Starting phenix.real_space_refine on Wed Sep 17 22:50:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mj5_48312/09_2025/9mj5_48312.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mj5_48312/09_2025/9mj5_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_48312/09_2025/9mj5_48312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mj5_48312/09_2025/9mj5_48312.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mj5_48312/09_2025/9mj5_48312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mj5_48312/09_2025/9mj5_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-2.0-5805/lib/python3.9/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: 3.28, per 1000 atoms: 0.28 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: 1.07 Conformation dependent library (CDL) restraints added in 482.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.52 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: 2.69 Time building geometry restraints manager: 1.46 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=" CB GLU C 451 " pdb=" CG GLU C 451 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" C SER S 587 " pdb=" N LYS S 588 " ideal model delta sigma weight residual 1.331 1.357 -0.026 2.07e-02 2.33e+03 1.57e+00 bond pdb=" CA THR S1003 " pdb=" CB THR S1003 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.39e+00 bond pdb=" CB ASP B 247 " pdb=" CG ASP B 247 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.33e+00 bond pdb=" CA MET A 16 " pdb=" CB MET A 16 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.36e-02 5.41e+03 1.20e+00 ... (remaining 12237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 16473 2.00 - 4.00: 226 4.00 - 6.00: 28 6.00 - 8.00: 10 8.00 - 9.99: 5 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=" CA GLU C 451 " pdb=" CB GLU C 451 " pdb=" CG GLU C 451 " ideal model delta sigma weight residual 114.10 120.88 -6.78 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA GLU A 68 " pdb=" CB GLU A 68 " pdb=" CG GLU A 68 " ideal model delta sigma weight residual 114.10 120.82 -6.72 2.00e+00 2.50e-01 1.13e+01 angle pdb=" N GLY A 29 " pdb=" CA GLY A 29 " pdb=" C GLY A 29 " ideal model delta sigma weight residual 110.58 114.95 -4.37 1.35e+00 5.49e-01 1.05e+01 angle pdb=" CA MET A 56 " pdb=" CB MET A 56 " pdb=" CG MET A 56 " ideal model delta sigma weight residual 114.10 120.55 -6.45 2.00e+00 2.50e-01 1.04e+01 ... (remaining 16737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 7000 34.85 - 69.71: 394 69.71 - 104.56: 27 104.56 - 139.41: 0 139.41 - 174.26: 1 Dihedral angle restraints: 7422 sinusoidal: 3374 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 7419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1312 0.037 - 0.073: 397 0.073 - 0.110: 140 0.110 - 0.146: 35 0.146 - 0.183: 6 Chirality restraints: 1890 Sorted by residual: 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 chirality pdb=" CA GLU B 62 " pdb=" N GLU B 62 " pdb=" C GLU B 62 " pdb=" CB GLU B 62 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.960 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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= 0.187 Angle : 0.702 25.215 16748 Z= 0.326 Chirality : 0.043 0.183 1890 Planarity : 0.004 0.030 1995 Dihedral : 19.125 174.263 4794 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 aren 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 covalent geometry : bond 0.00288 (12242) covalent geometry : angle 0.61049 (16742) hydrogen bonds : bond 0.14644 ( 520) hydrogen bonds : angle 5.60690 ( 1451) metal coordination : bond 0.21273 ( 4) metal coordination : angle 18.36158 ( 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 : 0.411 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: 0.1015 time to fit residues: 18.9769 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 : 0.296 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.8980 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: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN C 441 ASN C 564 ASN S 549 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.111354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.082514 restraints weight = 30722.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.085118 restraints weight = 16717.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.086811 restraints weight = 11563.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.087854 restraints weight = 9283.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.088523 restraints weight = 8132.292| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12246 Z= 0.157 Angle : 0.562 9.042 16748 Z= 0.293 Chirality : 0.042 0.162 1890 Planarity : 0.004 0.032 1995 Dihedral : 16.340 175.423 2020 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.16 % Rotamer: Outliers : 3.64 % Allowed : 23.81 % Favored : 72.55 % 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 aren not related in a simple way. whole: 0.71 (0.23), residues: 1364 helix: 2.01 (0.24), residues: 487 sheet: 0.14 (0.30), residues: 291 loop : -0.66 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 9 TYR 0.012 0.001 TYR A 99 PHE 0.017 0.001 PHE S 341 TRP 0.005 0.001 TRP S 746 HIS 0.003 0.001 HIS S1154 Details of bonding type rmsd covalent geometry : bond 0.00366 (12242) covalent geometry : angle 0.55165 (16742) hydrogen bonds : bond 0.05107 ( 520) hydrogen bonds : angle 4.57316 ( 1451) metal coordination : bond 0.00707 ( 4) metal coordination : angle 5.57542 ( 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 158 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8764 (mpp) cc_final: 0.7159 (ppp) REVERT: A 68 GLU cc_start: 0.8268 (pp20) cc_final: 0.7867 (pp20) REVERT: B 123 GLU cc_start: 0.7925 (pp20) cc_final: 0.7651 (pp20) REVERT: B 237 MET cc_start: 0.7140 (ppp) cc_final: 0.6697 (ppp) REVERT: S 797 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7424 (t80) REVERT: S 1124 LEU cc_start: 0.7593 (tt) cc_final: 0.7348 (tp) REVERT: S 1168 LYS cc_start: 0.8057 (mmtm) cc_final: 0.7465 (ptmt) outliers start: 45 outliers final: 25 residues processed: 150 average time/residue: 0.0849 time to fit residues: 19.6370 Evaluate side-chains 133 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 159 ILE Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain S residue 435 VAL Chi-restraints excluded: chain S residue 540 MET 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 915 ILE Chi-restraints excluded: chain S residue 946 GLN Chi-restraints excluded: chain S residue 983 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.110199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.080524 restraints weight = 30845.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.083157 restraints weight = 16339.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.084879 restraints weight = 11176.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.085971 restraints weight = 8897.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.086629 restraints weight = 7742.718| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12246 Z= 0.182 Angle : 0.571 8.266 16748 Z= 0.298 Chirality : 0.043 0.157 1890 Planarity : 0.004 0.033 1995 Dihedral : 16.403 176.250 2018 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 4.78 % Allowed : 23.64 % Favored : 71.58 % 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 aren not related in a simple way. whole: 0.58 (0.23), residues: 1364 helix: 1.96 (0.24), residues: 488 sheet: -0.01 (0.30), residues: 291 loop : -0.75 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 30 TYR 0.015 0.001 TYR S 978 PHE 0.020 0.002 PHE S 341 TRP 0.005 0.001 TRP S 746 HIS 0.004 0.001 HIS S 707 Details of bonding type rmsd covalent geometry : bond 0.00433 (12242) covalent geometry : angle 0.56138 (16742) hydrogen bonds : bond 0.05493 ( 520) hydrogen bonds : angle 4.54385 ( 1451) metal coordination : bond 0.00677 ( 4) metal coordination : angle 5.60668 ( 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 166 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 107 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8816 (mpp) cc_final: 0.7024 (ppp) REVERT: A 12 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8392 (mm) REVERT: A 89 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6983 (tp30) REVERT: B 123 GLU cc_start: 0.8068 (pp20) cc_final: 0.7800 (pp20) REVERT: B 237 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6639 (ppp) REVERT: S 445 ASP cc_start: 0.7951 (t0) cc_final: 0.7723 (t0) REVERT: S 797 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7541 (t80) REVERT: S 1168 LYS cc_start: 0.8172 (mmtm) cc_final: 0.7445 (ptmt) outliers start: 59 outliers final: 35 residues processed: 155 average time/residue: 0.0947 time to fit residues: 22.2160 Evaluate side-chains 141 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 69 VAL Chi-restraints excluded: chain A residue 80 LEU 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 159 ILE 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 529 VAL Chi-restraints excluded: chain C residue 531 CYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain S residue 369 SER 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 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 946 GLN 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: 8.9990 chunk 123 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 114 optimal weight: 0.5980 chunk 137 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS C 493 GLN S1111 ASN S1215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.108449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.079528 restraints weight = 31128.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.082062 restraints weight = 17020.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.083687 restraints weight = 11801.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.084714 restraints weight = 9540.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.085357 restraints weight = 8384.510| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 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 = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12246 Z= 0.207 Angle : 0.585 7.037 16748 Z= 0.305 Chirality : 0.043 0.159 1890 Planarity : 0.004 0.035 1995 Dihedral : 16.520 176.549 2018 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 5.18 % Allowed : 24.05 % Favored : 70.77 % 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 aren not related in a simple way. whole: 0.45 (0.23), residues: 1364 helix: 1.87 (0.24), residues: 488 sheet: -0.11 (0.30), residues: 287 loop : -0.82 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 30 TYR 0.015 0.001 TYR S 978 PHE 0.021 0.002 PHE S 341 TRP 0.005 0.001 TRP S 513 HIS 0.008 0.001 HIS B 158 Details of bonding type rmsd covalent geometry : bond 0.00496 (12242) covalent geometry : angle 0.57787 (16742) hydrogen bonds : bond 0.05680 ( 