Starting phenix.real_space_refine on Tue Jun 10 19:49:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mj5_48312/06_2025/9mj5_48312.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mj5_48312/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mj5_48312/06_2025/9mj5_48312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mj5_48312/06_2025/9mj5_48312.map" model { file = "/net/cci-nas-00/data/ceres_data/9mj5_48312/06_2025/9mj5_48312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mj5_48312/06_2025/9mj5_48312.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.69, per 1000 atoms: 0.73 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: 2.78 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 3.64 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: 4.73 Time building geometry restraints manager: 3.32 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 35.680 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.570 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (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 TRP 0.011 0.001 TRP B 107 HIS 0.003 0.001 HIS S 707 PHE 0.019 0.001 PHE S 855 TYR 0.009 0.001 TYR S 957 ARG 0.006 0.000 ARG A 9 Details of bonding type rmsd hydrogen bonds : bond 0.14644 ( 520) hydrogen bonds : angle 5.60690 ( 1451) metal coordination : bond 0.21273 ( 4) metal coordination : angle 18.36158 ( 6) covalent geometry : bond 0.00288 (12242) covalent geometry : angle 0.61049 (16742) *********************** 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 : 1.338 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: 0.2422 time to fit residues: 45.3999 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 : 1.345 ------------------------------------------------------------------------------- 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 117 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 126 optimal weight: 0.0470 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN S 549 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.114174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.085931 restraints weight = 30710.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.088637 restraints weight = 16672.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090377 restraints weight = 11480.667| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12246 Z= 0.107 Angle : 0.524 9.507 16748 Z= 0.271 Chirality : 0.041 0.159 1890 Planarity : 0.003 0.030 1995 Dihedral : 16.192 174.071 2020 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 2.83 % Allowed : 23.56 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1364 helix: 2.20 (0.24), residues: 485 sheet: 0.36 (0.31), residues: 280 loop : -0.58 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 528 HIS 0.002 0.001 HIS S 707 PHE 0.013 0.001 PHE S 855 TYR 0.014 0.001 TYR A 99 ARG 0.003 0.000 ARG A 9 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 520) hydrogen bonds : angle 4.41410 ( 1451) metal coordination : bond 0.00596 ( 4) metal coordination : angle 5.45344 ( 6) covalent geometry : bond 0.00228 (12242) covalent geometry : angle 0.51393 (16742) *********************** 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 157 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8731 (mpp) cc_final: 0.7564 (ppp) REVERT: A 40 MET cc_start: 0.5468 (OUTLIER) cc_final: 0.3818 (ppp) REVERT: B 123 GLU cc_start: 0.7867 (pp20) cc_final: 0.7577 (pp20) REVERT: B 237 MET cc_start: 0.7214 (ppp) cc_final: 0.6884 (ppp) REVERT: S 797 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7406 (t80) outliers start: 35 outliers final: 21 residues processed: 149 average time/residue: 0.2089 time to fit residues: 47.9105 Evaluate side-chains 137 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain S residue 435 VAL Chi-restraints excluded: chain S residue 609 VAL Chi-restraints excluded: chain S residue 670 MET 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 915 ILE Chi-restraints excluded: chain S residue 983 ILE Chi-restraints excluded: chain S residue 1127 SER Chi-restraints excluded: chain S residue 1231 ASP Chi-restraints excluded: chain S residue 1239 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 91 optimal weight: 2.9990 chunk 102 optimal weight: 0.0050 chunk 76 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS C 441 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.110583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.081839 restraints weight = 31170.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084439 restraints weight = 16978.