Starting phenix.real_space_refine on Mon Aug 25 23:40:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s3e_19691/08_2025/8s3e_19691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s3e_19691/08_2025/8s3e_19691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s3e_19691/08_2025/8s3e_19691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s3e_19691/08_2025/8s3e_19691.map" model { file = "/net/cci-nas-00/data/ceres_data/8s3e_19691/08_2025/8s3e_19691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s3e_19691/08_2025/8s3e_19691.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 8 Type Number sf(0) Gaussians Ca 8 9.91 5 K 4 8.98 5 P 24 5.49 5 Mg 4 5.21 5 S 208 5.16 5 C 20632 2.51 5 N 5012 2.21 5 O 5693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31585 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7192 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 27, 'TRANS': 874} Chain breaks: 4 Chain: "B" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7192 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 27, 'TRANS': 874} Chain breaks: 4 Chain: "C" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7192 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 27, 'TRANS': 874} Chain breaks: 4 Chain: "D" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7192 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 27, 'TRANS': 874} Chain breaks: 4 Chain: "E" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 367 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "F" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 367 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "G" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 367 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "H" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 367 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "A" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 335 Unusual residues: {' K': 2, ' CA': 2, ' MG': 1, '6PL': 9, 'CLR': 4} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 244 Planarities with less than four sites: {'6PL:plan-2': 3} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 334 Unusual residues: {' K': 1, ' CA': 2, ' MG': 1, '6PL': 9, 'CLR': 4} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 244 Planarities with less than four sites: {'6PL:plan-2': 3} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Unusual residues: {' CA': 2, ' MG': 1, '6PL': 9, 'CLR': 4} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 244 Planarities with less than four sites: {'6PL:plan-2': 3} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 334 Unusual residues: {' K': 1, ' CA': 2, ' MG': 1, '6PL': 9, 'CLR': 4} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 244 Planarities with less than four sites: {'6PL:plan-2': 3} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 7.60, per 1000 atoms: 0.24 Number of scatterers: 31585 At special positions: 0 Unit cell: (142.12, 142.12, 129.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 8 19.99 K 4 19.00 S 208 16.00 P 24 15.00 Mg 4 11.99 O 5693 8.00 N 5012 7.00 C 20632 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7200 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 24 sheets defined 58.3% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 21 through 54 removed outlier: 4.514A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 106 Processing helix chain 'A' and resid 109 through 134 Processing helix chain 'A' and resid 147 through 171 removed outlier: 3.774A pdb=" N GLN A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.564A pdb=" N LEU A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 200 Proline residue: A 191 - end of helix removed outlier: 3.987A pdb=" N TYR A 198 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 229 through 260 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.547A pdb=" N ASN A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 328 removed outlier: 3.819A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 removed outlier: 3.500A pdb=" N VAL A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 432 through 451 removed outlier: 3.509A pdb=" N GLU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 470 removed outlier: 3.786A pdb=" N HIS A 468 " --> pdb=" O HIS A 464 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.598A pdb=" N MET A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.813A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 601 through 610 removed outlier: 3.836A pdb=" N ARG A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 609 " --> pdb=" O VAL A 605 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.876A pdb=" N VAL A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 699 through 704' Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 removed outlier: 3.524A pdb=" N VAL A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 743 Processing helix chain 'A' and resid 747 through 751 Processing helix chain 'A' and resid 759 through 767 Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 785 through 793 removed outlier: 3.520A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 797 Processing helix chain 'A' and resid 806 through 808 No H-bonds generated for 'chain 'A' and resid 806 through 808' Processing helix chain 'A' and resid 812 through 816 Processing helix chain 'A' and resid 817 through 829 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 884 through 891 removed outlier: 3.540A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 916 through 921 removed outlier: 3.570A pdb=" N VAL A 919 " --> pdb=" O ALA A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 930 removed outlier: 3.594A pdb=" N ALA A 926 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 942 Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 965 through 970 removed outlier: 3.687A pdb=" N LEU A 969 " --> pdb=" O PRO A 966 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 970 " --> pdb=" O GLN A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 986 No H-bonds generated for 'chain 'A' and resid 984 through 986' Processing helix chain 'A' and resid 987 through 992 Processing helix chain 'A' and resid 995 through 1008 removed outlier: 3.613A pdb=" N LEU A 999 " --> pdb=" O CYS A 995 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 54 removed outlier: 4.514A pdb=" N PHE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 106 Processing helix chain 'B' and resid 109 through 134 Processing helix chain 'B' and resid 147 through 171 removed outlier: 3.774A pdb=" N GLN B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 removed outlier: 3.564A pdb=" N LEU B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 200 Proline residue: B 191 - end of helix removed outlier: 3.986A pdb=" N TYR B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 229 through 260 Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.546A pdb=" N ASN B 265 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 328 removed outlier: 3.819A pdb=" N LEU B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 432 through 451 removed outlier: 3.510A pdb=" N GLU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.786A pdb=" N HIS B 468 " --> pdb=" O HIS B 464 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 500 Processing helix chain 'B' and resid 502 through 512 removed outlier: 3.599A pdb=" N MET B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 511 " --> pdb=" O LEU B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 533 removed outlier: 3.813A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 601 through 610 removed outlier: 3.836A