520) hydrogen bonds : angle 4.57377 ( 1451) metal coordination : bond 0.00717 ( 4) metal coordination : angle 4.99879 ( 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 170 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 106 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8373 (mm) REVERT: A 40 MET cc_start: 0.5638 (OUTLIER) cc_final: 0.4130 (ppp) REVERT: A 89 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6724 (tp30) REVERT: B 123 GLU cc_start: 0.7973 (pp20) cc_final: 0.7737 (pp20) REVERT: B 237 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6587 (ppp) REVERT: S 445 ASP cc_start: 0.7897 (t0) cc_final: 0.7673 (t0) REVERT: S 797 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7490 (t80) REVERT: S 1096 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8959 (tt) REVERT: S 1168 LYS cc_start: 0.8175 (mmtm) cc_final: 0.7560 (ptmt) outliers start: 64 outliers final: 44 residues processed: 160 average time/residue: 0.0905 time to fit residues: 21.6100 Evaluate side-chains 152 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 102 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 40 MET 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 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 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 ILE 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 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 C residue 592 MET Chi-restraints excluded: chain S residue 369 SER 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 68 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.111335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.083045 restraints weight = 31058.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.085645 restraints weight = 16879.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.087362 restraints weight = 11707.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.088473 restraints weight = 9340.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089159 restraints weight = 8127.462| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12246 Z= 0.111 Angle : 0.523 9.981 16748 Z= 0.271 Chirality : 0.042 0.188 1890 Planarity : 0.003 0.035 1995 Dihedral : 16.357 174.512 2018 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 3.97 % Allowed : 25.34 % 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 aren not related in a simple way. whole: 0.67 (0.23), residues: 1364 helix: 2.07 (0.24), residues: 487 sheet: 0.17 (0.31), residues: 271 loop : -0.78 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.012 0.001 TYR A 99 PHE 0.009 0.001 PHE S 583 TRP 0.007 0.001 TRP C 528 HIS 0.003 0.001 HIS S 707 Details of bonding type rmsd covalent geometry : bond 0.00245 (12242) covalent geometry : angle 0.51674 (16742) hydrogen bonds : bond 0.03858 ( 520) hydrogen bonds : angle 4.20560 ( 1451) metal coordination : bond 0.00553 ( 4) metal coordination : angle 4.34006 ( 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 170 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8769 (mpp) cc_final: 0.7166 (ppp) REVERT: A 12 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8274 (mm) REVERT: A 40 MET cc_start: 0.5537 (OUTLIER) cc_final: 0.4105 (ppp) REVERT: B 123 GLU cc_start: 0.7904 (pp20) cc_final: 0.7644 (pp20) REVERT: B 237 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6641 (ppp) REVERT: C 471 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9230 (pp) REVERT: S 544 MET cc_start: 0.7941 (ptt) cc_final: 0.7708 (ptt) REVERT: S 797 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7475 (t80) REVERT: S 1168 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7437 (ptmt) outliers start: 49 outliers final: 31 residues processed: 158 average time/residue: 0.0961 time to fit residues: 22.6338 Evaluate side-chains 148 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 80 LEU Chi-restraints excluded: chain A residue 89 GLU 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 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 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 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 591 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 635 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 722 VAL Chi-restraints excluded: chain S residue 797 TYR 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 1231 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 46 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 10 optimal weight: 0.0070 chunk 55 optimal weight: 0.0670 chunk 80 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.112781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.084543 restraints weight = 31236.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.087224 restraints weight = 16980.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.088991 restraints weight = 11638.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090087 restraints weight = 9273.