Starting phenix.real_space_refine on Fri Jul 3 03:54:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mj5_48312/07_2026/9mj5_48312.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mj5_48312/07_2026/9mj5_48312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mj5_48312/07_2026/9mj5_48312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mj5_48312/07_2026/9mj5_48312.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mj5_48312/07_2026/9mj5_48312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mj5_48312/07_2026/9mj5_48312.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 1.012 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 44 5.49 5 Mg 1 5.21 5 S 68 5.16 5 C 7460 2.51 5 N 2022 2.21 5 O 2323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11919 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 924 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "B" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1615 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain breaks: 1 Chain: "C" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1474 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "P" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'DNA': 2, 'RNA': 9} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 7008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 7008 Classifications: {'peptide': 873} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 829} Chain breaks: 2 Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2894 SG CYS C 481 47.947 20.076 23.775 1.00167.33 S ATOM 2931 SG CYS C 486 46.552 22.050 21.138 1.00167.15 S ATOM 3047 SG CYS C 500 44.588 19.326 23.956 1.00182.05 S ATOM 3071 SG CYS C 503 46.637 18.385 19.916 1.00180.28 S Time building chain proxies: 2.39, per 1000 atoms: 0.20 Number of scatterers: 11919 At special positions: 0 Unit cell: (97.92, 116.64, 146.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 68 16.00 P 44 15.00 Mg 1 11.99 O 2323 8.00 N 2022 7.00 C 7460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 379.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 503 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 500 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 481 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 486 " Number of angles added : 6 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 15 sheets defined 40.2% alpha, 24.6% beta 10 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.740A pdb=" N MET A 16 " --> pdb=" O ASN A 13 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A 17 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ALA A 18 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 109 removed outlier: 3.854A pdb=" N TYR A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 115 through 119 removed outlier: 3.505A pdb=" N VAL B 119 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 175 Processing helix chain 'B' and resid 206 through 219 removed outlier: 3.723A pdb=" N CYS B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 234 Processing helix chain 'B' and resid 238 through 252 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 532 through 541 Processing helix chain 'C' and resid 543 through 554 removed outlier: 3.923A pdb=" N GLU C 549 " --> pdb=" O ALA C 545 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU C 550 " --> pdb=" O TYR C 546 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 565 removed outlier: 3.803A pdb=" N ALA C 565 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 616 removed outlier: 3.586A pdb=" N LEU C 615 " --> pdb=" O ARG C 611 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET C 616 " --> pdb=" O ARG C 612 " (cutoff:3.500A) Processing helix chain 'S' and resid 409 through 420 Processing helix chain 'S' and resid 420 through 426 Processing helix chain 'S' and resid 482 through 492 Processing helix chain 'S' and resid 597 through 606 Processing helix chain 'S' and resid 614 through 630 Processing helix chain 'S' and resid 642 through 655 Processing helix chain 'S' and resid 658 through 663 removed outlier: 3.672A pdb=" N LYS S 661 " --> pdb=" O HIS S 658 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE S 662 " --> pdb=" O TRP S 659 " (cutoff:3.500A) Processing helix chain 'S' and resid 678 through 685 Processing helix chain 'S' and resid 693 through 701 Processing helix chain 'S' and resid 707 through 716 Processing helix chain 'S' and resid 725 through 733 removed outlier: 3.898A pdb=" N GLN S 729 " --> pdb=" O GLU S 726 " (cutoff:3.500A) Processing helix chain 'S' and resid 734 through 760 removed outlier: 3.515A pdb=" N LEU S 738 " --> pdb=" O GLU S 734 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN S 760 " --> pdb=" O MET S 756 " (cutoff:3.500A) Processing helix chain 'S' and resid 760 through 773 removed outlier: 4.116A pdb=" N LEU S 764 " --> pdb=" O ASN S 760 " (cutoff:3.500A) Processing helix chain 'S' and resid 775 through 782 Processing helix chain 'S' and resid 784 through 799 removed outlier: 3.681A pdb=" N ASN S 788 " --> pdb=" O ARG S 784 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN S 799 " --> pdb=" O ALA S 795 " (cutoff:3.500A) Processing helix chain 'S' and resid 863 through 873 Processing helix chain 'S' and resid 909 through 931 removed outlier: 4.029A pdb=" N ARG S 922 " --> pdb=" O LEU S 918 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS S 923 " --> pdb=" O VAL S 919 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN S 924 " --> pdb=" O GLU S 920 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL S 925 " --> pdb=" O ARG S 921 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN S 931 " --> pdb=" O GLN S 927 " (cutoff:3.500A) Processing helix chain 'S' and resid 935 through 959 Processing helix chain 'S' and resid 960 through 962 No H-bonds generated for 'chain 'S' and resid 960 through 962' Processing helix chain 'S' and resid 970 through 994 removed outlier: 3.954A pdb=" N VAL S 976 " --> pdb=" O LEU S 972 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET S 994 " --> pdb=" O MET S 990 " (cutoff:3.500A) Processing helix chain 'S' and resid 1014 through 1031 removed outlier: 3.561A pdb=" N VAL S1018 " --> pdb=" O ASN S1014 " (cutoff:3.500A) Processing helix chain 'S' and resid 1085 through 1101 Processing helix chain 'S' and resid 1104 through 1126 Processing helix chain 'S' and resid 1129 through 1134 removed outlier: 3.502A pdb=" N GLN S1132 " --> pdb=" O PRO S1129 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU S1134 " --> pdb=" O SER S1131 " (cutoff:3.500A) Processing helix chain 'S' and resid 1142 through 1146 removed outlier: 4.107A pdb=" N TYR