pdb=" N ARG B 607 " --> pdb=" O LYS B 603 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE B 609 " --> pdb=" O VAL B 605 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 610 " --> pdb=" O LYS B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.876A pdb=" N VAL B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 699 through 704' Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 739 removed outlier: 3.525A pdb=" N VAL B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 743 Processing helix chain 'B' and resid 747 through 751 Processing helix chain 'B' and resid 759 through 767 Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 785 through 793 removed outlier: 3.521A pdb=" N LEU B 789 " --> pdb=" O SER B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 797 Processing helix chain 'B' and resid 806 through 808 No H-bonds generated for 'chain 'B' and resid 806 through 808' Processing helix chain 'B' and resid 812 through 816 Processing helix chain 'B' and resid 817 through 829 Processing helix chain 'B' and resid 874 through 876 No H-bonds generated for 'chain 'B' and resid 874 through 876' Processing helix chain 'B' and resid 884 through 891 removed outlier: 3.541A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 916 through 921 removed outlier: 3.569A pdb=" N VAL B 919 " --> pdb=" O ALA B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 930 removed outlier: 3.594A pdb=" N ALA B 926 " --> pdb=" O SER B 922 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 942 Processing helix chain 'B' and resid 946 through 957 Processing helix chain 'B' and resid 965 through 970 removed outlier: 3.686A pdb=" N LEU B 969 " --> pdb=" O PRO B 966 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA B 970 " --> pdb=" O GLN B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 986 No H-bonds generated for 'chain 'B' and resid 984 through 986' Processing helix chain 'B' and resid 987 through 992 Processing helix chain 'B' and resid 995 through 1008 removed outlier: 3.613A pdb=" N LEU B 999 " --> pdb=" O CYS B 995 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 54 removed outlier: 4.513A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 106 Processing helix chain 'C' and resid 109 through 134 Processing helix chain 'C' and resid 147 through 171 removed outlier: 3.774A pdb=" N GLN C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 removed outlier: 3.565A pdb=" N LEU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 200 Proline residue: C 191 - end of helix removed outlier: 3.986A pdb=" N TYR C 198 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 229 through 260 Processing helix chain 'C' and resid 261 through 265 removed outlier: 3.547A pdb=" N ASN C 265 " --> pdb=" O PRO C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 328 removed outlier: 3.819A pdb=" N LEU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 removed outlier: 3.501A pdb=" N VAL C 414 " --> pdb=" O ASP C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 432 through 451 removed outlier: 3.510A pdb=" N GLU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 removed outlier: 3.786A pdb=" N HIS C 468 " --> pdb=" O HIS C 464 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 Processing helix chain 'C' and resid 502 through 512 removed outlier: 3.599A pdb=" N MET C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 511 " --> pdb=" O LEU C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 533 removed outlier: 3.813A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 601 through 610 removed outlier: 3.500A pdb=" N VAL C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG C 607 " --> pdb=" O LYS C 603 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA C 608 " --> pdb=" O GLU C 604 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE C 609 " --> pdb=" O VAL C 605 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 610 " --> pdb=" O LYS C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 704 removed outlier: 3.877A pdb=" N VAL C 703 " --> pdb=" O GLU C 699 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 704 " --> pdb=" O ILE C 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 699 through 704' Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 739 removed outlier: 3.524A pdb=" N VAL C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 743 Processing helix chain 'C' and resid 747 through 751 Processing helix chain 'C' and resid 759 through 767 Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 785 through 793 removed outlier: 3.521A pdb=" N LEU C 789 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 797 Processing helix chain 'C' and resid 806 through 808 No H-bonds generated for 'chain 'C' and resid 806 through 808' Processing helix chain 'C' and resid 812 through 816 Processing helix chain 'C' and resid 817 through 829 Processing helix chain 'C' and resid 874 through 876 No H-bonds generated for 'chain 'C' and resid 874 through 876' Processing helix chain 'C' and resid 884 through 891 removed outlier: 3.540A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 916 through 921 removed outlier: 3.569A pdb=" N VAL C 919 " --> pdb=" O ALA C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 930 removed outlier: 3.595A pdb=" N ALA C 926 " --> pdb=" O SER C 922 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 932 through 942 Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 965 through 970 removed outlier: 3.687A pdb=" N LEU C 969 " --> pdb=" O PRO C 966 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA C 970 " --> pdb=" O GLN C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 986 No H-bonds generated for 'chain 'C' and resid 984 through 986' Processing helix chain 'C' and resid 987 through 992 Processing helix chain 'C' and resid 995 through 1008 removed outlier: 3.613A pdb=" N LEU C 999 " --> pdb=" O CYS C 995 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 54 removed outlier: 4.514A pdb=" N PHE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 106 Processing helix chain 'D' and resid 109 through 134 Processing helix chain 'D' and resid 147 through 171 removed outlier: 3.774A pdb=" N GLN D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 removed outlier: 3.563A pdb=" N LEU D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 200 Proline residue: D 191 - end of helix removed outlier: 3.986A pdb=" N TYR D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 229 through 260 Processing helix chain 'D' and resid 261 through 265 removed outlier: 3.546A pdb=" N ASN D 265 " --> pdb=" O PRO D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 297 through 328 removed outlier: 3.819A pdb=" N LEU D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 414 removed outlier: 3.501A pdb=" N VAL D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 432 through 451 removed outlier: 3.510A pdb=" N GLU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 470 removed outlier: 3.786A pdb=" N HIS D 468 " --> pdb=" O HIS D 464 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 500 Processing helix chain 'D' and resid 502 through 512 removed outlier: 3.599A pdb=" N MET D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE D 511 " --> pdb=" O LEU D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 533 removed outlier: 3.813A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 601 through 610 removed outlier: 3.500A pdb=" N VAL D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG D 607 " --> pdb=" O LYS D 603 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA D 608 " --> pdb=" O GLU D 604 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE D 609 " --> pdb=" O VAL D 605 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 610 " --> pdb=" O LYS D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 704 removed outlier: 3.876A pdb=" N VAL D 703 " --> pdb=" O GLU D 699 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 704 " --> pdb=" O ILE D 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 699 through 704' Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 739 removed outlier: 3.524A pdb=" N VAL D 738 " --> pdb=" O LEU D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 743 Processing helix chain 'D' and resid 747 through 751 Processing helix chain 'D' and resid 759 through 767 Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 785 through 793 removed outlier: 3.521A pdb=" N LEU D 789 " --> pdb=" O SER D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 797 Processing helix chain 'D' and resid 806 through 808 No H-bonds generated for 'chain 'D' and resid 806 through 808' Processing helix chain 'D' and resid 812 through 816 Processing helix chain 'D' and resid 817 through 829 Processing helix chain 'D' and resid 874 through 876 No H-bonds generated for 'chain 'D' and resid 874 through 876' Processing helix chain 'D' and resid 884 through 891 removed outlier: 3.540A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 911 Processing helix chain 'D' and resid 916 through 921 removed outlier: 3.569A pdb=" N VAL D 919 " --> pdb=" O ALA D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 930 removed outlier: 3.595A pdb=" N ALA D 926 " --> pdb=" O SER D 922 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN D 930 " --> pdb=" O ALA D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 932 through 942 Processing helix chain 'D' and resid 946 through 957 Processing helix chain 'D' and resid 965 through 970 removed outlier: 3.687A pdb=" N LEU D 969 " --> pdb=" O PRO D 966 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA D 970 " --> pdb=" O GLN D 967 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 986 No H-bonds generated for 'chain 'D' and resid 984 through 986' Processing helix chain 'D' and resid 987 through 992 Processing helix chain 'D' and resid 995 through 1008 removed outlier: 3.614A pdb=" N LEU D 999 " --> pdb=" O CYS D 995 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN D1008 " --> pdb=" O LEU D1004 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 297 removed outlier: 5.270A pdb=" N GLY E 269 " --> pdb=" O ILE E 265 " (cutoff:3.500A) Proline residue: E 270 - end of helix Processing helix chain 'F' and resid 258 through 297 removed outlier: 5.270A pdb=" N GLY F 269 " --> pdb=" O ILE F 265 " (cutoff:3.500A) Proline residue: F 270 - end of helix Processing helix chain 'G' and resid 258 through 297 removed outlier: 5.270A pdb=" N GLY G 269 " --> pdb=" O ILE G 265 " (cutoff:3.500A) Proline residue: G 270 - end of helix Processing helix chain 'H' and resid 258 through 297 removed outlier: 5.269A pdb=" N GLY H 269 " --> pdb=" O ILE H 265 " (cutoff:3.500A) Proline residue: H 270 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 402 removed outlier: 4.636A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 459 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 540 removed outlier: 4.043A pdb=" N ALA A 567 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 598 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N MET A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.713A pdb=" N HIS A 718 " --> pdb=" O MET A 799 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL A 801 " --> pdb=" O HIS A 718 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 720 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU A 803 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N CYS A 722 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 831 through 832 Processing sheet with id=AA6, first strand: chain 'A' and resid 976 through 981 removed outlier: 5.072A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AA8, first strand: chain 'B' and resid 398 through 402 removed outlier: 4.636A pdb=" N GLY B 349 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN B 459 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 535 through 540 removed outlier: 4.042A pdb=" N ALA B 567 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE B 598 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N MET B 565 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.712A pdb=" N HIS B 718 " --> pdb=" O MET B 799 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N VAL B 801 " --> pdb=" O HIS B 718 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL B 720 " --> pdb=" O VAL B 801 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU B 803 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N CYS B 722 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 831 through 832 Processing sheet with id=AB3, first strand: chain 'B' and resid 976 through 981 removed outlier: 5.072A pdb=" N GLY B1013 " --> pdb=" O PHE B1050 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AB5, first strand: chain 'C' and resid 398 through 402 removed outlier: 4.636A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN C 459 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 535 through 540 removed outlier: 4.043A pdb=" N ALA C 567 " --> pdb=" O PHE C 596 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE C 598 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N MET C 565 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.712A pdb=" N HIS C 718 " --> pdb=" O MET C 799 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL C 801 " --> pdb=" O HIS C 718 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL C 720 " --> pdb=" O VAL C 801 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU C 803 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N CYS C 722 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 831 through 832 Processing sheet with id=AB9, first strand: chain 'C' and resid 976 through 981 removed outlier: 5.072A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AC2, first strand: chain 'D' and resid 398 through 402 removed outlier: 4.635A pdb=" N GLY D 349 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN D 459 " --> pdb=" O ILE D 424 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 535 through 540 removed outlier: 4.042A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.712A pdb=" N HIS D 718 " --> pdb=" O MET D 799 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL D 801 " --> pdb=" O HIS D 718 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL D 720 " --> pdb=" O VAL D 801 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU D 803 " --> pdb=" O VAL D 720 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N CYS D 722 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 831 through 832 Processing sheet with id=AC6, first strand: chain 'D' and resid 976 through 981 removed outlier: 5.072A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) 1567 hydrogen bonds defined for protein. 