Starting phenix.real_space_refine on Sun Apr 5 17:09:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uyp_64621/04_2026/9uyp_64621.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uyp_64621/04_2026/9uyp_64621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uyp_64621/04_2026/9uyp_64621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uyp_64621/04_2026/9uyp_64621.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uyp_64621/04_2026/9uyp_64621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uyp_64621/04_2026/9uyp_64621.map" } resolution = 3.51 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= 0.032 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 2 5.49 5 S 76 5.16 5 C 7453 2.51 5 N 2023 2.21 5 O 2170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11724 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 5860 Classifications: {'peptide': 764} Link IDs: {'CIS': 1, 'PTRANS': 41, 'TRANS': 721} Chain breaks: 4 Chain: "B" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5842 Classifications: {'peptide': 762} Link IDs: {'PTRANS': 40, 'TRANS': 721} Chain breaks: 5 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 2.83, per 1000 atoms: 0.24 Number of scatterers: 11724 At special positions: 0 Unit cell: (90.736, 99.216, 184.864, 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 76 16.00 P 2 15.00 O 2170 8.00 N 2023 7.00 C 7453 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 518 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 522 " - pdb=" SG CYS A 540 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 536 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 383 " distance=2.03 Simple disulfide: pdb=" SG CYS B 423 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 518 " - pdb=" SG CYS B 537 " distance=2.03 Simple disulfide: pdb=" SG CYS B 522 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 555 " distance=2.03 Simple disulfide: pdb=" SG CYS B 558 " - pdb=" SG CYS B 571 " distance=2.03 Simple disulfide: pdb=" SG CYS B 650 " - pdb=" SG CYS B 744 " distance=2.03 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: 0.90 Conformation dependent library (CDL) restraints added in 542.1 milliseconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2814 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 19 sheets defined 47.8% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 61 through 81 removed outlier: 4.963A pdb=" N HIS A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ARG A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 4.178A pdb=" N SER A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 165 removed outlier: 3.595A pdb=" N ILE A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.532A pdb=" N SER A 182 " --> pdb=" O PRO A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 225 through 241 removed outlier: 3.847A pdb=" N ALA A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 268 removed outlier: 3.637A pdb=" N LYS A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 319 through 324 removed outlier: 4.151A pdb=" N VAL A 324 " --> pdb=" O ASP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 Processing helix chain 'A' and resid 356 through 365 removed outlier: 3.680A pdb=" N PHE A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE A 365 " --> pdb=" O TRP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 423 removed outlier: 3.694A pdb=" N VAL A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 446 removed outlier: 3.573A pdb=" N LEU A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 609 removed outlier: 3.501A pdb=" N LEU A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 620 Processing helix chain 'A' and resid 620 through 642 removed outlier: 3.538A pdb=" N VAL A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A 642 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 676 removed outlier: 5.308A pdb=" N LEU A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG A 674 " --> pdb=" O THR A 670 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 675 " --> pdb=" O LYS A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 719 removed outlier: 3.872A pdb=" N ILE A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 701 " --> pdb=" O GLN A 697 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 709 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 738 removed outlier: 3.684A pdb=" N ALA A 738 " --> pdb=" O PRO A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 752 Processing helix chain 'A' and resid 755 through 772 removed outlier: 3.802A pdb=" N TYR A 768 " --> pdb=" O THR A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 806 removed outlier: 3.789A pdb=" N ILE A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 800 " --> pdb=" O TRP A 796 " (cutoff:3.500A) Proline residue: A 801 - end of helix Processing helix chain 'A' and resid 811 through 835 removed