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.086116 restraints weight = 11786.885| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12246 Z= 0.156 Angle : 0.550 7.615 16748 Z= 0.285 Chirality : 0.042 0.156 1890 Planarity : 0.003 0.033 1995 Dihedral : 16.199 175.519 2017 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 3.97 % Allowed : 23.97 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.23), residues: 1364 helix: 2.10 (0.24), residues: 487 sheet: 0.16 (0.30), residues: 291 loop : -0.66 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 746 HIS 0.008 0.001 HIS B 158 PHE 0.018 0.001 PHE S 341 TYR 0.012 0.001 TYR S 978 ARG 0.002 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.04976 ( 520) hydrogen bonds : angle 4.43947 ( 1451) metal coordination : bond 0.00585 ( 4) metal coordination : angle 5.24916 ( 6) covalent geometry : bond 0.00367 (12242) covalent geometry : angle 0.54074 (16742) *********************** 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 162 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 113 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8720 (mpp) cc_final: 0.7016 (ppp) REVERT: A 79 ILE cc_start: 0.8616 (mm) cc_final: 0.8230 (tp) REVERT: B 123 GLU cc_start: 0.7934 (pp20) cc_final: 0.7661 (pp20) REVERT: B 237 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6806 (ppp) REVERT: C 440 THR cc_start: 0.6988 (OUTLIER) cc_final: 0.6734 (m) REVERT: S 797 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7455 (t80) REVERT: S 1124 LEU cc_start: 0.7743 (tp) cc_final: 0.7530 (tt) REVERT: S 1168 LYS cc_start: 0.8027 (mmtm) cc_final: 0.7459 (ptmt) outliers start: 49 outliers final: 35 residues processed: 150 average time/residue: 0.2236 time to fit residues: 51.6302 Evaluate side-chains 147 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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 67 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 237 MET Chi-restraints excluded: chain B residue 252 GLU 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 C residue 592 MET Chi-restraints excluded: chain S residue 369 SER 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 137 optimal weight: 10.0000 chunk 26 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.111250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.081423 restraints weight = 30921.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.084058 restraints weight = 16694.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.085762 restraints weight = 11549.156| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12246 Z= 0.172 Angle : 0.553 6.922 16748 Z= 0.289 Chirality : 0.043 0.158 1890 Planarity : 0.003 0.034 1995 Dihedral : 16.293 175.916 2017 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.16 % Rotamer: Outliers : 5.02 % Allowed : 23.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1364 helix: 1.99 (0.24), residues: 488 sheet: 0.05 (0.30), residues: 287 loop : -0.75 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 746 HIS 0.004 0.001 HIS S 707 PHE 0.019 0.001 PHE S 341 TYR 0.013 0.001 TYR S 978 ARG 0.002 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.05117 ( 520) hydrogen bonds : angle 4.44650 ( 1451) metal coordination : bond 0.00659 ( 4) metal coordination : angle 4.68190 ( 6) covalent geometry : bond 0.00407 (12242) covalent geometry : angle 0.54602 (16742) *********************** 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: 62 poor density : 108 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8764 (mm) cc_final: 0.8348 (tp) REVERT: A 89 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.7002 (tp30) REVERT: B 123 GLU cc_start: 0.8090 (pp20) cc_final: 0.7822 (pp20) REVERT: B 237 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6604 (ppp) REVERT: S 797 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.7552 (t80) REVERT: S 1124 LEU cc_start: 0.7802 (tp) cc_final: 0.7544 (tt) REVERT: S 1168 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7394 (ptmt) outliers start: 62 outliers final: 39 residues processed: 158 average time/residue: 0.2227 time to fit residues: 52.3543 Evaluate side-chains 147 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain 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 166 HIS Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 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 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 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 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 81 optimal weight: 3.9990 chunk 132 optimal weight: 0.0000 chunk 25 optimal weight: 0.0370 chunk 125 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 10 optimal weight: 0.0470 chunk 23 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.3560 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.115359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.085873 restraints weight = 31891.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.088672 restraints weight = 17419.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.090503 restraints weight = 12064.273| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12246 Z= 0.099 Angle : 0.505 9.991 16748 Z= 0.261 Chirality : 0.041 0.159 1890 Planarity : 0.003 0.033 1995 Dihedral : 16.070 173.634 2017 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 2.91 % Allowed : 24.94 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1364 helix: 2.25 (0.24), residues: 479 sheet: 0.27 (0.32), residues: 268 loop : -0.71 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 528 HIS 0.002 0.000 HIS S 707 PHE 0.009 0.001 PHE C 562 TYR 0.008 0.001 TYR S 957 ARG 0.002 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 520) hydrogen bonds : angle 4.08643 ( 1451) metal coordination : bond 0.00474 ( 4) metal coordination : angle 3.95394 ( 6) covalent geometry : bond 0.00205 (12242) covalent geometry : angle 0.49958 (16742) *********************** 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 156 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.8844 (mpp) cc_final: 0.7010 (ppp) REVERT: A 40 MET cc_start: 0.5519 (OUTLIER) cc_final: 0.4080 (ppp) REVERT: B 123 GLU cc_start: 0.7987 (pp20) cc_final: 0.7709 (pp20) REVERT: B 237 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.7049 (ppp) REVERT: C 471 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9259 (pp) REVERT: S 797 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7484 (t80) outliers start: 36 outliers final: 22 residues processed: 148 average time/residue: 0.2233 time to fit residues: 50.4444 Evaluate side-chains 139 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 471 LEU Chi-restraints excluded: chain C residue 529 VAL 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 C residue 592 MET Chi-restraints excluded: chain S residue 609 VAL Chi-restraints excluded: chain S residue 635 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 718 THR Chi-restraints excluded: chain S residue 722 VAL Chi-restraints excluded: chain S residue 797 TYR Chi-restraints excluded: chain S residue 972 LEU Chi-restraints excluded: chain S residue 983 ILE Chi-restraints excluded: chain S residue 1127 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 137 optimal weight: 10.0000 chunk 118 optimal weight: 0.0040 chunk 134 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS C 475 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.113850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.083828 restraints weight = 31238.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.086602 restraints weight = 16934.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.088387 restraints weight = 11716.841| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12246 Z= 0.112 Angle : 0.524 9.468 16748 Z= 0.267 Chirality : 0.041 0.157 1890 Planarity : 0.003 0.033 1995 Dihedral : 16.051 174.475 2015 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 3.56 % Allowed : 25.59 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1364 helix: 2.26 (0.24), residues: 480 sheet: 0.47 (0.32), residues: 266 loop : -0.63 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 528 HIS 0.009 0.001 HIS B 158 PHE 0.011 0.001 PHE S 341 TYR 0.008 0.001 TYR S 957 ARG 0.002 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 520) hydrogen bonds : angle 4.08331 ( 1451) metal coordination : bond 0.00453 ( 4) metal coordination : angle 3.75037 ( 6) covalent geometry : bond 0.00251 (12242) covalent geometry : angle 0.51930 (16742) *********************** 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 158 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.8843 (mpp) cc_final: 0.7045 (ppp) REVERT: B 123 GLU cc_start: 0.8011 (pp20) cc_final: 0.7728 (pp20) REVERT: B 237 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6900 (ppp) REVERT: C 471 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9284 (pp) REVERT: C 473 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8470 (ptpp) REVERT: S 797 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7466 (t80) outliers start: 44 outliers final: 33 residues processed: 147 average time/residue: 0.2312 time to fit residues: 51.0455 Evaluate side-chains 147 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain 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 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 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 471 LEU Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 562 PHE 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 609 VAL Chi-restraints excluded: chain S residue 635 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 718 THR Chi-restraints excluded: chain S residue 722 VAL Chi-restraints excluded: chain S residue 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 1173 ASP Chi-restraints excluded: chain S residue 1231 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 50 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 99 optimal weight: 0.0030 chunk 109 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 44 optimal weight: 8.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.113632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.085457 restraints weight = 31366.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.088140 restraints weight = 17099.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.089905 restraints weight = 11829.535| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12246 Z= 0.102 Angle : 0.535 11.667 16748 Z= 0.269 Chirality : 0.042 0.162 1890 Planarity : 0.003 0.033 1995 Dihedral : 15.975 174.007 2015 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.89 % Favored : 96.04 % Rotamer: Outliers : 3.08 % Allowed : 25.91 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1364 helix: 2.21 (0.24), residues: 485 sheet: 0.49 (0.32), residues: 258 loop : -0.59 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 528 HIS 0.002 0.000 HIS S 707 PHE 0.009 0.001 PHE S 583 TYR 0.008 0.001 TYR S 957 ARG 0.002 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 520) hydrogen bonds : angle 4.03876 ( 1451) metal coordination : bond 0.00418 ( 4) metal coordination : angle 3.50978 ( 6) covalent geometry : bond 0.00220 (12242) covalent geometry : angle 0.53142 (16742) *********************** 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 152 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.8731 (mpp) cc_final: 0.7083 (ppp) REVERT: A 109 PHE cc_start: 0.8926 (m-80) cc_final: 0.8693 (m-10) REVERT: B 123 