Starting phenix.real_space_refine on Mon May 13 08:53:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh6_44534/05_2024/9bh6_44534.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh6_44534/05_2024/9bh6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh6_44534/05_2024/9bh6_44534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh6_44534/05_2024/9bh6_44534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh6_44534/05_2024/9bh6_44534.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bh6_44534/05_2024/9bh6_44534.pdb" } 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 Residue "A PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 12.12, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 8.78 Conformation dependent library (CDL) restraints added in 4.3 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: 3.10 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: 9.79 Time building geometry restraints manager: 9.62 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: 100.13 - 106.93: 587 106.93 - 113.72: 14253 113.72 - 120.52: 9570 120.52 - 127.32: 8858 127.32 - 134.11: 236 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 2.440 nonbonded pdb=" OH TYR C 113 " pdb=" O LYS C 121 " model vdw 2.354 2.440 nonbonded pdb=" OH TYR A 113 " pdb=" O LYS A 121 " model vdw 2.355 2.440 nonbonded pdb=" OE1 GLU A 332 " pdb=" NH2 ARG A 456 " model vdw 2.404 2.520 nonbonded pdb=" O GLY D 615 " pdb=" OG1 THR D 618 " model vdw 2.404 2.440 ... (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 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: 2.170 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: 7.940 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 63.260 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.150 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.720 ------------------------------------------------------------------------------- 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= 0.183 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 608 time to evaluate : 2.811 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: 0.4501 time to fit residues: 401.3678 Evaluate side-chains 389 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 3.189 ------------------------------------------------------------------------------- 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: 0.8980 chunk 233 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 279 optimal weight: 0.3980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 835 ASN A 888 GLN B 366 HIS B 416 HIS B 520 GLN B 835 ASN B 888 GLN C 73 ASN C 180 HIS ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 835 ASN D 73 ASN ** D 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 HIS D 835 ASN D 888 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 24808 Z= 0.247 Angle : 0.590 11.064 33504 Z= 0.309 Chirality : 0.042 0.145 3908 Planarity : 0.004 0.040 4204 Dihedral : 5.220 31.037 3332 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 1.12 % Allowed : 5.87 % Favored : 93.01 % 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: 0.34 (0.14), residues: 3048 helix: 0.34 (0.11), residues: 1796 sheet: 0.41 (0.29), residues: 248 loop : 0.29 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 588 HIS 0.009 0.001 HIS C 85 PHE 0.019 0.002 PHE A 594 TYR 0.014 0.001 TYR B 113 ARG 0.006 0.000 ARG A 396 *********************** 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 450 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 420 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.7451 (mmm) cc_final: 0.7239 (mmm) REVERT: A 859 MET cc_start: 0.6407 (mmt) cc_final: 0.6042 (mmt) REVERT: B 153 LYS cc_start: 0.8955 (tppt) cc_final: 0.8394 (tptp) REVERT: B 212 MET cc_start: 0.8864 (ttm) cc_final: 0.8651 (ttt) REVERT: B 307 MET cc_start: 0.6212 (mmm) cc_final: 0.5993 (tpp) REVERT: B 637 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7811 (ttt-90) REVERT: B 860 ARG cc_start: 0.7276 (mtt90) cc_final: 0.7072 (mtm-85) REVERT: C 212 MET cc_start: 0.8891 (ttm) cc_final: 0.8582 (ttt) REVERT: C 225 HIS cc_start: 0.7330 (p-80) cc_final: 0.7051 (p-80) REVERT: D 122 THR cc_start: 0.8847 (p) cc_final: 0.8332 (p) REVERT: D 131 LYS cc_start: 0.8644 (tptt) cc_final: 