outlier: 4.586A pdb=" N SER A 831 " --> pdb=" O SER A 827 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 843 removed outlier: 3.817A pdb=" N ILE A 843 " --> pdb=" O LYS A 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 80 removed outlier: 3.831A pdb=" N ALA B 71 " --> pdb=" O HIS B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.725A pdb=" N GLU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 165 removed outlier: 3.993A pdb=" N VAL B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 196 through 211 removed outlier: 4.330A pdb=" N GLN B 200 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 241 Processing helix chain 'B' and resid 259 through 268 Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 336 through 345 removed outlier: 3.846A pdb=" N ASP B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 365 removed outlier: 3.604A pdb=" N PHE B 365 " --> pdb=" O TRP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 400 No H-bonds generated for 'chain 'B' and resid 398 through 400' Processing helix chain 'B' and resid 401 through 423 removed outlier: 3.533A pdb=" N ILE B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 437 through 446 Processing helix chain 'B' and resid 500 through 504 Processing helix chain 'B' and resid 586 through 610 removed outlier: 3.561A pdb=" N LEU B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 643 removed outlier: 3.968A pdb=" N VAL B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N THR B 638 " --> pdb=" O ILE B 634 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N PHE B 639 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 678 removed outlier: 3.922A pdb=" N ARG B 654 " --> pdb=" O CYS B 650 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 657 " --> pdb=" O ARG B 653 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 660 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 719 removed outlier: 3.941A pdb=" N VAL B 699 " --> pdb=" O THR B 695 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 714 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TRP B 715 " --> pdb=" O GLY B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 772 removed outlier: 3.611A pdb=" N LEU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE B 752 " --> pdb=" O ASP B 748 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR B 757 " --> pdb=" O GLY B 753 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N SER B 758 " --> pdb=" O CYS B 754 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 767 " --> pdb=" O VAL B 763 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR B 768 " --> pdb=" O THR B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 775 No H-bonds generated for 'chain 'B' and resid 773 through 775' Processing helix chain 'B' and resid 782 through 806 removed outlier: 3.730A pdb=" N VAL B 800 " --> pdb=" O TRP B 796 " (cutoff:3.500A) Proline residue: B 801 - end of helix removed outlier: 3.599A pdb=" N PHE B 804 " --> pdb=" O VAL B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 809 No H-bonds generated for 'chain 'B' and resid 807 through 809' Processing helix chain 'B' and resid 811 through 834 removed outlier: 3.966A pdb=" N THR B 821 " --> pdb=" O THR B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 844 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.407A pdb=" N LEU A 39 " --> pdb=" O GLY A 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 45 removed outlier: 3.568A pdb=" N PHE A 45 " --> pdb=" O LEU A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 251 removed outlier: 7.824A pdb=" N VAL A 216 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER A 248 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR A 218 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LYS A 250 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA A 220 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY A 275 " --> pdb=" O TYR A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 331 removed outlier: 3.561A pdb=" N GLN A 476 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 486 " --> pdb=" O GLN A 476 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 450 through 451 removed outlier: 3.603A pdb=" N PHE A 450 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 530 Processing sheet with id=AA7, first strand: chain 'A' and resid 548 through 549 Processing sheet with id=AA8, first strand: chain 'A' and resid 562 through 564 Processing sheet with id=AA9, first strand: chain 'A' and resid 724 through 726 Processing sheet with id=AB1, first strand: chain 'B' and resid 92 through 93 removed outlier: 7.733A pdb=" N THR B 40 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 44 through 45 removed outlier: 3.720A pdb=" N PHE B 45 " --> pdb=" O LEU B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 171 through 173 removed outlier: 6.061A pdb=" N GLN B 171 " --> pdb=" O