GLU cc_start: 0.7848 (pp20) cc_final: 0.7584 (pp20) REVERT: C 471 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9229 (pp) REVERT: C 473 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8231 (ptpp) REVERT: S 797 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7366 (t80) outliers start: 38 outliers final: 29 residues processed: 141 average time/residue: 0.2212 time to fit residues: 47.1721 Evaluate side-chains 143 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 80 LEU 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 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 471 LEU Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 562 PHE 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 609 VAL Chi-restraints excluded: chain S residue 635 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 718 THR Chi-restraints excluded: chain S residue 722 VAL Chi-restraints excluded: chain S residue 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 1058 LEU Chi-restraints excluded: chain S residue 1127 SER Chi-restraints excluded: chain S residue 1173 ASP Chi-restraints excluded: chain S residue 1231 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 0.0270 chunk 86 optimal weight: 2.9990 overall best weight: 1.1040 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.111927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.083521 restraints weight = 31319.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.086122 restraints weight = 17208.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087830 restraints weight = 11925.306| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12246 Z= 0.126 Angle : 0.555 9.822 16748 Z= 0.281 Chirality : 0.042 0.162 1890 Planarity : 0.003 0.033 1995 Dihedral : 16.008 174.025 2015 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 3.64 % Allowed : 25.51 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.23), residues: 1364 helix: 2.14 (0.24), residues: 485 sheet: 0.51 (0.32), residues: 265 loop : -0.60 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 746 HIS 0.003 0.001 HIS S 707 PHE 0.032 0.001 PHE B 135 TYR 0.008 0.001 TYR S 978 ARG 0.002 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 520) hydrogen bonds : angle 4.13388 ( 1451) metal coordination : bond 0.00467 ( 4) metal coordination : angle 3.55183 ( 6) covalent geometry : bond 0.00290 (12242) covalent geometry : angle 0.55125 (16742) *********************** 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 157 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 112 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.8746 (mpp) cc_final: 0.7620 (ppp) REVERT: A 12 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7846 (mm) REVERT: A 40 MET cc_start: 0.5526 (OUTLIER) cc_final: 0.4093 (ppp) REVERT: A 109 PHE cc_start: 0.8914 (m-80) cc_final: 0.8683 (m-10) REVERT: B 123 GLU cc_start: 0.7881 (pp20) cc_final: 0.7614 (pp20) REVERT: B 166 HIS cc_start: 0.8864 (OUTLIER) cc_final: 0.8620 (m-70) REVERT: C 471 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9231 (pp) REVERT: C 473 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8303 (ptpp) REVERT: S 797 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.7443 (t80) outliers start: 45 outliers final: 34 residues processed: 146 average time/residue: 0.2204 time to fit residues: 48.6452 Evaluate side-chains 149 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 166 HIS Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 531 CYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain 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 609 VAL Chi-restraints excluded: chain S residue 635 VAL 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 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 1127 SER Chi-restraints excluded: chain S residue 1231 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.109529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.080836 restraints weight = 31254.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.083425 restraints weight = 17189.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.085069 restraints weight = 11912.683| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12246 Z= 0.177 Angle : 0.606 9.352 16748 Z= 0.309 Chirality : 0.043 0.202 1890 Planarity : 0.003 0.033 1995 Dihedral : 16.163 174.099 2013 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 3.89 % Allowed : 25.18 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.23), residues: 1364 helix: 1.95 (0.24), residues: 488 sheet: 0.26 (0.32), residues: 268 loop : -0.71 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 746 HIS 0.003 0.001 HIS S 707 PHE 0.018 0.001 PHE S 341 TYR 0.012 0.001 TYR S 978 ARG 0.002 0.000 ARG S 784 Details of bonding type rmsd hydrogen bonds : bond 0.05139 ( 520) hydrogen bonds : angle 4.38240 ( 1451) metal coordination : bond 0.00611 ( 4) metal coordination : angle 3.93422 ( 6) covalent geometry : bond 0.00424 (12242) covalent geometry : angle 0.60165 (16742) *********************** 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 158 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 110 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.8726 (mpp) cc_final: 0.7102 (ppp) REVERT: A 40 MET cc_start: 0.5622 (OUTLIER) cc_final: 0.4104 (ppp) REVERT: B 123 GLU cc_start: 0.7911 (pp20) cc_final: 0.7662 (pp20) REVERT: B 