Starting phenix.real_space_refine on Mon Aug 25 01:05:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh6_44534/08_2025/9bh6_44534.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh6_44534/08_2025/9bh6_44534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bh6_44534/08_2025/9bh6_44534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh6_44534/08_2025/9bh6_44534.map" model { file = "/net/cci-nas-00/data/ceres_data/9bh6_44534/08_2025/9bh6_44534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh6_44534/08_2025/9bh6_44534.cif" } resolution = 3.3 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= 0.005 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 160 5.16 5 C 15592 2.51 5 N 4232 2.21 5 O 4404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24388 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6097 Classifications: {'peptide': 774} Link IDs: {'PTRANS': 23, 'TRANS': 750} Chain breaks: 5 Chain: "B" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6097 Classifications: {'peptide': 774} Link IDs: {'PTRANS': 23, 'TRANS': 750} Chain breaks: 5 Chain: "C" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6097 Classifications: {'peptide': 774} Link IDs: {'PTRANS': 23, 'TRANS': 750} Chain breaks: 5 Chain: "D" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6097 Classifications: {'peptide': 774} Link IDs: {'PTRANS': 23, 'TRANS': 750} Chain breaks: 5 Time building chain proxies: 6.17, per 1000 atoms: 0.25 Number of scatterers: 24388 At special positions: 0 Unit cell: (142.443, 130.781, 139.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 160 16.00 O 4404 8.00 N 4232 7.00 C 15592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5808 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 16 sheets defined 62.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.734A pdb=" N LEU A 106 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 108 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.723A pdb=" N GLY A 120 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 removed outlier: 4.412A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 162 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 191 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.685A pdb=" N GLY A 222 " --> pdb=" O HIS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 247 removed outlier: 3.580A pdb=" N GLU A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.504A pdb=" N VAL A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 removed outlier: 4.367A pdb=" N THR A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 368 Processing helix chain 'A' and resid 383 through 396 removed outlier: 3.654A pdb=" N LEU A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 421 through 434 Processing helix chain 'A' and resid 445 through 450 removed outlier: 4.043A pdb=" N GLY A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 450' Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 528 through 541 Processing helix chain 'A' and resid 546 through 555 Processing helix chain 'A' and resid 557 through 564 Processing helix chain 'A' and resid 578 through 592 removed outlier: 3.612A pdb=" N GLU A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 624 through 640 removed outlier: 3.655A pdb=" N LEU A 629 " --> pdb=" O PRO A 625 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 655 removed outlier: 3.666A pdb=" N LEU A 653 " --> pdb=" O HIS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 676 removed outlier: 4.155A pdb=" N LYS A 675 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 688 removed outlier: 3.951A pdb=" N VAL A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 700 Processing helix chain 'A' and resid 706 through 730 removed outlier: 3.951A pdb=" N HIS A 716 " --> pdb=" O GLN A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 744 through 770 removed outlier: 3.672A pdb=" N GLN A 753 " --> pdb=" O GLN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 779 removed outlier: 3.534A pdb=" N LEU A 777 " --> pdb=" O ASN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 788 Processing helix chain 'A' and resid 792 through 797 removed outlier: 4.480A pdb=" N LEU A 796 " --> pdb=" O GLU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 814 Processing helix chain 'A' and resid 817 through 824 Processing helix chain 'A' and resid 825 through 837 Processing helix chain 'A' and resid 871 through 892 Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.542A pdb=" N GLY B 75 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 93 through 101 Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.810A pdb=" N LEU B 106 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B 108 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.720A pdb=" N GLY B 120 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 136 removed outlier: 4.377A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 191 through 205 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 227 through 247 removed outlier: 3.613A pdb=" N GLU B 231 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 325 through 335 Processing helix chain 'B' and resid 346 through 368 Processing helix chain 'B' and resid 383 through 396 removed outlier: 3.529A pdb=" N LEU B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 3.822A pdb=" N LYS B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 434 Processing helix chain 'B' and resid 444 through 449 removed outlier: 3.936A pdb=" N SER B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 449 " --> pdb=" O THR B 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 444 through 449' Processing helix chain 'B' and resid 470 through 479 Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 528 through 541 Processing helix chain 'B' and resid 546 through 555 Processing helix chain 'B' and resid 557 through 564 Processing helix chain 'B' and resid 578 through 592 removed outlier: 3.682A pdb=" N GLU B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 621 Processing helix chain 'B' and resid 624 through 640 removed outlier: 3.564A pdb=" N LEU B 629 " --> pdb=" O PRO B 625 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 655 removed outlier: 3.566A pdb=" N LEU B 653 " --> pdb=" O HIS B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 674 Processing helix chain 'B' and resid 677 through 688 removed outlier: 4.005A pdb=" N VAL B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 700 removed outlier: 3.569A pdb=" N GLY B 700 " --> pdb=" O ARG B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 730 removed outlier: 3.549A pdb=" N GLN B 712 " --> pdb=" O ARG B 708 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS B 716 " --> pdb=" O GLN B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 744 through 770 removed outlier: 3.652A pdb=" N GLN B 753 " --> pdb=" O GLN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 780 removed outlier: 3.579A pdb=" N LEU B 777 " --> pdb=" O ASN B 773 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN B 780 " --> pdb=" O LEU B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 788 Processing helix chain 'B' and resid 790 through 799 removed outlier: 4.318A pdb=" N ASP B 795 " --> pdb=" O GLU B 792 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL B 797 " --> pdb=" O CYS B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 814 Processing helix chain 'B' and resid 817 through 824 removed