Starting phenix.real_space_refine on Thu May 29 05:29:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s3e_19691/05_2025/8s3e_19691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s3e_19691/05_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_19691/05_2025/8s3e_19691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s3e_19691/05_2025/8s3e_19691.map" model { file = "/net/cci-nas-00/data/ceres_data/8s3e_19691/05_2025/8s3e_19691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s3e_19691/05_2025/8s3e_19691.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 2.53s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 20.29, per 1000 atoms: 0.64 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: 8.53 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 4.13 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: 13.31 Time building geometry restraints manager: 9.08 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: 16.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 71.600 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.060 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), 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 TRP 0.012 0.001 TRP A 93 HIS 0.004 0.001 HIS C 586 PHE 0.025 0.001 PHE D 550 TYR 0.013 0.001 TYR B1032 ARG 0.005 0.000 ARG B 20 Details of bonding type rmsd hydrogen bonds : bond 0.13084 ( 1567) hydrogen bonds : angle 5.50381 ( 4353) covalent geometry : bond 0.00333 (32252) covalent geometry : angle 0.76353 (43716) 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 : 3.621 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: 1.1561 time to fit residues: 601.3757 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 : 3.215 ------------------------------------------------------------------------------- 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 317 optimal weight: 0.8980 chunk 284 optimal weight: 0.4980 chunk 158 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 152 optimal weight: 0.3980 chunk 294 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 179 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 341 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 A1058 ASN B 142 GLN B 222 GLN B 771 HIS B1058 ASN C 142 GLN C 222 GLN C 747 HIS ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 ASN D 142 GLN D 222 GLN D 771 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.200150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.149075 restraints weight = 36659.669| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.41 r_work: 0.3685 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 32256 Z= 0.108 Angle : 0.688 30.758 43716 Z= 0.296 Chirality : 0.063 1.761 4972 Planarity : 0.003 0.047 5324 Dihedral : 13.935 179.994 5900 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.17 % Allowed : 13.72 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.14), residues: 3752 helix: 1.47 (0.12), residues: 1888 sheet: 0.11 (0.28), residues: 356 loop : 0.45 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 93 HIS 0.005 0.001 HIS D 718 PHE 0.017 0.001 PHE D 144 TYR 0.015 0.001 TYR C 762 ARG 0.003 0.000 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 1567) hydrogen bonds : angle 4.41520 ( 4353) covalent geometry : bond 0.00228 (32252) covalent geometry : angle 0.68844 (43716) Misc. bond : bond 0.00115 ( 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 476 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 371 time to evaluate : 3.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 GLU cc_start: 0.6254 (mt-10) cc_final: 0.5953 (mt-10) REVERT: A 604 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6180 (mp0) REVERT: A 953 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7398 (mp) REVERT: B 604 GLU cc_start: 0.6797 (mm-30) cc_final: 0.5981 (mp0) REVERT: B 794 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7232 (tp) REVERT: B 1007 TYR cc_start: 0.7434 (m-10) cc_final: 0.7229 (m-10) REVERT: C 30 MET cc_start: 0.7414 (tpt) cc_final: 0.7155 (tpt) REVERT: C 281 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8372 (mp) REVERT: D 723 ILE cc_start: 0.6261 (OUTLIER) cc_final: 0.4846 (pp) REVERT: D 794 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7206 (tp) REVERT: E 264 MET cc_start: 0.6752 (ptm) cc_final: 0.6450 (ptt) REVERT: F 264 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6408 (ptt) REVERT: G 264 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.6283 (ptt) REVERT: H 264 MET cc_start: 0.6472 (OUTLIER) cc_final: 0.6272 (ptt) outliers start: 105 outliers final: 36 residues processed: 437 average time/residue: 1.1007 time to fit residues: 594.7745 Evaluate side-chains 383 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 339 time to evaluate : 3.253 ------------------------------------------------------------------------------- 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 304 MET 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 416 ILE 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 281 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 565 MET 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 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 416 ILE 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 188 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 318 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 330 optimal weight: 10.0000 chunk 130 optimal weight: 0.0770 chunk 240 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.6342 ------------------------------------------------------------------------------- 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 771 HIS C 142 GLN C 200 ASN ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4344 r_free = 0.4344 target = 0.198797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.146954 restraints weight = 36592.981| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.45 r_work: 0.3657 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 32256 Z= 0.110 Angle : 0.685 30.870 43716 Z= 0.293 Chirality : 0.063 1.759 4972 Planarity : 0.003 0.048 5324 Dihedral : 13.532 178.395 5859 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.56 % Allowed : 14.11 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.14), residues: 3752 helix: 1.62 (0.12), residues: 1884 sheet: -0.00 (0.28), residues: 356 loop : 0.47 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 767 HIS 0.004 0.001 HIS C 718 PHE 0.020 0.001 PHE D 144 TYR 0.016 0.001 TYR D1007 ARG 0.006 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 1567) hydrogen bonds : angle 4.25866 ( 4353) covalent geometry : bond 0.00238 (32252) covalent geometry : angle 0.68488 (43716) Misc. bond : bond 0.00137 ( 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 500 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 382 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 GLU cc_start: 0.7344 (pm20) cc_final: 0.7110 (pm20) REVERT: A 603 LYS cc_start: 0.7464 (mttt) cc_final: 0.7212 (mttt) REVERT: A 604 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6114 (mp0) REVERT: A 794 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7377 (tp) REVERT: A 953 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7411 (mp) REVERT: B 604 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6464 (mp0) REVERT: B 794 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7220 (tp) REVERT: C 281 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8400 (mp) REVERT: C 304 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8392 (mmm) REVERT: C 565 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7497 (ttm) REVERT: C 685 LYS cc_start: 0.5060 (OUTLIER) cc_final: 0.4647 (ptmt) REVERT: C 794 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7415 (tp) REVERT: D 329 ARG cc_start: 0.7264 (ppt90) cc_final: 0.6559 (ptt90) REVERT: D 794 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7249 (tp) REVERT: E 264 MET cc_start: 0.6790 (ptm) cc_final: 0.6516 (ptt) REVERT: F 264 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6488 (ptt) outliers start: 118 outliers final: 45 residues processed: 449 average time/residue: 1.1478 time to fit residues: 630.4151 Evaluate side-chains 396 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 341 time to evaluate : 3.180 ------------------------------------------------------------------------------- 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 416 ILE Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 794 ILE 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 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 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 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 416 ILE Chi-restraints excluded: chain C residue 565 MET Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 685 LYS Chi-restraints excluded: chain C residue 794 ILE 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 416 ILE Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 755 VAL 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 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 267 LEU Chi-restraints excluded: chain H residue 267 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 5.9990 chunk 312 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 356 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 253 optimal weight: 0.0980 chunk 355 optimal weight: 4.9990 chunk 283 optimal weight: 0.5980 chunk 351 optimal weight: 5.9990 chunk 304 optimal weight: 3.