Starting phenix.real_space_refine on Sat Oct 24 05:38:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m8f_63709/10_2026/9m8f_63709.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m8f_63709/10_2026/9m8f_63709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m8f_63709/10_2026/9m8f_63709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m8f_63709/10_2026/9m8f_63709.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m8f_63709/10_2026/9m8f_63709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m8f_63709/10_2026/9m8f_63709.map" } resolution = 3.48 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= 0.001 sd= 0.085 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 38 5.16 5 C 7765 2.51 5 N 2168 2.21 5 O 2274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12249 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6111 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 730} Chain breaks: 4 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 6086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6086 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 729} Chain breaks: 4 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'TPP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.90, per 1000 atoms: 0.24 Number of scatterers: 12249 At special positions: 0 Unit cell: (113.98, 94.3, 111.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 4 15.00 O 2274 8.00 N 2168 7.00 C 7765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 525.2 milliseconds 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2830 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 6 sheets defined 48.5% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 103 through 125 Processing helix chain 'A' and resid 141 through 150 removed outlier: 4.088A pdb=" N GLY A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 171 through 182 removed outlier: 3.533A pdb=" N ILE A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 225 through 243 removed outlier: 4.047A pdb=" N LEU A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 265 through 271 removed outlier: 3.948A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 275 removed outlier: 3.514A pdb=" N GLY A 275 " --> pdb=" O ALA A 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 303 through 316 Processing helix chain 'A' and resid 328 through 335 Processing helix chain 'A' and resid 338 through 346 removed outlier: 3.656A pdb=" N THR A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 358 Processing helix chain 'A' and resid 371 through 378 removed outlier: 4.144A pdb=" N LYS A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 388 removed outlier: 4.005A pdb=" N ASN A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 444 through 455 removed outlier: 3.622A pdb=" N LYS A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 466 removed outlier: 4.321A pdb=" N ASN A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 493 removed outlier: 3.569A pdb=" N ARG A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 491 " --> pdb=" O ASP A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 541 removed outlier: 3.737A pdb=" N VAL A 533 " --> pdb=" O THR A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 604 through 617 Processing helix chain 'A' and resid 617 through 622 removed outlier: 3.870A pdb=" N HIS A 622 " --> pdb=" O SER A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 651 Processing helix chain 'A' and resid 678 through 686 removed outlier: 3.711A pdb=" N THR A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 712 removed outlier: 3.643A pdb=" N ALA A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 769 through 785 removed outlier: 4.374A pdb=" N ALA A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 783 " --> pdb=" O GLN A 779 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP A 785 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 814 removed outlier: 3.893A pdb=" N LEU A 800 " --> pdb=" O SER A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 Processing helix chain 'A' and resid 844 through 853 removed outlier: 3.617A pdb=" N GLN A 848 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 849 " --> pdb=" O PRO A 846 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 850 " --> pdb=" O GLU A 847 " (cutoff:3.500A) Proline residue: A 851 - end of helix Processing helix chain 'A' and resid 870 through 878 Processing helix chain 'A' and resid 881 through 896 Processing helix chain 'A' and resid 901 through 912 removed outlier: 4.066A pdb=" N VAL A 905 " --> pdb=" O PRO A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.854A pdb=" N ALA A 919 " --> pdb=" O VAL A 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 123 removed outlier: 3.594A pdb=" N ALA B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 141 through 152 removed outlier: 3.667A pdb=" N GLY B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 171 through 183 removed outlier: 3.782A pdb=" N ILE B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 226 through 244 Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 265 through 271 removed outlier: 3.888A pdb=" N ARG B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 278 removed outlier: 3.991A pdb=" N ALA B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 316 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 338 through 347 removed outlier: 3.556A pdb=" N ASN B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 355 Processing helix chain 'B' and resid 359 through 366 removed outlier: 4.098A pdb=" N VAL B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 378 removed outlier: 4.148A pdb=" N LYS B 375 " --> pdb=" O ASP B 371 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA B 376 " --> pdb=" O PRO B 372 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL B 378 " --> pdb=" O THR B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.626A pdb=" N TRP B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 388' Processing helix chain 'B' and resid 391 through 394 Processing helix chain 'B' and resid 395 through 409 removed outlier: 3.807A pdb=" N ALA B 402 " --> pdb=" O LYS B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 454 removed outlier: 3.608A pdb=" N ARG B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 479 through 493 removed outlier: 3.735A pdb=" N TYR B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 519 removed outlier: 3.594A pdb=" N LYS B 518 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 514 through 519' Processing helix chain 'B' and resid 527 through 539 Processing helix chain 'B' and resid 545 through 547 No H-bonds generated for 'chain 'B' and resid 545 through 547' Processing helix chain 'B' and resid 604 through 617 Processing helix chain 'B' and resid 617 through 622 Processing helix chain 'B' and resid 641 through 651 Processing helix chain 'B' and resid 671 through 675 removed outlier: 3.649A pdb=" N ALA B 675 " --> pdb=" O LEU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 Processing helix chain 'B' and resid 697 through 712 removed outlier: 3.714A pdb=" N ALA B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 702 " --> pdb=" O TYR B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 769 No H-bonds generated for 'chain 'B' and resid 767 through 769' Processing helix chain 'B' and resid 770 through 782 Processing helix chain 'B' and resid 797 through 814 Processing helix chain 'B' and resid 822 through 829 Processing helix chain 'B' and resid 844 through 848 removed outlier: 3.649A pdb=" N GLN B 848 " --> pdb=" O VAL B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 853 removed outlier: 3.581A pdb=" N TRP B 852 " --> pdb=" O ILE B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 878 Processing helix chain 'B' and resid 881 through 896 Processing helix chain 'B' and resid 901 through 912 removed outlier: 3.735A pdb=" N VAL B 905 " --> pdb=" O PRO B 901 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 166 removed outlier: 3.857A pdb=" N PHE A 257 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL A 254 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL A 286 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N CYS A 256 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ASN A 288 " --> pdb=" O CYS A 256 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU A 258 " --> pdb=" O ASN A 288 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE A 285 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA A 418 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 287 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASN A 318 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU A 417 " --> pdb=" O ASN A 318 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 320 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N LYS A 419 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL A 322 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 549 through 552 removed outlier: 7.667A pdb=" N LEU A 658 " --> pdb=" O PRO A 628 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TYR A 630 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA A 660 " --> pdb=" O TYR A 630 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE A 632 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 690 " --> pdb=" O PHE A 720 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 748 through 752 removed outlier: 5.444A pdb=" N ARG A 750 " --> pdb=" O SER A 793 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N SER A 793 " --> pdb=" O ARG A 750 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASN A 760 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASP A 790 " --> pdb=" O ASN A 760 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA A 762 " --> pdb=" O ASP A 790 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N TRP A 792 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE A 764 " --> pdb=" O TRP A 792 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL A 794 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA A 766 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 835 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU A 860 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA A 837 " --> pdb=" O LEU A 860 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 166 removed outlier: 6.463A pdb=" N GLN B 164 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE B 257 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE B 166 " --> pdb=" O PHE B 257 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL B 254 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL B 286 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS B 256 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASN B 288 " --> pdb=" O CYS B 256 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 258 " --> pdb=" O ASN B 288 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 283 " --> pdb=" O THR B 414 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE B 416 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE B 285 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA B 418 " --> pdb=" O PHE B 285 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE B 287 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASN B 318 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU B 417 " --> pdb=" O ASN B 318 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 320 " --> pdb=" O LEU B 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 549 through 552 removed outlier: 7.684A pdb=" N LEU B 658 " --> pdb=" O PRO B 628 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR B 630 " --> pdb=" O LEU B 658 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA B 660 " --> pdb=" O TYR B 630 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE B 632 " --> pdb=" O ALA B 660 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 657 " --> pdb=" O ILE B 723 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL B 725 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY B 659 " --> pdb=" O VAL B 725 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 750 through 752 removed outlier: 3.553A pdb=" N TYR B 751 " --> pdb=" O VAL B 791 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 791 " --> pdb=" O TYR B 751 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 762 " --> pdb=" O ALA B 788 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ILE B 836 " --> pdb=" O LYS B 761 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLN B 763 " --> pdb=" O ILE B 836 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL B 838 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU B 765 " --> pdb=" O VAL B 838 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1287 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: 1.94 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4124 1.34 - 1.46: 2218 1.46 - 1.57: 6170 1.57 - 1.69: 8 1.69 - 1.81: 68 Bond restraints: 12588 Sorted by residual: bond pdb=" N ASP B 446 " pdb=" CA ASP B 446 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.16e-02 7.43e+03 6.19e+00 bond pdb=" N GLU B 445 " pdb=" CA GLU B 445 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.23e-02 6.61e+03 5.36e+00 bond pdb=" N LEU B 444 " pdb=" CA LEU B 444 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.34e+00 bond pdb=" CB PRO A 127 " pdb=" CG PRO A 127 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.66e+00 bond pdb=" N THR B 443 " pdb=" CA THR B 443 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.53e+00 ... (remaining 12583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 16936 2.39 - 4.77: 190 4.77 - 7.16: 20 7.16 - 9.54: 2 9.54 - 11.93: 1 Bond angle restraints: 17149 Sorted by residual: angle pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" CD PRO A 127 " ideal model delta sigma weight residual 112.00 105.00 7.00 1.40e+00 5.10e-01 2.50e+01 angle pdb=" N ILE B 246 " pdb=" CA ILE B 246 " pdb=" C ILE B 246 " ideal model delta sigma weight residual 112.96 108.84 4.12 1.00e+00 1.00e+00 1.69e+01 angle pdb=" CA GLN B 544 " pdb=" CB GLN B 544 " pdb=" CG GLN B 544 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 angle pdb=" C TYR A 87 " pdb=" N VAL A 88 " pdb=" CA VAL A 88 " ideal model delta sigma weight residual 121.97 128.62 -6.65 1.80e+00 3.09e-01 1.37e+01 angle pdb=" CA GLU A 464 " pdb=" CB GLU A 464 " pdb=" CG GLU A 464 " ideal model delta sigma weight residual 114.10 120.96 -6.86 2.00e+00 2.50e-01 1.18e+01 ... (remaining 17144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6192 17.98 - 35.96: 865 35.96 - 53.94: 228 53.94 - 71.92: 43 71.92 - 89.90: 19 Dihedral angle restraints: 7347 sinusoidal: 2897 harmonic: 4450 Sorted by residual: dihedral pdb=" CA GLU B 445 " pdb=" C GLU B 445 " pdb=" N ASP B 446 " pdb=" CA ASP B 446 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA LYS B 543 " pdb=" C LYS B 543 " pdb=" N GLN B 544 " pdb=" CA GLN B 544 " ideal model delta harmonic sigma weight residual 180.00 163.33 16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ASP A 900 " pdb=" CB ASP A 900 " pdb=" CG ASP A 900 " pdb=" OD1 ASP A 900 " ideal model delta sinusoidal sigma weight residual -30.00 -86.50 56.50 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 7344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1506 0.060 - 0.119: 261 0.119 - 0.179: 25 0.179 - 0.238: 0 0.238 - 0.298: 1 Chirality restraints: 1793 Sorted by residual: chirality pdb=" CB VAL A 88 " pdb=" CA VAL A 88 " pdb=" CG1 VAL A 88 " pdb=" CG2 VAL A 88 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA LEU B 444 " pdb=" N LEU B 444 " pdb=" C LEU B 444 " pdb=" CB LEU B 444 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA ILE B 719 " pdb=" N ILE B 719 " pdb=" C ILE B 719 " pdb=" CB ILE B 719 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1790 not shown) Planarity restraints: 2276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 845 " -0.061 5.00e-02 4.00e+02 9.47e-02 1.44e+01 pdb=" N PRO B 846 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 846 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 846 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 126 " -0.051 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO A 127 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 127 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 127 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 158 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO A 159 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " -0.032 5.00e-02 4.00e+02 ... (remaining 2273 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 154 2.64 - 3.21: 10988 3.21 - 3.77: 18452 3.77 - 4.34: 24442 4.34 - 4.90: 41297 Nonbonded interactions: 95333 Sorted by model distance: nonbonded pdb=" OH TYR B 109 " pdb=" OE1 GLU B 146 " model vdw 2.076 3.040 nonbonded pdb=" OG SER A 140 " pdb=" O ILE A 421 " model vdw 2.205 3.040 nonbonded pdb=" OG SER A 634 " pdb=" OD2 ASP A 676 " model vdw 2.214 3.040 nonbonded