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.090787 restraints weight = 8072.993| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12246 Z= 0.102 Angle : 0.529 9.454 16748 Z= 0.270 Chirality : 0.041 0.179 1890 Planarity : 0.003 0.034 1995 Dihedral : 16.241 174.081 2015 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 4.13 % Allowed : 25.26 % 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 aren not related in a simple way. whole: 0.77 (0.23), residues: 1364 helix: 2.21 (0.24), residues: 485 sheet: 0.17 (0.31), residues: 266 loop : -0.72 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.010 0.001 TYR A 99 PHE 0.009 0.001 PHE S 583 TRP 0.007 0.001 TRP C 528 HIS 0.003 0.001 HIS S 794 Details of bonding type rmsd covalent geometry : bond 0.00219 (12242) covalent geometry : angle 0.52421 (16742) hydrogen bonds : bond 0.03418 ( 520) hydrogen bonds : angle 4.07926 ( 1451) metal coordination : bond 0.00451 ( 4) metal coordination : angle 3.77790 ( 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 166 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 115 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.8713 (mpp) cc_final: 0.7077 (ppp) REVERT: A 12 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8224 (mm) REVERT: A 40 MET cc_start: 0.5485 (OUTLIER) cc_final: 0.4103 (ppp) REVERT: B 123 GLU cc_start: 0.7820 (pp20) cc_final: 0.7568 (pp20) REVERT: C 471 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9205 (pp) REVERT: C 473 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8331 (ptpp) REVERT: S 797 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7411 (t80) outliers start: 51 outliers final: 37 residues processed: 152 average time/residue: 0.0909 time to fit residues: 20.9320 Evaluate side-chains 154 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 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 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 ILE 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 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 571 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 592 MET Chi-restraints excluded: chain S residue 435 VAL 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 983 ILE Chi-restraints excluded: chain S residue 1012 SER Chi-restraints excluded: chain S residue 1058 LEU Chi-restraints excluded: chain S residue 1173 ASP 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: 0.9990 chunk 84 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 115 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.110964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.082463 restraints weight = 31045.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.085035 restraints weight = 17021.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.086724 restraints weight = 11832.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.087822 restraints weight = 9478.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088510 restraints weight = 8259.979| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- 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 = 0.38 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 = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12246 Z= 0.132 Angle : 0.552 9.722 16748 Z= 0.281 Chirality : 0.042 0.171 1890 Planarity : 0.003 0.033 1995 Dihedral : 16.256 174.919 2015 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.33 % Favored : 95.60 % Rotamer: Outliers : 4.21 % Allowed : 25.10 % 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 aren not related in a simple way. whole: 0.77 (0.23), residues: 1364 helix: 2.14 (0.24), residues: 485 sheet: 0.23 (0.31), residues: 271 loop : -0.70 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.008 0.001 TYR S 957 PHE 0.014 0.001 PHE S 341 TRP 0.004 0.001 TRP C 528 HIS 0.004 0.001 HIS S 707 Details of bonding type rmsd covalent geometry : bond 0.00305 (12242) covalent geometry : angle 0.54708 (16742) hydrogen bonds : bond 0.04246 ( 520) hydrogen bonds : angle 4.19697 ( 1451) metal coordination : bond 0.00502 ( 4) metal coordination : angle 3.83846 ( 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 165 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 113 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8707 (mpp) cc_final: 0.7062 (ppp) REVERT: A 12 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8222 (mm) REVERT: A 40 MET cc_start: 0.5545 (OUTLIER) cc_final: 0.4154 (ppp) REVERT: B 123 GLU cc_start: 0.7870 (pp20) cc_final: 0.7622 (pp20) REVERT: C 471 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9225 (pp) REVERT: C 473 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8350 (ptpp) REVERT: S 445 ASP cc_start: 0.7606 (t0) cc_final: 0.7398 (t0) REVERT: S 797 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7470 (t80) REVERT: S 1096 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8889 (tt) REVERT: S 1168 LYS cc_start: 0.7967 (mmtm) cc_final: 0.7441 (ptmt) outliers start: 52 outliers final: 40 residues processed: 152 average time/residue: 0.0894 time to fit residues: 20.4141 Evaluate side-chains 155 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 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 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 167 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 571 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 592 MET Chi-restraints excluded: chain S residue 433 LYS 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 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 1163 SER Chi-restraints excluded: chain S residue 1173 ASP 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: 5.9990 chunk 105 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 62 optimal weight: 0.0370 chunk 22 optimal weight: 5.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS S 727 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.110132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.080257 restraints weight = 30818.