S1146 " --> pdb=" O PRO S1143 " (cutoff:3.500A) Processing helix chain 'S' and resid 1152 through 1165 removed outlier: 3.592A pdb=" N ALA S1158 " --> pdb=" O HIS S1154 " (cutoff:3.500A) Processing helix chain 'S' and resid 1187 through 1190 Processing helix chain 'S' and resid 1194 through 1201 Processing helix chain 'S' and resid 1207 through 1215 removed outlier: 3.589A pdb=" N TYR S1211 " --> pdb=" O ASP S1207 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN S1215 " --> pdb=" O TYR S1211 " (cutoff:3.500A) Processing helix chain 'S' and resid 1216 through 1224 Processing helix chain 'S' and resid 1231 through 1239 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.420A pdb=" N SER A 10 " --> pdb=" O CYS A 26 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N VAL A 28 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU A 31 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N SER A 44 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 33 " --> pdb=" O ILE A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.420A pdb=" N SER A 10 " --> pdb=" O CYS A 26 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N VAL A 28 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 83 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 48 removed outlier: 3.772A pdb=" N THR B 75 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N HIS B 131 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA B 143 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG B 133 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU B 141 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE B 135 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LYS B 139 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASP B 103 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 141 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TRP B 107 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N LYS B 145 " --> pdb=" O TRP B 107 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASN B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS B 85 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 91 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA B 83 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS B 93 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 60 Processing sheet with id=AA5, first strand: chain 'B' and resid 255 through 256 Processing sheet with id=AA6, first strand: chain 'C' and resid 460 through 471 removed outlier: 5.453A pdb=" N VAL C 468 " --> pdb=" O ALA C 521 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA C 521 " --> pdb=" O VAL C 468 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR C 470 " --> pdb=" O ASN C 519 " (cutoff:3.500A) removed outlier: 12.351A pdb=" N ASN C 526 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N ALA C 589 " --> pdb=" O ASN C 526 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N TRP C 528 " --> pdb=" O ALA C 589 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL C 591 " --> pdb=" O TRP C 528 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR C 530 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASP C 593 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 579 " --> pdb=" O ARG C 586 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS C 577 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG C 573 " --> pdb=" O MET C 592 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL C 594 " --> pdb=" O ILE C 571 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE C 571 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N SER C 569 " --> pdb=" O PRO C 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 477 through 480 removed outlier: 4.104A pdb=" N TYR C 478 " --> pdb=" O ARG C 513 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS C 511 " --> pdb=" O ALA C 480 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 491 through 492 removed outlier: 3.555A pdb=" N ILE C 491 " --> pdb=" O ARG C 499 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG C 499 " --> pdb=" O ILE C 491 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 516 through 520 removed outlier: 9.693A pdb=" N VAL S 516 " --> pdb=" O HIS S 373 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER S 375 " --> pdb=" O VAL S 516 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N ALA S 518 " --> pdb=" O SER S 375 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS S 377 " --> pdb=" O ALA S 518 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA S 520 " --> pdb=" O CYS S 377 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N MET S 379 " --> pdb=" O ALA S 520 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS S 364 " --> pdb=" O TRP S 345 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N TRP S 345 " --> pdb=" O LYS S 364 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N TRP S 366 " --> pdb=" O PHE S 343 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N PHE S 343 " --> pdb=" O TRP S 366 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 431 through 438 removed outlier: 3.536A pdb=" N LYS S 437 " --> pdb=" O SER S 450 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER S 450 " --> pdb=" O LYS S 437 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU S 451 " --> pdb=" O PRO S 391 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR S 457 " --> pdb=" O ARG S 385 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS S 475 " --> pdb=" O LEU S 390 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 394 through 396 removed outlier: 7.249A pdb=" N LYS S 395 " --> pdb=" O THR S 404 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 609 through 611 removed outlier: 8.900A pdb=" N GLU S 610 " --> pdb=" O HIS S 582 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS S 584 " --> pdb=" O GLU S 610 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE S 557 " --> pdb=" O MET S 547 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET S 547 " --> pdb=" O ILE S 557 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA S 559 " --> pdb=" O LYS S 545 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER S 567 " --> pdb=" O LEU S 537 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU S 537 " --> pdb=" O SER S 567 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL S 538 " --> pdb=" O ILE S 633 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL S 635 " --> pdb=" O VAL S 538 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N MET S 540 " --> pdb=" O VAL S 635 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE S 634 " --> pdb=" O CYS S 691 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 