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- 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 747 HIS C 142 GLN C 200 ASN C 771 HIS D 108 GLN D 142 GLN D 747 HIS D 753 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.194225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.141377 restraints weight = 36212.573| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.42 r_work: 0.3587 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32256 Z= 0.159 Angle : 0.734 31.271 43716 Z= 0.321 Chirality : 0.064 1.746 4972 Planarity : 0.004 0.050 5324 Dihedral : 13.521 176.090 5847 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.22 % Allowed : 14.17 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.14), residues: 3752 helix: 1.49 (0.12), residues: 1884 sheet: -0.14 (0.28), residues: 356 loop : 0.36 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 43 HIS 0.007 0.001 HIS C 718 PHE 0.025 0.002 PHE D 144 TYR 0.015 0.002 TYR B1015 ARG 0.005 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.05065 ( 1567) hydrogen bonds : angle 4.39413 ( 4353) covalent geometry : bond 0.00365 (32252) covalent geometry : angle 0.73402 (43716) Misc. bond : bond 0.00072 ( 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 536 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 396 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 GLU cc_start: 0.7418 (pm20) cc_final: 0.7189 (pm20) REVERT: A 603 LYS cc_start: 0.7526 (mttt) cc_final: 0.7314 (mttt) REVERT: A 604 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6182 (mp0) REVERT: A 685 LYS cc_start: 0.5173 (OUTLIER) cc_final: 0.4718 (ptpt) REVERT: A 764 LYS cc_start: 0.8128 (ptpp) cc_final: 0.7812 (pttp) REVERT: A 1007 TYR cc_start: 0.7194 (m-10) cc_final: 0.6976 (m-10) REVERT: B 604 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6705 (mp0) REVERT: B 794 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7304 (tp) REVERT: B 1009 MET cc_start: 0.6000 (mmm) cc_final: 0.5708 (mmm) REVERT: C 304 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8445 (mmm) REVERT: C 794 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7425 (tp) REVERT: D 43 TRP cc_start: 0.5357 (t-100) cc_final: 0.4984 (t-100) REVERT: D 329 ARG cc_start: 0.7306 (ppt90) cc_final: 0.7073 (ppt90) REVERT: D 555 GLU cc_start: 0.6409 (mt-10) cc_final: 0.6014 (mt-10) REVERT: E 264 MET cc_start: 0.6870 (ptm) cc_final: 0.6627 (ptt) REVERT: F 264 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6641 (ptt) outliers start: 140 outliers final: 60 residues processed: 483 average time/residue: 1.1149 time to fit residues: 663.4766 Evaluate side-chains 431 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 366 time to evaluate : 3.446 ------------------------------------------------------------------------------- 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 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 685 LYS 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 99 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 308 ILE 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 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 304 MET 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 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 794 ILE 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 532 VAL Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 755 VAL 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 276 SER 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 267 LEU Chi-restraints excluded: chain G residue 287 LEU 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 307 optimal weight: 4.9990 chunk 333 optimal weight: 4.9990 chunk 306 optimal weight: 0.8980 chunk 362 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 319 optimal weight: 6.9990 chunk 141 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 449 ASN B 747 HIS C 142 GLN C 771 HIS D 468 HIS D 747 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.189886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.136713 restraints weight = 36041.440| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.37 r_work: 0.3529 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32256 Z= 0.230 Angle : 0.808 31.599 43716 Z= 0.362 Chirality : 0.067 1.734 4972 Planarity : 0.005 0.054 5324 Dihedral : 13.751 173.194 5847 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.22 % Allowed : 14.32 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.13), residues: 3752 helix: 1.13 (0.12), residues: 1868 sheet: -0.19 (0.27), residues: 348 loop : 0.09 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 694 HIS 0.009 0.002 HIS C 718 PHE 0.027 0.003 PHE B1012 TYR 0.031 0.003 TYR D 198 ARG 0.006 0.001 ARG D 974 Details of bonding type rmsd hydrogen bonds : bond 0.05898 ( 1567) hydrogen bonds : angle 4.61981 ( 4353) covalent geometry : bond 0.00546 (32252) covalent geometry : angle 0.80821 (43716) Misc. bond : bond 0.00267 ( 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 559 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 419 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ASN cc_start: 0.7569 (m-40) cc_final: 0.6000 (p0) REVERT: A 521 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: A 555 GLU cc_start: 0.6470 (mt-10) cc_final: 0.6110 (mt-10) REVERT: A 763 LEU cc_start: 0.6184 (mm) cc_final: 0.5864 (mm) REVERT: B 685 LYS cc_start: 0.5512 (OUTLIER) cc_final: 0.4875 (ptpt) REVERT: B 1009 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.5653 (mmm) REVERT: C 34 PHE cc_start: 0.7107 (m-80) cc_final: 0.6891 (m-80) REVERT: C 43 TRP cc_start: 0.5411 (t-100) cc_final: 0.5151 (t-100) REVERT: C 372 ASN cc_start: 0.7585 (m-40) cc_final: 0.6039 (p0) REVERT: D 43 TRP cc_start: 0.5449 (t-100) cc_final: 0.5073 (t-100) REVERT: D 329 ARG cc_start: 0.7333 (ppt90) cc_final: 0.7080 (ppt90) REVERT: D 372 ASN cc_start: 0.7577 (m-40) cc_final: 0.6010 (p0) REVERT: D 555 GLU cc_start: 0.6496 (mt-10) cc_final: 0.6123 (mt-10) REVERT: D 1007 TYR cc_start: 0.7379 (m-10) cc_final: 0.7170 (m-10) REVERT: D 1009 MET cc_start: 0.5958 (OUTLIER) cc_final: 0.5750 (mmm) REVERT: F 264 MET cc_start: 0.7108 (ptm) cc_final: 0.6900 (ptp) outliers start: 140 outliers final: 68 residues processed: 501 average time/residue: 1.0595 time to fit residues: 658.2507 Evaluate side-chains 461 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 389 time to evaluate : 3.191 ------------------------------------------------------------------------------- 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 281 LEU 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 521 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 720 VAL 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 871 THR 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 281 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 457 ILE 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 685 LYS Chi-restraints excluded: chain B residue 720 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 871 THR Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1009 MET Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 197 VAL 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 720 VAL 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 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 505 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 601 ASP 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 871 THR Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 1009 MET Chi-restraints excluded: chain E residue 267 LEU 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 267 LEU Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain H residue 267 LEU Chi-restraints excluded: chain H residue 287 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 177 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 111 optimal weight: 0.4980 chunk 115 optimal weight: 0.6980 chunk 314 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 268 ASN A 771 HIS B 142 GLN B 268 ASN B 753 HIS C 200 ASN C 268 ASN C 771 HIS D 268 ASN D 468 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.193216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.141334 restraints weight = 36034.061| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.35 r_work: 0.3582 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32256 Z= 0.126 Angle : 0.725 31.040 43716 Z= 0.314 Chirality : 0.064 1.741 4972 Planarity : 0.004 0.050 5324 Dihedral : 13.456 173.930 5847 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.29 % Allowed : 15.77 