SER B 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 216 through 221 removed outlier: 8.003A pdb=" N VAL B 216 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER B 248 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR B 218 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS B 250 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA B 220 " --> pdb=" O LYS B 250 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.824A pdb=" N ILE B 329 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR B 470 " --> pdb=" O GLN B 492 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLN B 492 " --> pdb=" O TYR B 470 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE B 472 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 449 through 451 removed outlier: 3.661A pdb=" N PHE B 450 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 526 through 530 Processing sheet with id=AB8, first strand: chain 'B' and resid 547 through 548 Processing sheet with id=AB9, first strand: chain 'B' and resid 562 through 564 Processing sheet with id=AC1, first strand: chain 'B' and resid 723 through 726 498 hydrogen bonds defined for protein. 1431 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: 1.90 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3836 1.34 - 1.46: 2755 1.46 - 1.58: 5272 1.58 - 1.70: 3 1.70 - 1.82: 110 Bond restraints: 11976 Sorted by residual: bond pdb=" O2P SEP A1001 " pdb=" P SEP A1001 " ideal model delta sigma weight residual 1.610 1.506 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" O3P SEP B1001 " pdb=" P SEP B1001 " ideal model delta sigma weight residual 1.610 1.506 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" O3P SEP A1001 " pdb=" P SEP A1001 " ideal model delta sigma weight residual 1.610 1.506 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" O2P SEP B1001 " pdb=" P SEP B1001 " ideal model delta sigma weight residual 1.610 1.507 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" O1P SEP B1001 " pdb=" P SEP B1001 " ideal model delta sigma weight residual 1.610 1.507 0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 11971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 16205 3.23 - 6.46: 65 6.46 - 9.70: 11 9.70 - 12.93: 0 12.93 - 16.16: 2 Bond angle restraints: 16283 Sorted by residual: angle pdb=" CA PRO B 431 " pdb=" N PRO B 431 " pdb=" CD PRO B 431 " ideal model delta sigma weight residual 112.00 105.26 6.74 1.40e+00 5.10e-01 2.32e+01 angle pdb=" CA LEU A 826 " pdb=" CB LEU A 826 " pdb=" CG LEU A 826 " ideal model delta sigma weight residual 116.30 132.46 -16.16 3.50e+00 8.16e-02 2.13e+01 angle pdb=" CA LEU B 761 " pdb=" CB LEU B 761 " pdb=" CG LEU B 761 " ideal model delta sigma weight residual 116.30 131.55 -15.25 3.50e+00 8.16e-02 1.90e+01 angle pdb=" CB MET B 641 " pdb=" CG MET B 641 " pdb=" SD MET B 641 " ideal model delta sigma weight residual 112.70 120.94 -8.24 3.00e+00 1.11e-01 7.54e+00 angle pdb=" N PRO B 431 " pdb=" CD PRO B 431 " pdb=" CG PRO B 431 " ideal model delta sigma weight residual 103.20 99.14 4.06 1.50e+00 4.44e-01 7.33e+00 ... (remaining 16278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 6103 17.56 - 35.13: 798 35.13 - 52.69: 225 52.69 - 70.26: 46 70.26 - 87.82: 17 Dihedral angle restraints: 7189 sinusoidal: 2806 harmonic: 4383 Sorted by residual: dihedral pdb=" CB CYS A 558 " pdb=" SG CYS A 558 " pdb=" SG CYS A 571 " pdb=" CB CYS A 571 " ideal model delta sinusoidal sigma weight residual -86.00 -168.91 82.91 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS B 558 " pdb=" SG CYS B 558 " pdb=" SG CYS B 571 " pdb=" CB CYS B 571 " ideal model delta sinusoidal sigma weight residual -86.00 -160.63 74.63 1 1.00e+01 1.00e-02 7.06e+01 dihedral pdb=" CB CYS A 367 " pdb=" SG CYS A 367 " pdb=" SG CYS A 383 " pdb=" CB CYS A 383 " ideal model delta sinusoidal sigma weight residual 93.00 31.28 61.72 1 1.00e+01 1.00e-02 5.05e+01 ... (remaining 7186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1537 0.054 - 0.109: 295 0.109 - 0.163: 30 0.163 - 0.218: 0 0.218 - 0.272: 2 Chirality restraints: 1864 Sorted by residual: chirality pdb=" CG LEU B 704 " pdb=" CB LEU B 704 " pdb=" CD1 LEU B 704 " pdb=" CD2 LEU B 704 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB THR A 819 " pdb=" CA THR A 819 " pdb=" OG1 THR A 819 " pdb=" CG2 THR A 819 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB THR B 766 " pdb=" CA THR B 766 " pdb=" OG1 THR B 766 " pdb=" CG2 THR B 766 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 1861 not shown) Planarity restraints: 2083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 430 " 0.066 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO B 431 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 431 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 431 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 565 " -0.036 