Starting phenix.real_space_refine on Fri Jun 20 23:26:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh6_44534/06_2025/9bh6_44534.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh6_44534/06_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_44534/06_2025/9bh6_44534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh6_44534/06_2025/9bh6_44534.map" model { file = "/net/cci-nas-00/data/ceres_data/9bh6_44534/06_2025/9bh6_44534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh6_44534/06_2025/9bh6_44534.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.94, per 1000 atoms: 0.57 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: 5.53 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 2.74 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: 9.06 Time building geometry restraints manager: 6.57 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.890 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: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 53.330 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.520 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.002 TRP C 588 HIS 0.005 0.001 HIS D 710 PHE 0.025 0.002 PHE A 787 TYR 0.025 0.004 TYR B 758 ARG 0.020 0.003 ARG D 745 Details of bonding type rmsd hydrogen bonds : bond 0.19638 ( 1357) hydrogen bonds : angle 7.48967 ( 3915) covalent geometry : bond 0.00281 (24808) covalent geometry : angle 0.60811 (33504) *********************** 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 : 2.794 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: 0.7327 (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: 0.8454 (tppt) REVERT: C 212 MET cc_start: 0.8913 (ttm) cc_final: 0.8550 (ttp) REVERT: C 217 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7677 (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: 0.7272 (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: 0.6487 (mmt) REVERT: D 336 ASP cc_start: 0.8113 (m-30) cc_final: 0.7875 (m-30) REVERT: D 470 ASP cc_start: 0.7388 (m-30) cc_final: 0.7174 (m-30) REVERT: D 495 ILE cc_start: 0.7953 (mt) cc_final: 0.7741 (mm) outliers start: 0 outliers final: 0 residues processed: 608 average time/residue: 0.4235 time to fit residues: 377.5884 Evaluate side-chains 389 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 0.0040 chunk 233 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 241 optimal weight: 0.0970 chunk 93 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 279 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 835 ASN D 73 ASN D 520 GLN D 716 HIS D 753 GLN D 835 ASN D 888 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.135120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114618 restraints weight = 38878.744| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.04 r_work: 0.3362 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2134 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= 0.131 Angle : 0.574 10.156 33504 Z= 0.304 Chirality : 0.041 0.156 3908 Planarity : 0.004 0.037 4204 Dihedral : 5.154 29.456 3332 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.05 % Allowed : 5.94 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3048 helix: 0.42 (0.11), residues: 1796 sheet: 0.51 (0.29), residues: 248 loop : 0.37 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 588 HIS 0.009 0.001 HIS C 85 PHE 0.016 0.002 PHE A 313 TYR 0.012 0.001 TYR D 171 ARG 0.007 0.000 ARG D 483 Details of bonding type rmsd hydrogen bonds : bond 0.04875 ( 1357) hydrogen bonds : angle 4.81450 ( 3915) covalent geometry : bond 0.00280 (24808) covalent geometry : angle 0.57427 (33504) *********************** 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 458 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 430 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.7946 (t0) cc_final: 0.7743 (t0) REVERT: A 463 ILE cc_start: 0.8938 (mm) cc_final: 0.8738 (mt) REVERT: A 587 MET cc_start: 0.7574 (mmm) cc_final: 0.7338 (mmm) REVERT: A 859 MET cc_start: 0.6311 (mmt) cc_final: 0.5881 (mmt) REVERT: B 152 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8187 (tm-30) REVERT: B 307 MET cc_start: 0.6165 (mmm) cc_final: 0.5934 (tpp) REVERT: B 470 ASP cc_start: 0.7920 (m-30) cc_final: 0.7705 (m-30) REVERT: B 637 ARG cc_start: 0.8281 (ttp80) cc_final: 0.8000 (ttt-90) REVERT: B 711 ARG cc_start: 0.7586 (ttt90) cc_final: 0.7380 (ttt90) REVERT: B 860 ARG cc_start: 0.7402 (mtt90) cc_final: 0.7194 (mtm-85) REVERT: C 212 MET cc_start: 0.8822 (ttm) cc_final: 0.8550 (ttt) REVERT: C 225 HIS cc_start: 0.7189 (p-80) cc_final: 0.6916 (p-80) REVERT: C 335 CYS cc_start: 0.8837 (m) cc_final: 0.8635 (p) REVERT: D 113 TYR cc_start: 0.9099 (p90) cc_final: 0.8831 (p90) REVERT: D 122 THR cc_start: 0.8841 (p) cc_final: 0.8286 (p) REVERT: D 126 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7285 (mp0) REVERT: D 131 LYS cc_start: 0.8704 (tptt) cc_final: 0.7730 (mmtt) REVERT: D 307 MET cc_start: 0.7103 (mmm) cc_final: 0.6708 (mmt) REVERT: D 860 ARG cc_start: 0.7418 (mtt90) cc_final: 0.7152 (mtm-85) REVERT: D 867 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7807 (mtt-85) outliers start: 28 outliers final: 17 residues processed: 443 average time/residue: 0.4198 time to fit residues: 280.6991 Evaluate side-chains 378 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 361 time to evaluate : 2.973 ------------------------------------------------------------------------------- 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 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 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 832 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 172 optimal weight: 7.9990 chunk 193 optimal weight: 2.9990 chunk 274 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 551 HIS ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110460 restraints weight = 39128.343| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.19 r_work: 0.3276 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 24808 Z= 0.287 Angle : 0.668 7.674 33504 Z= 0.340 Chirality : 0.045 0.219 3908 Planarity : 0.005 0.046 4204 Dihedral : 5.052 35.272 3332 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.72 % Allowed : 8.00 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3048 helix: 0.53 (0.12), residues: 1780 sheet: 0.31 (0.29), residues: 240 loop : 0.02 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 588 HIS 0.007 0.001 HIS C 366 PHE 0.030 0.003 PHE A 594 TYR 0.018 0.002 TYR D 171 ARG 0.006 0.001 ARG A 456 Details of bonding type rmsd hydrogen bonds : bond 0.05270 ( 1357) hydrogen bonds : angle 4.73092 ( 3915) covalent geometry : bond 0.00705 (24808) covalent geometry : angle 0.66835 (33504) *********************** 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 417 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 371 time to evaluate : 4.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8968 (p90) cc_final: 0.8600 (p90) REVERT: A 205 ASN cc_start: 0.8584 (t0) cc_final: 0.8090 (t0) REVERT: A 216 ASP cc_start: 0.8055 (t0) cc_final: 0.7833 (t0) REVERT: A 859 MET cc_start: 0.6469 (mmt) cc_final: 0.6074 (mmt) REVERT: B 153 LYS cc_start: 0.9010 (tppt) cc_final: 0.8598 (tptp) REVERT: B 205 ASN cc_start: 0.8594 (t0) cc_final: 0.8270 (t0) REVERT: B 216 ASP cc_start: 0.7955 (t0) cc_final: 0.7716 (t0) REVERT: B 637 ARG cc_start: 0.8250 (ttp80) cc_final: 0.8030 (ttt-90) REVERT: B 860 ARG cc_start: 0.7461 (mtt90) cc_final: 0.7207 (mtm-85) REVERT: B 863 TRP cc_start: 0.8937 (t-100) cc_final: 0.8703 (t-100) REVERT: C 100 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8283 (mp) REVERT: C 152 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8326 (tm-30) REVERT: C 612 THR cc_start: 0.7187 (OUTLIER) cc_final: 0.6185 (p) REVERT: D 131 LYS cc_start: 0.8725 (tptt) cc_final: 0.7836 (mmtt) REVERT: D 205 ASN cc_start: 0.8623 (t0) cc_final: 0.8210 (t0) REVERT: D 307 MET cc_start: 0.7331 (mmm) cc_final: 0.6958 (mmt) REVERT: D 488 THR cc_start: 0.8581 (m) cc_final: 0.8336 (p) REVERT: D 860 ARG cc_start: 0.7498 (mtt90) cc_final: 0.7271 (mtm-85) REVERT: D 867 ARG cc_start: 0.8046 (mtt90) cc_final: 0.7828 (mtt-85) outliers start: 46 outliers final: 31 residues processed: 393 average time/residue: 0.5139 time to fit residues: 312.7733 Evaluate side-chains 385 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 352 time to evaluate : 2.708 ------------------------------------------------------------------------------- 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 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 775 GLU Chi-restraints excluded: chain A residue 826 ILE 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 B residue 859 MET 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 316 MET Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 832 ILE 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 Chi-restraints excluded: chain D residue 826 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 292 optimal weight: 0.9980 chunk 