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.082925 restraints weight = 16465.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.084653 restraints weight = 11348.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.085728 restraints weight = 9033.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.086303 restraints weight = 7892.830| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1982 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= 0.170 Angle : 0.585 8.821 16748 Z= 0.300 Chirality : 0.043 0.177 1890 Planarity : 0.003 0.034 1995 Dihedral : 16.347 174.728 2015 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 4.86 % Allowed : 24.78 % Favored : 70.36 % 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 aren not related in a simple way. whole: 0.61 (0.23), residues: 1364 helix: 1.98 (0.24), residues: 487 sheet: 0.14 (0.32), residues: 267 loop : -0.78 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 834 TYR 0.012 0.001 TYR S 978 PHE 0.031 0.001 PHE B 135 TRP 0.005 0.001 TRP S 746 HIS 0.010 0.001 HIS B 158 Details of bonding type rmsd covalent geometry : bond 0.00404 (12242) covalent geometry : angle 0.57952 (16742) hydrogen bonds : bond 0.05169 ( 520) hydrogen bonds : angle 4.39084 ( 1451) metal coordination : bond 0.00615 ( 4) metal coordination : angle 4.17681 ( 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 171 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 111 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8823 (mpp) cc_final: 0.7060 (ppp) REVERT: A 12 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8357 (mm) REVERT: A 40 MET cc_start: 0.5543 (OUTLIER) cc_final: 0.4080 (ppp) REVERT: B 123 GLU cc_start: 0.8124 (pp20) cc_final: 0.7864 (pp20) REVERT: C 608 MET cc_start: 0.8911 (tpt) cc_final: 0.8687 (tpt) REVERT: S 445 ASP cc_start: 0.8179 (t0) cc_final: 0.7978 (t0) REVERT: S 767 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7834 (tt0) REVERT: S 797 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7521 (t80) REVERT: S 1168 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7473 (ptmt) outliers start: 60 outliers final: 46 residues processed: 158 average time/residue: 0.0833 time to fit residues: 19.9703 Evaluate side-chains 162 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 112 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 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 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 159 ILE 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 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 571 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 592 MET Chi-restraints excluded: chain S residue 369 SER Chi-restraints excluded: chain S residue 408 ILE 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 767 GLN 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 1163 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: 0.2980 chunk 119 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.108378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.079805 restraints weight = 30998.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.082305 restraints weight = 16954.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.083937 restraints weight = 11849.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084961 restraints weight = 9519.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.085498 restraints weight = 8345.598| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- 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 = 0.25 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 = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12246 Z= 0.189 Angle : 0.606 8.758 16748 Z= 0.312 Chirality : 0.044 0.202 1890 Planarity : 0.003 0.034 1995 Dihedral : 16.391 174.014 2015 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.94 % Rotamer: Outliers : 4.21 % Allowed : 25.51 % Favored : 70.28 % 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 aren not related in a simple way. whole: 0.44 (0.23), residues: 1364 helix: 1.87 (0.24), residues: 488 sheet: -0.03 (0.31), residues: 269 loop : -0.85 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 30 TYR 0.013 0.001 TYR S 978 PHE 0.019 0.001 PHE S 341 TRP 0.004 0.001 TRP S 746 HIS 0.004 0.001 HIS S 707 Details of bonding type rmsd covalent geometry : bond 0.00453 (12242) covalent geometry : angle 0.60062 (16742) hydrogen bonds : bond 0.05380 ( 520) hydrogen bonds : angle 4.45512 ( 1451) metal coordination : bond 0.00671 ( 4) metal coordination : angle 4.33045 ( 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 164 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 112 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8761 (mpp) cc_final: 0.7183 (ppp) REVERT: A 12 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8277 (mm) REVERT: A 40 MET cc_start: 0.5700 (OUTLIER) cc_final: 0.4180 (ppp) REVERT: A 89 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6714 (tp30) REVERT: B 123 GLU cc_start: 0.7992 (pp20) cc_final: 0.7761 (pp20) REVERT: B 244 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8576 (mm-40) REVERT: S 767 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: S 797 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7463 (t80) REVERT: S 1168 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7532 (ptmt) outliers start: 52 outliers final: 46 residues processed: 154 average