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.14), residues: 3752 helix: 1.37 (0.12), residues: 1892 sheet: -0.29 (0.27), residues: 356 loop : 0.17 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 694 HIS 0.006 0.001 HIS D 753 PHE 0.014 0.001 PHE A 516 TYR 0.023 0.002 TYR A1007 ARG 0.003 0.000 ARG D 20 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 1567) hydrogen bonds : angle 4.38380 ( 4353) covalent geometry : bond 0.00281 (32252) covalent geometry : angle 0.72520 (43716) Misc. bond : bond 0.00044 ( 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 516 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 407 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 GLU cc_start: 0.7467 (pm20) cc_final: 0.7241 (pm20) REVERT: A 604 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6021 (mp0) REVERT: A 764 LYS cc_start: 0.8176 (ptpp) cc_final: 0.7830 (pttp) REVERT: B 281 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8349 (mp) REVERT: B 723 ILE cc_start: 0.6443 (OUTLIER) cc_final: 0.6241 (mp) REVERT: B 972 ARG cc_start: 0.7081 (ptm160) cc_final: 0.6346 (ptm160) REVERT: C 43 TRP cc_start: 0.5371 (t-100) cc_final: 0.5073 (t-100) REVERT: C 281 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8366 (mp) REVERT: C 763 LEU cc_start: 0.6176 (mm) cc_final: 0.5971 (mm) REVERT: C 764 LYS cc_start: 0.8113 (ptpp) cc_final: 0.7783 (pttp) REVERT: C 1007 TYR cc_start: 0.7700 (m-80) cc_final: 0.6785 (m-80) REVERT: D 43 TRP cc_start: 0.5486 (t-100) cc_final: 0.5118 (t-100) REVERT: D 329 ARG cc_start: 0.7329 (ppt90) cc_final: 0.7057 (ppt90) REVERT: D 521 GLU cc_start: 0.7464 (pm20) cc_final: 0.7246 (pm20) REVERT: D 764 LYS cc_start: 0.8131 (ptpp) cc_final: 0.7771 (pttp) outliers start: 109 outliers final: 47 residues processed: 467 average time/residue: 1.1155 time to fit residues: 645.2613 Evaluate side-chains 422 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 372 time to evaluate : 3.618 ------------------------------------------------------------------------------- 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 339 VAL Chi-restraints excluded: chain A residue 343 LYS 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 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 587 LEU 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 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 281 LEU 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 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 10 optimal weight: 0.6980 chunk 370 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 32 optimal weight: 0.0040 chunk 334 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 289 optimal weight: 2.9990 chunk 207 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS B 142 GLN C 142 GLN C 771 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.195350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.143514 restraints weight = 36224.495| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.37 r_work: 0.3609 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 32256 Z= 0.108 Angle : 0.712 31.009 43716 Z= 0.305 Chirality : 0.063 1.739 4972 Planarity : 0.003 0.048 5324 Dihedral : 13.256 174.897 5847 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.86 % Allowed : 16.62 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.14), residues: 3752 helix: 1.56 (0.12), residues: 1896 sheet: -0.28 (0.27), residues: 356 loop : 0.25 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 694 HIS 0.005 0.001 HIS D 753 PHE 0.018 0.001 PHE C 34 TYR 0.027 0.001 TYR D1007 ARG 0.003 0.000 ARG D 20 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 1567) hydrogen bonds : angle 4.27730 ( 4353) covalent geometry : bond 0.00231 (32252) covalent geometry : angle 0.71233 (43716) Misc. bond : bond 0.00029 ( 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 487 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 392 time to evaluate : 3.