pdb=" OE2 GLU A 146 " pdb=" NH1 ARG A 178 " model vdw 2.218 3.120 nonbonded pdb=" OH TYR A 109 " pdb=" OE2 GLU A 146 " model vdw 2.249 3.040 ... (remaining 95328 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 84 through 354 or (resid 355 and (name N or name CA or nam \ e C or name O or name CB )) or resid 356 through 364 or (resid 365 and (name N o \ r name CA or name C or name O or name CB )) or resid 366 through 374 or (resid 3 \ 75 through 376 and (name N or name CA or name C or name O or name CB )) or resid \ 377 through 444 or (resid 445 and (name N or name CA or name C or name O or nam \ e CB )) or resid 446 through 518 or (resid 519 and (name N or name CA or name C \ or name O or name CB )) or resid 520 through 542 or (resid 543 and (name N or na \ me CA or name C or name O or name CB )) or resid 544 through 555 or resid 564 th \ rough 755 or (resid 756 and (name N or name CA or name C or name O or name CB )) \ or resid 757 through 917)) selection = (chain 'B' and (resid 84 through 291 or resid 301 through 302 or (resid 303 and \ (name N or name CA or name C or name O or name CB )) or resid 304 through 448 or \ (resid 449 and (name N or name CA or name C or name O or name CB )) or resid 45 \ 0 through 501 or (resid 502 and (name N or name CA or name C or name O or name C \ B )) or resid 503 through 575 or resid 595 through 669 or (resid 670 and (name N \ or name CA or name C or name O or name CB )) or resid 671 through 917)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.100 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 12588 Z= 0.139 Angle : 0.606 11.926 17149 Z= 0.326 Chirality : 0.044 0.298 1793 Planarity : 0.005 0.095 2276 Dihedral : 17.865 89.896 4517 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.00 % Favored : 94.87 % Rotamer: Outliers : 0.24 % Allowed : 28.61 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.21), residues: 1541 helix: 0.45 (0.21), residues: 650 sheet: 0.66 (0.42), residues: 175 loop : -1.90 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.024 0.001 TYR A 877 PHE 0.012 0.001 PHE A 867 TRP 0.014 0.001 TRP A 792 HIS 0.003 0.001 HIS B 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (12588) covalent geometry : angle 0.60583 / 0.33 (17149) hydrogen bonds : bond 0.17667 / 11.80 ( 439) hydrogen bonds : angle 6.06850 / 4.48 ( 1287) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.466 Fit side-chains REVERT: A 771 MET cc_start: 0.9056 (mmm) cc_final: 0.8814 (mmm) REVERT: B 309 GLU cc_start: 0.8000 (tt0) cc_final: 0.7662 (tt0) outliers start: 3 outliers final: 3 residues processed: 145 average time/residue: 0.0920 time to fit residues: 20.5165 Evaluate side-chains 140 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 415 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN ** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 GLN B 573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.104301 restraints weight = 19149.965| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.63 r_work: 0.3033 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 12588 Z= 0.338 Angle : 0.697 9.981 17149 Z= 0.364 Chirality : 0.051 0.201 1793 Planarity : 0.006 0.067 2276 Dihedral : 5.490 59.389 1751 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.88 % Favored : 92.99 % Rotamer: Outliers : 4.70 % Allowed : 25.45 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.21), residues: 1541 helix: 0.45 (0.20), residues: 666 sheet: 0.25 (0.41), residues: 182 loop : -2.23 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 850 TYR 0.025 0.002 TYR A 233 PHE 0.020 0.002 PHE B 720 TRP 0.015 0.002 TRP B 797 HIS 0.006 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00818 / 0.34 (12588) covalent geometry : angle 0.69715 / 0.36 (17149) hydrogen bonds : bond 0.05864 / 4.10 ( 439) hydrogen bonds : angle 4.71390 / 3.47 ( 1287) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 143 time to evaluate : 0.457 Fit side-chains REVERT: A 181 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9076 (mm) REVERT: A 381 MET cc_start: 0.4725 (mpp) cc_final: 0.4441 (mmm) REVERT: A 450 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.7784 (t80) REVERT: A 454 GLN cc_start: 0.7857 (mp10) cc_final: 0.7512 (mp10) REVERT: A 644 SER cc_start: 0.9359 (OUTLIER) cc_final: 0.9011 (m) REVERT: A 758 ARG cc_start: 0.8674 (mmt-90) cc_final: 0.8371 (mmt-90) REVERT: A 890 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8914 (mm) REVERT: B 224 MET cc_start: 0.8410 (mtt) cc_final: 0.8012 (mtt) REVERT: B 313 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7398 (ttp-170) REVERT: B 352 TYR cc_start: 0.7016 (OUTLIER) cc_final: 0.6714 (t80) REVERT: B 447 LEU cc_start: 0.8816 (tp) cc_final: 0.8536 (tp) REVERT: B 801 ASN cc_start: 0.8745 (t0) cc_final: 0.8526 (t0) outliers start: 58 outliers final: 26 residues processed: 185 average time/residue: 0.0958 time to fit residues: 27.1790 Evaluate side-chains 160 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 313 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 859 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [6, 29, 21, 10, 83, 48, 93, 80, 32, 81, 57] chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN A 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104660 restraints weight = 18978.363| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.61 r_work: 0.3034 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12588 Z= 0.124 Angle : 0.552 10.412 17149 Z= 0.279 Chirality : 0.044 0.190 1793 Planarity : 0.005 0.060 2276 Dihedral : 5.159 60.492 1751 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.87 % Favored : 95.00 % Rotamer: Outliers : 