time/residue: 0.0906 time to fit residues: 21.1879 Evaluate side-chains 160 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 109 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 A residue 89 GLU 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 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 159 ILE 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 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 571 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 592 MET Chi-restraints excluded: chain S residue 369 SER Chi-restraints excluded: chain S residue 408 ILE 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 767 GLN 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 1163 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: 1.9990 chunk 81 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 96 optimal weight: 0.0030 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 0.0870 chunk 87 optimal weight: 4.9990 overall best weight: 0.6970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN B 158 HIS S1111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.111299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083413 restraints weight = 31044.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.085984 restraints weight = 16825.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.087668 restraints weight = 11686.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.088787 restraints weight = 9320.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.089306 restraints weight = 8092.807| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12246 Z= 0.115 Angle : 0.577 9.173 16748 Z= 0.294 Chirality : 0.043 0.203 1890 Planarity : 0.003 0.034 1995 Dihedral : 16.256 172.695 2015 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.53 % Rotamer: Outliers : 3.97 % Allowed : 26.15 % Favored : 69.88 % 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 aren not related in a simple way. whole: 0.70 (0.23), residues: 1364 helix: 2.09 (0.24), residues: 485 sheet: 0.16 (0.31), residues: 271 loop : -0.73 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.008 0.001 TYR S 957 PHE 0.010 0.001 PHE B 155 TRP 0.009 0.001 TRP C 528 HIS 0.011 0.001 HIS B 158 Details of bonding type rmsd covalent geometry : bond 0.00257 (12242) covalent geometry : angle 0.57205 (16742) hydrogen bonds : bond 0.03854 ( 520) hydrogen bonds : angle 4.16380 ( 1451) metal coordination : bond 0.00519 ( 4) metal coordination : angle 3.93733 ( 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 159 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 110 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.8712 (mpp) cc_final: 0.7092 (ppp) REVERT: A 12 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8219 (mm) REVERT: A 40 MET cc_start: 0.5668 (OUTLIER) cc_final: 0.4132 (ppp) REVERT: B 123 GLU cc_start: 0.7910 (pp20) cc_final: 0.7681 (pp20) REVERT: B 237 MET cc_start: 0.6653 (ppp) cc_final: 0.6404 (ppp) REVERT: B 244 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8569 (mm-40) REVERT: C 473 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8390 (ptpp) REVERT: S 797 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7344 (t80) outliers start: 49 outliers final: 40 residues processed: 149 average time/residue: 0.0965 time to fit residues: 21.4914 Evaluate side-chains 155 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 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 139 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 167 MET 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 571 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 592 MET Chi-restraints excluded: chain S residue 369 SER Chi-restraints excluded: chain S residue 433 LYS 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 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 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: 0.0170 chunk 39 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.112066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084315 restraints weight = 30984.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086942 restraints weight = 16874.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.088644 restraints weight = 11676.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089756 restraints weight = 9309.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090400 restraints weight = 8081.665| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12246 Z= 0.115 Angle : 0.581 12.274 16748 Z= 0.294 Chirality : 0.042 0.205 1890 Planarity : 0.003 0.034 1995 Dihedral : 16.168 172.257 2015 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 3.32 % Allowed : 26.80 % Favored : 69.88 % 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 aren not related in a simple way. whole: 0.77 (0.23), residues: 1364 helix: 2.14 (0.24), residues: 485 sheet: 0.23 (0.32), residues: 257 loop : -0.67 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.008 0.001 TYR S 957 PHE 0.011 0.001 PHE B 64 TRP 0.009 0.001 TRP C 528 HIS 0.003 0.001 HIS S 707 Details of bonding type rmsd covalent geometry : bond 0.00257 (12242) covalent geometry : angle 0.57677 (16742) hydrogen bonds : bond 0.03653 ( 520) hydrogen bonds : angle 4.08392 ( 1451) metal coordination : bond 0.00448 ( 4) metal coordination : angle 3.53528 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2114.87 seconds wall clock time: 37 minutes 13.91 seconds (2233.91 seconds total)