 Planarity : 0.004 0.042 2352 Dihedral : 5.320 58.845 1882 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.41 % Favored : 94.19 % Rotamer: Outliers : 4.45 % Allowed : 28.53 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1774 helix: 1.50 (0.18), residues: 920 sheet: -0.66 (0.36), residues: 191 loop : -1.52 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 58 TYR 0.012 0.001 TYR A 806 PHE 0.017 0.001 PHE A 818 TRP 0.009 0.001 TRP A 278 HIS 0.005 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00272 (13918) covalent geometry : angle 0.58872 (18858) hydrogen bonds : bond 0.03986 ( 723) hydrogen bonds : angle 4.30487 ( 2112) Misc. bond : bond 0.00044 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 129 time to evaluate : 0.510 Fit side-chains REVERT: A 74 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8320 (tm) REVERT: A 432 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8677 (tppt) REVERT: A 445 MET cc_start: 0.8617 (tmm) cc_final: 0.8338 (tmm) REVERT: A 477 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8012 (mm) REVERT: A 507 MET cc_start: 0.8297 (mtm) cc_final: 0.8004 (mtm) REVERT: A 627 ARG cc_start: 0.8652 (mtp85) cc_final: 0.8174 (mtp180) REVERT: A 755 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8761 (mtt180) REVERT: C 47 LYS cc_start: 0.8800 (mmmm) cc_final: 0.8484 (tptp) REVERT: C 432 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7103 (tptp) REVERT: C 445 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6260 (mmp) REVERT: C 471 MET cc_start: 0.5001 (mmm) cc_final: 0.4770 (tpp) REVERT: C 475 CYS cc_start: 0.7463 (m) cc_final: 0.7054 (t) REVERT: C 507 MET cc_start: 0.7260 (ttp) cc_final: 0.6717 (tpp) REVERT: C 545 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7813 (mptt) REVERT: C 660 ASP cc_start: 0.8061 (m-30) cc_final: 0.7570 (t0) REVERT: C 745 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7628 (p0) REVERT: C 892 MET cc_start: 0.8530 (mtm) cc_final: 0.8193 (mmm) REVERT: C 893 MET cc_start: 0.8843 (mtt) cc_final: 0.8603 (mtp) outliers start: 68 outliers final: 26 residues processed: 186 average time/residue: 0.4919 time to fit residues: 101.7932 Evaluate side-chains 158 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 376 HIS Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 874 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 76 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.133687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.069720 restraints weight = 22012.345| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.32 r_work: 0.2722 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13920 Z= 0.164 Angle : 0.612 9.629 18858 Z= 0.312 Chirality : 0.043 0.171 2282 Planarity : 0.004 0.043 2352 Dihedral : 5.260 58.234 1879 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.26 % Favored : 93.29 % Rotamer: Outliers : 3.73 % Allowed : 29.12 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1774 helix: 1.43 (0.17), residues: 919 sheet: -0.69 (0.36), residues: 191 loop : -1.52 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 58 TYR 0.012 0.001 TYR A 806 PHE 0.018 0.001 PHE C 776 TRP 0.009 0.001 TRP A 302 HIS 0.004 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00392 (13918) covalent geometry : angle 0.61232 (18858) hydrogen bonds : bond 0.04402 ( 723) hydrogen bonds : angle 4.31835 ( 2112) Misc. bond : bond 0.00089 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 127 time to evaluate : 0.460 Fit side-chains REVERT: A 74 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8359 (tm) REVERT: A 432 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8640 (tppt) REVERT: A 445 MET cc_start: 0.8614 (tmm) cc_final: 0.8305 (tmm) REVERT: A 477 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8053 (mm) REVERT: A 507 MET cc_start: 0.8368 (mtm) cc_final: 0.8097 (mtm) REVERT: A 755 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8766 (mtt180) REVERT: C 47 LYS cc_start: 0.8803 (mmmm) cc_final: 0.8488 (tptp) REVERT: C 405 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8809 (mpp) REVERT: C 445 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6481 (mmp) REVERT: C 471 MET cc_start: 0.4924 (mmm) cc_final: 0.4649 (tpp) REVERT: C 475 CYS cc_start: 0.7560 (m) cc_final: 0.7092 (t) REVERT: C 507 MET cc_start: 0.7292 (ttp) cc_final: 0.6731 (tpp) REVERT: C 545 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7803 (mptt) REVERT: C 660 ASP cc_start: 0.8050 (m-30) cc_final: 0.7579 (t0) REVERT: C 892 MET cc_start: 0.8586 (mtm) cc_final: 0.8248 (mmm) outliers start: 57 outliers final: 34 residues processed: 173 average