3.40 % Allowed : 26.50 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1541 helix: 0.92 (0.21), residues: 658 sheet: 0.35 (0.40), residues: 180 loop : -2.03 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 154 TYR 0.018 0.001 TYR A 233 PHE 0.015 0.001 PHE B 720 TRP 0.013 0.001 TRP A 792 HIS 0.005 0.001 HIS B 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 (12588) covalent geometry : angle 0.55213 / 0.28 (17149) hydrogen bonds : bond 0.04022 / 2.81 ( 439) hydrogen bonds : angle 4.12104 / 3.03 ( 1287) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.445 Fit side-chains REVERT: A 181 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8893 (mm) REVERT: A 450 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7519 (t80) REVERT: A 454 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7200 (mp10) REVERT: A 484 TYR cc_start: 0.8052 (t80) cc_final: 0.7840 (t80) REVERT: A 644 SER cc_start: 0.9264 (OUTLIER) cc_final: 0.8971 (m) REVERT: A 758 ARG cc_start: 0.8666 (mmt-90) cc_final: 0.8239 (mmt-90) REVERT: A 890 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8860 (mm) REVERT: B 181 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8928 (mm) REVERT: B 224 MET cc_start: 0.8214 (mtt) cc_final: 0.7890 (mtt) REVERT: B 260 ASP cc_start: 0.7571 (m-30) cc_final: 0.7261 (m-30) REVERT: B 313 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7089 (ttp-170) REVERT: B 352 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6700 (t80) REVERT: B 444 LEU cc_start: 0.7732 (tt) cc_final: 0.7398 (mt) REVERT: B 455 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7346 (mtm-85) REVERT: B 540 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8404 (mt) outliers start: 42 outliers final: 21 residues processed: 174 average time/residue: 0.0944 time to fit residues: 24.9235 Evaluate side-chains 164 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 313 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 455 ARG Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 807 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [142, 26, 105, 6, 4, 12, 9, 88, 107, 70, 150] chunk 142 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 622 HIS B 252 GLN B 394 HIS B 544 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.098184 restraints weight = 19001.310| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.66 r_work: 0.2961 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12588 Z= 0.264 Angle : 0.633 7.581 17149 Z= 0.325 Chirality : 0.048 0.185 1793 Planarity : 0.005 0.064 2276 Dihedral : 5.316 59.040 1750 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.36 % Favored : 93.58 % Rotamer: Outliers : 5.43 % Allowed : 25.28 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.21), residues: 1541 helix: 0.87 (0.21), residues: 654 sheet: 0.23 (0.42), residues: 180 loop : -2.20 (0.21), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 850 TYR 0.021 0.002 TYR A 233 PHE 0.019 0.002 PHE B 720 TRP 0.010 0.001 TRP B 792 HIS 0.005 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.26 (12588) covalent geometry : angle 0.63289 / 0.33 (17149) hydrogen bonds : bond 0.05013 / 3.52 ( 439) hydrogen bonds : angle 4.34255 / 3.19 ( 1287) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 131 time to evaluate : 0.395 Fit side-chains REVERT: A 224 MET cc_start: 0.8518 (mtt) cc_final: 0.8263 (mtt) REVERT: A 450 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7510 (t80) REVERT: A 454 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7202 (mp10) REVERT: A 508 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6935 (mp) REVERT: A 565 TRP cc_start: 0.7639 (OUTLIER) cc_final: 0.7195 (m100) REVERT: A 644 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.9009 (m) REVERT: A 890 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8863 (mm) REVERT: B 146 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8290 (tp30) REVERT: B 224 MET cc_start: 0.8396 (mtt) cc_final: 0.8025 (mtt) REVERT: B 313 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7297 (ttp-170) REVERT: B 326 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8794 (tmm-80) REVERT: B 352 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.6827 (t80) REVERT: B 444 LEU cc_start: 0.7725 (tt) cc_final: 0.7499 (mt) REVERT: B 454 GLN cc_start: 0.7722 (mp10) cc_final: 0.7517 (mp10) REVERT: B 485 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7189 (mtp) REVERT: B 801 ASN cc_start: 0.8807 (t0) cc_final: 0.8562 (t0) outliers start: 67 outliers final: 38 residues processed: 183 average time/residue: 0.0987 time to fit residues: 26.8604 Evaluate side-chains 175 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 565 TRP Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 313 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 859 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [81, 141, 146, 14, 105, 149, 123, 37, 10, 154, 102] chunk 81 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 154 optimal weight: 0.0570 chunk 102 optimal weight: 0.0670 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 252 GLN B 544 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106208 restraints weight = 18837.413| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.64 r_work: 0.3087 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12588 Z= 0.105 Angle : 0.543 10.968 17149 Z= 0.271 Chirality : 0.043 0.181 1793 Planarity : 0.005 0.059 2276 Dihedral : 5.069 61.133 1750 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 3.81 % Allowed : 26.18 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.22), residues: 1541 helix: 1.18 (0.21), residues: 652 sheet: 0.23 (0.41), residues: 