outlier: 3.535A pdb=" N ARG B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 837 Processing helix chain 'B' and resid 871 through 892 Processing helix chain 'C' and resid 77 through 87 Processing helix chain 'C' and resid 93 through 101 Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.592A pdb=" N GLY C 120 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 134 removed outlier: 4.378A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 162 Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing helix chain 'C' and resid 180 through 184 Processing helix chain 'C' and resid 191 through 205 removed outlier: 3.784A pdb=" N GLY C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.739A pdb=" N GLY C 222 " --> pdb=" O HIS C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 247 removed outlier: 3.547A pdb=" N GLU C 231 " --> pdb=" O GLY C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 325 through 335 removed outlier: 4.313A pdb=" N THR C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 368 Processing helix chain 'C' and resid 383 through 397 removed outlier: 3.517A pdb=" N GLU C 389 " --> pdb=" O LYS C 385 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 397 " --> pdb=" O GLN C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 421 through 434 Processing helix chain 'C' and resid 444 through 449 removed outlier: 4.155A pdb=" N SER C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY C 449 " --> pdb=" O THR C 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 444 through 449' Processing helix chain 'C' and resid 470 through 479 Processing helix chain 'C' and resid 497 through 499 No H-bonds generated for 'chain 'C' and resid 497 through 499' Processing helix chain 'C' and resid 500 through 510 Processing helix chain 'C' and resid 528 through 541 removed outlier: 3.506A pdb=" N GLY C 541 " --> pdb=" O GLU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 555 Processing helix chain 'C' and resid 557 through 564 Processing helix chain 'C' and resid 578 through 592 removed outlier: 3.661A pdb=" N GLU C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN C 592 " --> pdb=" O TRP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 622 Processing helix chain 'C' and resid 624 through 640 removed outlier: 3.841A pdb=" N LEU C 629 " --> pdb=" O PRO C 625 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASP C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 655 removed outlier: 3.555A pdb=" N LEU C 653 " --> pdb=" O HIS C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 676 removed outlier: 3.680A pdb=" N LYS C 675 " --> pdb=" O CYS C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 688 removed outlier: 3.787A pdb=" N VAL C 683 " --> pdb=" O SER C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 700 removed outlier: 3.555A pdb=" N GLY C 700 " --> pdb=" O ARG C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 730 removed outlier: 3.599A pdb=" N GLN C 712 " --> pdb=" O ARG C 708 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS C 716 " --> pdb=" O GLN C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 Processing helix chain 'C' and resid 744 through 770 Processing helix chain 'C' and resid 771 through 788 removed outlier: 3.666A pdb=" N LEU C 777 " --> pdb=" O ASN C 773 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN C 780 " --> pdb=" O LEU C 776 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN C 782 " --> pdb=" O LEU C 778 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS C 783 " --> pdb=" O SER C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 797 removed outlier: 4.654A pdb=" N LEU C 796 " --> pdb=" O GLU C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 814 Processing helix chain 'C' and resid 817 through 824 Processing helix chain 'C' and resid 825 through 837 Processing helix chain 'C' and resid 871 through 892 Processing helix chain 'D' and resid 77 through 87 Processing helix chain 'D' and resid 93 through 101 Processing helix chain 'D' and resid 102 through 108 removed outlier: 3.791A pdb=" N LEU D 106 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.852A pdb=" N GLY D 120 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 136 removed outlier: 4.430A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 162 Processing helix chain 'D' and resid 180 through 184 Processing helix chain 'D' and resid 191 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 217 through 222 removed outlier: 3.707A pdb=" N GLY D 222 " --> pdb=" O HIS D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 247 removed outlier: 3.504A pdb=" N GLU D 231 " --> pdb=" O GLY D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 278 Processing helix chain 'D' and resid 325 through 335 removed outlier: 4.163A pdb=" N THR D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 368 Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 402 through 409 removed outlier: 4.050A pdb=" N LYS D 407 " --> pdb=" O SER D 403 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 434 Processing helix chain 'D' and resid 444 through 450 removed outlier: 4.207A pdb=" N SER D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 479 Processing helix chain 'D' and resid 500 through 510 Processing helix chain 'D' and resid 528 through 541 Processing helix chain 'D' and resid 546 through 555 Processing helix chain 'D' and resid 557 through 564 Processing helix chain 'D' and resid 578 through 592 removed outlier: 3.797A pdb=" N GLU D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 622 removed outlier: 3.512A pdb=" N THR D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 640 removed outlier: 3.518A pdb=" N LEU D 629 " --> pdb=" O PRO D 625 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP D 630 " --> pdb=" O ALA D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 655 Processing helix chain 'D' and resid 665 through 676 removed outlier: 3.831A pdb=" N LYS D 675 " --> pdb=" O CYS D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 677 through 688 removed outlier: 3.754A pdb=" N VAL D 683 " --> pdb=" O SER D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 700 Processing helix chain 'D' and resid 706 through 729 removed outlier: 4.083A pdb=" N HIS D 716 " --> pdb=" O GLN D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 744 through 770 Processing helix chain 'D' and resid 771 through 780 removed outlier: 3.805A pdb=" N LEU D 777 " --> pdb=" O ASN D 773 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN D 780 " --> pdb=" O LEU D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 788 Processing helix chain 'D' and resid 792 through 797 removed outlier: 4.536A pdb=" N LEU D 796 " --> pdb=" O GLU D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 814 Processing helix chain 'D' and resid 817 through 824 Processing helix chain 'D' and resid 825 through 837 Processing helix chain 'D' and resid 871 through 892 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 removed outlier: 6.971A pdb=" N ASP A 169 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N THR A 190 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TYR A 171 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA A 140 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N CYS A 189 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE A 142 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LYS A 139 