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO A 566 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 566 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 566 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 426 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" C HIS A 426 " -0.034 2.00e-02 2.50e+03 pdb=" O HIS A 426 " 0.013 2.00e-02 2.50e+03 pdb=" N THR A 427 " 0.011 2.00e-02 2.50e+03 ... (remaining 2080 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 285 2.69 - 3.24: 11373 3.24 - 3.79: 17284 3.79 - 4.35: 21555 4.35 - 4.90: 37261 Nonbonded interactions: 87758 Sorted by model distance: nonbonded pdb=" O ILE A 802 " pdb=" OG1 THR A 806 " model vdw 2.133 3.040 nonbonded pdb=" O GLY B 658 " pdb=" OG1 THR B 662 " model vdw 2.148 3.040 nonbonded pdb=" O ILE B 700 " pdb=" OG SER B 703 " model vdw 2.159 3.040 nonbonded pdb=" O SER A 152 " pdb=" OG SER A 152 " model vdw 2.225 3.040 nonbonded pdb=" N GLU B 84 " pdb=" OE1 GLU B 84 " model vdw 2.263 3.120 ... (remaining 87753 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 30 through 610 or resid 615 through 772 or resid 781 throu \ gh 844 or resid 1001)) selection = (chain 'B' and (resid 30 through 676 or resid 692 through 772 or resid 781 throu \ gh 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.880 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.004 0.108 11993 Z= 0.192 Angle : 0.593 16.161 16317 Z= 0.283 Chirality : 0.042 0.272 1864 Planarity : 0.004 0.097 2083 Dihedral : 17.097 87.823 4324 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.24 % Allowed : 32.80 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.22), residues: 1504 helix: 1.29 (0.21), residues: 643 sheet: -2.11 (0.41), residues: 172 loop : -1.38 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 578 TYR 0.031 0.001 TYR B 836 PHE 0.020 0.001 PHE B 632 TRP 0.006 0.001 TRP B 493 HIS 0.002 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00433 (11976) covalent geometry : angle 0.59165 (16283) SS BOND : bond 0.00202 ( 17) SS BOND : angle 0.95450 ( 34) hydrogen bonds : bond 0.17870 ( 498) hydrogen bonds : angle 5.82976 ( 1431) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 0.434 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 108 average time/residue: 0.0839 time to fit residues: 14.5215 Evaluate side-chains 104 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 116 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN B 479 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.144103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.091497 restraints weight = 19627.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.095083 restraints weight = 11930.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.095599 restraints weight = 8769.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.096870 restraints weight = 7140.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097147 restraints weight = 6691.935| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11993 Z= 0.180 Angle : 0.576 11.084 16317 Z= 0.286 Chirality : 0.042 0.200 1864 Planarity : 0.004 0.058 2083 Dihedral : 4.642 66.713 1679 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.23 % Allowed : 28.89 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.22), residues: 1504 helix: 1.40 (0.21), residues: 656 sheet: -2.02 (0.38), residues: 193 loop : -1.36 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 617 TYR 0.015 0.001 TYR A 757 PHE 0.013 0.001 PHE A 803 TRP 0.006 0.001 TRP B 493 HIS 0.002 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00429 (11976) covalent geometry : angle 0.57492 (16283) SS BOND : bond 0.00295 ( 17) SS BOND : angle 0.96782 ( 34) hydrogen bonds : bond 0.04631 ( 498) hydrogen bonds : angle 4.27879 ( 1431) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 111 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 117 ILE cc_start: 0.5788 (OUTLIER) cc_final: 0.5511 (tp) REVERT: A 204 MET cc_start: 0.8452 (mtt) cc_final: 0.8081 (mtt) REVERT: A 419 HIS cc_start: 0.7881 (OUTLIER) cc_final: 0.7439 (t70) REVERT: A 654 ARG cc_start: 0.7385 (tpm170) cc_final: 0.7152 (tpp-160) REVERT: A 762 MET cc_start: 0.9003 (mmm) cc_final: 0.8765 (mmm) REVERT: B 283 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7921 (t0) outliers start: 53 outliers final: 19 residues processed: 156 average time/residue: 0.0853 time to fit residues: 20.5153 Evaluate side-chains 123 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 837 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 82 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.093468 restraints weight = 19604.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097332 restraints weight = 11788.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.097963 restraints weight = 8530.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099188 restraints weight = 6802.