180 loop : -1.98 (0.21), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 455 TYR 0.016 0.001 TYR A 233 PHE 0.014 0.001 PHE B 720 TRP 0.012 0.001 TRP A 792 HIS 0.004 0.001 HIS B 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.10 (12588) covalent geometry : angle 0.54284 / 0.27 (17149) hydrogen bonds : bond 0.03475 / 2.43 ( 439) hydrogen bonds : angle 3.88941 / 2.86 ( 1287) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 0.415 Fit side-chains REVERT: A 224 MET cc_start: 0.8316 (mtt) cc_final: 0.8057 (mtt) REVERT: A 371 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7139 (t0) REVERT: A 450 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7423 (t80) REVERT: A 454 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: A 508 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6946 (mp) REVERT: A 623 ASN cc_start: 0.9227 (t0) cc_final: 0.8790 (t0) REVERT: A 644 SER cc_start: 0.9277 (OUTLIER) cc_final: 0.8956 (m) REVERT: B 146 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8188 (tp30) REVERT: B 224 MET cc_start: 0.8161 (mtt) cc_final: 0.7862 (mtt) REVERT: B 326 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8573 (tmm-80) REVERT: B 352 TYR cc_start: 0.6993 (OUTLIER) cc_final: 0.6704 (t80) REVERT: B 450 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8332 (t80) REVERT: B 454 GLN cc_start: 0.7739 (mp10) cc_final: 0.7267 (mp10) REVERT: B 485 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7106 (mtp) outliers start: 47 outliers final: 22 residues processed: 177 average time/residue: 0.0999 time to fit residues: 26.7644 Evaluate side-chains 164 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 849 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [82, 80, 72, 146, 116, 17, 155, 122, 104, 142, 0] chunk 82 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 116 optimal weight: 0.2980 chunk 17 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 122 optimal weight: 0.4980 chunk 104 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 GLN B 252 GLN B 544 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101842 restraints weight = 19035.416| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.65 r_work: 0.3023 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12588 Z= 0.237 Angle : 0.614 8.241 17149 Z= 0.311 Chirality : 0.047 0.181 1793 Planarity : 0.005 0.063 2276 Dihedral : 5.203 58.589 1750 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 5.19 % Allowed : 25.12 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.22), residues: 1541 helix: 1.11 (0.21), residues: 647 sheet: 0.22 (0.42), residues: 178 loop : -2.10 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 451 TYR 0.026 0.002 TYR A 109 PHE 0.020 0.002 PHE B 720 TRP 0.009 0.001 TRP B 852 HIS 0.008 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 (12588) covalent geometry : angle 0.61387 / 0.31 (17149) hydrogen bonds : bond 0.04545 / 3.20 ( 439) hydrogen bonds : angle 4.13922 / 3.03 ( 1287) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 133 time to evaluate : 0.272 Fit side-chains REVERT: A 224 MET cc_start: 0.8474 (mtt) cc_final: 0.8168 (mtt) REVERT: A 371 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7178 (t0) REVERT: A 450 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7456 (t80) REVERT: A 454 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: A 644 SER cc_start: 0.9325 (OUTLIER) cc_final: 0.9010 (m) REVERT: B 146 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8241 (tp30) REVERT: B 224 MET cc_start: 0.8335 (mtt) cc_final: 0.7926 (mtt) REVERT: B 252 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8247 (mt0) REVERT: B 277 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8091 (tt) REVERT: B 313 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7158 (ttp-170) REVERT: B 326 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8642 (tmm-80) REVERT: B 352 TYR cc_start: 0.6914 (OUTLIER) cc_final: 0.6684 (t80) REVERT: B 444 LEU cc_start: 0.7876 (tt) cc_final: 0.7631 (mt) REVERT: B 450 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8218 (t80) REVERT: B 454 GLN cc_start: 0.7787 (mp10) cc_final: 0.7236 (mp10) REVERT: B 485 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7045 (mtp) REVERT: B 817 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8610 (ptt-90) outliers start: 64 outliers final: 33 residues processed: 184 average time/residue: 0.0955 time to fit residues: 26.1328 Evaluate side-chains 176 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 313 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 817 ARG Chi-restraints excluded: chain B residue 849 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [126, 49, 81, 53, 50, 14, 10, 150, 154, 96, 100] chunk 126 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 154 optimal weight: 0.0170 chunk 96 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 252 GLN B 544 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106368 restraints weight = 18824.704| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.64 r_work: 0.3057 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12588 Z= 0.130 Angle : 0.565 11.931 17149 Z= 0.280 Chirality : 0.044 0.177 1793 Planarity : 0.005 0.059 2276 Dihedral : 5.095 59.459 1750 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.52 % Favored : 94.42 % Rotamer: Outliers : 4.54 % Allowed : 25.61 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.22), residues: 1541 helix: 1.20 (0.21), residues: 647 sheet: 0.25 (0.41), residues: 178 loop : -2.00 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 758 TYR 0.020 0.001 TYR A 109 PHE 0.016 0.001 PHE B 720 TRP 0.011 0.001 TRP A 792 