Starting phenix.real_space_refine on Tue Aug 26 05:06:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byq_45042/08_2025/9byq_45042.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byq_45042/08_2025/9byq_45042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byq_45042/08_2025/9byq_45042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byq_45042/08_2025/9byq_45042.map" model { file = "/net/cci-nas-00/data/ceres_data/9byq_45042/08_2025/9byq_45042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byq_45042/08_2025/9byq_45042.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 23 5.49 5 S 94 5.16 5 C 10361 2.51 5 N 2823 2.21 5 O 3607 1.98 5 H 16960 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33870 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 14447 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 934, 14411 Classifications: {'peptide': 934} Link IDs: {'PTRANS': 62, 'TRANS': 871} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 934, 14411 Classifications: {'peptide': 934} Link IDs: {'PTRANS': 62, 'TRANS': 871} Chain breaks: 5 bond proxies already assigned to first conformer: 14564 Conformer: "C" Number of residues, atoms: 934, 14403 Classifications: {'peptide': 934} Link IDs: {'PTRANS': 62, 'TRANS': 871} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 14564 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 376 Classifications: {'DNA': 12} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 11} Chain: "B" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1395 Classifications: {'peptide': 94} Link IDs: {'TRANS': 93} Chain breaks: 1 Chain: "F" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 383 Classifications: {'DNA': 12} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 14447 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 934, 14411 Classifications: {'peptide': 934} Link IDs: {'PTRANS': 62, 'TRANS': 871} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 934, 14411 Classifications: {'peptide': 934} Link IDs: {'PTRANS': 62, 'TRANS': 871} Chain breaks: 5 bond proxies already assigned to first conformer: 14564 Conformer: "C" Number of residues, atoms: 934, 14403 Classifications: {'peptide': 934} Link IDs: {'PTRANS': 62, 'TRANS': 871} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 14564 Chain: "E" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1395 Classifications: {'peptide': 94} Link IDs: {'TRANS': 93} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 696 Classifications: {'water': 232} Link IDs: {None: 231} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 699 Classifications: {'water': 233} Link IDs: {None: 232} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6520 SG CYS A 453 63.613 137.774 80.436 1.00 57.64 S ATOM 6561 SG CYS A 456 66.564 139.151 79.600 1.00 53.48 S ATOM 6668 SG CYS A 464 65.548 136.203 77.701 1.00 59.44 S ATOM 23121 SG CYS D 453 47.390 25.141 80.629 1.00 57.64 S ATOM 23162 SG CYS D 456 43.911 23.758 79.620 1.00 53.48 S ATOM 23269 SG CYS D 464 45.356 26.815 77.678 1.00 59.44 S Time building chain proxies: 13.04, per 1000 atoms: 0.39 Number of scatterers: 33870 At special positions: 0 Unit cell: (111.72, 163.8, 110.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 94 16.00 P 23 15.00 O 3607 8.00 N 2823 7.00 C 10361 6.00 H 16960 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 456 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 453 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 464 " pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 453 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 456 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 464 " 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 14 sheets defined 51.7% alpha, 19.8% beta 3 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 5.28 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.536A pdb=" N THR A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 107 through 119 Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.964A pdb=" N PHE A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.592A pdb=" N GLN A 203 " --> pdb=" O GLN A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.784A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 266 through 291 Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 296 through 308 removed outlier: 4.972A pdb=" N TYR A 301 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP A 302 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 305 - end of helix Processing helix chain 'A' and resid 312 through 337 removed outlier: 3.584A pdb=" N LEU A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 357 through 360 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.644A pdb=" N GLU A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 