4353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.09 Time building geometry restraints manager: 3.95 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: 5438 1.33 - 1.45: 8260 1.45 - 1.57: 18202 1.57 - 1.69: 48 1.69 - 1.81: 304 Bond restraints: 32252 Sorted by residual: bond pdb=" O1P 6PL C1202 " pdb=" P 6PL C1202 " ideal model delta sigma weight residual 1.502 1.652 -0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" O1P 6PL B1202 " pdb=" P 6PL B1202 " ideal model delta sigma weight residual 1.502 1.651 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" O4P 6PL C1202 " pdb=" P 6PL C1202 " ideal model delta sigma weight residual 1.651 1.502 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" O1P 6PL A1216 " pdb=" P 6PL A1216 " ideal model delta sigma weight residual 1.502 1.651 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" O4P 6PL B1202 " pdb=" P 6PL B1202 " ideal model delta sigma weight residual 1.651 1.502 0.149 2.00e-02 2.50e+03 5.54e+01 ... (remaining 32247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.98: 43660 5.98 - 11.97: 32 11.97 - 17.95: 12 17.95 - 23.93: 4 23.93 - 29.92: 8 Bond angle restraints: 43716 Sorted by residual: angle pdb=" C12 CLR C1206 " pdb=" C13 CLR C1206 " pdb=" C18 CLR C1206 " ideal model delta sigma weight residual 111.01 81.09 29.92 3.00e+00 1.11e-01 9.94e+01 angle pdb=" C12 CLR B1206 " pdb=" C13 CLR B1206 " pdb=" C18 CLR B1206 " ideal model delta sigma weight residual 111.01 81.13 29.88 3.00e+00 1.11e-01 9.92e+01 angle pdb=" C12 CLR A1204 " pdb=" C13 CLR A1204 " pdb=" C18 CLR A1204 " ideal model delta sigma weight residual 111.01 81.14 29.87 3.00e+00 1.11e-01 9.91e+01 angle pdb=" C12 CLR D1206 " pdb=" C13 CLR D1206 " pdb=" C18 CLR D1206 " ideal model delta sigma weight residual 111.01 81.16 29.85 3.00e+00 1.11e-01 9.90e+01 angle pdb=" C17 CLR B1206 " pdb=" C13 CLR B1206 " pdb=" C18 CLR B1206 " ideal model delta sigma weight residual 110.18 80.66 29.52 3.00e+00 1.11e-01 9.68e+01 ... (remaining 43711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 19404 35.11 - 70.21: 580 70.21 - 105.32: 4 105.32 - 140.42: 0 140.42 - 175.53: 20 Dihedral angle restraints: 20008 sinusoidal: 8896 harmonic: 11112 Sorted by residual: dihedral pdb=" C18 CLR C1206 " pdb=" C13 CLR C1206 " pdb=" C17 CLR C1206 " pdb=" C20 CLR C1206 " ideal model delta sinusoidal sigma weight residual 312.73 137.20 175.53 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C18 CLR D1206 " pdb=" C13 CLR D1206 " pdb=" C17 CLR D1206 " pdb=" C20 CLR D1206 " ideal model delta sinusoidal sigma weight residual 312.73 137.23 175.50 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C18 CLR A1204 " pdb=" C13 CLR A1204 " pdb=" C17 CLR A1204 " pdb=" C20 CLR A1204 " ideal model delta sinusoidal sigma weight residual 312.73 137.24 175.49 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 20005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.377: 4968 0.377 - 0.753: 0 0.753 - 1.130: 0 1.130 - 1.507: 0 1.507 - 1.883: 4 Chirality restraints: 4972 Sorted by residual: chirality pdb=" C13 CLR A1204 " pdb=" C12 CLR A1204 " pdb=" C14 CLR A1204 " pdb=" C17 CLR A1204 " both_signs ideal model delta sigma weight residual False -2.93 -1.05 -1.88 2.00e-01 2.50e+01 8.87e+01 chirality pdb=" C13 CLR D1206 " pdb=" C12 CLR D1206 " pdb=" C14 CLR D1206 " pdb=" C17 CLR D1206 " both_signs ideal model delta sigma weight residual False -2.93 -1.05 -1.88 2.00e-01 2.50e+01 8.86e+01 chirality pdb=" C13 CLR C1206 " pdb=" C12 CLR C1206 " pdb=" C14 CLR C1206 " pdb=" C17 CLR C1206 " both_signs ideal model delta sigma weight residual False -2.93 -1.05 -1.88 2.00e-01 2.50e+01 8.82e+01 ... (remaining 4969 not shown) Planarity restraints: 5324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 191 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO B 192 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 191 " 0.031 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 192 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 191 " -0.031 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO D 192 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 192 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 192 " -0.026 5.00e-02 4.00e+02 ... (remaining 5321 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.71: 890 2.71 - 3.32: 36450 3.32 - 3.93: 61704 3.93 - 4.53: 84823 4.53 - 5.14: 128688 Nonbonded interactions: 312555 Sorted by model distance: nonbonded pdb=" OG1 THR A 284 " pdb=" OH TYR B 290 " model vdw 2.107 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" OG1 THR D 284 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR C 284 " pdb=" OH TYR D 290 " model vdw 2.221 3.040 nonbonded pdb=" O ARG G 295 " pdb=" NE2 GLN G 298 " model vdw 2.238 3.120 nonbonded pdb=" O ARG F 295 " pdb=" NE2 GLN F 298 " model vdw 2.238 3.120 ... (remaining 312550 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 1060 or resid 1203 through 1204 or (resid 1209 \ and (name N or name C1 or name C11 or name C12 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or nam \ e O4P or name P )) or (resid 1210 and (name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C3 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name O11 or name O2 or name O3 or name O31)) or (resid 1 \ 211 and (name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C16 or name O11 or name O2 or name O3 or name O3P)) or (resid 1212 and (nam \ e C1 or name C11 or name C12 or name C2 or name C3 or name C31 or name C32 or na \ me C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 o \ r name O3 or name O31 or name O3P)) or (resid 1213 and (name C1 or name C11 or n \ ame C12 or name O11 or name O2 or name O3 or name O3P)) or resid 1214 or (resid \ 1216 and (name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C16 or name C17 or name C2 or name C3 or name O11 or name O1P or name O2 o \ r name O2P or name O3 or name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 19 through 1060 or resid 1203 through 1204 or resid 1209 o \ r (resid 1210 and (name C1 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 \ or name O11 or name O2 or name O3 or name O31)) or (resid 1211 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O11 \ or name O2 or name O3 or name O3P)) or (resid 1212 and (name C1 or name C11 or \ name C12 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name O3 or name O3 \ 1 or name O3P)) or (resid 1213 and (name C1 or name C11 or name C12 or name O11 \ or name O2 or name O3 or name O3P)) or resid 1214 or (resid 1216 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name C2 or name C3 or name O11 or name O1P or name O2 or name O2P or name O \ 3 or name O3P or name O4P or name P )))) selection = (chain 'C' and (resid 19 through 1060 or resid 1203 through 1204 or resid 1209 o \ r (resid 1210 and (name C1 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 \ or name O11 or name O2 or name O3 or name O31)) or (resid 1211 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O11 \ or name O2 or name O3 or name O3P)) or (resid 1212 and (name C1 or name C11 or \ name C12 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name O3 or name O3 \ 1 or name O3P)) or (resid 1213 and (name C1 or name C11 or name C12 or name O11 \ or name O2 or name O3 or name O3P)) or resid 1214 or (resid 1216 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name C2 or name C3 or name O11 or name O1P or name O2 or name O2P or name O \ 3 or name O3P or name O4P or name P )))) selection = (chain 'D' and (resid 19 through 1060 or resid 1203 through 1204 or resid 1209 o \ r (resid 1210 and (name C1 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 \ or name O11 or name O2 or name O3 or name O31)) or (resid 1211 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O11 \ or name O2 or name O3 or name O3P)) or (resid 1212 and (name C1 or name C11 or \ name C12 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 o \ r name C35 or name C36 or name C37 or name C38 or name C39 or name O3 or name O3 \ 1 or name O3P)) or (resid 1213 and (name C1 or name C11 or name C12 or name O11 \ or name O2 or name O3 or name O3P)) or resid 1214 or (resid 1216 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name