HIS 0.004 0.001 HIS B 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (12588) covalent geometry : angle 0.56476 / 0.28 (17149) hydrogen bonds : bond 0.03724 / 2.62 ( 439) hydrogen bonds : angle 3.91166 / 2.86 ( 1287) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 136 time to evaluate : 0.355 Fit side-chains REVERT: A 146 GLU cc_start: 0.8467 (tp30) cc_final: 0.8046 (tp30) REVERT: A 371 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7120 (t0) REVERT: A 448 LYS cc_start: 0.7790 (pttm) cc_final: 0.7539 (mppt) REVERT: A 450 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7404 (t80) REVERT: A 454 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7117 (mp10) REVERT: A 644 SER cc_start: 0.9288 (OUTLIER) cc_final: 0.8967 (m) REVERT: B 146 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8217 (tp30) REVERT: B 224 MET cc_start: 0.8199 (mtt) cc_final: 0.7877 (mtt) REVERT: B 260 ASP cc_start: 0.7791 (m-30) cc_final: 0.7546 (m-30) REVERT: B 277 LEU cc_start: 0.8370 (tt) cc_final: 0.8074 (tt) REVERT: B 313 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7038 (ttp-170) REVERT: B 326 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8639 (tmm-80) REVERT: B 352 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.6614 (t80) REVERT: B 444 LEU cc_start: 0.7932 (tt) cc_final: 0.7691 (mt) REVERT: B 450 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8272 (t80) REVERT: B 454 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: B 485 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.7029 (mtp) outliers start: 56 outliers final: 37 residues processed: 181 average time/residue: 0.0960 time to fit residues: 26.4830 Evaluate side-chains 176 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 129 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 313 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 859 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [92, 127, 21, 104, 155, 82, 65, 111, 90, 33, 117] chunk 92 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.143898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110898 restraints weight = 18834.171| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.54 r_work: 0.3091 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12588 Z= 0.203 Angle : 0.597 11.056 17149 Z= 0.300 Chirality : 0.046 0.177 1793 Planarity : 0.005 0.062 2276 Dihedral : 5.157 60.117 1750 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.23 % Favored : 93.71 % Rotamer: Outliers : 4.86 % Allowed : 24.80 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.22), residues: 1541 helix: 1.21 (0.21), residues: 640 sheet: 0.15 (0.42), residues: 180 loop : -2.05 (0.21), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 758 TYR 0.024 0.001 TYR A 109 PHE 0.019 0.002 PHE B 720 TRP 0.009 0.001 TRP B 852 HIS 0.007 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.20 (12588) covalent geometry : angle 0.59678 / 0.30 (17149) hydrogen bonds : bond 0.04223 / 2.98 ( 439) hydrogen bonds : angle 4.04269 / 2.96 ( 1287) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 133 time to evaluate : 0.398 Fit side-chains REVERT: A 146 GLU cc_start: 0.8458 (tp30) cc_final: 0.8095 (tp30) REVERT: A 371 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7142 (t0) REVERT: A 381 MET cc_start: 0.5512 (mmp) cc_final: 0.5093 (mmm) REVERT: A 448 LYS cc_start: 0.7846 (pttm) cc_final: 0.7595 (mppt) REVERT: A 450 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7387 (t80) REVERT: A 454 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7086 (mp10) REVERT: A 644 SER cc_start: 0.9330 (OUTLIER) cc_final: 0.9002 (m) REVERT: A 758 ARG cc_start: 0.8822 (mmt-90) cc_final: 0.8569 (mmm160) REVERT: A 890 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8897 (mm) REVERT: B 146 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8172 (tp30) REVERT: B 224 MET cc_start: 0.8280 (mtt) cc_final: 0.7890 (mtt) REVERT: B 303 LYS cc_start: 0.8524 (tptm) cc_final: 0.8302 (mmmt) REVERT: B 313 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7078 (ttp-170) REVERT: B 326 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8493 (tmm-80) REVERT: B 352 TYR cc_start: 0.6911 (OUTLIER) cc_final: 0.6510 (t80) REVERT: B 450 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8218 (t80) REVERT: B 454 GLN cc_start: 0.7833 (mp10) cc_final: 0.7221 (mp10) REVERT: B 485 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7090 (mtp) outliers start: 60 outliers final: 44 residues processed: 183 average time/residue: 0.0965 time to fit residues: 26.9022 Evaluate side-chains 184 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 130 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 313 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [31, 37, 138, 116, 100, 143, 74, 111, 115, 147, 25] chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 138 optimal weight: 0.2980 chunk 116 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 HIS B 252 GLN B 544 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113844 restraints weight = 18651.399| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.56 r_work: 0.3138 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12588 Z= 0.109 Angle : 0.553 11.251 17149 Z= 0.274 Chirality : 0.043 0.173 1793 Planarity : 0.005 0.058 2276 Dihedral : 5.026 61.407 1750 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.32 % Favored : 94.61 % Rotamer: Outliers : 4.46 % Allowed : 25.36 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.22), residues: 1541 helix: 1.41 (0.21), residues: 632 sheet: 0.04 (0.41), residues: 185 loop : -1.90 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 758 TYR 0.024 