0.7884 (mmtt) REVERT: D 307 MET cc_start: 0.6993 (mmm) cc_final: 0.6584 (mmt) REVERT: D 639 MET cc_start: 0.9335 (mtp) cc_final: 0.9133 (mtm) outliers start: 30 outliers final: 22 residues processed: 434 average time/residue: 0.4193 time to fit residues: 274.1103 Evaluate side-chains 377 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 355 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 286 ASP 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 680 MET Chi-restraints excluded: chain D residue 691 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 232 optimal weight: 0.8980 chunk 190 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 280 optimal weight: 0.5980 chunk 302 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 277 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 HIS B 219 HIS B 520 GLN ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 HIS ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 753 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2559 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= 0.335 Angle : 0.594 9.662 33504 Z= 0.304 Chirality : 0.042 0.145 3908 Planarity : 0.004 0.041 4204 Dihedral : 4.918 32.811 3332 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.72 % Allowed : 7.74 % Favored : 90.55 % 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: 0.64 (0.14), residues: 3048 helix: 0.76 (0.12), residues: 1780 sheet: 0.28 (0.29), residues: 248 loop : 0.11 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 588 HIS 0.008 0.001 HIS A 366 PHE 0.024 0.002 PHE A 594 TYR 0.016 0.002 TYR D 171 ARG 0.005 0.000 ARG A 132 *********************** 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 421 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 375 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7497 (mt) REVERT: A 200 ARG cc_start: 0.8509 (ttp80) cc_final: 0.8292 (ttp80) REVERT: A 205 ASN cc_start: 0.8273 (t0) cc_final: 0.7737 (t0) REVERT: A 216 ASP cc_start: 0.7378 (t0) cc_final: 0.7142 (t0) REVERT: B 131 LYS cc_start: 0.8386 (tptt) cc_final: 0.7577 (mmtt) REVERT: B 205 ASN cc_start: 0.8380 (t0) cc_final: 0.8026 (t0) REVERT: B 216 ASP cc_start: 0.7486 (t0) cc_final: 0.7137 (t0) REVERT: B 217 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7855 (mm-30) REVERT: B 516 ARG cc_start: 0.7753 (mmt-90) cc_final: 0.7353 (mpt180) REVERT: B 860 ARG cc_start: 0.7258 (mtt90) cc_final: 0.7046 (mtm-85) REVERT: B 863 TRP cc_start: 0.8918 (t-100) cc_final: 0.8711 (t-100) REVERT: C 612 THR cc_start: 0.6791 (OUTLIER) cc_final: 0.5750 (p) REVERT: D 131 LYS cc_start: 0.8612 (tptt) cc_final: 0.7895 (mmtt) REVERT: D 307 MET cc_start: 0.7222 (mmm) cc_final: 0.6851 (mmt) REVERT: D 488 THR cc_start: 0.8337 (m) cc_final: 0.8044 (p) outliers start: 46 outliers final: 37 residues processed: 399 average time/residue: 0.3939 time to fit residues: 241.3096 Evaluate side-chains 388 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 349 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 286 ASP 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 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 308 LYS Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 286 ASP 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 530 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 335 CYS Chi-restraints excluded: chain D residue 513 LYS Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 680 MET Chi-restraints excluded: chain D residue 691 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 0.7980 chunk 210 optimal weight: 0.2980 chunk 145 optimal weight: 0.3980 chunk 31 optimal weight: 4.9990 chunk 133 optimal weight: 0.2980 chunk 188 optimal weight: 3.9990 chunk 281 optimal weight: 0.6980 chunk 297 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 266 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 HIS D 451 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24808 Z= 0.150 Angle : 0.502 9.249 33504 Z= 0.259 Chirality : 0.039 0.158 3908 Planarity : 0.003 0.034 4204 Dihedral : 4.517 27.633 3332 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.49 % Allowed : 8.86 % Favored : 89.65 % 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: 1.10 (0.15), residues: 3048 helix: 1.21 (0.12), residues: 1808 sheet: 0.46 (0.29), residues: 248 loop : 0.09 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 588 HIS 0.005 0.001 HIS D 366 PHE 0.015 0.001 PHE D 313 TYR 0.015 0.001 TYR B 113 ARG 0.006 0.000 ARG D 396 *********************** 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 417 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 377 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8256 (ttp80) REVERT: A 205 ASN cc_start: 0.8219 (t0) cc_final: 0.7707 (t0) REVERT: A 216 ASP cc_start: 0.7337 (t0) cc_final: 0.7094 (t0) REVERT: A 727 ASP cc_start: 0.8395 (m-30) cc_final: 0.8112 (m-30) REVERT: B 131 LYS cc_start: 0.8381 (tptt) cc_final: 0.7586 (mmtt) REVERT: B 153 LYS cc_start: 0.8890 (tppt) cc_final: 0.8410 (tptp) REVERT: B 205 ASN cc_start: 0.8348 (t0) cc_final: 0.7984 (t0) REVERT: B 216 ASP cc_start: 0.7430 (t0) cc_final: 0.7047 (t0) REVERT: B 217 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7799 (mm-30) REVERT: C 212 MET cc_start: 0.8739 (ttm) cc_final: 0.8475 (ttt) REVERT: C 587 MET cc_start: 0.6996 (mmm) cc_final: 0.6695 (mmm) REVERT: C 612 THR cc_start: 0.6563 (OUTLIER) cc_final: 0.5449 (p) REVERT: D 131 LYS cc_start: 0.8562 (tptt) cc_final: 0.7873 (mmtt) REVERT: D 205 ASN cc_start: 0.8491 (t0) cc_final: 0.8098 (t0) REVERT: D 264 MET cc_start: 0.7896 (mtm) cc_final: 0.7554 (mtm) REVERT: D 267 THR cc_start: 0.7914 (p) cc_final: 0.7587 (p) REVERT: D 307 MET cc_start: 0.7152 (mmm) cc_final: 0.6891 (mmt) outliers start: 40 outliers final: 24 residues processed: 394 average time/residue: 0.3876 time to fit residues: 236.4035 Evaluate side-chains 369 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 344 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 286 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 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 296 VAL Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 513 LYS Chi-restraints excluded: chain D residue 548 GLN 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 247 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 221 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 254 optimal weight: 0.3980 chunk 205 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 267 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3015 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= 0.201 Angle : 0.512 8.378 33504 Z= 0.260 Chirality : 0.040 0.257 3908 Planarity : 0.003 0.034 4204 Dihedral : 4.380 28.503 3332 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.83 % Allowed : 9.68 % Favored : 88.49 % 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: 1.22 (0.15), residues: 3048 helix: 1.32 (0.12), residues: 1804 sheet: 0.50 (0.30), residues: 248 loop : 0.12 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 588 HIS 0.005 0.001 HIS C 366 PHE 0.015 0.001 PHE D 781 TYR 0.013 0.001 TYR D 171 ARG 0.004 0.000 ARG B 396 *********************** 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 422 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 373 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ARG cc_start: 0.8508 (ttp80) cc_final: 0.8267 (ttp80) REVERT: A 205 ASN cc_start: 0.8239 (t0) cc_final: 0.7710 (t0) REVERT: A 216 ASP cc_start: 0.7366 (t0) cc_final: 0.7159 (t0) REVERT: A 217 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7909 (mm-30) REVERT: A 313 PHE cc_start: 0.7527 (t80) cc_final: 0.7326 (t80) REVERT: A 727 ASP cc_start: 0.8261 (m-30) cc_final: 0.8055 (m-30) REVERT: B 126 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: B 131 LYS cc_start: 0.8351 (tptt) cc_final: 0.7581 (mmtt) REVERT: B 153 LYS cc_start: 0.8830 (tppt) cc_final: 0.8534 (tptp) REVERT: B 205 ASN cc_start: 0.8371 (t0) cc_final: 0.8009 (t0) REVERT: B 216 ASP cc_start: 0.7412 (t0) cc_final: 0.7091 (t0) REVERT: B 217 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7830 (mm-30) REVERT: C 126 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: C 212 MET cc_start: 0.8736 (ttm) cc_final: 0.8461 (ttt) REVERT: C 511 SER cc_start: 0.7988 (t) cc_final: 0.7666 (p) REVERT: C 520 GLN cc_start: 0.6227 (pp30) cc_final: 0.5851 (pp30) REVERT: C 612 THR cc_start: 0.6364 (OUTLIER) cc_final: 0.5151 (p) REVERT: D 122 THR cc_start: 0.8623 (p) cc_final: 0.8296 (p) REVERT: D 131 LYS cc_start: 0.8539 (tptt) cc_final: 0.7869 (mmtt) REVERT: D 205 ASN cc_start: 0.8500 (t0) cc_final: 0.8105 (t0) REVERT: D 264 MET cc_start: 0.7940 (mtm) cc_final: 0.7545 (mtm) REVERT: D 307 MET cc_start: 0.7223 (mmm) cc_final: 0.6965 (mmt) outliers start: 49 outliers final: 33 residues processed: 400 average time/residue: 0.3744 time to fit residues: 233.1781 Evaluate side-chains 382 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 346 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 403 SER 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 101 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 296 VAL Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 487 ASP Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain D residue 513 LYS Chi-restraints excluded: chain D residue 548 GLN 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 100 optimal weight: 8.9990 chunk 268 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 137 optimal weight: 9.9990 chunk 24 optimal weight: 0.0670 chunk 98 optimal weight: 0.1980 chunk 156 optimal weight: 1.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3211 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= 0.174 Angle : 0.497 8.725 33504 Z= 0.251 Chirality : 0.039 0.290 3908 Planarity : 0.003 0.033 4204 Dihedral : 4.219 27.419 3332 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.94 % Allowed : 10.35 % Favored : 87.71 % 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: 1.33 (0.15), residues: 3048 helix: 1.45 (0.12), residues: 1804 sheet: 0.60 (0.30), residues: 248 loop : 0.04 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 588 HIS 0.005 0.001 HIS C 366 PHE 0.013 0.001 PHE C 658 TYR 0.014 0.001 TYR B 113 ARG 0.005 0.000 ARG A 396 *********************** 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 418 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 366 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8253 (ttp80) REVERT: A 205 ASN cc_start: 0.8258 (t0) cc_final: 0.7736 (t0) REVERT: A 216 ASP cc_start: 0.7375 (t0) cc_final: 0.7160 (t0) REVERT: B 126 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: B 131 LYS cc_start: 0.8323 (tptt) cc_final: 0.7540 (mmtt) REVERT: B 153 LYS cc_start: 0.8903 (tppt) cc_final: 0.8544 (tptp) REVERT: B 205 ASN cc_start: 0.8374 (t0) cc_final: 0.8012 (t0) REVERT: B 216 ASP cc_start: 0.7396 (t0) cc_final: 0.7095 (t0) REVERT: B 217 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7810 (mm-30) REVERT: B 516 ARG cc_start: 0.7718 (mmt-90) cc_final: 0.7507 (mpt180) REVERT: B 660 ASP cc_start: 0.7714 (t70) cc_final: 0.7449 (t70) REVERT: C 126 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: C 212 MET cc_start: 0.8686 (ttm) cc_final: 0.8413 (ttt) REVERT: C 511 SER cc_start: 0.7982 (t) cc_final: 0.7636 (p) REVERT: C 520 GLN cc_start: 0.6386 (pp30) cc_final: 0.6007 (pp30) REVERT: C 587 MET cc_start: 0.7007 (mmm) cc_final: 0.6781 (mmm) REVERT: C 612 THR cc_start: 0.6146 (OUTLIER) cc_final: 0.4891 (p) REVERT: D 131 LYS cc_start: 0.8471 (tptt) cc_final: 0.7822 (mmtt) REVERT: D 205 ASN cc_start: 0.8511 (t0) cc_final: 0.8118 (t0) REVERT: D 264 MET cc_start: 0.7898 (mtm) cc_final: 0.7495 (mtm) REVERT: D 307 MET cc_start: 0.7183 (mmm) cc_final: 0.6976 (mmt) REVERT: D 511 SER cc_start: 0.7747 (t) cc_final: 0.7452 (p) outliers start: 52 outliers final: 35 residues processed: 395 average time/residue: 0.3693 time to fit residues: 231.4576 Evaluate side-chains 382 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 344 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 403 SER 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 831 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 126 GLU 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 403 SER Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 286 ASP 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 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 Chi-restraints excluded: chain D residue 743 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 0.0870 chunk 33 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 chunk 217 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 296 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3312 