258 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 57 optimal weight: 0.0060 chunk 303 optimal weight: 4.9990 chunk 294 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 160 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.134415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.115283 restraints weight = 39433.302| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.83 r_work: 0.3384 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24808 Z= 0.119 Angle : 0.516 9.284 33504 Z= 0.266 Chirality : 0.040 0.161 3908 Planarity : 0.004 0.036 4204 Dihedral : 4.603 29.389 3332 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.16 % Allowed : 9.57 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.15), residues: 3048 helix: 1.07 (0.12), residues: 1800 sheet: 0.27 (0.29), residues: 248 loop : 0.05 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 588 HIS 0.006 0.001 HIS D 366 PHE 0.015 0.001 PHE D 765 TYR 0.013 0.001 TYR B 113 ARG 0.004 0.000 ARG D 483 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 1357) hydrogen bonds : angle 4.33153 ( 3915) covalent geometry : bond 0.00269 (24808) covalent geometry : angle 0.51578 (33504) *********************** 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 404 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 373 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8938 (p90) cc_final: 0.8600 (p90) REVERT: A 141 LEU cc_start: 0.9148 (mp) cc_final: 0.8927 (mt) REVERT: A 200 ARG cc_start: 0.8722 (ttp80) cc_final: 0.8492 (ttp80) REVERT: A 205 ASN cc_start: 0.8414 (t0) cc_final: 0.7898 (t0) REVERT: A 216 ASP cc_start: 0.7843 (t0) cc_final: 0.7607 (t0) REVERT: A 389 GLU cc_start: 0.8463 (tt0) cc_final: 0.8142 (tt0) REVERT: A 859 MET cc_start: 0.6397 (mmt) cc_final: 0.6127 (mmp) REVERT: B 114 SER cc_start: 0.9325 (p) cc_final: 0.9034 (t) REVERT: B 153 LYS cc_start: 0.9008 (tppt) cc_final: 0.8536 (tptp) REVERT: B 205 ASN cc_start: 0.8416 (t0) cc_final: 0.8089 (t0) REVERT: B 216 ASP cc_start: 0.7729 (t0) cc_final: 0.7498 (t0) REVERT: B 217 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8284 (mt-10) REVERT: B 660 ASP cc_start: 0.8136 (t0) cc_final: 0.7900 (t70) REVERT: B 860 ARG cc_start: 0.7500 (mtt90) cc_final: 0.7229 (mtm-85) REVERT: C 113 TYR cc_start: 0.9017 (p90) cc_final: 0.8809 (p90) REVERT: C 114 SER cc_start: 0.9219 (p) cc_final: 0.9003 (t) REVERT: C 212 MET cc_start: 0.8824 (ttm) cc_final: 0.8588 (ttt) REVERT: C 587 MET cc_start: 0.7325 (mmm) cc_final: 0.7119 (mmm) REVERT: C 612 THR cc_start: 0.6774 (OUTLIER) cc_final: 0.5714 (p) REVERT: D 113 TYR cc_start: 0.9102 (p90) cc_final: 0.8845 (p90) REVERT: D 126 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7425 (mp0) REVERT: D 131 LYS cc_start: 0.8629 (tptt) cc_final: 0.7821 (mmtt) REVERT: D 205 ASN cc_start: 0.8577 (t0) cc_final: 0.8195 (t0) REVERT: D 264 MET cc_start: 0.8435 (mtm) cc_final: 0.8173 (mtm) REVERT: D 307 MET cc_start: 0.7182 (mmm) cc_final: 0.6801 (mmt) REVERT: D 313 PHE cc_start: 0.7597 (t80) cc_final: 0.7047 (t80) REVERT: D 587 MET cc_start: 0.7456 (mmm) cc_final: 0.7178 (mmm) REVERT: D 860 ARG cc_start: 0.7465 (mtt90) cc_final: 0.7251 (mtm-85) outliers start: 31 outliers final: 17 residues processed: 391 average time/residue: 0.3873 time to fit residues: 232.0389 Evaluate side-chains 356 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 338 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 101 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 488 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 403 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 513 LYS 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 180 optimal weight: 0.4980 chunk 87 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 226 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 120 optimal weight: 0.1980 chunk 117 optimal weight: 10.