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A 111 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N SER A 265 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TYR A 113 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 309 through 312 removed outlier: 6.554A pdb=" N LEU A 309 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASP A 304 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A 457 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE A 495 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 459 " --> pdb=" O ILE A 495 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AA4, first strand: chain 'A' and resid 595 through 598 Processing sheet with id=AA5, first strand: chain 'B' and resid 168 through 171 removed outlier: 7.029A pdb=" N ASP B 169 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N THR B 190 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR B 171 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA B 140 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N CYS B 189 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE B 142 " --> pdb=" O CYS B 189 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS B 139 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL B 213 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU B 141 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL B 215 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B 143 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 309 through 312 removed outlier: 6.338A pdb=" N VAL B 457 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE B 495 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE B 459 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU B 341 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 463 through 464 Processing sheet with id=AA8, first strand: chain 'B' and resid 595 through 598 Processing sheet with id=AA9, first strand: chain 'C' and resid 168 through 171 removed outlier: 6.996A pdb=" N ASP C 169 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N THR C 190 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR C 171 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA C 140 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N CYS C 189 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE C 142 " --> pdb=" O CYS C 189 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS C 139 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL C 213 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C 141 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL C 215 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 143 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU C 111 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N SER C 265 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR C 113 " --> pdb=" O SER C 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 309 through 312 removed outlier: 6.308A pdb=" N VAL C 457 " --> pdb=" O ILE C 493 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE C 495 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE C 459 " --> pdb=" O ILE C 495 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU C 341 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 463 through 464 Processing sheet with id=AB3, first strand: chain 'C' and resid 595 through 598 Processing sheet with id=AB4, first strand: chain 'D' and resid 168 through 171 removed outlier: 3.577A pdb=" N VAL D 188 " --> pdb=" O ASP D 169 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 190 " --> pdb=" O TYR D 171 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA D 140 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N CYS D 189 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PHE D 142 " --> pdb=" O CYS D 189 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LYS D 139 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU D 111 " --> pdb=" O GLY D 263 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N SER D 265 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR D 113 " --> pdb=" O SER D 265 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 309 through 312 removed outlier: 6.509A pdb=" N LEU D 309 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ASP D 304 " --> pdb=" O LEU D 309 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL D 457 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE D 495 " --> pdb=" O VAL D 457 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE D 459 " --> pdb=" O ILE D 495 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 463 through 464 Processing sheet with id=AB7, first strand: chain 'D' and resid 595 through 598 1357 hydrogen bonds defined for protein. 3915 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: 5.14 Time building geometry restraints manager: 2.80 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: 7962 1.34 - 1.46: 4149 1.46 - 1.58: 12445 1.58 - 1.69: 0 1.69 - 1.81: 252 Bond restraints: 24808 Sorted by residual: bond pdb=" CB VAL A 340 " pdb=" CG2 VAL A 340 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.13e-01 bond pdb=" C VAL D 409 " pdb=" N PRO D 410 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.94e-01 bond pdb=" CB VAL C 340 " pdb=" CG2 VAL C 340 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.53e-01 bond pdb=" CG GLU D 593 " pdb=" CD GLU D 593 " ideal model delta sigma weight residual 1.516 1.494 0.022 2.50e-02 1.60e+03 7.65e-01 bond pdb=" CB CYS B 496 " pdb=" SG CYS B 496 " ideal model delta sigma weight residual 1.808 1.779 0.029 3.30e-02 9.18e+02 7.55e-01 ... (remaining 24803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 32405 1.46 - 2.91: 967 2.91 - 4.37: 101 4.37 - 5.83: 20 5.83 - 7.28: 11 Bond angle restraints: 33504 Sorted by residual: angle pdb=" N VAL B 409 " pdb=" CA VAL B 409 " pdb=" C VAL B 409 " ideal model delta sigma weight residual 108.88 115.76 -6.88 2.16e+00 2.14e-01 1.01e+01 angle pdb=" N VAL A 409 " pdb=" CA VAL A 409 " pdb=" C VAL A 409 " ideal model delta sigma weight residual 108.88 115.04 -6.16 2.16e+00 2.14e-01 8.14e+00 angle pdb=" N VAL D 409 " pdb=" CA VAL D 409 " pdb=" C VAL D 409 " ideal model delta sigma weight residual 108.88 115.03 -6.15 2.16e+00 2.14e-01 8.10e+00 angle pdb=" N PHE D 781 " pdb=" CA PHE D 781 " pdb=" C PHE D 781 " ideal model delta sigma weight residual 112.54 115.81 -3.27 1.22e+00 6.72e-01 7.18e+00 angle pdb=" N PHE C 781 " pdb=" CA PHE C 781 " pdb=" C PHE C 781 " ideal model delta sigma weight residual 111.82 114.86 -3.04 1.16e+00 7.43e-01 6.85e+00 ... (remaining 33499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 14053 18.00 - 35.99: 790 35.99 - 53.98: 139 53.98 - 71.98: 52 71.98 - 89.97: 14 Dihedral angle restraints: 15048 sinusoidal: 6092 harmonic: 8956 Sorted by residual: dihedral pdb=" CA GLU A 593 " pdb=" C GLU A 593 " pdb=" N PHE A 594 " pdb=" CA PHE A 594 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA GLU B 593 " pdb=" C GLU B 593 " pdb=" N PHE B 594 " pdb=" CA PHE B 594 " ideal model delta harmonic sigma weight residual 180.00 150.51 29.49 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA GLU D 593 " pdb=" C GLU D 593 " pdb=" N PHE D 594 " pdb=" CA PHE D 594 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 15045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2647 0.039 - 0.078: 960 0.078 - 0.117: 255 0.117 - 0.157: 43 0.157 - 0.196: 3 Chirality restraints: 3908 Sorted by residual: chirality pdb=" CA PHE