850 through 852 removed outlier: 5.236A pdb=" N ILE S1040 " --> pdb=" O ASP S 860 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP S 860 " --> pdb=" O ILE S1040 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY S1042 " --> pdb=" O LEU S 858 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR S1000 " --> pdb=" O MET S1007 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN S1009 " --> pdb=" O VAL S 998 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL S 998 " --> pdb=" O ASN S1009 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 850 through 852 removed outlier: 12.257A pdb=" N GLY S1042 " --> pdb=" O PRO S1062 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE S1044 " --> pdb=" O VAL S1060 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL S1060 " --> pdb=" O PHE S1044 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER S1046 " --> pdb=" O LEU S1058 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LYS S1054 " --> pdb=" O LEU S1050 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 1135 through 1138 496 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3348 1.33 - 1.45: 2093 1.45 - 1.57: 6605 1.57 - 1.69: 86 1.69 - 1.81: 110 Bond restraints: 12242 Sorted by residual: bond pdb=" O3B DCP S1302 " pdb=" PG DCP S1302 " ideal model delta sigma weight residual 1.746 1.599 0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" O3A DCP S1302 " pdb=" PB DCP S1302 " ideal model delta sigma weight residual 1.672 1.590 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O5' DCP S1302 " pdb=" PA DCP S1302 " ideal model delta sigma weight residual 1.654 1.578 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3' DC T 20 " pdb=" C2' DC T 20 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.94e+00 bond pdb=" C1' DC T 20 " pdb=" N1 DC T 20 " ideal model delta sigma weight residual 1.468 1.506 -0.038 1.40e-02 5.10e+03 7.38e+00 ... (remaining 12237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 16598 2.78 - 5.57: 122 5.57 - 8.35: 17 8.35 - 11.14: 4 11.14 - 13.92: 1 Bond angle restraints: 16742 Sorted by residual: angle pdb=" C ASP S1002 " pdb=" N THR S1003 " pdb=" CA THR S1003 " ideal model delta sigma weight residual 121.54 131.53 -9.99 1.91e+00 2.74e-01 2.74e+01 angle pdb=" PB DCP S1302 " pdb=" O3B DCP S1302 " pdb=" PG DCP S1302 " ideal model delta sigma weight residual 125.87 139.79 -13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" N3 DT T 29 " pdb=" C4 DT T 29 " pdb=" O4 DT T 29 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT T 5 " pdb=" C4 DT T 5 " pdb=" O4 DT T 5 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" O4' DA T 6 " pdb=" C4' DA T 6 " pdb=" C3' DA T 6 " ideal model delta sigma weight residual 106.00 103.56 2.44 6.00e-01 2.78e+00 1.65e+01 ... (remaining 16737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 7004 34.85 - 69.71: 397 69.71 - 104.56: 27 104.56 - 139.41: 0 139.41 - 174.26: 1 Dihedral angle restraints: 7429 sinusoidal: 3381 harmonic: 4048 Sorted by residual: dihedral pdb=" CA MET B 152 " pdb=" C MET B 152 " pdb=" N ASN B 153 " pdb=" CA ASN B 153 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" C4' DA T 19 " pdb=" C3' DA T 19 " pdb=" O3' DA T 19 " pdb=" P DC T 20 " ideal model delta sinusoidal sigma weight residual -140.00 34.26 -174.26 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA PHE S 441 " pdb=" C PHE S 441 " pdb=" N GLU S 442 " pdb=" CA GLU S 442 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 7426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1278 0.037 - 0.074: 412 0.074 - 0.111: 158 0.111 - 0.148: 35 0.148 - 0.185: 7 Chirality restraints: 1890 Sorted by residual: chirality pdb=" C1' DCP S1302 " pdb=" C2' DCP S1302 " pdb=" N1 DCP S1302 " pdb=" O4' DCP S1302 " both_signs ideal model delta sigma weight residual False 2.25 2.43 -0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CG LEU C 453 " pdb=" CB LEU C 453 " pdb=" CD1 LEU C 453 " pdb=" CD2 LEU C 453 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" CA ILE B 146 " pdb=" N ILE B 146 " pdb=" C ILE B 146 " pdb=" CB ILE B 146 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 1887 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 223 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" CD GLU B 223 " 0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU B 223 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 223 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP S 524 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C ASP S 524 " 0.028 2.00e-02 2.50e+03 pdb=" O ASP S 524 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU S 525 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 451 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" C GLU C 451 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU C 451 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN C 452 " -0.009 2.00e-02 2.50e+03 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 8 2.51 - 3.11: 8299 3.11 - 3.71: 17607 3.71 - 4.30: 23108 4.30 - 4.90: 38680 Nonbonded interactions: 87702 Sorted by model distance: nonbonded pdb="MG MG S1301 " pdb=" O2B DCP S1302 " model vdw 1.915 2.170 nonbonded pdb="MG MG S1301 " pdb=" O3G DCP S1302 " model vdw 1.992 2.170 nonbonded pdb="MG MG S1301 " pdb=" O1A DCP S1302 " model vdw 2.026 2.170 nonbonded pdb="MG MG S1301 " pdb=" O3A DCP S1302 " model vdw 2.038 2.170 nonbonded pdb="MG MG S1301 " pdb=" PB DCP S1302 " model vdw 2.271 2.530 ... (remaining 87697 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.26 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 13.360 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 : 0.005 0.244 12246 Z= 0.272 Angle : 0.743 25.215 16748 Z= 0.392 Chirality : 0.044 0.185 1890 Planarity : 0.004 0.030 1995 Dihedral : 19.143 174.263 4801 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 0.73 % Allowed : 27.45 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.23), residues: 1364 helix: 2.02 (0.24), residues: 486 sheet: 0.33 (0.32), residues: 257 loop : -0.64 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 9 TYR 0.009 0.001 TYR S 957 PHE 0.019 0.001 PHE S 855 TRP 0.011 0.001 TRP B 107 HIS 0.003 0.001 HIS S 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.24 (12242) covalent geometry : angle 0.65700 / 0.39 (16742) hydrogen bonds : bond 0.14644 / 10.00 ( 520) hydrogen bonds : angle 5.60690 / 4.06 ( 1451) metal coordination : bond 0.21273 / 10.01 ( 4) metal coordination : angle 18.36158 / 8.