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 GLN ** 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 = 0.3821 r_free = 0.3821 target = 0.135355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.115493 restraints weight = 39476.013| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.02 r_work: 0.3376 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24808 Z= 0.113 Angle : 0.498 7.595 33504 Z= 0.256 Chirality : 0.039 0.258 3908 Planarity : 0.003 0.034 4204 Dihedral : 4.359 28.405 3332 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.38 % Allowed : 10.39 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.15), residues: 3048 helix: 1.28 (0.12), residues: 1804 sheet: 0.38 (0.30), residues: 248 loop : 0.14 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 588 HIS 0.006 0.001 HIS C 366 PHE 0.014 0.001 PHE D 765 TYR 0.013 0.001 TYR D 171 ARG 0.004 0.000 ARG B 396 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 1357) hydrogen bonds : angle 4.16316 ( 3915) covalent geometry : bond 0.00259 (24808) covalent geometry : angle 0.49809 (33504) *********************** 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 411 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 374 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8940 (p90) cc_final: 0.8567 (p90) REVERT: A 126 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7324 (mp0) REVERT: A 141 LEU cc_start: 0.9137 (mp) cc_final: 0.8925 (mt) REVERT: A 200 ARG cc_start: 0.8751 (ttp80) cc_final: 0.8516 (ttp80) REVERT: A 205 ASN cc_start: 0.8457 (t0) cc_final: 0.7961 (t0) REVERT: A 216 ASP cc_start: 0.7973 (t0) cc_final: 0.7709 (t0) REVERT: B 114 SER cc_start: 0.9349 (p) cc_final: 0.9022 (t) REVERT: B 126 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7447 (mp0) REVERT: B 205 ASN cc_start: 0.8470 (t0) cc_final: 0.8146 (t0) REVERT: B 216 ASP cc_start: 0.7798 (t0) cc_final: 0.7499 (t0) REVERT: B 660 ASP cc_start: 0.8111 (t0) cc_final: 0.7850 (t70) REVERT: B 860 ARG cc_start: 0.7529 (mtt90) cc_final: 0.7294 (mtm-85) REVERT: C 113 TYR cc_start: 0.9035 (p90) cc_final: 0.8830 (p90) REVERT: C 126 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7357 (mp0) REVERT: C 212 MET cc_start: 0.8850 (ttm) cc_final: 0.8636 (ttt) REVERT: C 511 SER cc_start: 0.8097 (t) cc_final: 0.7750 (p) REVERT: C 612 THR cc_start: 0.6561 (OUTLIER) cc_final: 0.5374 (p) REVERT: C 860 ARG cc_start: 0.7557 (mtt90) cc_final: 0.7174 (mtm-85) REVERT: D 126 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7525 (mp0) REVERT: D 131 LYS cc_start: 0.8595 (tptt) cc_final: 0.7792 (mmtt) REVERT: D 205 ASN cc_start: 0.8630 (t0) cc_final: 0.8250 (t0) REVERT: D 264 MET cc_start: 0.8430 (mtm) cc_final: 0.8174 (mtm) REVERT: D 307 MET cc_start: 0.7250 (mmm) cc_final: 0.6883 (mmt) REVERT: D 860 ARG cc_start: 0.7498 (mtt90) cc_final: 0.7259 (mtm-85) outliers start: 37 outliers final: 20 residues processed: 398 average time/residue: 0.3748 time to fit residues: 231.9116 Evaluate side-chains 369 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 348 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 713 MET Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain B residue 76 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 775 GLU 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 612 THR Chi-restraints excluded: chain C residue 832 ILE 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 691 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 299 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 69 optimal weight: 0.0470 chunk 54 optimal weight: 1.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 ASN C 325 HIS ** C 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3798 r_free = 0.3798 target = 0.133587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.114007 restraints weight = 39208.848| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.95 r_work: 0.3361 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3196 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= 0.168 Angle : 0.539 8.538 33504 Z= 0.271 Chirality : 0.040 0.196 3908 Planarity : 0.004 0.036 4204 Dihedral : 4.366 30.178 3332 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.72 % Allowed : 10.80 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.15), residues: 3048 helix: 1.28 (0.12), residues: 1800 sheet: 0.34 (0.30), residues: 248 loop : 0.01 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 588 HIS 0.005 0.001 HIS C 366 PHE 0.017 0.002 PHE D 781 TYR 0.015 0.001 TYR B 113 ARG 0.008 0.000 ARG B 516 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 1357) hydrogen bonds : angle 4.19549 ( 3915) covalent geometry : bond 0.00408 (24808) covalent geometry : angle 0.53918 (33504) *********************** 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 400 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 354 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8915 (p90) cc_final: 0.8530 (p90) REVERT: A 200 ARG cc_start: 0.8787 (ttp80) cc_final: 0.8556 (ttp80) REVERT: A 205 ASN cc_start: 0.8501 (t0) cc_final: 0.8008 (t0) REVERT: A 216 ASP cc_start: 0.7849 (t0) cc_final: 0.7590 (t0) REVERT: A 859 MET cc_start: 0.6934 (mmp) cc_final: 0.6552 (mmp) REVERT: B 205 ASN cc_start: 0.8513 (t0) cc_final: 0.8188 (t0) REVERT: B 216 ASP cc_start: 0.7810 (t0) cc_final: 0.7519 (t0) REVERT: B 660 ASP cc_start: 0.8085 (t0) cc_final: 0.7828 (t70) REVERT: C 212 MET cc_start: 0.8868 (ttm) cc_final: 0.8633 (ttt) REVERT: C 314 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: C 511 SER cc_start: 0.8140 (t) cc_final: 0.7784 (p) REVERT: C 612 THR cc_start: 0.6537 (OUTLIER) cc_final: 0.5357 (p) REVERT: C 860 ARG cc_start: 0.7610 (mtt90) cc_final: 0.7254 (mtm-85) REVERT: D 131 LYS cc_start: 0.8633 (tptt) cc_final: 0.7891 (mmtt) REVERT: D 205 ASN cc_start: 0.8611 (t0) cc_final: 0.8224 (t0) REVERT: D 264 MET cc_start: 0.8485 (mtm) cc_final: 0.8218 (mtm) REVERT: D 307 MET cc_start: 0.7344 (mmm) cc_final: 0.6976 (mmt) REVERT: D 511 SER cc_start: 0.7769 (t) cc_final: 0.7391 (p) REVERT: D 587 MET cc_start: 0.7615 (mmm) cc_final: 0.7320 (mmm) outliers start: 46 outliers final: 36 residues processed: 384 average time/residue: 0.3702 time to fit residues: 222.3119 Evaluate side-chains 375 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 337 time to evaluate : 2.956 ------------------------------------------------------------------------------- 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 403 SER Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 487 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 826 ILE 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 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 487 ASP Chi-restraints excluded: chain B residue 488 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 489 VAL Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 832 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 108 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 236 optimal weight: 0.6980 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 451 ASN ** 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 = 0.134687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115103 restraints weight = 39178.233| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.89 r_work: 0.3378 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3301 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= 0.122 Angle : 0.511 9.433 33504 Z= 0.259 Chirality : 0.039 0.177 3908 Planarity : 0.004 0.036 4204 Dihedral : 4.264 28.741 3332 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.61 % Allowed : 11.25 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.15), residues: 3048 helix: 1.40 (0.12), residues: 1800 sheet: 0.38 (0.30), residues: 248 loop : 0.02 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 588 HIS 0.004 0.001 HIS C 366 PHE 0.013 0.001 PHE D 781 TYR 0.012 0.001 TYR D 171 ARG 0.007 0.000 ARG B 516 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 1357) hydrogen bonds : angle 4.13249 ( 3915) covalent geometry : bond 0.00285 (24808) covalent geometry : angle 0.51069 (33504) *********************** 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 401 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 358 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8890 (p90) cc_final: 0.8518 (p90) REVERT: A 126 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7244 (mp0) REVERT: A 200 ARG cc_start: 0.8751 (ttp80) cc_final: 0.8507 (ttp80) REVERT: A 205 ASN cc_start: 0.8450 (t0) cc_final: 0.7958 (t0) REVERT: A 216 ASP cc_start: 0.7854 (t0) cc_final: 0.7599 (t0) REVERT: A 859 MET cc_start: 0.6861 (mmp) cc_final: 0.6493 (mmp) REVERT: B 114 SER cc_start: 0.9308 (p) cc_final: 0.9017 (t) REVERT: B 126 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: B 205 ASN cc_start: 0.8488 (t0) cc_final: 0.8167 (t0) REVERT: B 216 ASP cc_start: 0.7815 (t0) cc_final: 0.7534 (t0) REVERT: C 113 TYR cc_start: 0.9017 (p90) cc_final: 0.8810 (p90) REVERT: C 126 GLU cc_start: 0.7563 (mp0) cc_final: 0.7258 (mp0) REVERT: C 212 MET cc_start: 0.8829 (ttm) cc_final: 0.8594 (ttt) REVERT: C 314 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: C 511 SER cc_start: 0.8133 (t) cc_final: 0.7785 (p) REVERT: C 612 THR cc_start: 0.6445 (OUTLIER) cc_final: 0.5247 (p) REVERT: C 860 ARG cc_start: 0.7578 (mtt90) cc_final: 0.7246 (mtm-85) REVERT: D 113 TYR cc_start: 0.9080 (p90) cc_final: 0.8866 (p90) REVERT: D 126 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: D 131 LYS cc_start: 0.8594 (tptt) cc_final: 0.7825 (mmtt) REVERT: D 205 ASN cc_start: 0.8569 (t0) cc_final: 0.8187 (t0) REVERT: D 264 MET cc_start: 