Starting phenix.real_space_refine on Fri Jun 27 10:12:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s3e_19691/06_2025/8s3e_19691.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s3e_19691/06_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_19691/06_2025/8s3e_19691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s3e_19691/06_2025/8s3e_19691.map" model { file = "/net/cci-nas-00/data/ceres_data/8s3e_19691/06_2025/8s3e_19691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s3e_19691/06_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): 2.44s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 21.20, per 1000 atoms: 0.67 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: 9.16 Conformation dependent library (CDL) restraints added in 4.3 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: 5.12 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: 13.87 Time building geometry restraints manager: 10.66 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: 15.240 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: 0.050 Extract box with map and model: 1.420 Check model and map are aligned: 0.230 Set scattering table: 0.320 Process input model: 79.610 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.180 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:14.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.020 ------------------------------------------------------------------------------- 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 : 4.161 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: 1.4430 time to fit residues: 756.3115 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 : 3.929 ------------------------------------------------------------------------------- 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 = 61)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.149074 restraints weight = 36659.678| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.41 r_work: 0.3685 rms_B_bonded: 2.99 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 : 3.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 GLU cc_start: 0.6251 (mt-10) cc_final: 0.5950 (mt-10) REVERT: A 604 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6178 (mp0) REVERT: A 953 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7401 (mp) REVERT: B 604 GLU cc_start: 0.6795 (mm-30) cc_final: 0.5980 (mp0) REVERT: B 794 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7231 (tp) REVERT: B 1007 TYR cc_start: 0.7435 (m-10) cc_final: 0.7229 (m-10) REVERT: C 30 MET cc_start: 0.7417 (tpt) cc_final: 0.7158 (tpt) REVERT: C 281 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8373 (mp) REVERT: D 723 ILE cc_start: 0.6262 (OUTLIER) cc_final: 0.4847 (pp) REVERT: D 794 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7203 (tp) REVERT: E 264 MET cc_start: 0.6750 (ptm) cc_final: 0.6449 (ptt) REVERT: F 264 MET cc_start: 0.6695 (OUTLIER) cc_final: 0.6406 (ptt) REVERT: G 264 MET cc_start: 0.6485 (OUTLIER) cc_final: 0.6282 (ptt) REVERT: H 264 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.6270 (ptt) outliers start: 105 outliers final: 36 residues processed: 437 average time/residue: 1.1759 time to fit residues: 634.2574 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 : 3.522 ------------------------------------------------------------------------------- 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: 8.9990 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: 2.9990 chunk 46 optimal weight: 8.9990 chunk 330 optimal weight: 9.9990 chunk 130 optimal weight: 0.0670 chunk 240 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 771 HIS B 142 GLN B 771 HIS C 142 GLN C 200 ASN C 771 HIS D 142 GLN D 771 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.196546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.144392 restraints weight = 36404.669| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.43 r_work: 0.3621 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32256 Z= 0.133 Angle : 0.707 31.051 43716 Z= 0.306 Chirality : 0.064 1.755 4972 Planarity : 0.004 0.049 5324 Dihedral : 13.580 177.638 5859 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.01 % Allowed : 13.60 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.33 (0.14), residues: 3752 helix: 1.53 (0.12), residues: 1884 sheet: -0.02 (0.28), residues: 356 loop : 0.45 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 767 HIS 0.006 0.001 HIS C 718 PHE 0.021 0.002 PHE D 144 TYR 0.018 0.002 TYR D1007 ARG 0.006 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 1567) hydrogen bonds : angle 4.34402 ( 4353) covalent geometry : bond 0.00299 (32252) covalent geometry : angle 0.70692 (43716) Misc. bond : bond 0.00107 ( 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 519 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 386 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8399 (mp) REVERT: A 329 ARG cc_start: 0.7253 (ppt90) cc_final: 0.6529 (ptt90) REVERT: A 603 LYS cc_start: 0.7498 (mttt) cc_final: 0.7283 (mttt) REVERT: A 604 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6198 (mp0) REVERT: A 794 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7395 (tp) REVERT: A 953 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7446 (mp) REVERT: A 1007 TYR cc_start: 0.7291 (m-10) cc_final: 0.7076 (m-10) REVERT: B 604 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6462 (mp0) REVERT: B 794 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7271 (tp) REVERT: B 1009 MET cc_start: 0.6074 (mmm) cc_final: 0.5752 (mmm) REVERT: C 685 LYS cc_start: 0.5133 (OUTLIER) cc_final: 0.4696 (ptmt) REVERT: C 691 MET cc_start: 0.5650 (OUTLIER) cc_final: 0.5432 (mtm) REVERT: C 794 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7428 (tp) REVERT: D 281 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8398 (mp) REVERT: D 555 GLU cc_start: 0.6395 (mt-10) cc_final: 0.6015 (mt-10) REVERT: D 794 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7294 (tp) REVERT: D 1007 TYR cc_start: 0.7350 (m-10) cc_final: 0.7136 (m-10) REVERT: E 264 MET cc_start: 0.6847 (ptm) cc_final: 0.6575 (ptt) REVERT: F 264 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6529 (ptt) REVERT: F 276 SER cc_start: 0.7915 (t) cc_final: 0.7708 (p) outliers start: 133 outliers final: 53 residues processed: 463 average time/residue: 1.1679 time to fit residues: 662.1231 Evaluate side-chains 410 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 347 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 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 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 685 LYS Chi-restraints excluded: chain C residue 691 MET 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 281 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 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: 0.0770 chunk 87 optimal weight: 3.9990 chunk 356 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 253 optimal weight: 0.1980 chunk 355 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 351 optimal weight: 0.9980 chunk 304 optimal weight: 0.8980 overall best weight: 0.8340 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN C 142 GLN C 200 ASN C 771 HIS D 108 GLN D 142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.196356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.144141 restraints weight = 36341.752| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.43 r_work: 0.3623 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1457 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= 0.121 Angle : 0.697 30.985 43716 Z= 0.299 Chirality : 0.064 1.752 4972 Planarity : 0.003 0.050 5324 Dihedral : 13.486 176.944 5859 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.68 % Allowed : 14.63 % Favored : 81.69 % 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: 1.36 (0.14), residues: 3752 helix: 1.61 (0.12), residues: 1884 sheet: -0.13 (0.27), residues: 356 loop : 0.41 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 43 HIS 0.004 0.001 HIS C 718 PHE 0.013 0.001 PHE D 144 TYR 0.012 0.001 TYR D 198 ARG 0.004 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 1567) hydrogen bonds : angle 4.27811 ( 4353) covalent geometry : bond 0.00269 (32252) covalent geometry : angle 0.69653 (43716) Misc. bond : bond 0.00088 ( 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 507 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 385 time to evaluate : 11.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 LYS cc_start: 0.7502 (mttt) cc_final: 0.7268 (mttt) REVERT: A 604 GLU cc_start: 0.6939 (mm-30) cc_final: 0.5979 (mp0) REVERT: A 794 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7420 (tp) REVERT: A 1007 TYR cc_start: 0.7338 (m-10) cc_final: 0.7129 (m-10) REVERT: B 604 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6198 (mp0) REVERT: B 794 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7299 (tp) REVERT: B 972 ARG cc_start: 0.6874 (ptm160) cc_final: 0.5988 (ptm160) REVERT: C 521 GLU cc_start: 0.7409 (pm20) cc_final: 0.7193 (pm20) REVERT: C 794 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7433 (tp) REVERT: C 799 MET cc_start: 0.7548 (tpt) cc_final: 0.7296 (tpp) REVERT: D 442 MET cc_start: 0.5917 (mmt) cc_final: 0.5695 (mmt) REVERT: D 794 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7312 (tp) REVERT: E 264 MET cc_start: 0.6857 (ptm) cc_final: 0.6618 (ptt) REVERT: F 264 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6622 (ptt) outliers start: 122 outliers final: 58 residues processed: 455 average time/residue: 1.2831 time to fit residues: 718.7255 Evaluate side-chains 418 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 355 time to evaluate : 4.593 ------------------------------------------------------------------------------- 