D 781 " pdb=" N PHE D 781 " pdb=" C PHE D 781 " pdb=" CB PHE D 781 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CA PHE B 781 " pdb=" N PHE B 781 " pdb=" C PHE B 781 " pdb=" CB PHE B 781 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA PHE A 781 " pdb=" N PHE A 781 " pdb=" C PHE A 781 " pdb=" CB PHE A 781 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 3905 not shown) Planarity restraints: 4204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 758 " -0.010 2.00e-02 2.50e+03 1.75e-02 6.12e+00 pdb=" CG TYR B 758 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR B 758 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 758 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR B 758 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 758 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR B 758 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR B 758 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 455 " -0.175 9.50e-02 1.11e+02 7.87e-02 4.51e+00 pdb=" NE ARG C 455 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 455 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 455 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 455 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 745 " -0.160 9.50e-02 1.11e+02 7.23e-02 4.43e+00 pdb=" NE ARG D 745 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 745 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG D 745 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG D 745 " 0.001 2.00e-02 2.50e+03 ... (remaining 4201 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6404 2.82 - 3.34: 23892 3.34 - 3.86: 38322 3.86 - 4.38: 47200 4.38 - 4.90: 80849 Nonbonded interactions: 196667 Sorted by model distance: nonbonded pdb=" OH TYR D 113 " pdb=" O LYS D 121 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR C 113 " pdb=" O LYS C 121 " model vdw 2.354 3.040 nonbonded pdb=" OH TYR A 113 " pdb=" O LYS A 121 " model vdw 2.355 3.040 nonbonded pdb=" OE1 GLU A 332 " pdb=" NH2 ARG A 456 " model vdw 2.404 3.120 nonbonded pdb=" O GLY D 615 " pdb=" OG1 THR D 618 " model vdw 2.404 3.040 ... (remaining 196662 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 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: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.900 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24808 Z= 0.128 Angle : 0.608 7.284 33504 Z= 0.364 Chirality : 0.043 0.196 3908 Planarity : 0.008 0.079 4204 Dihedral : 12.638 89.974 9240 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 0.49 % Favored : 99.38 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.13), residues: 3048 helix: -1.46 (0.10), residues: 1764 sheet: 0.60 (0.30), residues: 240 loop : -0.15 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG D 745 TYR 0.025 0.004 TYR B 758 PHE 0.025 0.002 PHE A 787 TRP 0.026 0.002 TRP C 588 HIS 0.005 0.001 HIS D 710 Details of bonding type rmsd covalent geometry : bond 0.00281 (24808) covalent geometry : angle 0.60811 (33504) hydrogen bonds : bond 0.19638 ( 1357) hydrogen bonds : angle 7.48967 ( 3915) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 608 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8751 (t) cc_final: 0.8546 (t) REVERT: A 122 THR cc_start: 0.8800 (p) cc_final: 0.8266 (p) REVERT: A 336 ASP cc_start: 0.8151 (m-30) cc_final: 0.7868 (m-30) REVERT: A 859 MET cc_start: 0.6222 (mmt) cc_final: 0.6002 (mmt) REVERT: B 336 ASP cc_start: 0.8152 (m-30) cc_final: 0.7795 (p0) REVERT: B 426 ASP cc_start: 0.8287 (t0) cc_final: 0.8068 (t0) REVERT: B 470 ASP cc_start: 0.7528 (m-30) cc_final: 0.7326 (m-30) REVERT: B 637 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7835 (ttt-90) REVERT: B 817 THR cc_start: 0.8373 (p) cc_final: 0.8058 (m) REVERT: C 69 LEU cc_start: 0.8080 (mt) cc_final: 0.7813 (mp) REVERT: C 122 THR cc_start: 0.8856 (p) cc_final: 0.8118 (p) REVERT: C 153 LYS cc_start: 0.8669 (tptt) cc_final: 0.8455 (tppt) REVERT: C 212 MET cc_start: 0.8913 (ttm) cc_final: 0.8549 (ttp) REVERT: C 217 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7678 (mm-30) REVERT: C 713 MET cc_start: 0.8844 (tpp) cc_final: 0.8641 (tpt) REVERT: C 727 ASP cc_start: 0.8080 (m-30) cc_final: 0.7846 (m-30) REVERT: C 882 GLU cc_start: 0.7580 (tt0) cc_final: 0.7271 (tt0) REVERT: D 122 THR cc_start: 0.8949 (p) cc_final: 0.8375 (p) REVERT: D 131 LYS cc_start: 0.8266 (tptt) cc_final: 0.8021 (mmtt) REVERT: D 307 MET cc_start: 0.6880 (mmm) cc_final: 0.6495 (mmt) REVERT: D 336 ASP cc_start: 0.8113 (m-30) cc_final: 0.7876 (m-30) REVERT: D 470 ASP cc_start: 0.7388 (m-30) cc_final: 0.7172 (m-30) REVERT: D 495 ILE cc_start: 0.7953 (mt) cc_final: 0.7733 (mm) outliers start: 0 outliers final: 0 residues processed: 608 average time/residue: 0.2156 time to fit residues: 192.0596 Evaluate side-chains 388 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 180 HIS A 219 HIS A 366 HIS A 835 ASN A 888 GLN B 366 HIS B 416 HIS B 835 ASN B 888 GLN C 73 ASN C 180 HIS ** C 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 ASN ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 835 ASN D 73 ASN D 520 GLN D 592 ASN D 716 HIS D 753 GLN D 835 ASN D 888 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.134758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.114120 restraints weight = 39157.884| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.08 r_work: 0.3349 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24808 Z= 0.144 Angle : 0.584 10.203 33504 Z= 0.307 Chirality : 0.041 0.141 3908 Planarity : 0.004 0.038 4204 Dihedral : 5.158 30.283 3332 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.12 % Allowed : 6.05 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.14), residues: 3048 helix: 0.37 (0.11), residues: 1796 sheet: 0.47 (0.29), residues: 248 loop : 0.35 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 483 TYR 0.014 0.001 TYR B 113 PHE 0.016 0.002 PHE A 787 TRP 0.017 0.001 TRP C 588 HIS 0.012 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00319 (24808) covalent geometry : angle 0.58402 (33504) hydrogen bonds : bond 0.04856 ( 1357) hydrogen bonds : angle 4.81203 ( 3915) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 425 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 ILE cc_start: 0.8948 (mm) cc_final: 0.8745 (mt) REVERT: A 587 MET cc_start: 0.7593 (mmm) cc_final: 0.7359 (mmm) REVERT: A 859 MET cc_start: 0.6336 (mmt) cc_final: 0.5896 (mmt) REVERT: B 152 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8194 (tm-30) REVERT: B 307 MET cc_start: 0.6192 (mmm) cc_final: 0.5968 (tpp) REVERT: B 470 ASP cc_start: 0.7939 (m-30) cc_final: 0.7722 (m-30) REVERT: B 637 ARG cc_start: 0.8314 (ttp80) cc_final: 0.8039 (ttt-90) REVERT: B 860 ARG cc_start: 0.7395 (mtt90) cc_final: 0.7119 (mtm-85) REVERT: C 212 MET cc_start: 0.8837 (ttm) cc_final: 0.8568 (ttt) REVERT: C 225 HIS cc_start: 0.7208 (p-80) cc_final: 0.6938 (p-80) REVERT: D 113 TYR cc_start: 0.9112 (p90) cc_final: 0.8842 (p90) REVERT: D 122 THR cc_start: 0.8855 (p) cc_final: 0.8310 (p) REVERT: D 126 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7321 (mp0) REVERT: D 131 LYS cc_start: 0.8710 (tptt) cc_final: 0.7742 (mmtt) REVERT: D 303 TYR cc_start: 0.6756 (m-80) cc_final: 0.6513 (m-10) REVERT: D 307 MET cc_start: 0.7165 (mmm) cc_final: 0.6778 (mmt) REVERT: D 495 ILE cc_start: 0.7708 (mt) cc_final: 0.7463 (mm) REVERT: D 860 ARG cc_start: 0.7434 (mtt90) cc_final: 0.7154 (mtm-85) REVERT: D 867 ARG cc_start: 0.8118 (mtt90) cc_final: 0.7818 (mtt-85) outliers start: 30 outliers final: 20 residues processed: 438 average time/residue: 0.1980 time to fit residues: 129.6265 Evaluate side-chains 376 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 356 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 859 MET Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain D residue 513 LYS Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 680 MET Chi-restraints excluded: chain D residue 691 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 80 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 chunk 22 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 HIS B 520 GLN C 520 GLN ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.133546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113383 restraints weight = 39238.393| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.05 r_work: 0.3332 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24808 Z= 0.160 Angle : 0.550 8.837 33504 Z= 0.284 Chirality : 0.041 0.230 3908 Planarity : 0.004 0.036 4204 Dihedral : 4.754 30.710 3332 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.42 % Allowed : 7.74 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.15), residues: 3048 helix: 0.91 (0.12), residues: 1784 sheet: 0.43 (0.29), residues: 248 loop : 0.30 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 483 TYR 0.015 0.001 TYR D 171 PHE 0.017 0.002 PHE A 594 TRP 0.015 0.002 TRP C 588 HIS 0.006 0.001 HIS D 366 Details of bonding type rmsd covalent geometry : bond 0.00380 (24808) covalent geometry : angle 0.55040 (33504) hydrogen bonds : bond 0.04420 ( 1357) hydrogen bonds : angle 4.46003 ( 3915) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 391 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7495 (mt) REVERT: A 113 TYR cc_start: 0.8954 (p90) cc_final: 0.8648 (p90) REVERT: A 200 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8432 (ttp80) REVERT: A 205 ASN cc_start: 0.8467 (t0) cc_final: 0.7964 (t0) REVERT: A 216 ASP cc_start: 0.7923 (t0) cc_final: 0.7619 (t0) REVERT: A 217 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8340 (mm-30) REVERT: A 488 THR cc_start: 0.8186 (m) cc_final: 0.7922 (p) REVERT: A 859 MET cc_start: 0.6373 (mmt) cc_final: 0.6057 (mmt) REVERT: B 153 LYS cc_start: 0.8976 (tppt) cc_final: 0.8440 (tptp) REVERT: B 205 ASN cc_start: 0.8475 (t0) cc_final: 0.8152 (t0) REVERT: B 216 ASP cc_start: 0.7839 (t0) cc_final: 0.7491 (t0) REVERT: B 217 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8234 (mm-30) REVERT: B 660 ASP cc_start: 0.8224 (t0) cc_final: 0.7972 (t70) REVERT: B 860 ARG cc_start: 0.7415 (mtt90) cc_final: 0.7179 (mtm-85) REVERT: C 100 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8281 (mp) REVERT: C 113 TYR cc_start: 0.9017 (p90) cc_final: 0.8815 (p90) REVERT: C 212 MET cc_start: 0.8946 (ttm) cc_final: 0.8731 (ttt) REVERT: C 216 ASP cc_start: 0.7874 (t0) cc_final: 0.7646 (t0) REVERT: C 587 MET cc_start: 0.7412 (mmm) cc_final: 0.7172 (mmm) REVERT: C 612 THR cc_start: 0.6958 (OUTLIER) cc_final: 0.5948 (p) REVERT: C 727 ASP cc_start: 0.8427 (m-30) cc_final: 0.8178 (m-30) REVERT: D 126 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7416 (mp0) REVERT: D 131 LYS cc_start: 0.8716 (tptt) cc_final: 0.7792 (mmtt) REVERT: D 205 ASN cc_start: 0.8532 (t0) cc_final: 0.8117 (t0) REVERT: D 264 MET cc_start: 0.8558 (mtm) cc_final: 0.8261 (mtm) REVERT: D 307 MET cc_start: 0.7270 (mmm) cc_final: 0.6917 (mmt) REVERT: D 520 GLN cc_start: 0.7426 (mm-40) cc_final: 0.6838 (pp30) REVERT: D 860 ARG cc_start: 0.7402 (mtt90) cc_final: 0.7179 (mtm-85) outliers start: 38 outliers final: 23 residues processed: 413 average time/residue: 0.1685 time to fit residues: 106.1432 Evaluate side-chains 377 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 351 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 513 LYS Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 680 MET Chi-restraints excluded: chain D residue 691 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 206 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 277 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 242 optimal weight: 0.3980 chunk 75 optimal weight: 6.9990 chunk 235 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 268 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 520 GLN C 520 GLN C 551 HIS ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.134099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.114099 restraints weight = 39289.118| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.03 r_work: 0.3350 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24808 Z= 0.156 Angle : 0.531 7.952 33504 Z= 0.273 Chirality : 0.040 0.224 3908 Planarity : 0.004 0.036 4204 Dihedral : 4.562 30.314 3332 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.83 % Allowed : 8.63 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.15), residues: 3048 helix: 1.08 (0.12), residues: 1796 sheet: 0.41 (0.30), residues: 248 loop : 0.22 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 516 TYR 0.014 0.001 TYR D 171 PHE 0.016 0.002 PHE D 781 TRP 0.017 0.002 TRP C 588 HIS 0.006 0.001 HIS D 366 Details of bonding type rmsd covalent geometry : bond 0.00374 (24808) covalent geometry : angle 0.53147 (33504) hydrogen bonds : bond 0.04108 ( 1357) hydrogen bonds : angle 4.33596 ( 3915) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 359 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.9175 (mp) cc_final: 0.8959 (mt) REVERT: A 200 ARG cc_start: 0.8735 (ttp80) cc_final: 0.8510 (ttp80) REVERT: A 205 ASN cc_start: 0.8457 (t0) cc_final: 0.7966 (t0) REVERT: A 216 ASP cc_start: 0.7920 (t0) cc_final: 0.7715 (t0) REVERT: A 389 GLU cc_start: 0.8490 (tt0) cc_final: 0.8135 (tt0) REVERT: A 859 MET cc_start: 0.6444 (mmt) cc_final: 0.6163 (mmp) REVERT: B 205 ASN cc_start: 0.8451 (t0) cc_final: 0.8127 (t0) REVERT: B 216 ASP cc_start: 0.7804 (t0) cc_final: 0.7461 (t0) REVERT: B 217 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8186 (mm-30) REVERT: B 660 ASP cc_start: 0.8246 (t0) cc_final: 0.8003 (t70) REVERT: B 860 ARG cc_start: 0.7503 (mtt90) cc_final: 0.7245 (mtm-85) REVERT: C 113 TYR cc_start: 0.9054 (p90) cc_final: 0.8826 (p90) REVERT: C 212 MET cc_start: 0.8884 (ttm) cc_final: 0.8636 (ttt) REVERT: C 216 ASP cc_start: 0.7908 (t0) cc_final: 0.7678 (t0) REVERT: C 612 THR cc_start: 0.6747 (OUTLIER) cc_final: 0.5652 (p) REVERT: C 727 ASP cc_start: 0.8369 (m-30) cc_final: 0.8127 (m-30) REVERT: C 882 GLU cc_start: 0.8010 (tt0) cc_final: 0.7784 (tt0) REVERT: D 131 LYS cc_start: 0.8678 (tptt) cc_final: 0.7806 (mmtt) REVERT: D 205 ASN cc_start: 0.8627 (t0) cc_final: 0.8243 (t0) REVERT: D 264 MET cc_start: 0.8502 (mtm) cc_final: 0.8198 (mtm) REVERT: D 307 MET cc_start: 0.7307 (mmm) cc_final: 0.6985 (mmt) REVERT: D 860 ARG cc_start: 0.7482 (mtt90) cc_final: 0.7224 (mtm-85) outliers start: 49 outliers final: 26 residues processed: 385 average time/residue: 0.1793 time to fit residues: 106.7473 Evaluate side-chains 371 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 344 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 424 GLU Chi-restraints excluded: chain D residue 513 LYS Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 691 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 179 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 293 optimal weight: 0.8980 chunk 242 