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8775 (mpp) cc_final: 0.7202 (ppp) REVERT: B 123 GLU cc_start: 0.7958 (pp20) cc_final: 0.7646 (pp20) REVERT: B 133 ARG cc_start: 0.8772 (mmm160) cc_final: 0.8353 (ttm170) REVERT: S 797 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7488 (t80) REVERT: S 1124 LEU cc_start: 0.7515 (tt) cc_final: 0.7281 (tp) REVERT: S 1168 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7481 (ptmt) outliers start: 9 outliers final: 6 residues processed: 126 average time/residue: 0.0996 time to fit residues: 18.7532 Evaluate side-chains 117 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain S residue 609 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 718 THR Chi-restraints excluded: chain S residue 797 TYR Chi-restraints excluded: chain S residue 935 ASN Chi-restraints excluded: chain S residue 1239 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN S 549 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.112427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.083811 restraints weight = 30839.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.086421 restraints weight = 16715.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.088142 restraints weight = 11596.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.089247 restraints weight = 9263.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.089938 restraints weight = 8062.070| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12246 Z= 0.142 Angle : 0.569 12.305 16748 Z= 0.300 Chirality : 0.043 0.157 1890 Planarity : 0.003 0.034 1995 Dihedral : 16.347 172.606 2027 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 2.83 % Allowed : 24.13 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.23), residues: 1364 helix: 2.06 (0.24), residues: 491 sheet: 0.35 (0.32), residues: 265 loop : -0.69 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 9 TYR 0.013 0.001 TYR A 99 PHE 0.014 0.001 PHE S 341 TRP 0.006 0.001 TRP S 366 HIS 0.004 0.001 HIS S 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (12242) covalent geometry : angle 0.55076 / 0.30 (16742) hydrogen bonds : bond 0.04921 / 3.34 ( 520) hydrogen bonds : angle 4.76384 / 3.47 ( 1451) metal coordination : bond 0.00833 / 0.40 ( 4) metal coordination : angle 7.58278 / 3.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8725 (mpp) cc_final: 0.7285 (ppp) REVERT: A 40 MET cc_start: 0.5383 (OUTLIER) cc_final: 0.3715 (ppp) REVERT: B 123 GLU cc_start: 0.7869 (pp20) cc_final: 0.7568 (pp20) REVERT: B 237 MET cc_start: 0.7288 (ppp) cc_final: 0.6813 (ppp) REVERT: S 797 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7449 (t80) REVERT: S 1168 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7588 (ptmt) outliers start: 35 outliers final: 22 residues processed: 142 average time/residue: 0.0865 time to fit residues: 18.8775 Evaluate side-chains 134 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain S residue 369 SER Chi-restraints excluded: chain S residue 435 VAL Chi-restraints excluded: chain S residue 609 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 718 THR Chi-restraints excluded: chain S residue 722 VAL Chi-restraints excluded: chain S residue 797 TYR Chi-restraints excluded: chain S residue 935 ASN Chi-restraints excluded: chain S residue 983 ILE Chi-restraints excluded: chain S residue 1127 SER Chi-restraints excluded: chain S residue 1231 ASP Chi-restraints excluded: chain S residue 1239 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 74 optimal weight: 0.0770 chunk 134 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 441 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.111312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.082523 restraints weight = 30825.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.085098 restraints weight = 16711.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086822 restraints weight = 11574.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.087876 restraints weight = 9248.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088359 restraints weight = 8086.371| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12246 Z= 0.156 Angle : 0.549 9.288 16748 Z= 0.292 Chirality : 0.043 0.174 1890 Planarity : 0.003 0.034 1995 Dihedral : 16.365 172.987 2027 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 3.89 % Allowed : 24.21 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.23), residues: 1364 helix: 1.96 (0.24), residues: 492 sheet: 0.10 (0.30), residues: 291 loop : -0.70 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 834 TYR 0.010 0.001 TYR S 978 PHE 0.019 0.001 PHE C 507 TRP 0.005 0.001 TRP S 513 HIS 0.003 0.001 HIS S 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (12242) covalent geometry : angle 0.53774 / 0.29 (16742) hydrogen bonds : bond 0.05061 / 3.41 ( 520) hydrogen bonds : angle 4.56497 / 3.32 ( 1451) metal coordination : bond 0.00603 / 0.28 ( 4) metal coordination : angle 5.75792 / 2.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 113 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8723 (mpp) cc_final: 0.7093 (ppp) REVERT: A 40 MET cc_start: 0.5506 (OUTLIER) cc_final: 0.3865 (ppp) REVERT: B 123 GLU cc_start: 0.7858 (pp20) cc_final: 0.7582 (pp20) REVERT: B 237 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6756 (ppp) REVERT: C 440 THR cc_start: 0.6958 (OUTLIER) cc_final: 0.6718 (m) REVERT: S 797 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7454 (t80) REVERT: S 1168 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7508 (ptmt) outliers start: 48 outliers final: 31 residues processed: 150 average time/residue: 0.0880 time to fit residues: 20.0350 Evaluate side-chains 146 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain S residue 369 SER Chi-restraints excluded: chain S residue 433 LYS Chi-restraints excluded: chain S residue 435 VAL Chi-restraints excluded: chain S residue 609 VAL Chi-restraints excluded: chain S residue 646 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 718 THR Chi-restraints excluded: chain S residue 722 VAL Chi-restraints excluded: chain S residue 797 TYR Chi-restraints excluded: chain S residue 915 ILE Chi-restraints excluded: chain S residue 939 ILE Chi-restraints excluded: chain S residue 946 GLN Chi-restraints excluded: chain S residue 972 LEU Chi-restraints excluded: chain S residue 983 ILE Chi-restraints excluded: chain S residue 1012 SER Chi-restraints excluded: chain S residue 1127 SER Chi-restraints excluded: chain S residue 1231 ASP Chi-restraints excluded: chain S residue 1239 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 6 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 137 optimal weight: 30.0000 chunk 57 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 158 HIS C 487 ASN S1215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.107927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.078356 restraints weight = 31201.