0.8427 (mtm) cc_final: 0.8176 (mtm) REVERT: D 307 MET cc_start: 0.7327 (mmm) cc_final: 0.6941 (mmt) REVERT: D 511 SER cc_start: 0.7744 (t) cc_final: 0.7376 (p) REVERT: D 587 MET cc_start: 0.7536 (mmm) cc_final: 0.7308 (mmm) outliers start: 43 outliers final: 28 residues processed: 387 average time/residue: 0.3684 time to fit residues: 224.8952 Evaluate side-chains 374 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 342 time to evaluate : 2.903 ------------------------------------------------------------------------------- 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 257 ASN Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 487 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 B residue 76 LEU Chi-restraints excluded: chain B residue 126 GLU 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 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 314 GLU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 126 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 201 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 ASN ** 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 = 0.3798 r_free = 0.3798 target = 0.133677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114375 restraints weight = 39163.089| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.96 r_work: 0.3359 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3383 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 : 0.536 9.791 33504 Z= 0.269 Chirality : 0.040 0.164 3908 Planarity : 0.004 0.036 4204 Dihedral : 4.270 29.916 3332 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.72 % Allowed : 11.70 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.15), residues: 3048 helix: 1.33 (0.12), residues: 1804 sheet: 0.31 (0.30), residues: 248 loop : 0.01 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 588 HIS 0.005 0.001 HIS C 338 PHE 0.024 0.002 PHE A 313 TYR 0.015 0.001 TYR B 113 ARG 0.009 0.000 ARG B 516 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 1357) hydrogen bonds : angle 4.15792 ( 3915) covalent geometry : bond 0.00387 (24808) covalent geometry : angle 0.53567 (33504) *********************** 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 399 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 353 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8909 (p90) cc_final: 0.8534 (p90) REVERT: A 126 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7226 (mp0) REVERT: A 200 ARG cc_start: 0.8761 (ttp80) cc_final: 0.8517 (ttp80) REVERT: A 205 ASN cc_start: 0.8466 (t0) cc_final: 0.7973 (t0) REVERT: A 216 ASP cc_start: 0.7893 (t0) cc_final: 0.7617 (t0) REVERT: A 273 LEU cc_start: 0.8791 (tp) cc_final: 0.8587 (tp) REVERT: A 366 HIS cc_start: 0.5356 (OUTLIER) cc_final: 0.4363 (p-80) REVERT: A 614 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5892 (tp) REVERT: A 657 MET cc_start: 0.7400 (mmp) cc_final: 0.7190 (tpp) REVERT: A 859 MET cc_start: 0.6862 (mmp) cc_final: 0.6486 (mmp) REVERT: B 205 ASN cc_start: 0.8517 (t0) cc_final: 0.8201 (t0) REVERT: B 216 ASP cc_start: 0.7794 (t0) cc_final: 0.7537 (t0) REVERT: C 126 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: C 212 MET cc_start: 0.8870 (ttm) cc_final: 0.8631 (ttt) REVERT: C 314 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: C 511 SER cc_start: 0.8176 (t) cc_final: 0.7845 (p) REVERT: C 612 THR cc_start: 0.6436 (OUTLIER) cc_final: 0.5222 (p) REVERT: C 860 ARG cc_start: 0.7605 (mtt90) cc_final: 0.7280 (mtm-85) REVERT: D 126 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: D 131 LYS cc_start: 0.8573 (tptt) cc_final: 0.7835 (mmtt) REVERT: D 205 ASN cc_start: 0.8619 (t0) cc_final: 0.8233 (t0) REVERT: D 264 MET cc_start: 0.8526 (mtm) cc_final: 0.8259 (mtm) REVERT: D 307 MET cc_start: 0.7371 (mmm) cc_final: 0.7021 (mmt) REVERT: D 511 SER cc_start: 0.7773 (t) cc_final: 0.7402 (p) REVERT: D 545 SER cc_start: 0.8578 (t) cc_final: 0.8242 (m) REVERT: D 587 MET cc_start: 0.7642 (mmm) cc_final: 0.7422 (mmm) outliers start: 46 outliers final: 31 residues processed: 384 average time/residue: 0.3674 time to fit residues: 219.7315 Evaluate side-chains 377 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 340 time to evaluate : 2.841 ------------------------------------------------------------------------------- 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 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 487 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 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 