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 197 VAL Chi-restraints excluded: chain A residue 339 VAL 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 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 794 ILE 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 197 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 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 532 VAL Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 264 MET Chi-restraints excluded: chain F residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 307 optimal weight: 4.9990 chunk 333 optimal weight: 3.9990 chunk 306 optimal weight: 0.8980 chunk 362 optimal weight: 0.7980 chunk 256 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 319 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 139 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 GLN C 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.196528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.144287 restraints weight = 36262.267| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.44 r_work: 0.3624 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 32256 Z= 0.113 Angle : 0.692 30.956 43716 Z= 0.296 Chirality : 0.063 1.752 4972 Planarity : 0.003 0.049 5324 Dihedral : 13.352 176.661 5847 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.35 % Allowed : 15.23 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.14), residues: 3752 helix: 1.68 (0.12), residues: 1884 sheet: -0.18 (0.27), residues: 356 loop : 0.39 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 477 HIS 0.004 0.001 HIS A 718 PHE 0.013 0.001 PHE A 746 TYR 0.023 0.001 TYR D1007 ARG 0.004 0.000 ARG D 329 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 1567) hydrogen bonds : angle 4.22588 ( 4353) covalent geometry : bond 0.00247 (32252) covalent geometry : angle 0.69221 (43716) Misc. bond : bond 0.00068 ( 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 493 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 382 time to evaluate : 3.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 LYS cc_start: 0.7505 (mttt) cc_final: 0.7272 (mttt) REVERT: A 604 GLU cc_start: 0.6928 (mm-30) cc_final: 0.5961 (mp0) REVERT: A 746 PHE cc_start: 0.4683 (m-10) cc_final: 0.4296 (m-10) REVERT: A 799 MET cc_start: 0.7635 (tpt) cc_final: 0.7353 (tpp) REVERT: A 972 ARG cc_start: 0.6842 (ptm160) cc_final: 0.6294 (ptm160) REVERT: B 604 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6525 (mp0) REVERT: B 746 PHE cc_start: 0.4811 (m-10) cc_final: 0.4349 (m-10) REVERT: B 972 ARG cc_start: 0.6946 (ptm160) cc_final: 0.6054 (ptm160) REVERT: C 794 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7437 (tp) REVERT: D 43 TRP cc_start: 0.5343 (t-100) cc_final: 0.4991 (t-100) REVERT: D 555 GLU cc_start: 0.6365 (mt-10) cc_final: 0.5941 (mt-10) REVERT: E 264 MET cc_start: 0.6867 (ptm) cc_final: 0.6656 (ptt) outliers start: 111 outliers final: 52 residues processed: 447 average time/residue: 1.4091 time to fit residues: 776.8391 Evaluate side-chains 412 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 359 time to evaluate : 3.261 ------------------------------------------------------------------------------- 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 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain B residue 99 ASP 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 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 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 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 343 LYS Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain 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 287 LEU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 267 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 177 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 111 optimal weight: 0.1980 chunk 115 optimal weight: 0.6980 chunk 314 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 239 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 D 747 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.194886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.142494 restraints weight = 36145.289| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.42 r_work: 0.3600 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32256 Z= 0.135 Angle : 0.718 31.121 43716 Z= 0.310 Chirality : 0.064 1.747 4972 Planarity : 0.004 0.051 5324 Dihedral : 13.315 175.756 5847 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.47 % Allowed : 15.20 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.33 (0.14), residues: 3752 helix: 1.61 (0.12), residues: 1888 sheet: -0.20 (0.27), residues: 356 loop : 0.37 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 694 HIS 0.006 0.001 HIS C 718 PHE 0.016 0.002 PHE D 550 TYR 0.028 0.002 TYR A1007 ARG 0.004 0.000 ARG D 329 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 1567) hydrogen bonds : angle 4.28339 ( 4353) covalent geometry : bond 0.00307 (32252) covalent geometry : angle 0.71789 (43716) Misc. bond : bond 0.00065 ( 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 517 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 402 time to evaluate : 4.