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 255 optimal weight: 8.9990 chunk 269 optimal weight: 1.9990 chunk 234 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 520 GLN C 520 GLN ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.135908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.115891 restraints weight = 38950.261| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.97 r_work: 0.3387 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24808 Z= 0.117 Angle : 0.501 8.679 33504 Z= 0.256 Chirality : 0.039 0.174 3908 Planarity : 0.003 0.034 4204 Dihedral : 4.334 28.369 3332 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.64 % Allowed : 10.16 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.15), residues: 3048 helix: 1.30 (0.12), residues: 1804 sheet: 0.47 (0.30), residues: 248 loop : 0.15 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 516 TYR 0.012 0.001 TYR D 171 PHE 0.014 0.001 PHE D 765 TRP 0.017 0.001 TRP C 588 HIS 0.006 0.001 HIS D 366 Details of bonding type rmsd covalent geometry : bond 0.00270 (24808) covalent geometry : angle 0.50075 (33504) hydrogen bonds : bond 0.03665 ( 1357) hydrogen bonds : angle 4.14593 ( 3915) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 397 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8985 (p90) cc_final: 0.8618 (p90) REVERT: A 126 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7288 (mp0) REVERT: A 141 LEU cc_start: 0.9136 (mp) cc_final: 0.8932 (mt) REVERT: A 200 ARG cc_start: 0.8747 (ttp80) cc_final: 0.8518 (ttp80) REVERT: A 205 ASN cc_start: 0.8417 (t0) cc_final: 0.7874 (t0) REVERT: A 216 ASP cc_start: 0.7895 (t0) cc_final: 0.7672 (t0) REVERT: A 859 MET cc_start: 0.6696 (mmt) cc_final: 0.6429 (mmp) REVERT: B 114 SER cc_start: 0.9301 (p) cc_final: 0.8996 (t) REVERT: B 126 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7428 (mp0) REVERT: B 153 LYS cc_start: 0.9032 (tppt) cc_final: 0.8672 (tptp) REVERT: B 205 ASN cc_start: 0.8489 (t0) cc_final: 0.8157 (t0) REVERT: B 216 ASP cc_start: 0.7817 (t0) cc_final: 0.7502 (t0) REVERT: B 660 ASP cc_start: 0.8244 (t0) cc_final: 0.7988 (t70) REVERT: B 860 ARG cc_start: 0.7459 (mtt90) cc_final: 0.7201 (mtm-85) REVERT: C 113 TYR cc_start: 0.9046 (p90) cc_final: 0.8830 (p90) REVERT: C 126 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7354 (mp0) REVERT: C 212 MET cc_start: 0.8894 (ttm) cc_final: 0.8668 (ttt) REVERT: C 216 ASP cc_start: 0.7906 (t0) cc_final: 0.7645 (t0) REVERT: C 511 SER cc_start: 0.7981 (t) cc_final: 0.7637 (p) REVERT: C 587 MET cc_start: 0.7491 (mmm) cc_final: 0.7249 (mmm) REVERT: C 612 THR cc_start: 0.6562 (OUTLIER) cc_final: 0.5369 (p) REVERT: C 860 ARG cc_start: 0.7554 (mtt90) cc_final: 0.7118 (mtm-85) REVERT: D 126 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7491 (mp0) REVERT: D 130 LEU cc_start: 0.8465 (tp) cc_final: 0.8239 (tp) REVERT: D 131 LYS cc_start: 0.8585 (tptt) cc_final: 0.7727 (mmtt) REVERT: D 205 ASN cc_start: 0.8695 (t0) cc_final: 0.8320 (t0) REVERT: D 264 MET cc_start: 0.8443 (mtm) cc_final: 0.8140 (mtm) REVERT: D 307 MET cc_start: 0.7231 (mmm) cc_final: 0.6909 (mmt) REVERT: D 314 GLU cc_start: 0.8623 (mp0) cc_final: 0.8423 (mp0) REVERT: D 511 SER cc_start: 0.7741 (t) cc_final: 0.7385 (p) REVERT: D 587 MET cc_start: 0.7449 (mmm) cc_final: 0.7182 (mmm) REVERT: D 860 ARG cc_start: 0.7500 (mtt90) cc_final: 0.7225 (mtm-85) outliers start: 44 outliers final: 30 residues processed: 425 average time/residue: 0.1929 time to fit residues: 125.6272 Evaluate side-chains 392 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 361 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 513 LYS Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 691 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 93 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 56 optimal weight: 0.0870 chunk 156 optimal weight: 8.9990 chunk 204 optimal weight: 1.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 520 GLN C 325 HIS ** C 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 GLN C 592 ASN ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.133739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114324 restraints weight = 38990.392| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.96 r_work: 0.3346 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24808 Z= 0.188 Angle : 0.547 8.524 33504 Z= 0.276 Chirality : 0.041 0.160 3908 Planarity : 0.004 0.037 4204 Dihedral : 4.375 30.714 3332 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.94 % Allowed : 10.54 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.15), residues: 3048 helix: 1.26 (0.12), residues: 1800 sheet: 0.38 (0.30), residues: 248 loop : 0.01 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 521 TYR 0.014 0.001 TYR D 171 PHE 0.018 0.002 PHE D 781 TRP 0.019 0.002 TRP D 588 HIS 0.005 0.001 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.00454 (24808) covalent geometry : angle 0.54704 (33504) hydrogen bonds : bond 0.04046 ( 1357) hydrogen bonds : angle 4.22192 ( 3915) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 363 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8976 (p90) cc_final: 0.8574 (p90) REVERT: A 200 ARG cc_start: 0.8766 (ttp80) cc_final: 0.8545 (ttp80) REVERT: A 205 ASN cc_start: 0.8449 (t0) cc_final: 0.7919 (t0) REVERT: A 216 ASP cc_start: 0.7896 (t0) cc_final: 0.7657 (t0) REVERT: A 614 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.6005 (tp) REVERT: A 859 MET cc_start: 0.6559 (mmt) cc_final: 0.6282 (mmp) REVERT: B 126 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7433 (mp0) REVERT: B 153 LYS cc_start: 0.9062 (tppt) cc_final: 0.8712 (tptp) REVERT: B 205 ASN cc_start: 0.8492 (t0) cc_final: 0.8164 (t0) REVERT: B 216 ASP cc_start: 0.7830 (t0) cc_final: 0.7519 (t0) REVERT: B 520 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.6132 (pp30) REVERT: B 860 ARG cc_start: 0.7512 (mtt90) cc_final: 0.7278 (mtm-85) REVERT: C 205 ASN cc_start: 0.8548 (t0) cc_final: 0.8225 (t0) REVERT: C 212 MET cc_start: 0.8844 (ttm) cc_final: 0.8594 (ttt) REVERT: C 216 ASP cc_start: 0.7875 (t0) cc_final: 0.7596 (t0) REVERT: C 314 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: C 511 SER cc_start: 0.8025 (t) cc_final: 0.7703 (p) REVERT: C 587 MET cc_start: 0.7582 (mmm) cc_final: 0.7376 (mmm) REVERT: C 612 THR cc_start: 0.6525 (OUTLIER) cc_final: 0.5306 (p) REVERT: C 860 ARG cc_start: 0.7611 (mtt90) cc_final: 0.7216 (mtm-85) REVERT: D 131 LYS cc_start: 0.8601 (tptt) cc_final: 0.7767 (mmtt) REVERT: D 205 ASN cc_start: 0.8695 (t0) cc_final: 0.8298 (t0) REVERT: D 307 MET cc_start: 0.7274 (mmm) cc_final: 0.6898 (mmt) REVERT: D 511 SER cc_start: 0.7772 (t) cc_final: 0.7411 (p) REVERT: D 860 ARG cc_start: 0.7489 (mtt90) cc_final: 0.7276 (mtm-85) outliers start: 52 outliers final: 34 residues processed: 398 average time/residue: 0.1833 time to fit residues: 113.0303 Evaluate side-chains 383 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 345 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 657 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 513 LYS Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 691 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 139 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 306 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 520 GLN ** C 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.134529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115180 