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099576 restraints weight = 6245.843| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11993 Z= 0.116 Angle : 0.538 11.845 16317 Z= 0.262 Chirality : 0.041 0.226 1864 Planarity : 0.004 0.055 2083 Dihedral : 4.332 59.629 1677 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.59 % Allowed : 29.69 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.22), residues: 1504 helix: 1.48 (0.21), residues: 659 sheet: -1.91 (0.37), residues: 193 loop : -1.31 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 578 TYR 0.013 0.001 TYR A 757 PHE 0.010 0.001 PHE B 632 TRP 0.006 0.001 TRP B 493 HIS 0.003 0.000 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00266 (11976) covalent geometry : angle 0.53696 (16283) SS BOND : bond 0.00333 ( 17) SS BOND : angle 0.91454 ( 34) hydrogen bonds : bond 0.03873 ( 498) hydrogen bonds : angle 3.95964 ( 1431) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 0.456 Fit side-chains REVERT: A 69 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7884 (tt) REVERT: A 204 MET cc_start: 0.8438 (mtt) cc_final: 0.8123 (mtt) REVERT: A 337 ASP cc_start: 0.7473 (t70) cc_final: 0.7261 (t0) REVERT: A 396 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7796 (mm-30) REVERT: A 562 MET cc_start: 0.6197 (mmp) cc_final: 0.5851 (mmp) REVERT: A 654 ARG cc_start: 0.7433 (tpm170) cc_final: 0.7231 (tpp-160) REVERT: A 762 MET cc_start: 0.9070 (mmm) cc_final: 0.8760 (mmm) REVERT: A 803 PHE cc_start: 0.8521 (m-80) cc_final: 0.8212 (m-80) REVERT: B 835 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8229 (mm) outliers start: 45 outliers final: 23 residues processed: 154 average time/residue: 0.0807 time to fit residues: 20.0630 Evaluate side-chains 129 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 837 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 52 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 141 optimal weight: 0.0470 chunk 123 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.147349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.094878 restraints weight = 19542.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098374 restraints weight = 11864.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099300 restraints weight = 8489.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100379 restraints weight = 6986.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100722 restraints weight = 6486.772| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11993 Z= 0.101 Angle : 0.543 14.573 16317 Z= 0.258 Chirality : 0.041 0.292 1864 Planarity : 0.004 0.055 2083 Dihedral : 4.126 53.769 1675 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.43 % Allowed : 29.45 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.22), residues: 1504 helix: 1.62 (0.21), residues: 648 sheet: -1.82 (0.37), residues: 193 loop : -1.25 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 578 TYR 0.017 0.001 TYR B 836 PHE 0.008 0.001 PHE B 279 TRP 0.005 0.001 TRP B 361 HIS 0.002 0.000 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00224 (11976) covalent geometry : angle 0.54256 (16283) SS BOND : bond 0.00274 ( 17) SS BOND : angle 0.71024 ( 34) hydrogen bonds : bond 0.03429 ( 498) hydrogen bonds : angle 3.83148 ( 1431) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 0.431 Fit side-chains REVERT: A 69 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7845 (tt) REVERT: A 396 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7804 (mm-30) REVERT: A 762 MET cc_start: 0.9098 (mmm) cc_final: 0.8815 (mmm) REVERT: A 803 PHE cc_start: 0.8528 (m-80) cc_final: 0.8267 (m-80) REVERT: B 118 ARG cc_start: 0.4372 (OUTLIER) cc_final: 0.3126 (ptp-110) REVERT: B 762 MET cc_start: 0.8935 (tmm) cc_final: 0.8204 (mtm) REVERT: B 835 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8216 (mm) outliers start: 43 outliers final: 26 residues processed: 150 average time/residue: 0.0780 time to fit residues: 18.8338 Evaluate side-chains 133 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 837 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 121 optimal weight: 0.0980 chunk 73 optimal weight: 5.9990 chunk 119 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN B 708 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.147728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.094957 restraints weight = 19611.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098282 restraints weight = 11081.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.100460 restraints weight = 7856.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101899 restraints weight = 6348.