0.001 TYR A 109 PHE 0.014 0.001 PHE B 720 TRP 0.012 0.001 TRP A 792 HIS 0.004 0.000 HIS B 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (12588) covalent geometry : angle 0.55323 / 0.27 (17149) hydrogen bonds : bond 0.03414 / 2.40 ( 439) hydrogen bonds : angle 3.79850 / 2.78 ( 1287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 142 time to evaluate : 0.356 Fit side-chains REVERT: A 146 GLU cc_start: 0.8316 (tp30) cc_final: 0.7950 (tp30) REVERT: A 149 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8358 (t80) REVERT: A 224 MET cc_start: 0.8383 (mtt) cc_final: 0.8070 (mtt) REVERT: A 371 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7121 (t0) REVERT: A 381 MET cc_start: 0.5548 (mmp) cc_final: 0.5130 (mmm) REVERT: A 448 LYS cc_start: 0.7834 (pttm) cc_final: 0.7626 (mppt) REVERT: A 450 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7358 (t80) REVERT: A 454 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7076 (mp10) REVERT: A 644 SER cc_start: 0.9284 (OUTLIER) cc_final: 0.8948 (m) REVERT: A 758 ARG cc_start: 0.8785 (mmt-90) cc_final: 0.8543 (mmm160) REVERT: B 224 MET cc_start: 0.8138 (mtt) cc_final: 0.7855 (mtt) REVERT: B 277 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7968 (tt) REVERT: B 313 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7445 (mtp180) REVERT: B 326 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8379 (tmm-80) REVERT: B 352 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.6336 (t80) REVERT: B 450 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8198 (t80) REVERT: B 454 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: B 485 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.7010 (mtp) outliers start: 55 outliers final: 36 residues processed: 186 average time/residue: 0.0932 time to fit residues: 26.5179 Evaluate side-chains 181 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 313 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 859 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [139, 24, 105, 47, 38, 102, 121, 141, 128, 116, 44] chunk 139 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 121 optimal weight: 0.0870 chunk 141 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.148309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114875 restraints weight = 18678.619| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.59 r_work: 0.3153 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12588 Z= 0.103 Angle : 0.548 10.927 17149 Z= 0.271 Chirality : 0.043 0.223 1793 Planarity : 0.004 0.057 2276 Dihedral : 4.940 61.770 1750 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 3.65 % Allowed : 26.74 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.22), residues: 1541 helix: 1.47 (0.21), residues: 632 sheet: 0.08 (0.41), residues: 183 loop : -1.82 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 758 TYR 0.016 0.001 TYR A 233 PHE 0.013 0.001 PHE B 720 TRP 0.012 0.001 TRP A 792 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.10 (12588) covalent geometry : angle 0.54823 / 0.27 (17149) hydrogen bonds : bond 0.03178 / 2.24 ( 439) hydrogen bonds : angle 3.71528 / 2.71 ( 1287) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 224 MET cc_start: 0.8284 (mtt) cc_final: 0.7946 (mtt) REVERT: A 371 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7112 (t0) REVERT: A 381 MET cc_start: 0.5576 (mmp) cc_final: 0.5174 (mmm) REVERT: A 450 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7317 (t80) REVERT: A 454 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7021 (mp10) REVERT: A 758 ARG cc_start: 0.8770 (mmt-90) cc_final: 0.8565 (mmm160) REVERT: B 313 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7398 (mtp180) REVERT: B 444 LEU cc_start: 0.8036 (mt) cc_final: 0.7684 (tt) REVERT: B 450 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8174 (t80) REVERT: B 454 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7133 (mp10) REVERT: B 485 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.7044 (mtp) REVERT: B 840 ASP cc_start: 0.8648 (t0) cc_final: 0.7605 (t0) outliers start: 45 outliers final: 31 residues processed: 172 average time/residue: 0.0925 time to fit residues: 24.5541 Evaluate side-chains 173 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 313 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 859 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [22, 120, 62, 40, 130, 135, 21, 87, 102, 146, 47] chunk 22 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 40 optimal weight: 0.0030 chunk 130 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 252 GLN B 544 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114084 restraints weight = 18631.076| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.56 r_work: 0.3178 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12588 Z= 0.127 Angle : 0.554 10.633 17149 Z= 0.274 Chirality : 0.044 0.194 1793 Planarity : 0.004 0.059 2276 Dihedral : 4.924 60.301 1750 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 3.57 % Allowed : 26.26 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.22), residues: 1541 helix: 1.43 (0.21), residues: 639 sheet: 0.05 (0.41), residues: 183 loop : -1.87 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 758 TYR 0.022 0.001 TYR A 109 PHE 0.015 0.001 PHE B 720 TRP 0.009 0.001 TRP A 792 HIS 0.004 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (12588) covalent geometry : angle 0.55360 / 0.27 (17149) hydrogen bonds : bond 0.03408 / 2.41 ( 439) hydrogen bonds : angle 3.73441 / 2.73 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.13 seconds wall clock time: 39 minutes 29.25 seconds (2369.25 seconds total)