restraints weight = 38916.098| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.96 r_work: 0.3362 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24808 Z= 0.140 Angle : 0.522 9.471 33504 Z= 0.264 Chirality : 0.040 0.281 3908 Planarity : 0.004 0.038 4204 Dihedral : 4.295 29.656 3332 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.91 % Allowed : 10.87 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.15), residues: 3048 helix: 1.34 (0.12), residues: 1800 sheet: 0.39 (0.30), residues: 248 loop : -0.04 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 521 TYR 0.012 0.001 TYR D 171 PHE 0.014 0.001 PHE D 781 TRP 0.018 0.001 TRP C 588 HIS 0.005 0.001 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.00333 (24808) covalent geometry : angle 0.52211 (33504) hydrogen bonds : bond 0.03789 ( 1357) hydrogen bonds : angle 4.16892 ( 3915) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 373 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8958 (p90) cc_final: 0.8571 (p90) REVERT: A 126 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7213 (mp0) REVERT: A 200 ARG cc_start: 0.8770 (ttp80) cc_final: 0.8543 (ttp80) REVERT: A 205 ASN cc_start: 0.8434 (t0) cc_final: 0.7875 (t0) REVERT: A 216 ASP cc_start: 0.7907 (t0) cc_final: 0.7663 (t0) REVERT: A 366 HIS cc_start: 0.5389 (OUTLIER) cc_final: 0.4358 (p-80) REVERT: B 153 LYS cc_start: 0.9059 (tppt) cc_final: 0.8710 (tptp) REVERT: B 205 ASN cc_start: 0.8473 (t0) cc_final: 0.8144 (t0) REVERT: B 216 ASP cc_start: 0.7828 (t0) cc_final: 0.7516 (t0) REVERT: B 860 ARG cc_start: 0.7526 (mtt90) cc_final: 0.7299 (mtm-85) REVERT: C 126 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: C 205 ASN cc_start: 0.8517 (t0) cc_final: 0.8227 (t0) REVERT: C 212 MET cc_start: 0.8818 (ttm) cc_final: 0.8570 (ttt) REVERT: C 216 ASP cc_start: 0.7862 (t0) cc_final: 0.7560 (t0) REVERT: C 314 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: C 511 SER cc_start: 0.8078 (t) cc_final: 0.7724 (p) REVERT: C 612 THR cc_start: 0.6485 (OUTLIER) cc_final: 0.5265 (p) REVERT: C 860 ARG cc_start: 0.7636 (mtt90) cc_final: 0.7232 (mtm-85) REVERT: D 126 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7584 (mp0) REVERT: D 131 LYS cc_start: 0.8565 (tptt) cc_final: 0.7743 (mmtt) REVERT: D 205 ASN cc_start: 0.8684 (t0) cc_final: 0.8294 (t0) REVERT: D 264 MET cc_start: 0.8509 (mtm) cc_final: 0.8209 (mtm) REVERT: D 307 MET cc_start: 0.7308 (mmm) cc_final: 0.6934 (mmt) REVERT: D 511 SER cc_start: 0.7755 (t) cc_final: 0.7417 (p) REVERT: D 587 MET cc_start: 0.7459 (mmm) cc_final: 0.7140 (mmm) outliers start: 51 outliers final: 38 residues processed: 402 average time/residue: 0.1654 time to fit residues: 103.2751 Evaluate side-chains 392 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 350 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 657 MET Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 513 LYS Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 691 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 138 optimal weight: 0.9980 chunk 214 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 208 optimal weight: 0.8980 chunk 190 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 101 optimal weight: 0.0040 chunk 291 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 ASN ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.136137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.116504 restraints weight = 38940.353| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.90 r_work: 0.3394 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24808 Z= 0.108 Angle : 0.507 9.781 33504 Z= 0.256 Chirality : 0.039 0.244 3908 Planarity : 0.003 0.037 4204 Dihedral : 4.156 27.511 3332 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.53 % Allowed : 11.43 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.15), residues: 3048 helix: 1.48 (0.12), residues: 1796 sheet: 0.50 (0.30), residues: 248 loop : 0.08 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 396 TYR 0.042 0.001 TYR D 331 PHE 0.024 0.001 PHE A 313 TRP 0.020 0.001 TRP C 588 HIS 0.004 0.000 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.00248 (24808) covalent geometry : angle 0.50701 (33504) hydrogen bonds : bond 0.03440 ( 1357) hydrogen bonds : angle 4.05922 ( 3915) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 378 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8951 (p90) cc_final: 0.8563 (p90) REVERT: A 126 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7166 (mp0) REVERT: A 130 LEU cc_start: 0.8462 (tp) cc_final: 0.8249 (tp) REVERT: A 200 ARG cc_start: 0.8767 (ttp80) cc_final: 0.8537 (ttp80) REVERT: A 205 ASN cc_start: 0.8390 (t0) cc_final: 0.7869 (t0) REVERT: A 216 ASP cc_start: 0.7898 (t0) cc_final: 0.7649 (t0) REVERT: A 273 LEU cc_start: 0.8779 (tp) cc_final: 0.8560 (tp) REVERT: A 366 HIS cc_start: 0.5225 (OUTLIER) cc_final: 0.4319 (p-80) REVERT: A 657 MET cc_start: 0.7416 (mmp) cc_final: 0.7172 (tpp) REVERT: A 859 MET cc_start: 0.6785 (mmp) cc_final: 0.6479 (mmp) REVERT: B 153 LYS cc_start: 0.9053 (tppt) cc_final: 0.8726 (tptp) REVERT: B 205 ASN cc_start: 0.8449 (t0) cc_final: 0.8124 (t0) REVERT: B 216 ASP cc_start: 0.7825 (t0) cc_final: 0.7521 (t0) REVERT: C 113 TYR cc_start: 0.8971 (p90) cc_final: 0.8702 (p90) REVERT: C 205 ASN cc_start: 0.8466 (t0) cc_final: 0.8179 (t0) REVERT: C 212 MET cc_start: 0.8782 (ttm) cc_final: 0.8521 (ttt) REVERT: C 216 ASP cc_start: 0.7867 (t0) cc_final: 0.7583 (t0) REVERT: C 273 LEU cc_start: 0.8750 (tt) cc_final: 0.8549 (tp) REVERT: C 314 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: C 511 SER cc_start: 0.8063 (t) cc_final: 0.7708 (p) REVERT: C 612 THR cc_start: 0.6733 (OUTLIER) cc_final: 0.5456 (p) REVERT: C 860 ARG cc_start: 0.7605 (mtt90) cc_final: 0.7211 (mtm-85) REVERT: D 126 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7501 (mp0) REVERT: D 131 LYS cc_start: 0.8496 (tptt) cc_final: 0.7735 (mmtt) REVERT: D 205 ASN cc_start: 0.8651 (t0) cc_final: 0.8259 (t0) REVERT: D 264 MET cc_start: 0.8400 (mtm) cc_final: 0.8116 (mtm) REVERT: D 307 MET cc_start: 0.7292 (mmm) cc_final: 0.6919 (mmt) REVERT: D 511 SER cc_start: 0.7667 (t) cc_final: 0.7423 (p) REVERT: D 545 SER cc_start: 0.8534 (t) cc_final: 0.8222 (m) REVERT: D 587 MET cc_start: 0.7493 (mmm) cc_final: 0.7231 (mmm) outliers start: 41 outliers final: 27 residues processed: 404 average time/residue: 0.1661 time to fit residues: 105.0295 Evaluate side-chains 385 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 355 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 513 LYS Chi-restraints excluded: chain D residue 691 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 269 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 156 optimal weight: 0.4980 chunk 143 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 241 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 chunk 160 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 284 HIS ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.134385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115318 restraints weight = 39386.840| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.85 r_work: 0.3377 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24808 Z= 0.147 Angle : 0.543 10.476 33504 Z= 0.271 Chirality : 0.040 0.231 3908 Planarity : 0.004 0.033 4204 Dihedral : 4.197 29.349 3332 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.38 % Allowed : 