403 SER Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 471 ILE 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 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 612 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 126 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 279 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 264 optimal weight: 0.9980 chunk 69 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: 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 = 0.3818 r_free = 0.3818 target = 0.135046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.115627 restraints weight = 39120.925| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.86 r_work: 0.3385 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24808 Z= 0.118 Angle : 0.509 10.304 33504 Z= 0.257 Chirality : 0.039 0.168 3908 Planarity : 0.003 0.034 4204 Dihedral : 4.153 28.180 3332 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.72 % Allowed : 12.00 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.15), residues: 3048 helix: 1.50 (0.12), residues: 1796 sheet: 0.38 (0.30), residues: 248 loop : 0.08 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 588 HIS 0.007 0.001 HIS C 338 PHE 0.014 0.001 PHE A 313 TYR 0.014 0.001 TYR C 228 ARG 0.005 0.000 ARG B 516 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 1357) hydrogen bonds : angle 4.08730 ( 3915) covalent geometry : bond 0.00277 (24808) covalent geometry : angle 0.50860 (33504) *********************** 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 401 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 355 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8901 (p90) cc_final: 0.8485 (p90) REVERT: A 126 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7254 (mp0) REVERT: A 200 ARG cc_start: 0.8741 (ttp80) cc_final: 0.8503 (ttp80) REVERT: A 205 ASN cc_start: 0.8423 (t0) cc_final: 0.7930 (t0) REVERT: A 216 ASP cc_start: 0.7944 (t0) cc_final: 0.7664 (t0) REVERT: A 273 LEU cc_start: 0.8799 (tp) cc_final: 0.8587 (tp) REVERT: A 366 HIS cc_start: 0.5254 (OUTLIER) cc_final: 0.4338 (p-80) REVERT: B 126 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: B 205 ASN cc_start: 0.8437 (t0) cc_final: 0.8124 (t0) REVERT: B 216 ASP cc_start: 0.7793 (t0) cc_final: 0.7535 (t0) REVERT: C 113 TYR cc_start: 0.8978 (p90) cc_final: 0.8676 (p90) REVERT: C 126 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: C 212 MET cc_start: 0.8749 (ttm) cc_final: 0.8533 (ttt) REVERT: C 314 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: C 511 SER cc_start: 0.8167 (t) cc_final: 0.7850 (p) REVERT: C 550 MET cc_start: 0.7960 (mtt) cc_final: 0.7636 (mtt) REVERT: C 612 THR cc_start: 0.6650 (OUTLIER) cc_final: 0.5362 (p) REVERT: C 860 ARG cc_start: 0.7630 (mtt90) cc_final: 0.7279 (mtm-85) REVERT: D 126 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: D 131 LYS cc_start: 0.8522 (tptt) cc_final: 0.7824 (mmtt) REVERT: D 205 ASN cc_start: 0.8603 (t0) cc_final: 0.8226 (t0) REVERT: D 264 MET cc_start: 0.8401 (mtm) cc_final: 0.8114 (mtm) REVERT: D 307 MET cc_start: 0.7350 (mmm) cc_final: 0.7011 (mmt) REVERT: D 511 SER cc_start: 0.7737 (t) cc_final: 0.7448 (p) REVERT: D 545 SER cc_start: 0.8562 (t) cc_final: 0.8221 (m) outliers start: 46 outliers final: 28 residues processed: 386 average time/residue: 0.3706 time to fit residues: 224.8492 Evaluate side-chains 381 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 347 time to evaluate : 2.999 ------------------------------------------------------------------------------- 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 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 487 ASP Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 198 ILE 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 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 126 GLU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 126 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 31 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 281 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 ASN ** 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 = 0.3781 r_free = 0.3781 target = 0.132455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.113243 restraints weight = 39262.702| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.98 r_work: 0.3358 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24808 Z= 0.214 Angle : 0.591 11.193 33504 Z= 0.295 Chirality : 0.042 0.242 3908 Planarity : 0.004 0.037 4204 Dihedral : 