C2 or name C3 or name O11 or name O1P or name O2 or name O2P or name O \ 3 or name O3P or name O4P or name P )))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 29.640 Find NCS groups from input model: 0.910 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 32256 Z= 0.163 Angle : 0.764 29.916 43716 Z= 0.332 Chirality : 0.066 1.883 4972 Planarity : 0.003 0.046 5324 Dihedral : 16.608 175.530 12808 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.81 % Allowed : 14.63 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.14), residues: 3752 helix: 1.08 (0.12), residues: 1900 sheet: 0.44 (0.28), residues: 356 loop : 0.26 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 20 TYR 0.013 0.001 TYR B1032 PHE 0.025 0.001 PHE D 550 TRP 0.012 0.001 TRP A 93 HIS 0.004 0.001 HIS C 586 Details of bonding type rmsd covalent geometry : bond 0.00333 (32252) covalent geometry : angle 0.76353 (43716) hydrogen bonds : bond 0.13084 ( 1567) hydrogen bonds : angle 5.50381 ( 4353) Misc. bond : bond 0.02320 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 385 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 555 GLU cc_start: 0.6433 (mt-10) cc_final: 0.6074 (mt-10) REVERT: B 960 ARG cc_start: 0.4490 (pmt-80) cc_final: 0.4209 (ppt170) REVERT: G 287 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8407 (mt) outliers start: 60 outliers final: 35 residues processed: 426 average time/residue: 0.5994 time to fit residues: 311.3687 Evaluate side-chains 378 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 342 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 816 GLN Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 816 GLN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 816 GLN Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 288 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0370 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 747 HIS A 771 HIS B 142 GLN B 449 ASN B 747 HIS B 771 HIS B1058 ASN C 142 GLN C 222 GLN C 747 HIS C 771 HIS D 142 GLN D 747 HIS D 771 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.196309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.144235 restraints weight = 36515.807| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.43 r_work: 0.3622 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32256 Z= 0.147 Angle : 0.722 31.087 43716 Z= 0.315 Chirality : 0.064 1.755 4972 Planarity : 0.004 0.048 5324 Dihedral : 13.929 178.573 5900 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.35 % Allowed : 13.27 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.14), residues: 3752 helix: 1.35 (0.12), residues: 1888 sheet: 0.03 (0.28), residues: 356 loop : 0.42 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1031 TYR 0.019 0.002 TYR C1015 PHE 0.020 0.002 PHE D 144 TRP 0.008 0.001 TRP D 93 HIS 0.008 0.001 HIS D 718 Details of bonding type rmsd covalent geometry : bond 0.00332 (32252) covalent geometry : angle 0.72223 (43716) hydrogen bonds : bond 0.04811 ( 1567) hydrogen bonds : angle 4.49731 ( 4353) Misc. bond : bond 0.00119 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 388 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LYS cc_start: 0.5370 (mmtm) cc_final: 0.5150 (mmtm) REVERT: A 555 GLU cc_start: 0.6309 (mt-10) cc_final: 0.5988 (mt-10) REVERT: A 604 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6176 (mp0) REVERT: A 953 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7421 (mp) REVERT: B 555 GLU cc_start: 0.6014 (mt-10) cc_final: 0.5804 (mt-10) REVERT: B 560 LYS cc_start: 0.7685 (mmtm) cc_final: 0.7052 (mppt) REVERT: B 604 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6459 (mp0) REVERT: B 794 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7230 (tp) REVERT: B 1009 MET cc_start: 0.6248 (mmm) cc_final: 0.5946 (mmm) REVERT: D 555 GLU cc_start: 0.6420 (mt-10) cc_final: 0.6076 (mt-10) REVERT: D 794 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7276 (tp) REVERT: E 264 MET cc_start: 0.6772 (ptm) cc_final: 0.6466 (ptt) REVERT: F 264 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6474 (ptt) REVERT: G 264 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.6307 (ptt) REVERT: H 264 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.6267 (ptt) outliers start: 111 outliers final: 38 residues processed: 453 average time/residue: 0.5235 time to fit residues: 291.0971 Evaluate side-chains 386 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 342 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain F residue 264 MET Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 264 MET Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 264 MET Chi-restraints excluded: chain H residue 267 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 243 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 375 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 259 optimal weight: 2.9990 chunk 334 optimal weight: 0.5980 chunk 248 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 233 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 771 HIS B 142 GLN B 771 HIS C 200 ASN C 771 HIS D 142 GLN D 771 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.195230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.142966 restraints weight = 36344.663| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.43 r_work: 0.3604 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32256 Z= 0.139 Angle : 0.711 31.058 43716 Z= 0.308 Chirality : 0.064 1.754 4972 Planarity : 0.004 0.050 5324 Dihedral : 13.643 177.306 5859 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.22 % Allowed : 14.20 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.14), residues: 3752 helix: 1.41 (0.12), residues: 1884 sheet: -0.07 (0.28), residues: 356 loop : 0.40 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 20 TYR 0.016 0.002 TYR D1007 PHE 0.019 0.002 PHE D 144 TRP 0.008 0.001 TRP D 43 HIS 0.005 0.001 HIS D 718 Details of bonding type rmsd covalent geometry : bond 0.00317 (32252) covalent geometry : angle 0.71143 (43716) hydrogen bonds : bond 0.04780 ( 1567) hydrogen bonds : angle 4.41118 ( 4353) Misc. bond : bond 0.00045 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 388 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 GLU cc_start: 0.6348 (mt-10) cc_final: 0.5987 (mt-10) REVERT: A 604 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6209 (mp0) REVERT: A 764 LYS cc_start: 0.8103 (ptpp) cc_final: 0.7807 (pttp) REVERT: A 953 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7432 (mp) REVERT: A 1007 TYR cc_start: 0.7302 (m-10) cc_final: 0.7100 (m-10) REVERT: B 604 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6472 (mp0) REVERT: B 794 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7295 (tp) REVERT: B 924 MET cc_start: 0.7265 (mmt) cc_final: 0.7020 (mmt) REVERT: B 1009 MET cc_start: 0.6248 (mmm) cc_final: 0.6016 (mmm) REVERT: C 281 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8424 (mp) REVERT: D 555 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6072 (mt-10) REVERT: D 794 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7305 (tp) REVERT: E 264 MET cc_start: 0.6896 (ptm) cc_final: 0.6627 (ptt) REVERT: F 264 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6579 (ptt) REVERT: G 264 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6436 (ptt) REVERT: H 264 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.6412 (ptt) outliers start: 140 outliers final: 68 residues processed: 474 average time/residue: 0.4958 time to fit residues: 289.3978 Evaluate side-chains 436 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 361 