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.081000 restraints weight = 16558.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.082734 restraints weight = 11379.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.083766 restraints weight = 9052.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084338 restraints weight = 7946.205| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12246 Z= 0.253 Angle : 0.634 8.249 16748 Z= 0.337 Chirality : 0.045 0.153 1890 Planarity : 0.004 0.037 1995 Dihedral : 16.507 174.908 2025 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 5.59 % Allowed : 23.72 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.23), residues: 1364 helix: 1.81 (0.24), residues: 487 sheet: -0.07 (0.30), residues: 292 loop : -0.94 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG S1191 TYR 0.021 0.002 TYR A 113 PHE 0.026 0.002 PHE S 341 TRP 0.006 0.001 TRP S 513 HIS 0.008 0.002 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.25 (12242) covalent geometry : angle 0.62660 / 0.34 (16742) hydrogen bonds : bond 0.06471 / 4.36 ( 520) hydrogen bonds : angle 4.79955 / 3.47 ( 1451) metal coordination : bond 0.00717 / 0.37 ( 4) metal coordination : angle 5.28969 / 2.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 107 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 GLU cc_start: 0.8096 (pp20) cc_final: 0.7825 (pp20) REVERT: B 237 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6652 (ppp) REVERT: C 440 THR cc_start: 0.7192 (OUTLIER) cc_final: 0.6977 (m) REVERT: S 767 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: S 797 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7550 (t80) REVERT: S 1007 MET cc_start: 0.8730 (mtt) cc_final: 0.8421 (mtt) REVERT: S 1168 LYS cc_start: 0.8171 (mmtm) cc_final: 0.7460 (ptmt) outliers start: 69 outliers final: 46 residues processed: 165 average time/residue: 0.0861 time to fit residues: 21.7658 Evaluate side-chains 153 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 103 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 531 CYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 592 MET Chi-restraints excluded: chain S residue 369 SER Chi-restraints excluded: chain S residue 412 ASP Chi-restraints excluded: chain S residue 433 LYS Chi-restraints excluded: chain S residue 540 MET Chi-restraints excluded: chain S residue 609 VAL Chi-restraints excluded: chain S residue 646 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 718 THR Chi-restraints excluded: chain S residue 722 VAL Chi-restraints excluded: chain S residue 725 MET Chi-restraints excluded: chain S residue 767 GLN Chi-restraints excluded: chain S residue 771 ILE Chi-restraints excluded: chain S residue 788 ASN Chi-restraints excluded: chain S residue 797 TYR Chi-restraints excluded: chain S residue 915 ILE Chi-restraints excluded: chain S residue 935 ASN Chi-restraints excluded: chain S residue 939 ILE Chi-restraints excluded: chain S residue 946 GLN Chi-restraints excluded: chain S residue 983 ILE Chi-restraints excluded: chain S residue 1012 SER Chi-restraints excluded: chain S residue 1058 LEU Chi-restraints excluded: chain S residue 1099 ILE Chi-restraints excluded: chain S residue 1127 SER Chi-restraints excluded: chain S residue 1231 ASP Chi-restraints excluded: chain S residue 1239 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 68 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS S 954 ASN S1185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.110566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.080434 restraints weight = 31102.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.083121 restraints weight = 16575.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084832 restraints weight = 11362.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.085912 restraints weight = 9116.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.086623 restraints weight = 7967.880| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12246 Z= 0.166 Angle : 0.572 9.929 16748 Z= 0.303 Chirality : 0.044 0.190 1890 Planarity : 0.003 0.037 1995 Dihedral : 16.471 173.854 2025 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 4.62 % Allowed : 25.34 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.23), residues: 1364 helix: 1.88 (0.24), residues: 487 sheet: -0.08 (0.30), residues: 287 loop : -0.91 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 921 TYR 0.012 0.001 TYR S 978 PHE 0.017 0.001 PHE S 341 TRP 0.005 0.001 TRP S 513 HIS 0.004 0.001 HIS S 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (12242) covalent geometry : angle 0.56348 / 0.30 (16742) hydrogen bonds : bond 0.05353 / 3.61 ( 520) hydrogen bonds : angle 4.58915 / 3.33 ( 1451) metal coordination : bond 0.00647 / 0.34 ( 4) metal coordination : angle 5.10394 / 2.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 105 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8836 (mpp) cc_final: 0.7153 (ppp) REVERT: B 123 GLU cc_start: 0.8098 (pp20) cc_final: 0.7827 (pp20) REVERT: B 237 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6687 (ppp) REVERT: S 544 MET cc_start: 0.8268 (ptt) cc_final: 0.8039 (ptt) REVERT: S 797 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7510 (t80) REVERT: S 1096 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8740 (tt) REVERT: S 1168 LYS cc_start: 0.8173 (mmtm) cc_final: 0.7435 (ptmt) outliers start: 57 outliers final: 41 residues processed: 152 average time/residue: 0.0852 time to fit residues: 19.8092 Evaluate side-chains 148 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 531 CYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 592 MET Chi-restraints excluded: chain S residue 369 SER Chi-restraints excluded: chain S residue 412 ASP Chi-restraints excluded: chain S residue 433 LYS Chi-restraints excluded: chain S residue 540 MET Chi-restraints excluded: chain S residue 593 ILE Chi-restraints excluded: chain S residue 609 VAL Chi-restraints excluded: chain S residue 635 VAL Chi-restraints excluded: chain S residue 646 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 718 THR Chi-restraints excluded: chain S residue 722 VAL Chi-restraints excluded: chain S residue 788 ASN Chi-restraints excluded: chain S residue 797 TYR Chi-restraints excluded: chain S residue 915 ILE Chi-restraints excluded: chain S residue 939 ILE Chi-restraints excluded: chain S residue 946 GLN Chi-restraints excluded: chain S residue 983 ILE Chi-restraints excluded: chain S residue 1012 SER Chi-restraints excluded: chain S residue 1096 ILE Chi-restraints excluded: chain S residue 1099 ILE Chi-restraints excluded: chain S residue 1127 SER Chi-restraints excluded: chain S residue 1231 ASP Chi-restraints excluded: chain S residue 1239 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 46 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 55 optimal weight: 0.0970 chunk 80 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 475 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.112503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.082792 restraints weight = 31283.