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.102673 restraints weight = 5535.861| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11993 Z= 0.100 Angle : 0.541 13.499 16317 Z= 0.257 Chirality : 0.041 0.311 1864 Planarity : 0.004 0.055 2083 Dihedral : 4.063 49.809 1675 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.47 % Allowed : 28.25 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.22), residues: 1504 helix: 1.59 (0.21), residues: 651 sheet: -1.72 (0.37), residues: 193 loop : -1.19 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 654 TYR 0.012 0.001 TYR A 665 PHE 0.015 0.001 PHE B 632 TRP 0.006 0.001 TRP B 303 HIS 0.003 0.000 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00221 (11976) covalent geometry : angle 0.53932 (16283) SS BOND : bond 0.00228 ( 17) SS BOND : angle 0.95462 ( 34) hydrogen bonds : bond 0.03319 ( 498) hydrogen bonds : angle 3.74670 ( 1431) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 117 time to evaluate : 0.438 Fit side-chains REVERT: A 69 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7819 (tt) REVERT: A 117 ILE cc_start: 0.5717 (OUTLIER) cc_final: 0.5417 (tp) REVERT: A 396 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7789 (mm-30) REVERT: A 562 MET cc_start: 0.6096 (mmp) cc_final: 0.5722 (mmp) REVERT: A 762 MET cc_start: 0.9125 (mmm) cc_final: 0.8874 (mmm) REVERT: B 118 ARG cc_start: 0.4608 (OUTLIER) cc_final: 0.3331 (ptp-110) REVERT: B 762 MET cc_start: 0.8941 (tmm) cc_final: 0.8219 (mtt) REVERT: B 835 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8236 (mm) outliers start: 56 outliers final: 37 residues processed: 166 average time/residue: 0.0765 time to fit residues: 20.9134 Evaluate side-chains 147 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 825 SER Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 837 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 130 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 148 optimal weight: 0.0870 chunk 67 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.147478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.094032 restraints weight = 19591.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.097488 restraints weight = 10762.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.099769 restraints weight = 7515.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.101283 restraints weight = 6029.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102212 restraints weight = 5226.147| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11993 Z= 0.108 Angle : 0.539 14.323 16317 Z= 0.257 Chirality : 0.041 0.340 1864 Planarity : 0.004 0.056 2083 Dihedral : 4.024 48.015 1675 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.39 % Allowed : 28.49 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.22), residues: 1504 helix: 1.65 (0.21), residues: 649 sheet: -1.67 (0.37), residues: 193 loop : -1.16 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 654 TYR 0.018 0.001 TYR B 836 PHE 0.015 0.001 PHE B 632 TRP 0.006 0.001 TRP B 303 HIS 0.001 0.000 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00252 (11976) covalent geometry : angle 0.53788 (16283) SS BOND : bond 0.00193 ( 17) SS BOND : angle 0.95983 ( 34) hydrogen bonds : bond 0.03318 ( 498) hydrogen bonds : angle 3.71700 ( 1431) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 114 time to evaluate : 0.402 Fit side-chains REVERT: A 69 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7801 (tt) REVERT: A 117 ILE cc_start: 0.5737 (OUTLIER) cc_final: 0.5437 (tp) REVERT: A 396 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7793 (mm-30) REVERT: A 754 CYS cc_start: 0.7110 (t) cc_final: 0.6906 (t) REVERT: A 762 MET cc_start: 0.9034 (mmm) cc_final: 0.8730 (mmm) REVERT: B 118 ARG cc_start: 0.4562 (OUTLIER) cc_final: 0.3301 (ptp-170) REVERT: B 762 MET cc_start: 0.8937 (tmm) cc_final: 0.8198 (mtt) outliers start: 55 outliers final: 40 residues processed: 162 average time/residue: 0.0718 time to fit residues: 19.1684 Evaluate side-chains 152 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 837 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 42 optimal weight: 0.0030 chunk 61 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 108 optimal weight: 0.0030 chunk 91 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.148333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.096248 restraints weight = 19510.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.099311 restraints weight = 11349.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.100149 restraints weight = 8597.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101351 restraints weight = 7025.