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 760 ILE Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 264 MET Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 264 MET Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain H residue 264 MET Chi-restraints excluded: chain H residue 267 LEU Chi-restraints excluded: chain H residue 287 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 246 optimal weight: 0.0270 chunk 86 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 253 optimal weight: 1.9990 chunk 282 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 356 optimal weight: 9.9990 chunk 184 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 771 HIS B 142 GLN C 200 ASN D 108 GLN D 142 GLN D 771 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.196326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.144292 restraints weight = 36188.569| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.42 r_work: 0.3625 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32256 Z= 0.110 Angle : 0.694 30.908 43716 Z= 0.297 Chirality : 0.063 1.752 4972 Planarity : 0.003 0.050 5324 Dihedral : 13.519 177.046 5859 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.59 % Allowed : 14.99 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.14), residues: 3752 helix: 1.59 (0.12), residues: 1884 sheet: -0.15 (0.27), residues: 356 loop : 0.39 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 20 TYR 0.015 0.001 TYR D 762 PHE 0.014 0.001 PHE C 34 TRP 0.007 0.001 TRP A 767 HIS 0.003 0.001 HIS C 718 Details of bonding type rmsd covalent geometry : bond 0.00240 (32252) covalent geometry : angle 0.69358 (43716) hydrogen bonds : bond 0.04302 ( 1567) hydrogen bonds : angle 4.29571 ( 4353) Misc. bond : bond 0.00039 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 392 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 LYS cc_start: 0.7524 (mttt) cc_final: 0.7303 (mttt) REVERT: A 604 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6197 (mp0) REVERT: A 746 PHE cc_start: 0.4778 (m-10) cc_final: 0.4307 (m-10) REVERT: A 972 ARG cc_start: 0.6786 (ptm160) cc_final: 0.6207 (ptm160) REVERT: B 521 GLU cc_start: 0.7374 (pm20) cc_final: 0.7141 (pm20) REVERT: B 555 GLU cc_start: 0.6023 (mt-10) cc_final: 0.5798 (mp0) REVERT: B 604 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6178 (mp0) REVERT: B 763 LEU cc_start: 0.6361 (mm) cc_final: 0.6152 (mm) REVERT: B 972 ARG cc_start: 0.6911 (ptm160) cc_final: 0.6056 (ptm160) REVERT: C 154 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7641 (tpp) REVERT: D 948 GLU cc_start: 0.7589 (tt0) cc_final: 0.7335 (tm-30) REVERT: E 264 MET cc_start: 0.6846 (ptm) cc_final: 0.6614 (ptt) REVERT: F 264 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.6629 (ptt) REVERT: G 264 MET cc_start: 0.6641 (OUTLIER) cc_final: 0.6441 (ptt) REVERT: H 264 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.6436 (ptt) outliers start: 119 outliers final: 54 residues processed: 463 average time/residue: 0.5357 time to fit residues: 303.1237 Evaluate side-chains 425 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 367 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 760 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 264 MET Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 264 MET Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 264 MET Chi-restraints excluded: chain H residue 267 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 199 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 245 optimal weight: 0.0670 chunk 218 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 340 optimal weight: 2.9990 chunk 221 optimal weight: 0.5980 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 HIS A 771 HIS B 142 GLN B 328 ASN B 747 HIS C 142 GLN C 200 ASN C 747 HIS D 142 GLN D 468 HIS D 747 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.190969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138196 restraints weight = 36014.740| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.36 r_work: 0.3543 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 32256 Z= 0.204 Angle : 0.780 31.601 43716 Z= 0.346 Chirality : 0.066 1.737 4972 Planarity : 0.004 0.052 5324 Dihedral : 13.618 174.435 5847 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.01 % Allowed : 14.60 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.14), residues: 3752 helix: 1.26 (0.12), residues: 1880 sheet: -0.17 (0.27), residues: 348 loop : 0.16 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 260 TYR 0.019 0.002 TYR D 762 PHE 0.022 0.002 PHE B1012 TRP 0.012 0.002 TRP D 43 HIS 0.008 0.001 HIS A 718 Details of bonding type rmsd covalent geometry : bond 0.00474 (32252) covalent geometry : angle 0.78023 (43716) hydrogen bonds : bond 0.05678 ( 1567) hydrogen bonds : angle 4.54116 ( 4353) Misc. bond : bond 0.00088 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 408 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 GLU cc_start: 0.6377 (mt-10) cc_final: 0.6011 (mt-10) REVERT: A 764 LYS cc_start: 0.8198 (ptpp) cc_final: 0.7830 (pttp) REVERT: A 1007 TYR cc_start: 0.7294 (m-10) cc_final: 0.7086 (m-10) REVERT: A 1010 LEU cc_start: 0.5606 (OUTLIER) cc_final: 0.5325 (tm) REVERT: B 442 MET cc_start: 0.5898 (mmt) cc_final: 0.5670 (mmt) REVERT: B 604 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6443 (mp0) REVERT: B 764 LYS cc_start: 0.8185 (ptpp) cc_final: 0.7801 (pttp) REVERT: C 304 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8476 (mmm) REVERT: C 764 LYS cc_start: 0.8224 (ptpp) cc_final: 0.7858 (pttp) REVERT: D 329 ARG cc_start: 0.7284 (ppt90) cc_final: 0.6874 (ppt90) REVERT: D 555 GLU cc_start: 0.6454 (mt-10) cc_final: 0.6074 (mt-10) REVERT: D 948 GLU cc_start: 0.7599 (tt0) cc_final: 0.7264 (tm-30) outliers start: 133 outliers final: 63 residues processed: 480 average time/residue: 0.5546 time to fit residues: 327.4661 Evaluate side-chains 449 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 384 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 871 THR Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 264 MET Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 264 MET Chi-restraints excluded: chain H residue 267 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 259 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 366 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 293 optimal weight: 0.6980 chunk 255 optimal weight: 0.5980 chunk 355 optimal weight: 4.9990 chunk 375 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS B 142 GLN B 268 ASN B 753 HIS C 142 GLN C 200 ASN C 268 ASN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.193397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.141207 restraints weight = 36116.729| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.36 r_work: 0.3579 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32256 Z= 0.129 Angle : 0.721 31.036 43716 Z= 0.313 Chirality : 0.064 1.742 4972 Planarity : 0.004 0.051 5324 Dihedral : 13.439 174.624 5847 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.50 % Allowed : 15.17 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.14), residues: 3752 helix: 1.43 (0.12), residues: 1896 sheet: -0.12 (0.28), residues: 332 loop : 0.16 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.012 0.002 TYR B 996 PHE 0.018 0.001 PHE B1000 TRP 0.010 0.001 TRP C 694 HIS 0.004 0.001 HIS C 718 Details of bonding type rmsd covalent geometry : bond 0.00289 (32252) covalent geometry : angle 0.72057 (43716) hydrogen bonds : bond 0.04673 ( 1567) hydrogen bonds : angle 4.37536 ( 4353) Misc. bond : bond 0.00016 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 