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= 0.166 Angle : 0.489 9.501 33504 Z= 0.246 Chirality : 0.039 0.174 3908 Planarity : 0.003 0.036 4204 Dihedral : 4.122 26.961 3332 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.72 % Allowed : 10.84 % Favored : 87.44 % 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: 1.46 (0.15), residues: 3048 helix: 1.56 (0.12), residues: 1804 sheet: 0.69 (0.30), residues: 248 loop : 0.07 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 588 HIS 0.004 0.000 HIS C 366 PHE 0.020 0.001 PHE A 313 TYR 0.018 0.001 TYR A 156 ARG 0.004 0.000 ARG B 396 *********************** 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 399 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 353 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ARG cc_start: 0.8514 (ttp80) cc_final: 0.8253 (ttp80) REVERT: A 205 ASN cc_start: 0.8244 (t0) cc_final: 0.7690 (t0) REVERT: B 126 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: B 131 LYS cc_start: 0.8342 (tptt) cc_final: 0.7557 (mmtt) REVERT: B 153 LYS cc_start: 0.8885 (tppt) cc_final: 0.8522 (tptp) REVERT: B 205 ASN cc_start: 0.8386 (t0) cc_final: 0.8030 (t0) REVERT: B 216 ASP cc_start: 0.7422 (t0) cc_final: 0.7111 (t0) REVERT: B 217 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7765 (mm-30) REVERT: B 660 ASP cc_start: 0.7676 (t70) cc_final: 0.7383 (t70) REVERT: C 126 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: C 212 MET cc_start: 0.8646 (ttm) cc_final: 0.8386 (ttt) REVERT: C 314 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: C 511 SER cc_start: 0.7997 (t) cc_final: 0.7682 (p) REVERT: C 520 GLN cc_start: 0.6434 (pp30) cc_final: 0.6076 (pp30) REVERT: C 612 THR cc_start: 0.6371 (OUTLIER) cc_final: 0.5026 (p) REVERT: D 131 LYS cc_start: 0.8399 (tptt) cc_final: 0.7740 (mmtt) REVERT: D 205 ASN cc_start: 0.8499 (t0) cc_final: 0.8122 (t0) REVERT: D 264 MET cc_start: 0.7869 (mtm) cc_final: 0.7440 (mtm) REVERT: D 511 SER cc_start: 0.7740 (t) cc_final: 0.7463 (p) outliers start: 46 outliers final: 32 residues processed: 382 average time/residue: 0.3793 time to fit residues: 229.3316 Evaluate side-chains 381 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 345 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 403 SER 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 831 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 126 GLU 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 403 SER Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 743 CYS 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 691 GLU Chi-restraints excluded: chain D residue 743 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 0.0770 chunk 118 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 202 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 233 optimal weight: 7.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 HIS ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24808 Z= 0.203 Angle : 0.514 9.798 33504 Z= 0.256 Chirality : 0.039 0.196 3908 Planarity : 0.003 0.035 4204 Dihedral : 4.115 27.975 3332 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.83 % Allowed : 11.25 % Favored : 86.92 % 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: 1.41 (0.15), residues: 3048 helix: 1.56 (0.12), residues: 1804 sheet: 0.70 (0.30), residues: 248 loop : -0.04 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 588 HIS 0.006 0.001 HIS C 85 PHE 0.015 0.001 PHE A 313 TYR 0.017 0.001 TYR A 156 ARG 0.004 0.000 ARG B 516 *********************** 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 402 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 353 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: A 200 ARG cc_start: 0.8523 (ttp80) cc_final: 0.8263 (ttp80) REVERT: A 205 ASN cc_start: 0.8254 (t0) cc_final: 0.7718 (t0) REVERT: A 366 HIS cc_start: 0.5071 (OUTLIER) cc_final: 0.4279 (p-80) REVERT: B 126 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: B 131 LYS cc_start: 0.8363 (tptt) cc_final: 0.7598 (mmtt) REVERT: B 153 LYS cc_start: 0.8888 (tppt) cc_final: 0.8535 (tptp) REVERT: B 205 ASN cc_start: 0.8404 (t0) cc_final: 0.8049 (t0) REVERT: B 216 ASP cc_start: 0.7428 (t0) cc_final: 0.7220 (t0) REVERT: B 660 ASP cc_start: 0.7689 (t70) cc_final: 0.7366 (t70) REVERT: C 126 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: C 212 MET cc_start: 0.8672 (ttm) cc_final: 0.8409 (ttt) REVERT: C 314 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: C 511 SER cc_start: 0.8011 (t) cc_final: 0.7690 (p) REVERT: C 520 GLN cc_start: 0.6483 (pp30) cc_final: 0.6115 (pp30) REVERT: C 612 THR cc_start: 0.6452 (OUTLIER) cc_final: 0.5145 (p) REVERT: C 657 MET cc_start: 0.6898 (mmp) cc_final: 0.6650 (mmt) REVERT: D 131 LYS cc_start: 0.8384 (tptt) cc_final: 0.7745 (mmtt) REVERT: D 205 ASN cc_start: 0.8522 (t0) cc_final: 0.8131 (t0) REVERT: D 511 SER cc_start: 0.7758 (t) cc_final: 0.7472 (p) REVERT: D 545 SER cc_start: 0.8601 (t) cc_final: 0.8312 (m) outliers start: 49 outliers final: 37 residues processed: 383 average time/residue: 0.3648 time to fit residues: 221.1675 Evaluate side-chains 386 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 343 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 286 ASP 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 831 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 126 GLU 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 403 SER Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 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 257 ASN Chi-restraints excluded: chain D residue 513 LYS Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 743 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 0.6980 chunk 284 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 276 optimal weight: 0.0970 chunk 166 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 84 optimal weight: 0.2980 chunk 249 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 275 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24808 Z= 0.152 Angle : 0.495 10.451 33504 Z= 0.248 Chirality : 0.038 0.164 3908 Planarity : 0.003 0.034 4204 Dihedral : 4.024 26.217 3332 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.68 % Allowed : 11.81 % Favored : 86.51 % 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: 1.61 (0.15), residues: 3048 helix: 1.70 (0.12), residues: 1796 sheet: 0.78 (0.30), residues: 248 loop : 0.09 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 588 HIS 0.004 0.000 HIS C 85 PHE 0.012 0.001 PHE A 313 TYR 0.017 0.001 TYR A 156 ARG 0.004 0.000 ARG A 516 *********************** 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 413 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 368 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8828 (mp) cc_final: 0.8620 (mt) REVERT: A 200 ARG cc_start: 0.8520 (ttp80) cc_final: 0.8249 (ttp80) REVERT: A 205 ASN cc_start: 0.8236 (t0) cc_final: 0.7665 (t0) REVERT: A 366 HIS cc_start: 0.5003 (OUTLIER) cc_final: 0.4273 (p-80) REVERT: A 511 SER cc_start: 0.7811 (t) cc_final: 0.7467 (p) REVERT: B 126 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: B 131 LYS cc_start: 0.8356 (tptt) cc_final: 0.7600 (mmtt) REVERT: B 153 LYS cc_start: 0.8875 (tppt) cc_final: 0.8559 (tptp) REVERT: B 205 ASN cc_start: 0.8394 (t0) cc_final: 0.8044 (t0) REVERT: B 216 ASP cc_start: 0.7432 (t0) cc_final: 0.7208 (t0) REVERT: C 126 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: C 212 MET cc_start: 0.8637 (ttm) cc_final: 0.8382 (ttt) REVERT: C 314 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: C 511 SER cc_start: 0.8056 (t) cc_final: 0.7778 (p) REVERT: C 520 GLN cc_start: 0.6514 (pp30) cc_final: 0.6134 (pp30) REVERT: C 612 THR cc_start: 0.6400 (OUTLIER) cc_final: 0.5092 (p) REVERT: D 131 LYS cc_start: 0.8332 (tptt) cc_final: 0.7749 (mmtt) REVERT: D 205 ASN cc_start: 0.8500 (t0) cc_final: 0.8111 (t0) REVERT: D 513 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8333 (pttm) REVERT: D 545 SER cc_start: 0.8603 (t) cc_final: 0.8346 (m) outliers start: 45 outliers final: 30 residues processed: 399 average time/residue: 0.3633 time to fit residues: 230.3451 Evaluate side-chains 383 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 347 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 403 SER 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 A residue 831 VAL Chi-restraints excluded: chain B residue 126 GLU 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 487 ASP Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 513 