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 GLU cc_start: 0.6965 (mm-30) cc_final: 0.5978 (mp0) REVERT: B 442 MET cc_start: 0.5990 (mmt) cc_final: 0.5720 (mmt) REVERT: B 604 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6497 (mp0) REVERT: B 746 PHE cc_start: 0.4884 (m-10) cc_final: 0.4407 (m-10) REVERT: B 972 ARG cc_start: 0.7025 (ptm160) cc_final: 0.6106 (ptm160) REVERT: B 1007 TYR cc_start: 0.7544 (m-80) cc_final: 0.6601 (m-80) REVERT: C 794 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7476 (tp) REVERT: D 43 TRP cc_start: 0.5428 (t-100) cc_final: 0.5070 (t-100) outliers start: 115 outliers final: 58 residues processed: 472 average time/residue: 1.7054 time to fit residues: 1003.9356 Evaluate side-chains 430 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 371 time to evaluate : 7.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 308 ILE 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 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 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 C residue 21 MET 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 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 794 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 175 LEU 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 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 723 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 287 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 10 optimal weight: 0.5980 chunk 370 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 334 optimal weight: 4.9990 chunk 61 optimal weight: 0.0980 chunk 113 optimal weight: 0.0980 chunk 31 optimal weight: 0.6980 chunk 289 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS B 142 GLN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.197446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.145693 restraints weight = 36252.920| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.38 r_work: 0.3635 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1789 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= 0.101 Angle : 0.696 30.818 43716 Z= 0.296 Chirality : 0.063 1.752 4972 Planarity : 0.003 0.049 5324 Dihedral : 13.173 176.271 5847 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.86 % Allowed : 16.22 % Favored : 80.91 % 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: 1.47 (0.14), residues: 3752 helix: 1.80 (0.12), residues: 1880 sheet: -0.21 (0.27), residues: 356 loop : 0.35 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 694 HIS 0.003 0.000 HIS A 586 PHE 0.019 0.001 PHE A1000 TYR 0.014 0.001 TYR D1007 ARG 0.004 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 1567) hydrogen bonds : angle 4.18211 ( 4353) covalent geometry : bond 0.00214 (32252) covalent geometry : angle 0.69615 (43716) Misc. bond : bond 0.00032 ( 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 488 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 393 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 GLU cc_start: 0.6817 (mm-30) cc_final: 0.5837 (mp0) REVERT: A 746 PHE cc_start: 0.4594 (m-10) cc_final: 0.4187 (m-10) REVERT: A 972 ARG cc_start: 0.6862 (ptm160) cc_final: 0.6425 (ptm160) REVERT: B 604 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6379 (mp0) REVERT: B 1007 TYR cc_start: 0.7553 (m-80) cc_final: 0.6590 (m-80) REVERT: D 43 TRP cc_start: 0.5438 (t-100) cc_final: 0.5060 (t-100) REVERT: D 746 PHE cc_start: 0.4591 (m-10) cc_final: 0.4037 (m-10) REVERT: D 972 ARG cc_start: 0.6826 (ptm160) cc_final: 0.6174 (ptm160) outliers start: 95 outliers final: 46 residues processed: 451 average time/residue: 1.1154 time to fit residues: 620.4202 Evaluate side-chains 417 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 371 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 831 GLN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 975 CYS Chi-restraints excluded: chain C residue 21 MET 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 723 ILE Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 831 GLN Chi-restraints excluded: chain 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 565 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 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 Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 267 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 246 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 343 optimal weight: 0.8980 chunk 304 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 299 optimal weight: 0.7980 chunk 339 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 