403 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8344 (mp) REVERT: A 521 GLU cc_start: 0.7380 (pm20) cc_final: 0.7148 (pm20) REVERT: A 604 GLU cc_start: 0.6990 (mm-30) cc_final: 0.5999 (mp0) REVERT: A 764 LYS cc_start: 0.8177 (ptpp) cc_final: 0.7837 (pttp) REVERT: A 1010 LEU cc_start: 0.5597 (OUTLIER) cc_final: 0.5266 (tm) REVERT: B 281 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8344 (mp) REVERT: B 604 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6410 (mp0) REVERT: B 972 ARG cc_start: 0.7059 (ptm160) cc_final: 0.6257 (ptm160) REVERT: C 281 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8348 (mp) REVERT: C 685 LYS cc_start: 0.5177 (OUTLIER) cc_final: 0.4719 (ptpt) REVERT: D 281 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8350 (mp) REVERT: D 329 ARG cc_start: 0.7262 (ppt90) cc_final: 0.6798 (ppt90) REVERT: D 521 GLU cc_start: 0.7459 (pm20) cc_final: 0.7217 (pm20) REVERT: D 764 LYS cc_start: 0.8166 (ptpp) cc_final: 0.7737 (pttp) REVERT: D 948 GLU cc_start: 0.7557 (tt0) cc_final: 0.7211 (tm-30) outliers start: 116 outliers final: 63 residues processed: 466 average time/residue: 0.5737 time to fit residues: 328.5326 Evaluate side-chains 443 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 374 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 975 CYS Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 685 LYS Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 760 ILE Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain H residue 264 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 57 optimal weight: 0.7980 chunk 293 optimal weight: 0.2980 chunk 280 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 369 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 299 optimal weight: 0.7980 chunk 352 optimal weight: 0.8980 chunk 297 optimal weight: 0.0570 chunk 217 optimal weight: 0.2980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS C 142 GLN C 200 ASN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 753 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.195877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144057 restraints weight = 36289.956| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.38 r_work: 0.3616 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32256 Z= 0.106 Angle : 0.704 30.957 43716 Z= 0.301 Chirality : 0.063 1.743 4972 Planarity : 0.003 0.047 5324 Dihedral : 13.231 175.504 5847 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.02 % Allowed : 16.01 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.14), residues: 3752 helix: 1.63 (0.12), residues: 1896 sheet: -0.28 (0.27), residues: 356 loop : 0.31 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.025 0.001 TYR A1007 PHE 0.016 0.001 PHE B1000 TRP 0.011 0.001 TRP C 477 HIS 0.004 0.001 HIS B 753 Details of bonding type rmsd covalent geometry : bond 0.00226 (32252) covalent geometry : angle 0.70376 (43716) hydrogen bonds : bond 0.04159 ( 1567) hydrogen bonds : angle 4.25058 ( 4353) Misc. bond : bond 0.00030 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 399 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 GLU cc_start: 0.7393 (pm20) cc_final: 0.7152 (pm20) REVERT: A 604 GLU cc_start: 0.6908 (mm-30) cc_final: 0.5926 (mp0) REVERT: A 746 PHE cc_start: 0.4648 (m-10) cc_final: 0.4241 (m-10) REVERT: A 972 ARG cc_start: 0.6993 (ptm160) cc_final: 0.6504 (ptm160) REVERT: B 604 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6360 (mp0) REVERT: B 746 PHE cc_start: 0.4828 (m-10) cc_final: 0.4401 (m-10) REVERT: B 972 ARG cc_start: 0.7041 (ptm160) cc_final: 0.6243 (ptm160) REVERT: C 30 MET cc_start: 0.7393 (mmm) cc_final: 0.7188 (tpt) REVERT: C 685 LYS cc_start: 0.5172 (OUTLIER) cc_final: 0.4656 (ptpt) REVERT: D 329 ARG cc_start: 0.7269 (ppt90) cc_final: 0.6655 (ptt90) REVERT: D 521 GLU cc_start: 0.7491 (pm20) cc_final: 0.7243 (pm20) REVERT: D 555 GLU cc_start: 0.6293 (mt-10) cc_final: 0.5874 (mp0) REVERT: D 746 PHE cc_start: 0.4682 (m-10) cc_final: 0.4457 (m-10) REVERT: D 799 MET cc_start: 0.7473 (tpt) cc_final: 0.7263 (tpp) outliers start: 100 outliers final: 56 residues processed: 467 average time/residue: 0.5812 time to fit residues: 332.7814 Evaluate side-chains 431 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 374 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 831 GLN Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 975 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 685 LYS Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 831 GLN Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 760 ILE Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 933 ILE Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 264 MET Chi-restraints excluded: chain H residue 264 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 183 optimal weight: 8.9990 chunk 98 optimal weight: 0.4980 chunk 160 optimal weight: 1.9990 chunk 232 optimal weight: 0.0040 chunk 337 optimal weight: 0.5980 chunk 361 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 365 optimal weight: 3.9990 chunk 340 optimal weight: 0.8980 chunk 270 optimal weight: 8.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS B 142 GLN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 HIS ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.194727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.142485 restraints weight = 36154.916| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.37 r_work: 0.3595 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32256 Z= 0.124 Angle : 0.723 31.153 43716 Z= 0.312 Chirality : 0.064 1.738 4972 Planarity : 0.003 0.049 5324 Dihedral : 13.171 175.342 5847 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.80 % Allowed : 16.92 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.14), residues: 3752 helix: 1.67 (0.12), residues: 1888 sheet: -0.35 (0.27), residues: 364 loop : 0.31 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 20 TYR 0.018 0.001 TYR D1032 PHE 0.021 0.001 PHE B 34 TRP 0.014 0.001 TRP C 477 HIS 0.004 0.001 HIS B 753 Details of bonding type rmsd covalent geometry : bond 0.00278 (32252) covalent geometry : angle 0.72267 (43716) hydrogen bonds : bond 0.04449 ( 1567) hydrogen bonds : angle 4.26337 ( 4353) Misc. bond : bond 0.00047 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 389 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7310 (ppt90) cc_final: 0.6962 (ppt90) REVERT: A 521 GLU cc_start: 0.7423 (pm20) cc_final: 0.7161 (pm20) REVERT: A 604 GLU cc_start: 0.6900 (mm-30) cc_final: 0.5909 (mp0) REVERT: A 746 PHE cc_start: 0.4782 (m-10) cc_final: 0.4400 (m-10) REVERT: A 972 ARG cc_start: 0.7047 (ptm160) cc_final: 0.6569 (ptm160) REVERT: B 604 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6323 (mp0) REVERT: B 746 PHE cc_start: 0.4828 (m-10) cc_final: 0.4486 (m-10) REVERT: B 972 ARG cc_start: 0.7080 (ptm160) cc_final: 0.6398 (ptm160) REVERT: C 43 TRP cc_start: 0.5384 (t-100) cc_final: 0.5087 (t-100) REVERT: C 685 LYS cc_start: 0.5209 (OUTLIER) cc_final: 0.4689 (ptpt) REVERT: D 329 ARG cc_start: 0.7243 (ppt90) cc_final: 0.6616 (ppt90) REVERT: D 521 GLU cc_start: 0.7493 (pm20) cc_final: 0.7232 (pm20) REVERT: D 723 ILE cc_start: 0.6435 (OUTLIER) cc_final: 0.6191 (mp) REVERT: F 264 MET cc_start: 0.6947 (ptm) cc_final: 0.6737 (ptt) outliers start: 93 outliers final: 57 residues processed: 455 average time/residue: 0.5899 time to fit residues: 327.8837 Evaluate side-chains 434 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 375 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 975 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 685 LYS Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 