12.14 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.15), residues: 3048 helix: 1.40 (0.12), residues: 1804 sheet: 0.49 (0.30), residues: 248 loop : -0.05 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 396 TYR 0.019 0.001 TYR A 156 PHE 0.018 0.002 PHE C 658 TRP 0.018 0.002 TRP A 411 HIS 0.006 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00354 (24808) covalent geometry : angle 0.54276 (33504) hydrogen bonds : bond 0.03695 ( 1357) hydrogen bonds : angle 4.11090 ( 3915) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 355 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7289 (mp0) REVERT: A 200 ARG cc_start: 0.8715 (ttp80) cc_final: 0.8490 (ttp80) REVERT: A 205 ASN cc_start: 0.8375 (t0) cc_final: 0.7858 (t0) REVERT: A 216 ASP cc_start: 0.7858 (t0) cc_final: 0.7624 (t0) REVERT: A 273 LEU cc_start: 0.8793 (tp) cc_final: 0.8589 (tp) REVERT: A 366 HIS cc_start: 0.5341 (OUTLIER) cc_final: 0.4334 (p-80) REVERT: A 511 SER cc_start: 0.7900 (t) cc_final: 0.7544 (p) REVERT: B 205 ASN cc_start: 0.8426 (t0) cc_final: 0.8112 (t0) REVERT: B 216 ASP cc_start: 0.7725 (t0) cc_final: 0.7478 (t0) REVERT: C 113 TYR cc_start: 0.9033 (p90) cc_final: 0.8751 (p90) REVERT: C 126 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: C 205 ASN cc_start: 0.8391 (t0) cc_final: 0.8093 (t0) REVERT: C 212 MET cc_start: 0.8766 (ttm) cc_final: 0.8508 (ttt) REVERT: C 216 ASP cc_start: 0.7774 (t0) cc_final: 0.7513 (t0) REVERT: C 314 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: C 511 SER cc_start: 0.8128 (t) cc_final: 0.7768 (p) REVERT: C 520 GLN cc_start: 0.6672 (pp30) cc_final: 0.6363 (pp30) REVERT: C 612 THR cc_start: 0.6447 (OUTLIER) cc_final: 0.5276 (p) REVERT: C 860 ARG cc_start: 0.7579 (mtt90) cc_final: 0.7240 (mtm-85) REVERT: D 126 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7500 (mp0) REVERT: D 131 LYS cc_start: 0.8469 (tptt) cc_final: 0.7766 (mmtt) REVERT: D 205 ASN cc_start: 0.8557 (t0) cc_final: 0.8169 (t0) REVERT: D 307 MET cc_start: 0.7316 (mmm) cc_final: 0.6957 (mmt) REVERT: D 511 SER cc_start: 0.7751 (t) cc_final: 0.7464 (p) REVERT: D 545 SER cc_start: 0.8521 (t) cc_final: 0.8235 (m) REVERT: D 587 MET cc_start: 0.7503 (mmm) cc_final: 0.7268 (mmm) outliers start: 37 outliers final: 29 residues processed: 378 average time/residue: 0.1544 time to fit residues: 91.7490 Evaluate side-chains 375 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 342 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 513 LYS Chi-restraints excluded: chain D residue 691 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 243 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 227 optimal weight: 0.0870 chunk 13 optimal weight: 0.9990 chunk 214 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.135527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.115658 restraints weight = 39223.874| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.98 r_work: 0.3382 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24808 Z= 0.114 Angle : 0.530 11.585 33504 Z= 0.263 Chirality : 0.039 0.219 3908 Planarity : 0.003 0.032 4204 Dihedral : 4.100 27.562 3332 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.31 % Allowed : 12.37 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.15), residues: 3048 helix: 1.54 (0.12), residues: 1796 sheet: 0.53 (0.30), residues: 248 loop : 0.02 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 516 TYR 0.018 0.001 TYR A 156 PHE 0.014 0.001 PHE A 313 TRP 0.019 0.001 TRP C 588 HIS 0.006 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00266 (24808) covalent geometry : angle 0.53023 (33504) hydrogen bonds : bond 0.03405 ( 1357) hydrogen bonds : angle 4.04594 ( 3915) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 368 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7328 (mm-30) REVERT: A 113 TYR cc_start: 0.8928 (p90) cc_final: 0.8532 (p90) REVERT: A 126 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7235 (mp0) REVERT: A 200 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8494 (ttp80) REVERT: A 205 ASN cc_start: 0.8471 (t0) cc_final: 0.7953 (t0) REVERT: A 216 ASP cc_start: 0.7984 (t0) cc_final: 0.7722 (t0) REVERT: A 273 LEU cc_start: 0.8833 (tp) cc_final: 0.8630 (tp) REVERT: A 366 HIS cc_start: 0.5365 (OUTLIER) cc_final: 0.4347 (p-80) REVERT: A 511 SER cc_start: 0.7877 (t) cc_final: 0.7518 (p) REVERT: B 153 LYS cc_start: 0.8996 (tppt) cc_final: 0.8676 (tptp) REVERT: B 205 ASN cc_start: 0.8505 (t0) cc_final: 0.8202 (t0) REVERT: B 216 ASP cc_start: 0.7854 (t0) cc_final: 0.7580 (t0) REVERT: B 426 ASP cc_start: 0.8484 (t0) cc_final: 0.8069 (t0) REVERT: B 863 TRP cc_start: 0.8697 (t-100) cc_final: 0.8295 (t-100) REVERT: C 113 TYR cc_start: 0.9043 (p90) cc_final: 0.8727 (p90) REVERT: C 126 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: C 205 ASN cc_start: 0.8472 (t0) cc_final: 0.8177 (t0) REVERT: C 212 MET cc_start: 0.8793 (ttm) cc_final: 0.8568 (ttt) REVERT: C 216 ASP cc_start: 0.7901 (t0) cc_final: 0.7616 (t0) REVERT: C 314 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: C 511 SER cc_start: 0.8020 (t) cc_final: 0.7648 (p) REVERT: C 520 GLN cc_start: 0.6572 (pp30) cc_final: 0.6229 (pp30) REVERT: C 612 THR cc_start: 0.6638 (OUTLIER) cc_final: 0.5329 (p) REVERT: C 860 ARG cc_start: 0.7590 (mtt90) cc_final: 0.7175 (mtm-85) REVERT: D 126 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7427 (mp0) REVERT: D 131 LYS cc_start: 0.8465 (tptt) cc_final: 0.7699 (mmtt) REVERT: D 205 ASN cc_start: 0.8618 (t0) cc_final: 0.8237 (t0) REVERT: D 264 MET cc_start: 0.8427 (mtm) cc_final: 0.8122 (mtm) REVERT: D 307 MET cc_start: 0.7265 (mmm) cc_final: 0.6931 (mmt) REVERT: D 511 SER cc_start: 0.7766 (t) cc_final: 0.7478 (p) REVERT: D 545 SER cc_start: 0.8656 (t) cc_final: 0.8324 (m) REVERT: D 587 MET cc_start: 0.7633 (mmm) cc_final: 0.7372 (mmm) outliers start: 35 outliers final: 26 residues processed: 391 average time/residue: 0.1815 time to fit residues: 110.4508 Evaluate side-chains 376 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 346 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 513 LYS Chi-restraints excluded: chain D residue 691 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 132 optimal weight: 0.0270 chunk 19 optimal weight: 5.9990 chunk 297 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN ** C 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.135355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115526 restraints weight = 39405.167| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.93 r_work: 0.3382 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24808 Z= 0.121 Angle : 0.538 13.033 33504 Z= 0.266 Chirality : 0.039 0.205 3908 Planarity : 0.003 0.032 4204 Dihedral : 4.079 28.172 3332 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.42 % Allowed : 12.97 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.15), residues: 3048 helix: 1.57 (0.12), residues: 1796 sheet: 0.25 (0.29), residues: 268 loop : 0.05 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 516 TYR 0.017 0.001 TYR A 156 PHE 0.013 0.001 PHE D 765 TRP 0.018 0.001 TRP C 588 HIS 0.007 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00285 (24808) covalent geometry : angle 0.53829 (33504) hydrogen bonds : bond 0.03446 ( 1357) hydrogen bonds : angle 4.04079 ( 3915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6326.94 seconds wall clock time: 108 minutes 56.69 seconds (6536.69 seconds total)