449 ASN A 771 HIS B 142 GLN B 747 HIS C 142 GLN C 449 ASN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 HIS D 753 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.194254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141828 restraints weight = 36134.577| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.37 r_work: 0.3586 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32256 Z= 0.140 Angle : 0.735 31.199 43716 Z= 0.318 Chirality : 0.064 1.741 4972 Planarity : 0.004 0.050 5324 Dihedral : 13.165 175.225 5844 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.96 % Allowed : 16.68 % Favored : 80.37 % 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: 1.34 (0.14), residues: 3752 helix: 1.64 (0.12), residues: 1888 sheet: -0.23 (0.27), residues: 356 loop : 0.35 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.005 0.001 HIS A 718 PHE 0.023 0.002 PHE C 34 TYR 0.018 0.002 TYR A1032 ARG 0.004 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 1567) hydrogen bonds : angle 4.27918 ( 4353) covalent geometry : bond 0.00321 (32252) covalent geometry : angle 0.73470 (43716) Misc. bond : bond 0.00103 ( 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 479 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 381 time to evaluate : 4.604 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: 0.7300 (ppt90) cc_final: 0.6944 (ppt90) REVERT: A 604 GLU cc_start: 0.6891 (mm-30) cc_final: 0.5910 (mp0) REVERT: B 442 MET cc_start: 0.5940 (mmt) cc_final: 0.5709 (mmt) REVERT: B 604 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6444 (mp0) REVERT: C 43 TRP cc_start: 0.5377 (t-100) cc_final: 0.5092 (t-100) REVERT: D 43 TRP cc_start: 0.5442 (t-100) cc_final: 0.5064 (t-100) REVERT: E 264 MET cc_start: 0.6867 (ptm) cc_final: 0.6652 (ptt) outliers start: 98 outliers final: 62 residues processed: 447 average time/residue: 1.1736 time to fit residues: 651.2062 Evaluate side-chains 428 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 366 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 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 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 532 VAL 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 778 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 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 532 VAL Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 276 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 11 optimal weight: 0.9980 chunk 375 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 142 optimal weight: 0.0870 chunk 110 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 ** 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 = 0.4303 r_free = 0.4303 target = 0.195374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.143377 restraints weight = 36113.074| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.37 r_work: 0.3607 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32256 Z= 0.119 Angle : 0.720 31.021 43716 Z= 0.311 Chirality : 0.064 1.745 4972 Planarity : 0.003 0.050 5324 Dihedral : 13.107 175.397 5844 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.47 % Allowed : 16.92 % Favored : 80.61 % 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: 1.36 (0.14), residues: 3752 helix: 1.68 (0.12), residues: 1888 sheet: -0.27 (0.27), residues: 356 loop : 0.34 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 477 HIS 0.005 0.001 HIS D 753 PHE 0.028 0.001 PHE C 34 TYR 0.018 0.001 TYR A1032 ARG 0.004 0.000 ARG D 329 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 1567) hydrogen bonds : angle 4.24760 ( 4353) covalent geometry : bond 0.00266 (32252) covalent geometry : angle 0.72045 (43716) Misc. bond : bond 0.00039 ( 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 459 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 377 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7309 (ppt90) cc_final: 0.6952 (ppt90) REVERT: A 604 GLU cc_start: 0.6858 (mm-30) cc_final: 0.5862 (mp0) REVERT: A 746 PHE cc_start: 0.4734 (m-10) cc_final: 0.4404 (m-10) REVERT: A 972 ARG cc_start: 0.7004 (ptm160) cc_final: 0.6540 (ptm160) REVERT: B 604 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6358 (mp0) REVERT: C 30 MET cc_start: 0.7533 (mmm) cc_final: 0.7260 (tpt) REVERT: C 43 TRP cc_start: 0.5391 (t-100) cc_final: 0.5095 (t-100) REVERT: C 1009 MET cc_start: 0.4910 (mmm) cc_final: 0.4661 (mmm) REVERT: D 43 TRP cc_start: 0.5556 (t-100) cc_final: 0.5149 (t-100) REVERT: D 746 PHE cc_start: 0.4671 (m-10) cc_final: 0.4164 (m-10) REVERT: D 972 ARG cc_start: 0.6995 (ptm160) cc_final: 0.6280 (ptm160) REVERT: E 264 MET cc_start: 0.6875 (ptm) cc_final: 0.6666 (ptt) outliers start: 82 outliers final: 59 residues processed: 437 average time/residue: 1.1660 time to fit residues: 626.4700 Evaluate side-chains 427 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 368 