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7292 (ppt90) cc_final: 0.6988 (ppt90) REVERT: A 521 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: A 603 LYS cc_start: 0.7675 (mttt) cc_final: 0.7421 (mttt) REVERT: A 604 GLU cc_start: 0.6900 (mm-30) cc_final: 0.5904 (mp0) REVERT: A 746 PHE cc_start: 0.4679 (m-10) cc_final: 0.4280 (m-10) REVERT: A 799 MET cc_start: 0.7530 (tpt) cc_final: 0.7327 (tpp) REVERT: A 972 ARG cc_start: 0.6983 (ptm160) cc_final: 0.6503 (ptm160) REVERT: B 723 ILE cc_start: 0.6445 (OUTLIER) cc_final: 0.6194 (mp) REVERT: B 924 MET cc_start: 0.7202 (mmt) cc_final: 0.6898 (mmt) REVERT: B 972 ARG cc_start: 0.7068 (ptm160) cc_final: 0.6275 (ptm160) REVERT: C 43 TRP cc_start: 0.5375 (t-100) cc_final: 0.5065 (t-100) REVERT: C 1007 TYR cc_start: 0.7689 (m-80) cc_final: 0.6768 (m-80) REVERT: D 43 TRP cc_start: 0.5502 (t-100) cc_final: 0.5112 (t-100) REVERT: D 329 ARG cc_start: 0.7321 (ppt90) cc_final: 0.6656 (ptt90) REVERT: D 521 GLU cc_start: 0.7486 (pm20) cc_final: 0.7250 (pm20) REVERT: D 746 PHE cc_start: 0.4673 (m-10) cc_final: 0.4155 (m-10) REVERT: D 972 ARG cc_start: 0.6965 (ptm160) cc_final: 0.6274 (ptm160) outliers start: 95 outliers final: 48 residues processed: 454 average time/residue: 1.0968 time to fit residues: 613.8004 Evaluate side-chains 419 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 369 time to evaluate : 3.269 ------------------------------------------------------------------------------- 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 175 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 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 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 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 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 175 LEU 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 700 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 31 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 339 VAL Chi-restraints excluded: chain D residue 343 LYS 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 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 E residue 287 LEU Chi-restraints excluded: chain F residue 287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 246 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 343 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 278 optimal weight: 0.7980 chunk 299 optimal weight: 0.7980 chunk 339 optimal weight: 0.9990 chunk 220 optimal weight: 0.6980 chunk 287 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 C 200 ASN C 753 HIS C 771 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.194505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.142476 restraints weight = 36086.860| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.36 r_work: 0.3595 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32256 Z= 0.122 Angle : 0.729 31.158 43716 Z= 0.314 Chirality : 0.064 1.735 4972 Planarity : 0.003 0.049 5324 Dihedral : 13.189 174.972 5847 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.50 % Allowed : 17.25 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.14), residues: 3752 helix: 1.58 (0.12), residues: 1892 sheet: -0.34 (0.27), residues: 364 loop : 0.26 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 694 HIS 0.005 0.001 HIS D 753 PHE 0.023 0.001 PHE A 34 TYR 0.020 0.001 TYR A1032 ARG 0.003 0.000 ARG D 960 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 1567) hydrogen bonds : angle 4.27770 ( 4353) covalent geometry : bond 0.00274 (32252) covalent geometry : angle 0.72854 (43716) Misc. bond : bond 0.00056 ( 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 464 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 381 time to evaluate : 3.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7290 (ppt90) cc_final: 0.6970 (ppt90) REVERT: A 521 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: A 604 GLU cc_start: 0.6904 (mm-30) cc_final: 0.5915 (mp0) REVERT: A 723 ILE cc_start: 0.6479 (OUTLIER) cc_final: 0.6270 (mp) REVERT: A 742 ARG cc_start: 0.4996 (OUTLIER) cc_final: 0.4374 (mmp-170) REVERT: A 746 PHE cc_start: 0.4756 (m-10) cc_final: 0.4371 (m-10) REVERT: A 972 ARG cc_start: 0.7002 (ptm160) cc_final: 0.6507 (ptm160) REVERT: B 723 ILE cc_start: 0.6466 (OUTLIER) cc_final: 0.6199 (mp) REVERT: B 972 ARG cc_start: 0.7122 (ptm160) cc_final: 0.6388 (ptm160) REVERT: C 43 TRP cc_start: 0.5404 (t-100) cc_final: 0.5085 (t-100) REVERT: C 723 ILE cc_start: 0.6450 (OUTLIER) cc_final: 0.6157 (mp) REVERT: C 1007 TYR cc_start: 0.7692 (m-80) cc_final: 0.6737 (m-80) REVERT: D 43 TRP cc_start: 0.5557 (t-100) cc_final: 0.5159 (t-100) REVERT: D 329 ARG cc_start: 0.7317 (ppt90) cc_final: 0.7003 (ppt90) REVERT: D 521 GLU cc_start: 0.7493 (pm20) cc_final: 0.7244 (pm20) REVERT: D 746 PHE cc_start: 0.4697 (m-10) cc_final: 0.4490 (m-10) outliers start: 83 outliers final: 49 residues processed: 439 average time/residue: 1.1673 time to fit residues: 629.4658 Evaluate side-chains 422 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 368 time to evaluate : 3.289 ------------------------------------------------------------------------------- 