4.341 31.168 3332 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.49 % Allowed : 12.33 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.15), residues: 3048 helix: 1.26 (0.12), residues: 1792 sheet: -0.12 (0.30), residues: 268 loop : -0.07 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 588 HIS 0.006 0.001 HIS C 338 PHE 0.019 0.002 PHE A 594 TYR 0.044 0.002 TYR D 331 ARG 0.007 0.000 ARG B 516 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 1357) hydrogen bonds : angle 4.23977 ( 3915) covalent geometry : bond 0.00521 (24808) covalent geometry : angle 0.59130 (33504) ********************** 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 386 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 346 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8907 (p90) cc_final: 0.8487 (p90) REVERT: A 126 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7298 (mp0) REVERT: A 205 ASN cc_start: 0.8480 (t0) cc_final: 0.7967 (t0) REVERT: A 216 ASP cc_start: 0.7879 (t0) cc_final: 0.7622 (t0) REVERT: A 273 LEU cc_start: 0.8842 (tp) cc_final: 0.8630 (tp) REVERT: A 366 HIS cc_start: 0.5466 (OUTLIER) cc_final: 0.4349 (p-80) REVERT: A 511 SER cc_start: 0.7816 (t) cc_final: 0.7453 (p) REVERT: A 614 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.5999 (tp) REVERT: A 859 MET cc_start: 0.6991 (mmp) cc_final: 0.6656 (mmp) REVERT: B 153 LYS cc_start: 0.9020 (tppt) cc_final: 0.8702 (tptp) REVERT: B 205 ASN cc_start: 0.8563 (t0) cc_final: 0.8240 (t0) REVERT: B 216 ASP cc_start: 0.7812 (t0) cc_final: 0.7565 (t0) REVERT: C 113 TYR cc_start: 0.9072 (p90) cc_final: 0.8795 (p90) REVERT: C 126 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: C 212 MET cc_start: 0.8927 (ttm) cc_final: 0.8694 (ttt) REVERT: C 314 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: C 511 SER cc_start: 0.8199 (t) cc_final: 0.7873 (p) REVERT: C 520 GLN cc_start: 0.6819 (pp30) cc_final: 0.6503 (pp30) REVERT: C 550 MET cc_start: 0.7995 (mtt) cc_final: 0.7648 (mtt) REVERT: C 612 THR cc_start: 0.6436 (OUTLIER) cc_final: 0.5260 (p) REVERT: C 860 ARG cc_start: 0.7694 (mtt90) cc_final: 0.7379 (mtm-85) REVERT: D 131 LYS cc_start: 0.8544 (tptt) cc_final: 0.7864 (mmtt) REVERT: D 205 ASN cc_start: 0.8655 (t0) cc_final: 0.8271 (t0) REVERT: D 264 MET cc_start: 0.8553 (mtm) cc_final: 0.8282 (mtm) REVERT: D 307 MET cc_start: 0.7348 (mmm) cc_final: 0.7003 (mmt) REVERT: D 511 SER cc_start: 0.7818 (t) cc_final: 0.7464 (p) outliers start: 40 outliers final: 29 residues processed: 374 average time/residue: 0.3650 time to fit residues: 213.9572 Evaluate side-chains 370 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 336 time to evaluate : 2.898 ------------------------------------------------------------------------------- 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 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 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 B residue 76 LEU Chi-restraints excluded: chain B residue 134 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 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 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 612 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 126 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 125 optimal weight: 0.0050 chunk 226 optimal weight: 0.9990 chunk 205 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 269 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.134672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115878 restraints weight = 39004.911| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.90 r_work: 0.3386 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24808 Z= 0.116 Angle : 0.525 11.046 33504 Z= 0.265 Chirality : 0.039 0.163 3908 Planarity : 0.004 0.082 4204 Dihedral : 4.202 28.328 3332 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.27 % Allowed : 12.86 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.15), residues: 3048 helix: 1.46 (0.12), residues: 1792 sheet: 0.01 (0.30), residues: 268 loop : -0.00 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 588 HIS 0.005 0.001 HIS C 338 PHE 0.013 0.001 PHE D 765 TYR 0.018 0.001 TYR A 156 ARG 0.006 0.000 ARG A 226 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 1357) hydrogen bonds : angle 4.11077 ( 3915) covalent geometry : bond 0.00268 (24808) covalent geometry : angle 0.52538 (33504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14150.65 seconds wall clock time: 245 minutes 46.69 seconds (14746.69 seconds total)