time/residue: 0.4780 time to fit residues: 92.1525 Evaluate side-chains 163 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 376 HIS Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 871 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.1980 chunk 137 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 165 optimal weight: 0.0370 chunk 5 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 157 optimal weight: 0.0170 chunk 175 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.135265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.071662 restraints weight = 22059.503| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.32 r_work: 0.2770 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13920 Z= 0.115 Angle : 0.597 9.579 18858 Z= 0.301 Chirality : 0.041 0.171 2282 Planarity : 0.004 0.041 2352 Dihedral : 5.154 58.203 1879 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.52 % Favored : 93.97 % Rotamer: Outliers : 3.53 % Allowed : 29.45 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1774 helix: 1.63 (0.18), residues: 913 sheet: -0.83 (0.35), residues: 197 loop : -1.50 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 58 TYR 0.012 0.001 TYR A 806 PHE 0.017 0.001 PHE A 818 TRP 0.009 0.001 TRP A 278 HIS 0.004 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00252 (13918) covalent geometry : angle 0.59651 (18858) hydrogen bonds : bond 0.03807 ( 723) hydrogen bonds : angle 4.23144 ( 2112) Misc. bond : bond 0.00031 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 128 time to evaluate : 0.512 Fit side-chains REVERT: A 47 LYS cc_start: 0.8140 (tppt) cc_final: 0.7681 (tppt) REVERT: A 74 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8312 (tm) REVERT: A 95 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8578 (mp) REVERT: A 432 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8703 (tppt) REVERT: A 435 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: A 445 MET cc_start: 0.8613 (tmm) cc_final: 0.8348 (tmm) REVERT: A 477 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8068 (mm) REVERT: A 507 MET cc_start: 0.8278 (mtm) cc_final: 0.7967 (mtm) REVERT: A 627 ARG cc_start: 0.8637 (mtp85) cc_final: 0.8160 (mtp180) REVERT: A 755 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8748 (mtt180) REVERT: C 47 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8571 (tptp) REVERT: C 432 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6919 (tmtt) REVERT: C 445 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6275 (mmp) REVERT: C 507 MET cc_start: 0.7252 (ttp) cc_final: 0.6666 (tpp) REVERT: C 545 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7777 (mptt) REVERT: C 660 ASP cc_start: 0.8012 (m-30) cc_final: 0.7507 (t0) REVERT: C 892 MET cc_start: 0.8481 (mtm) cc_final: 0.8148 (mmm) REVERT: C 893 MET cc_start: 0.8833 (mtt) cc_final: 0.8557 (mtp) outliers start: 54 outliers final: 26 residues processed: 172 average time/residue: 0.5066 time to fit residues: 97.0878 Evaluate side-chains 158 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 376 HIS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 871 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 119 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 169 optimal weight: 0.0970 chunk 118 optimal weight: 0.5980 chunk 162 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN C 111 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.134573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.070942 restraints weight = 21922.125| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.30 r_work: 0.2750 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13920 Z= 0.132 Angle : 0.607 11.855 18858 Z= 0.305 Chirality : 0.042 0.176 2282 Planarity : 0.004 0.042 2352 Dihedral : 5.165 57.415 1879 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.03 % Favored : 93.46 % Rotamer: Outliers : 3.47 % Allowed : 29.71 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1774 helix: 1.60 (0.18), residues: 913 sheet: -0.82 (0.36), residues: 192 loop : -1.47 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 444 TYR 0.011 0.001 TYR A 806 PHE 0.016 0.001 PHE A 818 TRP 0.009 0.001 TRP A 302 HIS 0.004 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00306 (13918) covalent geometry : angle 0.60707 (18858) hydrogen bonds : bond 0.04035 ( 723) hydrogen bonds : angle 4.24063 ( 2112) Misc. bond : bond 0.00060 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 126 time to evaluate : 0.568 Fit side-chains REVERT: A 47 LYS cc_start: 0.8307 (tppt) cc_final: 0.7867 (tppt) REVERT: A 74 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8340 (tm) REVERT: A 95 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8600 (mp) REVERT: A 192 LYS cc_start: 0.8495 (pmmt) cc_final: 0.7991 (pptt) REVERT: A 432 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8719 (tppt) REVERT: A 435 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: A 445 MET cc_start: 0.8616 (tmm) cc_final: 0.8315 (tmm) REVERT: A 477 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8118 (mm) REVERT: A 507 MET cc_start: 0.8325 (mtm) cc_final: 0.8079 (mtm) REVERT: A 627 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8256 (mtp180) REVERT: A 755 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8742 (mtt180) REVERT: C 47 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8614 (tptp) REVERT: C 432 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6954 (tmtt) REVERT: C 445 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6374 (mmp) REVERT: C 479 GLU cc_start: 0.5891 (OUTLIER) cc_final: 0.5661 (tm-30) REVERT: C 507 MET cc_start: 0.7202 (ttp) cc_final: 0.6600 (tpp) REVERT: C 545 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7762 (mptt) REVERT: C 660 ASP cc_start: 0.8012 (m-30) cc_final: 0.7537 (t0) REVERT: C 892 MET cc_start: 0.8542 (mtm) cc_final: 0.8212 (mmm) REVERT: C 893 MET cc_start: 0.8863 (mtt) cc_final: 0.8569 (mtp) outliers start: 53 outliers final: 28 residues processed: 170 average time/residue: 0.5152 time to fit residues: 97.3930 Evaluate side-chains 163 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 376 HIS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 845 SER Chi-restraints excluded: chain C residue 871 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 111 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 117 optimal weight: 0.0870 chunk 18 optimal weight: 3.9990 chunk 172 optimal weight: 0.4980 chunk 165 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 147 optimal weight: 0.3980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.134887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.071329 restraints weight = 22096.824| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.34 r_work: 0.2756 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13920 Z= 0.126 Angle : 0.618 12.535 18858 Z= 0.309 Chirality : 0.042 0.164 2282 Planarity : 0.004 0.041 2352 Dihedral : 5.154 57.338 1879 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.64 % Favored : 93.80 % Rotamer: Outliers : 3.08 % Allowed : 29.97 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1774 helix: 1.61 (0.18), residues: 913 sheet: -0.82 (0.37), residues: 180 loop : -1.44 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 492 TYR 0.012 0.001 TYR A 806 PHE 0.017 0.001 PHE C 540 TRP 0.008 0.001 TRP A 302 HIS 0.004 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00291 (13918) covalent geometry : angle 0.61772 (18858) hydrogen bonds : bond 0.03963 ( 723) hydrogen bonds : angle 4.23682 ( 2112) Misc. bond : bond 0.00046 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 0.371 Fit side-chains REVERT: A 74 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8328 (tm) REVERT: A 95 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8567 (mp) REVERT: A 192 LYS cc_start: 0.8476 (pmmt) cc_final: 0.7967 (pptt) REVERT: A 432 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8704 (tppt) REVERT: A 435 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: A 445 MET cc_start: 0.8610 (tmm) cc_final: 0.8310 (tmm) REVERT: A 477 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8112 (mm) REVERT: A 507 MET cc_start: 0.8272 (mtm) cc_final: 0.8022 (mtm) REVERT: A 627 ARG cc_start: 0.8602 (mtp85) cc_final: 0.8215 (mtp180) REVERT: A 755 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8723 (mtt180) REVERT: C 47 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8581 (tptp) REVERT: C 121 MET cc_start: 0.8612 (mtt) cc_final: 0.8388 (mtp) REVERT: C 432 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6863 (tmtt) REVERT: C 445 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.6166 (mmp) REVERT: C 479 GLU cc_start: 0.5866 (OUTLIER) cc_final: 0.5619 (tm-30) REVERT: C 507 MET cc_start: 0.7191 (ttp) cc_final: 0.6597 (tpp) REVERT: C 540 PHE cc_start: 0.7331 (m-10) cc_final: 0.7056 (m-10) REVERT: C 545 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7638 (mptt) REVERT: C 660 ASP cc_start: 0.7981 (m-30) cc_final: 0.7501 (t0) REVERT: C 892 MET cc_start: 0.8506 (mtm) cc_final: 0.8162 (mmm) REVERT: C 893 MET cc_start: 0.8830 (mtt) cc_final: 0.8544 (mtp) outliers start: 47 outliers final: 28 residues processed: 165 average time/residue: 0.5334 time to fit residues: 99.2410 Evaluate