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 521 GLU Chi-restraints excluded: chain A residue 565 MET 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 742 ARG 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 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 175 LEU 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 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 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 738 VAL 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 D residue 975 CYS Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 11 optimal weight: 0.6980 chunk 375 optimal weight: 0.9980 chunk 82 optimal weight: 0.0060 chunk 3 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 C 771 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.194973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.143025 restraints weight = 36098.636| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.37 r_work: 0.3602 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32256 Z= 0.118 Angle : 0.726 31.130 43716 Z= 0.313 Chirality : 0.064 1.736 4972 Planarity : 0.003 0.048 5324 Dihedral : 13.133 175.236 5847 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.29 % Allowed : 17.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.14), residues: 3752 helix: 1.59 (0.12), residues: 1896 sheet: -0.32 (0.27), residues: 364 loop : 0.28 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 694 HIS 0.004 0.001 HIS D 753 PHE 0.026 0.001 PHE A 34 TYR 0.019 0.001 TYR A1032 ARG 0.007 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 1567) hydrogen bonds : angle 4.26623 ( 4353) covalent geometry : bond 0.00263 (32252) covalent geometry : angle 0.72555 (43716) Misc. bond : bond 0.00040 ( 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 464 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 388 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7302 (ppt90) cc_final: 0.6973 (ppt90) REVERT: A 521 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7245 (pm20) REVERT: A 603 LYS cc_start: 0.7511 (mttt) cc_final: 0.7242 (mttt) REVERT: A 604 GLU cc_start: 0.6899 (mm-30) cc_final: 0.5893 (mp0) REVERT: A 723 ILE cc_start: 0.6471 (OUTLIER) cc_final: 0.6208 (mp) REVERT: A 746 PHE cc_start: 0.4816 (m-10) cc_final: 0.4417 (m-10) REVERT: A 972 ARG cc_start: 0.7035 (ptm160) cc_final: 0.6534 (ptm160) REVERT: B 723 ILE cc_start: 0.6455 (OUTLIER) cc_final: 0.6194 (mp) REVERT: B 746 PHE cc_start: 0.4857 (m-10) cc_final: 0.4514 (m-10) REVERT: B 972 ARG cc_start: 0.7127 (ptm160) cc_final: 0.6476 (ptm160) REVERT: C 43 TRP cc_start: 0.5377 (t-100) cc_final: 0.5056 (t-100) REVERT: C 723 ILE cc_start: 0.6386 (OUTLIER) cc_final: 0.6171 (mp) REVERT: D 43 TRP cc_start: 0.5563 (t-100) cc_final: 0.5153 (t-100) REVERT: D 329 ARG cc_start: 0.7346 (ppt90) cc_final: 0.7022 (ppt90) REVERT: D 521 GLU cc_start: 0.7518 (pm20) cc_final: 0.7265 (pm20) REVERT: D 746 PHE cc_start: 0.4708 (m-10) cc_final: 0.4182 (m-10) REVERT: D 972 ARG cc_start: 0.7036 (ptm160) cc_final: 0.6514 (ptm160) outliers start: 76 outliers final: 49 residues processed: 447 average time/residue: 1.1489 time to fit residues: 628.1796 Evaluate side-chains 426 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 373 time to evaluate : 3.505 ------------------------------------------------------------------------------- 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 521 GLU 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 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 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 175 LEU 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 601 ASP 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 324 GLU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 738 VAL 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 258 SER Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 126 optimal weight: 0.2980 chunk 254 optimal weight: 0.0870 chunk 221 optimal weight: 0.3980 chunk 108 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 337 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 142 GLN C 200 ASN C 771 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.195805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.144168 restraints weight = 36253.348| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.37 r_work: 0.3616 rms_B_bonded: 2.90 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: 0.7244 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 32256 