removed outlier: 3.605A pdb=" N LEU A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 450 Processing helix chain 'A' and resid 464 through 473 Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 526 through 541 Processing helix chain 'A' and resid 555 through 584 Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 604 through 608 removed outlier: 3.636A pdb=" N GLN A 608 " --> pdb=" O PRO A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 641 removed outlier: 3.753A pdb=" N THR A 615 " --> pdb=" O CYS A 611 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 616 " --> pdb=" O PRO A 612 " (cutoff:3.500A) Proline residue: A 632 - end of helix Processing helix chain 'A' and resid 647 through 667 removed outlier: 3.995A pdb=" N GLY A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLN A 657 " --> pdb=" O LYS A 653 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THR A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 697 removed outlier: 3.580A pdb=" N GLN A 697 " --> pdb=" O ASP A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 740 removed outlier: 4.086A pdb=" N PHE A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 762 through 767 Processing helix chain 'A' and resid 773 through 785 Processing helix chain 'A' and resid 794 through 816 removed outlier: 3.830A pdb=" N TYR A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 841 Processing helix chain 'A' and resid 864 through 871 Proline residue: A 867 - end of helix Processing helix chain 'A' and resid 877 through 886 Processing helix chain 'A' and resid 900 through 907 removed outlier: 4.079A pdb=" N VAL A 904 " --> pdb=" O CYS A 900 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 907 " --> pdb=" O GLN A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 948 Processing helix chain 'B' and resid 989 through 1003 removed outlier: 3.504A pdb=" N ASN B 993 " --> pdb=" O TYR B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1023 Processing helix chain 'B' and resid 1024 through 1029 removed outlier: 3.770A pdb=" N SER B1028 " --> pdb=" O ALA B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1039 Processing helix chain 'B' and resid 1040 through 1043 removed outlier: 5.299A pdb=" N VAL B1043 " --> pdb=" O ARG B1040 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1040 through 1043' Processing helix chain 'B' and resid 1044 through 1059 removed outlier: 3.505A pdb=" N THR B1054 " --> pdb=" O GLU B1050 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B1059 " --> pdb=" O ILE B1055 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1072 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 32 through 40 removed outlier: 3.548A pdb=" N THR D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 107 through 119 Processing helix chain 'D' and resid 133 through 138 removed outlier: 3.996A pdb=" N PHE D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 157 through 164 Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 199 through 203 removed outlier: 3.589A pdb=" N GLN D 203 " --> pdb=" O GLN D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 217 Processing helix chain 'D' and resid 217 through 226 removed outlier: 3.772A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 266 through 291 Proline residue: D 286 - end of helix Processing helix chain 'D' and resid 296 through 308 removed outlier: 4.935A pdb=" N TYR D 301 " --> pdb=" O SER D 298 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASP D 302 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 305 - end of helix Processing helix chain 'D' and resid 312 through 337 removed outlier: 3.579A pdb=" N LEU D 327 " --> pdb=" O TYR D 323 " (cutoff:3.500A) Proline residue: D 329 - end of helix Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 357 through 360 Processing helix chain 'D' and resid 367 through 373 removed outlier: 3.663A pdb=" N GLU D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 410 removed outlier: 3.586A pdb=" N LEU D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 425 Processing helix chain 'D' and resid 439 through 446 Processing helix chain 'D' and resid 447 through 450 Processing helix chain 'D' and resid 464 through 473 Processing helix chain 'D' and resid 474 through 476 No H-bonds generated for 'chain 'D' and resid 474 through 476' Processing helix chain 'D' and resid 526 through 541 Processing helix chain 'D' and resid 555 through 584 removed outlier: 3.509A pdb=" N VAL D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 592 Processing helix chain 'D' and resid 604 through 608 removed outlier: 3.620A pdb=" N GLN D 608 " --> pdb=" O PRO D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 641 removed outlier: 3.749A pdb=" N THR D 615 " --> pdb=" O CYS D 611 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN D 616 " --> pdb=" O PRO D 612 " (cutoff:3.500A) Proline residue: D 632 - end of helix Processing helix chain 'D' and resid 647 through 667 removed outlier: 3.980A pdb=" N GLY D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLN D 657 " --> pdb=" O LYS D 653 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N THR D 658 " --> pdb=" O GLY D 654 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR D 661 " --> pdb=" O GLN D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 697 removed outlier: 3.537A pdb=" N GLN D 697 " --> pdb=" O ASP D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 740 removed outlier: 4.057A pdb=" N PHE D 739 " --> pdb=" O LEU D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 762 Processing helix chain 'D' and resid 762 through 767 Processing helix chain 'D' and resid 773 through 785 Processing helix chain 'D' and resid 794 through 816 removed outlier: 3.900A pdb=" N TYR D 798 " --> pdb=" O SER D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 841 Processing helix chain 'D' and resid 864 through 871 Proline residue: D 867 - end of helix Processing helix chain 'D' and resid 877 through 886 Processing helix chain 'D' and resid 900 through 906 removed outlier: 4.121A pdb=" N VAL D 904 " --> pdb=" O CYS D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 948 Processing helix chain 'E' and resid 989 through 1003 Processing helix chain 'E' and resid 1010 through 1023 Processing helix chain 'E' and resid 1024 through 1029 removed outlier: 3.723A pdb=" N SER E1028 " --> pdb=" O ALA E1025 " (cutoff:3.500A) Processing helix chain 'E' and resid 1030 through 1039 Processing helix chain 'E' and resid 1040 through 1043 removed outlier: 5.277A pdb=" N VAL E1043 " --> pdb=" O ARG E1040 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1040 through 1043' Processing helix chain 'E' and resid 1044 through 1059 removed outlier: 3.591A pdb=" N GLY E1059 " --> pdb=" O ILE E1055 " (cutoff:3.500A) Processing helix chain 'E' and resid 1063 through 1072 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 7.153A pdb=" N GLY A 18 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ARG A 72 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU A 80 " --> pdb=" O HIS A 71 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG A 73 " --> pdb=" O CYS A 78 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS A 78 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 52 removed outlier: 6.907A pdb=" N ASP A 89 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE A 153 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY A 149 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA A 182 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 52 removed outlier: 6.907A pdb=" N ASP A 89 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE A 153 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY A 149 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA A 182 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 344 through 349 removed outlier: 3.693A pdb=" N GLY A 346 " --> pdb=" O THR A 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 493 removed outlier: 22.923A pdb=" N ILE A 929 " --> pdb=" O PRO A 717 " (cutoff:3.500A) removed outlier: 17.360A pdb=" N ASN A 719 " --> pdb=" O ILE A 929 " (cutoff:3.500A) removed outlier: 12.351A pdb=" N GLN A 931 " --> pdb=" O ASN A 719 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N LYS A 721 " --> pdb=" O GLN A 931 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY A 933 " --> pdb=" O LYS A 721 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG A 725 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A 674 " --> pdb=" O ARG A 718 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 596 through 602 removed outlier: 22.923A pdb=" N ILE A 929 " --> pdb=" O PRO A 717 " (cutoff:3.500A) removed outlier: 17.360A pdb=" N ASN A 719 " --> pdb=" O ILE A 929 " (cutoff:3.500A) removed outlier: 12.351A pdb=" N GLN A 931 " --> pdb=" O ASN A 719 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N LYS A 721 " --> pdb=" O GLN A 931 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY A 933 " --> pdb=" O LYS A 721 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG A 725 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N PHE A 968 " --> pdb=" O PRO A 914 " (cutoff:3.500A) removed outlier: 13.914A pdb=" N THR A 916 " --> pdb=" O LYS A 966 " (cutoff:3.500A) removed outlier: 16.610A pdb=" N LYS A 966 " --> pdb=" O THR A 916 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 786 through 787 Processing sheet with id=AA8, first strand: chain 'D' and resid 17 through 18 removed outlier: 7.129A pdb=" N GLY D 