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 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 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 532 VAL 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 778 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 287 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 H residue 267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 126 optimal weight: 0.8980 chunk 254 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 337 optimal weight: 0.0010 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 105 optimal weight: 0.0970 chunk 134 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1058 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.196014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144237 restraints weight = 36278.557| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.37 r_work: 0.3615 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32256 Z= 0.114 Angle : 0.725 30.993 43716 Z= 0.311 Chirality : 0.064 1.745 4972 Planarity : 0.003 0.049 5324 Dihedral : 13.028 175.682 5844 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.05 % Allowed : 17.49 % Favored : 80.46 % 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: 1.39 (0.14), residues: 3752 helix: 1.71 (0.12), residues: 1888 sheet: -0.26 (0.27), residues: 356 loop : 0.35 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 477 HIS 0.004 0.001 HIS D 753 PHE 0.029 0.001 PHE C 34 TYR 0.017 0.001 TYR A1032 ARG 0.006 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 1567) hydrogen bonds : angle 4.24138 ( 4353) covalent geometry : bond 0.00252 (32252) covalent geometry : angle 0.72514 (43716) Misc. bond : bond 0.00042 ( 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 449 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 381 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7297 (ppt90) cc_final: 0.6936 (ppt90) REVERT: A 604 GLU cc_start: 0.6836 (mm-30) cc_final: 0.5862 (mp0) REVERT: A 746 PHE cc_start: 0.4721 (m-10) cc_final: 0.4381 (m-10) REVERT: A 972 ARG cc_start: 0.7020 (ptm160) cc_final: 0.6567 (ptm160) REVERT: A 1007 TYR cc_start: 0.7562 (m-80) cc_final: 0.6661 (m-80) REVERT: A 1009 MET cc_start: 0.4936 (mmm) cc_final: 0.4542 (mmm) REVERT: B 521 GLU cc_start: 0.7276 (pm20) cc_final: 0.7067 (pm20) REVERT: B 604 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6310 (mp0) REVERT: B 746 PHE cc_start: 0.4733 (m-10) cc_final: 0.4477 (m-10) REVERT: C 43 TRP cc_start: 0.5377 (t-100) cc_final: 0.5066 (t-100) REVERT: C 746 PHE cc_start: 0.4762 (m-10) cc_final: 0.4492 (m-10) REVERT: C 972 ARG cc_start: 0.6993 (ptm160) cc_final: 0.6589 (ptm160) REVERT: C 1007 TYR cc_start: 0.7470 (m-80) cc_final: 0.6689 (m-80) REVERT: D 43 TRP cc_start: 0.5548 (t-100) cc_final: 0.5159 (t-100) outliers start: 68 outliers final: 58 residues processed: 430 average time/residue: 1.1706 time to fit residues: 617.8768 Evaluate side-chains 423 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 365 time to evaluate : 3.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 700 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 339 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 532 VAL 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 778 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 287 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 H residue 267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 214 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 173 optimal weight: 20.0000 chunk 336 optimal weight: 2.9990 chunk 277 optimal weight: 0.9990 chunk 252 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 222 optimal weight: 0.2980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 753 HIS D 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.194985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.143011 restraints weight = 36134.041| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.37 r_work: 0.3600 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32256 Z= 0.127 Angle : 0.738 31.111 43716 Z= 0.319 Chirality : 0.064 1.742 4972 Planarity : 0.004 0.050 5324 Dihedral : 13.023 175.427 5844 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.11 % Allowed : 17.55 % Favored : 80.34 % 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: 1.33 (0.14), residues: 3752 helix: 1.66 (0.12), residues: 1888 sheet: -0.26 (0.27), residues: 356 loop : 0.33 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 477 HIS 0.004 0.001 HIS D 753 PHE 0.034 0.002 PHE C 34 TYR 0.018 0.001 TYR A1032 ARG 0.005 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 1567) hydrogen bonds : angle 4.26712 ( 4353) covalent geometry : bond 0.00290 (32252) covalent geometry : angle 0.73843 (43716) Misc. bond : bond 0.00052 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39068.20 seconds wall clock time: 679 minutes 49.53 seconds (40789.53 seconds total)