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.085528 restraints weight = 16603.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.087296 restraints weight = 11349.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.088405 restraints weight = 9042.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.089106 restraints weight = 7868.049| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12246 Z= 0.114 Angle : 0.535 9.047 16748 Z= 0.283 Chirality : 0.043 0.155 1890 Planarity : 0.003 0.036 1995 Dihedral : 16.385 172.662 2025 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.96 % Favored : 95.97 % Rotamer: Outliers : 4.29 % Allowed : 25.10 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1364 helix: 2.01 (0.24), residues: 487 sheet: 0.14 (0.31), residues: 281 loop : -0.87 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 921 TYR 0.009 0.001 TYR S 957 PHE 0.010 0.001 PHE S 583 TRP 0.006 0.001 TRP C 528 HIS 0.003 0.001 HIS S 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (12242) covalent geometry : angle 0.52774 / 0.28 (16742) hydrogen bonds : bond 0.04225 / 2.87 ( 520) hydrogen bonds : angle 4.34564 / 3.17 ( 1451) metal coordination : bond 0.00537 / 0.28 ( 4) metal coordination : angle 4.68364 / 2.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 110 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8810 (mpp) cc_final: 0.7091 (ppp) REVERT: A 40 MET cc_start: 0.5486 (OUTLIER) cc_final: 0.4041 (ppp) REVERT: B 123 GLU cc_start: 0.8041 (pp20) cc_final: 0.7763 (pp20) REVERT: B 237 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6726 (ppp) REVERT: C 471 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9248 (pp) REVERT: C 473 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8303 (ptpp) REVERT: S 797 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7443 (t80) REVERT: S 1168 LYS cc_start: 0.8133 (mmtm) cc_final: 0.7394 (ptmt) outliers start: 53 outliers final: 37 residues processed: 150 average time/residue: 0.0955 time to fit residues: 21.7467 Evaluate side-chains 151 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 531 CYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 592 MET Chi-restraints excluded: chain S residue 377 CYS Chi-restraints excluded: chain S residue 433 LYS Chi-restraints excluded: chain S residue 540 MET Chi-restraints excluded: chain S residue 593 ILE Chi-restraints excluded: chain S residue 609 VAL Chi-restraints excluded: chain S residue 635 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 718 THR Chi-restraints excluded: chain S residue 722 VAL Chi-restraints excluded: chain S residue 771 ILE Chi-restraints excluded: chain S residue 797 TYR Chi-restraints excluded: chain S residue 915 ILE Chi-restraints excluded: chain S residue 946 GLN Chi-restraints excluded: chain S residue 972 LEU Chi-restraints excluded: chain S residue 983 ILE Chi-restraints excluded: chain S residue 1012 SER Chi-restraints excluded: chain S residue 1058 LEU Chi-restraints excluded: chain S residue 1099 ILE Chi-restraints excluded: chain S residue 1127 SER Chi-restraints excluded: chain S residue 1231 ASP Chi-restraints excluded: chain S residue 1239 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 9 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 124 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.112123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.082204 restraints weight = 31052.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.084973 restraints weight = 16441.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.086754 restraints weight = 11212.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.087883 restraints weight = 8950.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.088619 restraints weight = 7785.196| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12246 Z= 0.120 Angle : 0.536 8.651 16748 Z= 0.281 Chirality : 0.042 0.188 1890 Planarity : 0.003 0.034 1995 Dihedral : 16.363 172.530 2025 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.33 % Favored : 95.60 % Rotamer: Outliers : 4.45 % Allowed : 25.10 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1364 helix: 2.05 (0.24), residues: 486 sheet: 0.28 (0.32), residues: 271 loop : -0.86 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.009 0.001 TYR S 957 PHE 0.011 0.001 PHE S 341 TRP 0.004 0.001 TRP S 366 HIS 0.003 0.001 HIS S 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (12242) covalent geometry : angle 0.52977 / 0.28 (16742) hydrogen bonds : bond 0.04262 / 2.89 ( 520) hydrogen bonds : angle 4.27924 / 3.12 ( 1451) metal coordination : bond 0.00510 / 0.26 ( 4) metal coordination : angle 4.40926 / 2.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 114 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8827 (mpp) cc_final: 0.7012 (ppp) REVERT: B 123 GLU cc_start: 0.8065 (pp20) cc_final: 0.7782 (pp20) REVERT: B 237 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6693 (ppp) REVERT: C 471 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9275 (pp) REVERT: C 473 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8361 (ptpp) REVERT: S 797 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7460 (t80) REVERT: S 1096 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8689 (tt) REVERT: S 1168 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7354 (ptmt) outliers start: 55 outliers final: 46 residues processed: 157 average time/residue: 0.0932 time to fit residues: 22.4576 Evaluate side-chains 162 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 111 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 531 CYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain S residue 377 CYS Chi-restraints excluded: chain S residue 433 LYS Chi-restraints excluded: chain S residue 540 MET Chi-restraints excluded: chain S residue 593 ILE Chi-restraints excluded: chain S residue 609 VAL Chi-restraints excluded: chain S residue 635 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 718 THR Chi-restraints excluded: chain S residue 722 VAL Chi-restraints excluded: chain S residue 771 ILE Chi-restraints excluded: chain S residue 788 ASN Chi-restraints excluded: chain S residue 797 TYR Chi-restraints excluded: chain S residue 915 ILE Chi-restraints excluded: chain S residue 946 GLN Chi-restraints excluded: chain S residue 972 LEU Chi-restraints excluded: chain S residue 983 ILE Chi-restraints excluded: chain S residue 1012 SER Chi-restraints excluded: chain S residue 1058 LEU Chi-restraints excluded: chain S residue 1096 ILE Chi-restraints excluded: chain S residue 1099 ILE Chi-restraints excluded: chain S residue 1127 SER Chi-restraints excluded: chain S residue 1131 SER Chi-restraints excluded: chain S residue 1231 ASP Chi-restraints excluded: chain S residue 1239 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 74 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.108739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.079894 restraints weight = 30910.