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.101661 restraints weight = 6432.124| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11993 Z= 0.097 Angle : 0.543 15.117 16317 Z= 0.258 Chirality : 0.041 0.333 1864 Planarity : 0.004 0.056 2083 Dihedral : 3.947 43.887 1675 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.75 % Allowed : 29.21 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.22), residues: 1504 helix: 1.66 (0.21), residues: 651 sheet: -1.64 (0.38), residues: 188 loop : -1.14 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 654 TYR 0.018 0.001 TYR B 836 PHE 0.017 0.001 PHE B 632 TRP 0.005 0.001 TRP B 361 HIS 0.003 0.000 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00215 (11976) covalent geometry : angle 0.54129 (16283) SS BOND : bond 0.00218 ( 17) SS BOND : angle 1.17809 ( 34) hydrogen bonds : bond 0.03202 ( 498) hydrogen bonds : angle 3.67448 ( 1431) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 112 time to evaluate : 0.433 Fit side-chains REVERT: A 69 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7783 (tt) REVERT: A 117 ILE cc_start: 0.5760 (OUTLIER) cc_final: 0.5508 (tp) REVERT: A 396 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7808 (mm-30) REVERT: A 562 MET cc_start: 0.5966 (mmp) cc_final: 0.5709 (mmp) REVERT: A 726 ASP cc_start: 0.7591 (t0) cc_final: 0.7335 (t70) REVERT: A 762 MET cc_start: 0.9021 (mmm) cc_final: 0.8785 (mmm) REVERT: A 803 PHE cc_start: 0.8428 (m-80) cc_final: 0.8137 (m-80) REVERT: B 118 ARG cc_start: 0.4434 (OUTLIER) cc_final: 0.3191 (ptp-170) REVERT: B 762 MET cc_start: 0.8977 (tmm) cc_final: 0.8744 (tmm) outliers start: 47 outliers final: 34 residues processed: 150 average time/residue: 0.0744 time to fit residues: 18.2627 Evaluate side-chains 145 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 837 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 74 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 0.0870 chunk 108 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.146863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.094191 restraints weight = 19737.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097152 restraints weight = 12303.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098299 restraints weight = 8814.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099383 restraints weight = 7239.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099706 restraints weight = 6639.022| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11993 Z= 0.131 Angle : 0.555 14.788 16317 Z= 0.265 Chirality : 0.041 0.324 1864 Planarity : 0.004 0.057 2083 Dihedral : 4.024 46.128 1675 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.91 % Allowed : 29.37 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.22), residues: 1504 helix: 1.66 (0.21), residues: 648 sheet: -1.65 (0.38), residues: 188 loop : -1.17 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 654 TYR 0.023 0.001 TYR A 836 PHE 0.017 0.001 PHE B 632 TRP 0.006 0.001 TRP B 303 HIS 0.001 0.000 HIS A 511 Details of bonding type rmsd covalent geometry : bond 0.00310 (11976) covalent geometry : angle 0.55345 (16283) SS BOND : bond 0.00225 ( 17) SS BOND : angle 1.13840 ( 34) hydrogen bonds : bond 0.03492 ( 498) hydrogen bonds : angle 3.72773 ( 1431) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 108 time to evaluate : 0.309 Fit side-chains REVERT: A 117 ILE cc_start: 0.5797 (OUTLIER) cc_final: 0.5539 (tp) REVERT: A 396 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7805 (mm-30) REVERT: A 562 MET cc_start: 0.6058 (mmp) cc_final: 0.5728 (mmp) REVERT: A 762 MET cc_start: 0.9045 (mmm) cc_final: 0.8783 (mmm) REVERT: A 803 PHE cc_start: 0.8416 (m-80) cc_final: 0.8103 (m-80) REVERT: B 440 MET cc_start: 0.8076 (tpp) cc_final: 0.7842 (tpp) REVERT: B 762 MET cc_start: 0.8968 (tmm) cc_final: 0.8747 (tmm) outliers start: 49 outliers final: 42 residues processed: 150 average time/residue: 0.0725 time to fit residues: 18.2370 Evaluate side-chains 149 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 106 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 825 SER Chi-restraints excluded: chain B residue 837 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 54 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 45 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 0.0010 chunk 117 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.148272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.096199 restraints weight = 19357.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100119 restraints weight = 11666.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100383 restraints weight = 8467.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.101515 restraints weight = 6946.