side-chains 162 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 376 HIS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 871 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 11 optimal weight: 0.1980 chunk 124 optimal weight: 6.9990 chunk 20 optimal weight: 0.0980 chunk 119 optimal weight: 2.9990 chunk 23 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 chunk 169 optimal weight: 0.1980 chunk 105 optimal weight: 6.9990 overall best weight: 0.2298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.136334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.073069 restraints weight = 22048.265| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.31 r_work: 0.2803 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13920 Z= 0.111 Angle : 0.621 12.773 18858 Z= 0.307 Chirality : 0.042 0.195 2282 Planarity : 0.004 0.040 2352 Dihedral : 5.077 57.059 1879 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.86 % Favored : 93.57 % Rotamer: Outliers : 2.75 % Allowed : 30.37 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1774 helix: 1.74 (0.18), residues: 912 sheet: -0.80 (0.37), residues: 180 loop : -1.41 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 492 TYR 0.012 0.001 TYR A 806 PHE 0.016 0.001 PHE A 818 TRP 0.010 0.001 TRP C 817 HIS 0.004 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00243 (13918) covalent geometry : angle 0.62108 (18858) hydrogen bonds : bond 0.03564 ( 723) hydrogen bonds : angle 4.17393 ( 2112) Misc. bond : bond 0.00013 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 0.504 Fit side-chains REVERT: A 74 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8329 (tm) REVERT: A 192 LYS cc_start: 0.8503 (pmmt) cc_final: 0.7992 (pptt) REVERT: A 432 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8754 (tppt) REVERT: A 435 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: A 445 MET cc_start: 0.8621 (tmm) cc_final: 0.8367 (tmm) REVERT: A 507 MET cc_start: 0.8157 (mtm) cc_final: 0.7930 (mtm) REVERT: A 541 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.6886 (pt) REVERT: A 627 ARG cc_start: 0.8554 (mtp85) cc_final: 0.7954 (mtp180) REVERT: A 755 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8720 (mtt180) REVERT: C 47 LYS cc_start: 0.8873 (mmmm) cc_final: 0.8562 (tptp) REVERT: C 146 MET cc_start: 0.7624 (pmm) cc_final: 0.7405 (mpp) REVERT: C 432 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6885 (tmtt) REVERT: C 445 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.6139 (mmp) REVERT: C 479 GLU cc_start: 0.5972 (OUTLIER) cc_final: 0.5675 (tm-30) REVERT: C 507 MET cc_start: 0.7180 (ttp) cc_final: 0.6672 (tpp) REVERT: C 540 PHE cc_start: 0.7319 (m-10) cc_final: 0.7030 (m-10) REVERT: C 545 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7693 (mptt) REVERT: C 660 ASP cc_start: 0.7957 (m-30) cc_final: 0.7484 (t0) REVERT: C 892 MET cc_start: 0.8441 (mtm) cc_final: 0.8171 (mmm) REVERT: C 893 MET cc_start: 0.8802 (mtt) cc_final: 0.8502 (mtp) outliers start: 42 outliers final: 20 residues processed: 164 average time/residue: 0.5175 time to fit residues: 94.1584 Evaluate side-chains 155 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 376 HIS Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 479 GLU Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 871 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 157 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 117 optimal weight: 0.0070 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.135824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.072334 restraints weight = 22245.917| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.36 r_work: 0.2806 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13920 Z= 0.120 Angle : 0.632 12.959 18858 Z= 0.312 Chirality : 0.042 0.263 2282 Planarity : 0.004 0.058 2352 Dihedral : 5.052 56.942 1878 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.58 % Favored : 93.97 % Rotamer: Outliers : 2.09 % Allowed : 31.35 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.21), residues: 1774 helix: 1.71 (0.18), residues: 912 sheet: -0.70 (0.39), residues: 173 loop : -1.38 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 492 TYR 0.012 0.001 TYR A 806 PHE 0.016 0.001 PHE A 818 TRP 0.009 0.001 TRP A 817 HIS 0.003 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00272 (13918) covalent geometry : angle 0.63247 (18858) hydrogen bonds : bond 0.03702 ( 723) hydrogen bonds : angle 4.17431 ( 2112) Misc. bond : bond 0.00033 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7174.25 seconds wall clock time: 122 minutes 19.09 seconds (7339.09 seconds total)