166 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.8689 (m-70) REVERT: C 471 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9245 (pp) REVERT: C 473 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8376 (ptpp) REVERT: S 797 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7486 (t80) REVERT: S 1168 LYS cc_start: 0.8013 (mmtm) cc_final: 0.7486 (ptmt) outliers start: 48 outliers final: 35 residues processed: 146 average time/residue: 0.2223 time to fit residues: 48.6726 Evaluate side-chains 150 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 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 233 GLN Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 531 CYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 592 MET Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain S residue 433 LYS Chi-restraints excluded: chain S residue 609 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 718 THR Chi-restraints excluded: chain S residue 722 VAL Chi-restraints excluded: chain S residue 771 ILE Chi-restraints excluded: chain S residue 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 1127 SER Chi-restraints excluded: chain S residue 1231 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 5 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.111632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.082058 restraints weight = 31030.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.084765 restraints weight = 16631.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.086541 restraints weight = 11407.842| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12246 Z= 0.144 Angle : 0.591 9.364 16748 Z= 0.299 Chirality : 0.043 0.186 1890 Planarity : 0.003 0.033 1995 Dihedral : 16.118 173.605 2013 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 3.16 % Allowed : 25.99 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1364 helix: 2.01 (0.24), residues: 486 sheet: 0.22 (0.32), residues: 268 loop : -0.75 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 746 HIS 0.003 0.001 HIS S 794 PHE 0.014 0.001 PHE S 341 TYR 0.010 0.001 TYR S 978 ARG 0.002 0.000 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 520) hydrogen bonds : angle 4.28332 ( 1451) metal coordination : bond 0.00592 ( 4) metal coordination : angle 3.86878 ( 6) covalent geometry : bond 0.00337 (12242) covalent geometry : angle 0.58637 (16742) ********************** 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 149 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.8789 (mpp) cc_final: 0.7069 (ppp) REVERT: A 40 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.4090 (ppp) REVERT: B 123 GLU cc_start: 0.8045 (pp20) cc_final: 0.7786 (pp20) REVERT: B 166 HIS cc_start: 0.9050 (OUTLIER) cc_final: 0.8778 (m-70) REVERT: B 244 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8579 (mm-40) REVERT: C 471 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9279 (pp) REVERT: C 473 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8549 (ptpp) REVERT: S 797 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7498 (t80) outliers start: 39 outliers final: 34 residues processed: 141 average time/residue: 0.2469 time to fit residues: 52.2425 Evaluate side-chains 146 residues out of total 1235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 HIS Chi-restraints excluded: chain B residue 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 233 GLN Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 463 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 531 CYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain 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 609 VAL Chi-restraints excluded: chain S residue 707 HIS Chi-restraints excluded: chain S residue 718 THR Chi-restraints excluded: chain S residue 722 VAL Chi-restraints excluded: chain S residue 771 ILE Chi-restraints excluded: chain S residue 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 1127 SER Chi-restraints excluded: chain S residue 1231 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 15 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.110834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.082471 restraints weight = 31144.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.085062 restraints weight = 17135.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086715 restraints weight = 11920.022| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12246 Z= 0.136 Angle : 0.591 9.380 16748 Z= 0.299 Chirality : 0.042 0.186 1890 Planarity : 0.003 0.033 1995 Dihedral : 16.098 173.513 2013 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.16 % Rotamer: Outliers : 3.16 % Allowed : 26.40 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1364 helix: 2.05 (0.24), residues: 486 sheet: 0.22 (0.32), residues: 268 loop : -0.72 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 528 HIS 0.003 0.001 HIS S 707 PHE 0.028 0.001 PHE A 109 TYR 0.009 0.001 TYR S 978 ARG 0.002 0.000 ARG S 834 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 520) hydrogen bonds : angle 4.23437 ( 1451) metal coordination : bond 0.00548 ( 4) metal coordination : angle 3.73143 ( 6) covalent geometry : bond 0.00317 (12242) covalent geometry : angle 0.58733 (16742) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4155.26 seconds wall clock time: 72 minutes 35.17 seconds (4355.17 seconds total)