LYS Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 743 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.9980 chunk 292 optimal weight: 7.9990 chunk 178 optimal weight: 0.0050 chunk 138 optimal weight: 7.9990 chunk 203 optimal weight: 0.3980 chunk 306 optimal weight: 0.3980 chunk 282 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24808 Z= 0.153 Angle : 0.504 10.856 33504 Z= 0.252 Chirality : 0.039 0.166 3908 Planarity : 0.003 0.035 4204 Dihedral : 3.976 25.993 3332 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.35 % Allowed : 12.59 % Favored : 86.06 % 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: 1.65 (0.15), residues: 3048 helix: 1.74 (0.12), residues: 1796 sheet: 0.85 (0.30), residues: 248 loop : 0.07 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 588 HIS 0.005 0.001 HIS C 85 PHE 0.013 0.001 PHE A 313 TYR 0.041 0.001 TYR D 331 ARG 0.005 0.000 ARG B 516 ********************** 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 393 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 357 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8755 (mp) cc_final: 0.8533 (mt) REVERT: A 200 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8256 (ttp80) REVERT: A 205 ASN cc_start: 0.8250 (t0) cc_final: 0.7678 (t0) REVERT: A 366 HIS cc_start: 0.5069 (OUTLIER) cc_final: 0.4337 (p-80) REVERT: A 511 SER cc_start: 0.7800 (t) cc_final: 0.7467 (p) REVERT: B 126 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: B 131 LYS cc_start: 0.8316 (tptt) cc_final: 0.7542 (mmtt) REVERT: B 153 LYS cc_start: 0.8870 (tppt) cc_final: 0.8556 (tptp) REVERT: B 205 ASN cc_start: 0.8404 (t0) cc_final: 0.8070 (t0) REVERT: B 216 ASP cc_start: 0.7402 (t0) cc_final: 0.7184 (t0) REVERT: C 126 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: C 212 MET cc_start: 0.8611 (ttm) cc_final: 0.8365 (ttt) REVERT: C 231 GLU cc_start: 0.8319 (tp30) cc_final: 0.8103 (tp30) REVERT: C 314 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: C 463 ILE cc_start: 0.9007 (mm) cc_final: 0.8744 (mt) REVERT: C 511 SER cc_start: 0.8061 (t) cc_final: 0.7790 (p) REVERT: C 520 GLN cc_start: 0.6509 (pp30) cc_final: 0.6152 (pp30) REVERT: C 612 THR cc_start: 0.6330 (OUTLIER) cc_final: 0.4985 (p) REVERT: D 131 LYS cc_start: 0.8316 (tptt) cc_final: 0.7738 (mmtt) REVERT: D 205 ASN cc_start: 0.8495 (t0) cc_final: 0.8079 (t0) REVERT: D 545 SER cc_start: 0.8615 (t) cc_final: 0.8343 (m) outliers start: 36 outliers final: 29 residues processed: 380 average time/residue: 0.3967 time to fit residues: 241.3990 Evaluate side-chains 379 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 345 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 366 HIS 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 A residue 831 VAL Chi-restraints excluded: chain B residue 126 GLU 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 487 ASP Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 743 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 8.9990 chunk 260 optimal weight: 20.0000 chunk 74 optimal weight: 0.3980 chunk 225 optimal weight: 0.9980 chunk 36 optimal weight: 0.0370 chunk 67 optimal weight: 2.9990 chunk 244 optimal weight: 0.1980 chunk 102 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 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 = 0.3848 r_free = 0.3848 target = 0.136920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.118295 restraints weight = 39400.547| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.82 r_work: 0.3432 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24808 Z= 0.137 Angle : 0.491 11.092 33504 Z= 0.246 Chirality : 0.038 0.165 3908 Planarity : 0.003 0.034 4204 Dihedral : 3.888 25.052 3332 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.42 % Allowed : 12.56 % Favored : 86.02 % 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: 1.76 (0.15), residues: 3048 helix: 1.82 (0.12), residues: 1800 sheet: 0.97 (0.31), residues: 248 loop : 0.12 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 588 HIS 0.005 0.001 HIS C 85 PHE 0.013 0.001 PHE D 632 TYR 0.019 0.001 TYR A 156 ARG 0.004 0.000 ARG B 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5707.61 seconds wall clock time: 104 minutes 39.22 seconds (6279.22 seconds total)