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.082428 restraints weight = 16840.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.084055 restraints weight = 11680.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.085149 restraints weight = 9428.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.085645 restraints weight = 8224.864| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 12246 Z= 0.208 Angle : 0.597 8.371 16748 Z= 0.314 Chirality : 0.044 0.168 1890 Planarity : 0.004 0.034 1995 Dihedral : 16.471 173.330 2025 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.94 % Rotamer: Outliers : 5.34 % Allowed : 24.70 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.23), residues: 1364 helix: 1.89 (0.24), residues: 486 sheet: 0.15 (0.32), residues: 267 loop : -0.95 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.021 0.001 TYR A 113 PHE 0.021 0.002 PHE S 341 TRP 0.006 0.001 TRP S 746 HIS 0.004 0.001 HIS S 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (12242) covalent geometry : angle 0.59164 / 0.31 (16742) hydrogen bonds : bond 0.05562 / 3.77 ( 520) hydrogen bonds : angle 4.49008 / 3.26 ( 1451) metal coordination : bond 0.00618 / 0.32 ( 4) metal coordination : angle 4.32455 / 2.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 106 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8717 (mpp) cc_final: 0.7040 (ppp) REVERT: B 123 GLU cc_start: 0.7909 (pp20) cc_final: 0.7643 (pp20) REVERT: B 237 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6738 (ppp) REVERT: C 471 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9238 (pp) REVERT: C 473 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8169 (ptpp) REVERT: S 445 ASP cc_start: 0.7658 (t0) cc_final: 0.7277 (t0) REVERT: S 797 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7540 (t80) REVERT: S 1007 MET cc_start: 0.8629 (mtt) cc_final: 0.8345 (mtt) REVERT: S 1096 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8901 (tt) REVERT: S 1168 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7577 (ptmt) outliers start: 66 outliers final: 46 residues processed: 159 average time/residue: 0.0894 time to fit residues: 21.7389 Evaluate side-chains 154 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 103 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 531 CYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain S residue 369 SER Chi-restraints excluded: chain S residue 433 LYS Chi-restraints excluded: chain S residue 528 VAL Chi-restraints excluded: chain S residue 540 MET Chi-restraints excluded: chain S residue 593 ILE Chi-restraints excluded: chain S residue 609 VAL Chi-restraints excluded: chain S residue 646 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 718 THR Chi-restraints excluded: chain S residue 722 VAL Chi-restraints excluded: chain S residue 725 MET Chi-restraints excluded: chain S residue 771 ILE Chi-restraints excluded: chain S residue 788 ASN Chi-restraints excluded: chain S residue 797 TYR Chi-restraints excluded: chain S residue 915 ILE Chi-restraints excluded: chain S residue 946 GLN Chi-restraints excluded: chain S residue 983 ILE Chi-restraints excluded: chain S residue 1012 SER Chi-restraints excluded: chain S residue 1058 LEU Chi-restraints excluded: chain S residue 1096 ILE Chi-restraints excluded: chain S residue 1099 ILE Chi-restraints excluded: chain S residue 1127 SER Chi-restraints excluded: chain S residue 1131 SER Chi-restraints excluded: chain S residue 1231 ASP Chi-restraints excluded: chain S residue 1239 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 20 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 493 GLN S 954 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.108878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.078301 restraints weight = 30487.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.080952 restraints weight = 16390.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.082655 restraints weight = 11281.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.083700 restraints weight = 9066.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.084358 restraints weight = 7961.213| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 12246 Z= 0.224 Angle : 0.631 9.097 16748 Z= 0.328 Chirality : 0.045 0.219 1890 Planarity : 0.004 0.035 1995 Dihedral : 16.575 173.461 2025 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.94 % Rotamer: Outliers : 4.45 % Allowed : 25.99 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.23), residues: 1364 helix: 1.74 (0.24), residues: 489 sheet: 0.05 (0.32), residues: 267 loop : -1.09 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 30 TYR 0.014 0.001 TYR S 978 PHE 0.021 0.002 PHE S 341 TRP 0.006 0.001 TRP S 746 HIS 0.005 0.001 HIS S 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 (12242) covalent geometry : angle 0.62475 / 0.33 (16742) hydrogen bonds : bond 0.05893 / 4.00 ( 520) hydrogen bonds : angle 4.62670 / 3.36 ( 1451) metal coordination : bond 0.00728 / 0.38 ( 4) metal coordination : angle 4.53519 / 2.