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.101959 restraints weight = 6387.521| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11993 Z= 0.096 Angle : 0.544 16.190 16317 Z= 0.257 Chirality : 0.041 0.334 1864 Planarity : 0.004 0.056 2083 Dihedral : 3.909 40.655 1675 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.59 % Allowed : 29.61 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.22), residues: 1504 helix: 1.66 (0.21), residues: 650 sheet: -1.60 (0.38), residues: 188 loop : -1.13 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 654 TYR 0.017 0.001 TYR A 836 PHE 0.019 0.001 PHE B 632 TRP 0.005 0.001 TRP B 361 HIS 0.002 0.000 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00215 (11976) covalent geometry : angle 0.54348 (16283) SS BOND : bond 0.00177 ( 17) SS BOND : angle 0.89452 ( 34) hydrogen bonds : bond 0.03197 ( 498) hydrogen bonds : angle 3.64481 ( 1431) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 107 time to evaluate : 0.312 Fit side-chains REVERT: A 117 ILE cc_start: 0.5771 (OUTLIER) cc_final: 0.5507 (tp) REVERT: A 396 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7789 (mm-30) REVERT: A 562 MET cc_start: 0.6084 (mmp) cc_final: 0.5813 (mmp) REVERT: A 762 MET cc_start: 0.9049 (mmm) cc_final: 0.8805 (mmm) REVERT: A 803 PHE cc_start: 0.8369 (m-80) cc_final: 0.8051 (m-80) REVERT: B 118 ARG cc_start: 0.4564 (OUTLIER) cc_final: 0.3483 (ptp-110) REVERT: B 440 MET cc_start: 0.8015 (tpp) cc_final: 0.7758 (tpp) REVERT: B 762 MET cc_start: 0.8988 (tmm) cc_final: 0.8776 (tmm) outliers start: 45 outliers final: 39 residues processed: 148 average time/residue: 0.0759 time to fit residues: 18.5313 Evaluate side-chains 147 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 825 SER Chi-restraints excluded: chain B residue 837 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 0.0870 chunk 23 optimal weight: 0.5980 chunk 81 optimal weight: 0.0870 chunk 48 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 72 optimal weight: 0.5980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.148626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.095165 restraints weight = 19661.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.098713 restraints weight = 10711.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.101021 restraints weight = 7438.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.102471 restraints weight = 5936.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.103449 restraints weight = 5160.802| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11993 Z= 0.095 Angle : 0.544 16.201 16317 Z= 0.256 Chirality : 0.041 0.325 1864 Planarity : 0.004 0.057 2083 Dihedral : 3.833 36.909 1675 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.43 % Allowed : 29.45 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.22), residues: 1504 helix: 1.65 (0.21), residues: 651 sheet: -1.54 (0.38), residues: 182 loop : -1.13 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 654 TYR 0.012 0.001 TYR A 836 PHE 0.021 0.001 PHE B 632 TRP 0.006 0.001 TRP B 303 HIS 0.001 0.000 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00213 (11976) covalent geometry : angle 0.54282 (16283) SS BOND : bond 0.00188 ( 17) SS BOND : angle 0.86357 ( 34) hydrogen bonds : bond 0.03077 ( 498) hydrogen bonds : angle 3.61327 ( 1431) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 0.426 Fit side-chains REVERT: A 117 ILE cc_start: 0.5751 (OUTLIER) cc_final: 0.5461 (tp) REVERT: A 396 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 803 PHE cc_start: 0.8378 (m-80) cc_final: 0.8042 (m-80) REVERT: B 762 MET cc_start: 0.8963 (tmm) cc_final: 0.8753 (tmm) outliers start: 43 outliers final: 39 residues processed: 147 average time/residue: 0.0708 time to fit residues: 17.5343 Evaluate side-chains 145 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 105 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 825 SER Chi-restraints excluded: chain B residue 837 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 51 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.147422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.095146 restraints weight = 19466.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098252 restraints weight = 11755.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099084 restraints weight = 8898.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101244 restraints weight = 7117.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101171 restraints weight = 5740.401| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11993 Z= 0.119 Angle : 0.557 15.720 16317 Z= 0.264 Chirality : 0.041 0.331 1864 Planarity : 0.004 0.057 2083 Dihedral : 3.898 38.512 1675 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.67 % Allowed : 29.61 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.22), residues: 1504 helix: 1.65 (0.21), residues: 648 sheet: -1.59 (0.38), residues: 188 loop : -1.11 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 654 TYR 0.022 0.001 TYR A 836 PHE 0.017 0.001 PHE B 632 TRP 0.006 0.001 TRP B 303 HIS 0.002 0.000 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00279 (11976) covalent geometry : angle 0.55560 (16283) SS BOND : bond 0.00218 ( 17) SS BOND : angle 0.93145 ( 34) hydrogen bonds : bond 0.03369 ( 498) hydrogen bonds : angle 3.66751 ( 1431) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2129.97 seconds wall clock time: 37 minutes 27.45 seconds (2247.45 seconds total)