760 ILE Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 933 ILE Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 264 MET Chi-restraints excluded: chain H residue 264 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 356 optimal weight: 10.0000 chunk 367 optimal weight: 4.9990 chunk 348 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 317 optimal weight: 0.9980 chunk 304 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 52 optimal weight: 0.0670 chunk 124 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 HIS A 771 HIS B 142 GLN B 449 ASN B 747 HIS C 142 GLN C 747 HIS ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.191429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.138616 restraints weight = 35934.832| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.37 r_work: 0.3550 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32256 Z= 0.178 Angle : 0.780 31.527 43716 Z= 0.344 Chirality : 0.065 1.726 4972 Planarity : 0.004 0.053 5324 Dihedral : 13.329 173.697 5847 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.74 % Allowed : 17.22 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.14), residues: 3752 helix: 1.40 (0.12), residues: 1892 sheet: -0.39 (0.27), residues: 356 loop : 0.21 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 20 TYR 0.020 0.002 TYR D1032 PHE 0.026 0.002 PHE D 34 TRP 0.019 0.001 TRP C 477 HIS 0.006 0.001 HIS B 753 Details of bonding type rmsd covalent geometry : bond 0.00417 (32252) covalent geometry : angle 0.77968 (43716) hydrogen bonds : bond 0.05336 ( 1567) hydrogen bonds : angle 4.45625 ( 4353) Misc. bond : bond 0.00092 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 388 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7327 (ppt90) cc_final: 0.6983 (ppt90) REVERT: A 521 GLU cc_start: 0.7493 (pm20) cc_final: 0.7248 (pm20) REVERT: A 764 LYS cc_start: 0.8169 (ptpp) cc_final: 0.7772 (pttp) REVERT: B 764 LYS cc_start: 0.8174 (ptpp) cc_final: 0.7785 (pttp) REVERT: C 43 TRP cc_start: 0.5370 (t-100) cc_final: 0.5074 (t-100) REVERT: D 329 ARG cc_start: 0.7274 (ppt90) cc_final: 0.6683 (ppt90) REVERT: D 521 GLU cc_start: 0.7497 (pm20) cc_final: 0.7216 (pm20) REVERT: D 723 ILE cc_start: 0.6438 (OUTLIER) cc_final: 0.6207 (mp) REVERT: D 764 LYS cc_start: 0.8133 (ptpp) cc_final: 0.7747 (pttp) REVERT: F 264 MET cc_start: 0.7012 (ptm) cc_final: 0.6801 (ptt) outliers start: 91 outliers final: 62 residues processed: 452 average time/residue: 0.5850 time to fit residues: 323.9708 Evaluate side-chains 438 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 375 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 738 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 975 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 760 ILE Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 831 GLN Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 264 MET Chi-restraints excluded: chain H residue 264 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 165 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 339 optimal weight: 0.9990 chunk 266 optimal weight: 0.0870 chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 253 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 268 ASN A 753 HIS A 771 HIS ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN D1058 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.194190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.142656 restraints weight = 36182.523| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.36 r_work: 0.3600 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32256 Z= 0.118 Angle : 0.733 31.077 43716 Z= 0.318 Chirality : 0.064 1.734 4972 Planarity : 0.003 0.049 5324 Dihedral : 13.206 174.953 5847 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.23 % Allowed : 17.91 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.14), residues: 3752 helix: 1.55 (0.12), residues: 1896 sheet: -0.32 (0.27), residues: 356 loop : 0.29 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 20 TYR 0.020 0.001 TYR D1032 PHE 0.024 0.001 PHE B 34 TRP 0.016 0.001 TRP C 477 HIS 0.004 0.001 HIS B 753 Details of bonding type rmsd covalent geometry : bond 0.00261 (32252) covalent geometry : angle 0.73342 (43716) hydrogen bonds : bond 0.04425 ( 1567) hydrogen bonds : angle 4.33374 ( 4353) Misc. bond : bond 0.00030 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 385 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7305 (ppt90) cc_final: 0.6959 (ppt90) REVERT: A 521 GLU cc_start: 0.7499 (pm20) cc_final: 0.7258 (pm20) REVERT: A 603 LYS cc_start: 0.7503 (mttt) cc_final: 0.7205 (mttt) REVERT: A 604 GLU cc_start: 0.6899 (mm-30) cc_final: 0.5897 (mp0) REVERT: A 746 PHE cc_start: 0.4774 (m-10) cc_final: 0.4455 (m-10) REVERT: A 972 ARG cc_start: 0.6961 (ptm160) cc_final: 0.6473 (ptm160) REVERT: B 746 PHE cc_start: 0.4904 (m-10) cc_final: 0.4608 (m-10) REVERT: B 972 ARG cc_start: 0.7096 (ptm160) cc_final: 0.6505 (ptm160) REVERT: B 1007 TYR cc_start: 0.7441 (m-80) cc_final: 0.6450 (m-80) REVERT: C 43 TRP cc_start: 0.5395 (t-100) cc_final: 0.5100 (t-100) REVERT: C 1007 TYR cc_start: 0.7425 (m-80) cc_final: 0.6651 (m-80) REVERT: D 329 ARG cc_start: 0.7252 (ppt90) cc_final: 0.6947 (ppt90) REVERT: D 521 GLU cc_start: 0.7506 (pm20) cc_final: 0.7243 (pm20) REVERT: D 555 GLU cc_start: 0.6361 (mt-10) cc_final: 0.6021 (mt-10) REVERT: D 723 ILE cc_start: 0.6405 (OUTLIER) cc_final: 0.6126 (mp) REVERT: D 764 LYS cc_start: 0.8032 (ptpp) cc_final: 0.7681 (pttp) REVERT: E 264 MET cc_start: 0.6845 (ptm) cc_final: 0.6585 (ptt) REVERT: F 264 MET cc_start: 0.7055 (ptm) cc_final: 0.6849 (ptt) outliers start: 74 outliers final: 62 residues processed: 439 average time/residue: 0.5960 time to fit residues: 319.7499 Evaluate side-chains 424 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 361 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 975 CYS Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 760 ILE Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 264 MET Chi-restraints excluded: chain H residue 264 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 244 optimal weight: 1.9990 chunk 353 optimal weight: 4.9990 chunk 331 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 135 optimal weight: 0.4980 chunk 327 optimal weight: 0.0030 chunk 203 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 253 optimal weight: 0.0870 overall best weight: 0.4368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS C1058 ASN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.195812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.144263 restraints weight = 36278.707| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.38 r_work: 0.3616 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32256 Z= 0.110 Angle : 0.722 31.100 43716 Z= 0.310 Chirality : 0.064 1.735 4972 Planarity : 0.003 0.048 5324 Dihedral : 13.082 175.993 5847 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.20 % Allowed : 17.82 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.14), residues: 3752 helix: 1.68 (0.12), residues: 1892 sheet: -0.32 (0.27), residues: 356 loop : 0.29 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 20 TYR 0.018 0.001 TYR B1032 PHE 0.028 0.001 PHE B 34 TRP 0.016 0.001 TRP C 477 HIS 0.004 0.001 HIS D 753 Details of bonding type rmsd covalent geometry : bond 0.00240 (32252) covalent geometry : angle 0.72236 (43716) hydrogen bonds : bond 0.04144 ( 1567) hydrogen bonds : angle 4.25707 ( 4353) Misc. bond : bond 0.00026 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18215.86 seconds wall clock time: 309 minutes 44.08 seconds (18584.08 seconds total)