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 106 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8836 (mpp) cc_final: 0.7098 (ppp) REVERT: A 16 MET cc_start: 0.8884 (pmm) cc_final: 0.8299 (pmm) REVERT: B 123 GLU cc_start: 0.8099 (pp20) cc_final: 0.7826 (pp20) REVERT: B 166 HIS cc_start: 0.9153 (OUTLIER) cc_final: 0.8867 (m-70) REVERT: B 237 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6647 (ppp) REVERT: C 473 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8472 (ptpp) REVERT: S 445 ASP cc_start: 0.8072 (t0) cc_final: 0.7749 (t0) REVERT: S 797 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7514 (t80) REVERT: S 1007 MET cc_start: 0.8725 (mtt) cc_final: 0.8424 (mtt) REVERT: S 1096 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8759 (tt) REVERT: S 1168 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7440 (ptmt) outliers start: 55 outliers final: 46 residues processed: 153 average time/residue: 0.0876 time to fit residues: 20.3938 Evaluate side-chains 153 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 102 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 531 CYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain S residue 369 SER Chi-restraints excluded: chain S residue 412 ASP Chi-restraints excluded: chain S residue 433 LYS Chi-restraints excluded: chain S residue 528 VAL Chi-restraints excluded: chain S residue 540 MET Chi-restraints excluded: chain S residue 593 ILE Chi-restraints excluded: chain S residue 609 VAL Chi-restraints excluded: chain S residue 646 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 718 THR Chi-restraints excluded: chain S residue 722 VAL Chi-restraints excluded: chain S residue 771 ILE Chi-restraints excluded: chain S residue 788 ASN Chi-restraints excluded: chain S residue 797 TYR Chi-restraints excluded: chain S residue 915 ILE Chi-restraints excluded: chain S residue 939 ILE Chi-restraints excluded: chain S residue 946 GLN Chi-restraints excluded: chain S residue 983 ILE Chi-restraints excluded: chain S residue 1012 SER Chi-restraints excluded: chain S residue 1058 LEU Chi-restraints excluded: chain S residue 1096 ILE Chi-restraints excluded: chain S residue 1099 ILE Chi-restraints excluded: chain S residue 1127 SER Chi-restraints excluded: chain S residue 1131 SER Chi-restraints excluded: chain S residue 1231 ASP Chi-restraints excluded: chain S residue 1239 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 88 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 72 optimal weight: 0.0050 chunk 135 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.110881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.082524 restraints weight = 30787.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.085136 restraints weight = 16762.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.086810 restraints weight = 11618.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.087900 restraints weight = 9324.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.088567 restraints weight = 8139.034| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 12246 Z= 0.118 Angle : 0.589 9.344 16748 Z= 0.303 Chirality : 0.044 0.162 1890 Planarity : 0.003 0.037 1995 Dihedral : 16.470 171.635 2025 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 3.64 % Allowed : 27.13 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.23), residues: 1364 helix: 2.00 (0.24), residues: 486 sheet: 0.20 (0.32), residues: 275 loop : -0.96 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.021 0.001 TYR A 113 PHE 0.015 0.001 PHE S 679 TRP 0.010 0.001 TRP C 528 HIS 0.006 0.001 HIS S 794 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (12242) covalent geometry : angle 0.58240 / 0.30 (16742) hydrogen bonds : bond 0.04289 / 2.93 ( 520) hydrogen bonds : angle 4.35143 / 3.18 ( 1451) metal coordination : bond 0.00560 / 0.29 ( 4) metal coordination : angle 4.58078 / 2.28 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8767 (mpp) cc_final: 0.7092 (ppp) REVERT: A 40 MET cc_start: 0.5568 (OUTLIER) cc_final: 0.4090 (ppp) REVERT: B 123 GLU cc_start: 0.7928 (pp20) cc_final: 0.7670 (pp20) REVERT: B 166 HIS cc_start: 0.8944 (OUTLIER) cc_final: 0.8706 (m-70) REVERT: B 237 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6727 (ppp) REVERT: C 473 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8156 (ptpp) REVERT: S 445 ASP cc_start: 0.7850 (t0) cc_final: 0.7531 (t0) REVERT: S 797 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7436 (t80) REVERT: S 1168 LYS cc_start: 0.8076 (mmtm) cc_final: 0.7464 (ptmt) outliers start: 45 outliers final: 38 residues processed: 149 average time/residue: 0.0875 time to fit residues: 19.8850 Evaluate side-chains 151 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 108 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 531 CYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain S residue 433 LYS Chi-restraints excluded: chain S residue 528 VAL Chi-restraints excluded: chain S residue 540 MET Chi-restraints excluded: chain S residue 593 ILE Chi-restraints excluded: chain S residue 609 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 718 THR Chi-restraints excluded: chain S residue 722 VAL Chi-restraints excluded: chain S residue 771 ILE Chi-restraints excluded: chain S residue 788 ASN Chi-restraints excluded: chain S residue 797 TYR Chi-restraints excluded: chain S residue 915 ILE Chi-restraints excluded: chain S residue 946 GLN Chi-restraints excluded: chain S residue 983 ILE Chi-restraints excluded: chain S residue 1012 SER Chi-restraints excluded: chain S residue 1058 LEU Chi-restraints excluded: chain S residue 1099 ILE Chi-restraints excluded: chain S residue 1127 SER Chi-restraints excluded: chain S residue 1131 SER Chi-restraints excluded: chain S residue 1231 ASP Chi-restraints excluded: chain S residue 1239 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.110565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.082235 restraints weight = 30799.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.084831 restraints weight = 16732.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.086511 restraints weight = 11542.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.087571 restraints weight = 9269.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.088135 restraints weight = 8109.742| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12246 Z= 0.124 Angle : 0.582 8.977 16748 Z= 0.300 Chirality : 0.043 0.158 1890 Planarity : 0.003 0.035 1995 Dihedral : 16.453 171.605 2025 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 3.89 % Allowed : 26.80 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1364 helix: 2.01 (0.24), residues: 485 sheet: 0.22 (0.32), residues: 271 loop : -0.89 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.014 0.001 TYR A 113 PHE 0.012 0.001 PHE S 679 TRP 0.006 0.001 TRP C 528 HIS 0.003 0.001 HIS S 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (12242) covalent geometry : angle 0.57645 / 0.30 (16742) hydrogen bonds : bond 0.04309 / 2.93 ( 520) hydrogen bonds : angle 4.30284 / 3.14 ( 1451) metal coordination : bond 0.00540 / 0.28 ( 4) metal coordination : angle 4.22208 / 2.08 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2130.52 seconds wall clock time: 37 minutes 38.83 seconds (2258.83 seconds total)