Z= 0.111 Angle : 0.723 31.078 43716 Z= 0.310 Chirality : 0.064 1.737 4972 Planarity : 0.003 0.047 5324 Dihedral : 13.053 175.816 5847 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.81 % Allowed : 18.03 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.14), residues: 3752 helix: 1.67 (0.12), residues: 1892 sheet: -0.28 (0.27), residues: 364 loop : 0.29 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 694 HIS 0.004 0.001 HIS D 753 PHE 0.031 0.001 PHE A 34 TYR 0.019 0.001 TYR A1032 ARG 0.006 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 1567) hydrogen bonds : angle 4.24638 ( 4353) covalent geometry : bond 0.00245 (32252) covalent geometry : angle 0.72320 (43716) Misc. bond : bond 0.00033 ( 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 447 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 387 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7305 (ppt90) cc_final: 0.6978 (ppt90) REVERT: A 521 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: A 604 GLU cc_start: 0.6840 (mm-30) cc_final: 0.5842 (mp0) REVERT: A 723 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.6131 (mp) REVERT: A 746 PHE cc_start: 0.4793 (m-10) cc_final: 0.4384 (m-10) REVERT: A 972 ARG cc_start: 0.7029 (ptm160) cc_final: 0.6505 (ptm160) REVERT: B 723 ILE cc_start: 0.6402 (OUTLIER) cc_final: 0.6166 (mp) REVERT: B 746 PHE cc_start: 0.4738 (m-10) cc_final: 0.4416 (m-10) REVERT: B 972 ARG cc_start: 0.7135 (ptm160) cc_final: 0.6509 (ptm160) REVERT: B 1007 TYR cc_start: 0.7345 (m-80) cc_final: 0.6456 (m-80) REVERT: C 30 MET cc_start: 0.7834 (tpt) cc_final: 0.7572 (mmm) REVERT: C 43 TRP cc_start: 0.5394 (t-100) cc_final: 0.5071 (t-100) REVERT: C 723 ILE cc_start: 0.6434 (OUTLIER) cc_final: 0.6224 (mp) REVERT: C 1007 TYR cc_start: 0.7663 (m-80) cc_final: 0.6634 (t80) REVERT: D 43 TRP cc_start: 0.5525 (t-100) cc_final: 0.5120 (t-100) REVERT: D 329 ARG cc_start: 0.7355 (ppt90) cc_final: 0.7033 (ppt90) REVERT: D 521 GLU cc_start: 0.7507 (pm20) cc_final: 0.7277 (pm20) REVERT: D 746 PHE cc_start: 0.4713 (m-10) cc_final: 0.4193 (m-10) REVERT: D 972 ARG cc_start: 0.7055 (ptm160) cc_final: 0.6556 (ptm160) outliers start: 60 outliers final: 49 residues processed: 437 average time/residue: 1.1402 time to fit residues: 610.5212 Evaluate side-chains 422 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 369 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 521 GLU 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 175 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 587 LEU 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 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 175 LEU 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 601 ASP 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 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 175 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 601 ASP Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 738 VAL 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 D residue 975 CYS Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 214 optimal weight: 0.4980 chunk 23 optimal weight: 0.3980 chunk 173 optimal weight: 20.0000 chunk 336 optimal weight: 0.5980 chunk 277 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 285 optimal weight: 0.5980 chunk 180 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS B 142 GLN C 142 GLN C 771 HIS ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.195447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.143670 restraints weight = 36176.625| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.37 r_work: 0.3609 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32256 Z= 0.115 Angle : 0.727 31.130 43716 Z= 0.312 Chirality : 0.064 1.736 4972 Planarity : 0.003 0.048 5324 Dihedral : 13.022 175.918 5844 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.17 % Allowed : 17.94 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.14), residues: 3752 helix: 1.67 (0.12), residues: 1896 sheet: -0.20 (0.27), residues: 356 loop : 0.30 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 694 HIS 0.004 0.001 HIS D 753 PHE 0.030 0.001 PHE A 34 TYR 0.019 0.001 TYR A1032 ARG 0.007 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 1567) hydrogen bonds : angle 4.25143 ( 4353) covalent geometry : bond 0.00257 (32252) covalent geometry : angle 0.72727 (43716) Misc. bond : bond 0.00042 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35491.42 seconds wall clock time: 610 minutes 48.55 seconds (36648.55 seconds total)