18 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ARG D 72 " --> pdb=" O GLY D 18 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU D 80 " --> pdb=" O HIS D 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 49 through 52 removed outlier: 6.925A pdb=" N ASP D 89 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE D 153 " --> pdb=" O ASP D 89 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY D 149 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA D 182 " --> pdb=" O PRO D 27 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 49 through 52 removed outlier: 6.925A pdb=" N ASP D 89 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE D 153 " --> pdb=" O ASP D 89 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY D 149 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA D 182 " --> pdb=" O PRO D 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 344 through 349 removed outlier: 3.708A pdb=" N GLY D 346 " --> pdb=" O THR D 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 488 through 493 removed outlier: 22.872A pdb=" N ILE D 929 " --> pdb=" O PRO D 717 " (cutoff:3.500A) removed outlier: 17.333A pdb=" N ASN D 719 " --> pdb=" O ILE D 929 " (cutoff:3.500A) removed outlier: 12.357A pdb=" N GLN D 931 " --> pdb=" O ASN D 719 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N LYS D 721 " --> pdb=" O GLN D 931 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY D 933 " --> pdb=" O LYS D 721 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ARG D 725 " --> pdb=" O LEU D 935 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR D 674 " --> pdb=" O ARG D 718 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 596 through 602 removed outlier: 22.872A pdb=" N ILE D 929 " --> pdb=" O PRO D 717 " (cutoff:3.500A) removed outlier: 17.333A pdb=" N ASN D 719 " --> pdb=" O ILE D 929 " (cutoff:3.500A) removed outlier: 12.357A pdb=" N GLN D 931 " --> pdb=" O ASN D 719 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N LYS D 721 " --> pdb=" O GLN D 931 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY D 933 " --> pdb=" O LYS D 721 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ARG D 725 " --> pdb=" O LEU D 935 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N PHE D 968 " --> pdb=" O PRO D 914 " (cutoff:3.500A) removed outlier: 13.888A pdb=" N THR D 916 " --> pdb=" O LYS D 966 " (cutoff:3.500A) removed outlier: 16.592A pdb=" N LYS D 966 " --> pdb=" O THR D 916 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY D 853 " --> pdb=" O THR D 898 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 786 through 788 831 hydrogen bonds defined for protein. 2319 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 7 hydrogen bonds 14 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 7.25 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.10: 16904 1.10 - 1.28: 2660 1.28 - 1.47: 5483 1.47 - 1.65: 8646 1.65 - 1.83: 130 Bond restraints: 33823 Sorted by residual: bond pdb=" HB2 LYS A 721 " pdb=" CB BLYS A 721 " ideal model delta sigma weight residual 0.970 1.170 -0.200 2.00e-02 2.50e+03 9.98e+01 bond pdb=" HB2 LYS A 721 " pdb=" CB CLYS A 721 " ideal model delta sigma weight residual 0.970 1.170 -0.200 2.00e-02 2.50e+03 9.98e+01 bond pdb=" HB2 LYS D 721 " pdb=" CB BLYS D 721 " ideal model delta sigma weight residual 0.970 1.162 -0.192 2.00e-02 2.50e+03 9.18e+01 bond pdb=" HB2 LYS D 721 " pdb=" CB CLYS D 721 " ideal model delta sigma weight residual 0.970 1.162 -0.192 2.00e-02 2.50e+03 9.18e+01 bond pdb=" HB2 LYS A 721 " pdb=" CB ALYS A 721 " ideal model delta sigma weight residual 0.970 1.141 -0.171 2.00e-02 2.50e+03 7.33e+01 ... (remaining 33818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 51479 2.82 - 5.64: 6528 5.64 - 8.46: 1706 8.46 - 11.28: 28 11.28 - 14.11: 42 Bond angle restraints: 59783 Sorted by residual: angle pdb=" C LEU A 472 " pdb=" N ARG A 473 " pdb=" CA ARG A 473 " ideal model delta sigma weight residual 120.54 129.19 -8.65 1.35e+00 5.49e-01 4.10e+01 angle pdb=" C LEU D 472 " pdb=" N ARG D 473 " pdb=" CA ARG D 473 " ideal model delta sigma weight residual 120.54 128.83 -8.29 1.35e+00 5.49e-01 3.77e+01 angle pdb=" CA ASP D 377 " pdb=" CB ASP D 377 " pdb=" CG ASP D 377 " ideal model delta sigma weight residual 112.60 118.22 -5.62 1.00e+00 1.00e+00 3.15e+01 angle pdb=" CA ASP D 544 " pdb=" CB ASP D 544 " pdb=" CG ASP D 544 " ideal model delta sigma weight residual 112.60 118.12 -5.52 1.00e+00 1.00e+00 3.05e+01 angle pdb=" CA ASP A 377 " pdb=" CB ASP A 377 " pdb=" CG ASP A 377 " ideal model delta sigma weight residual 112.60 118.00 -5.40 1.00e+00 1.00e+00 2.91e+01 ... (remaining 59778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.23: 14294 18.23 - 36.47: 762 36.47 - 54.70: 330 54.70 - 72.93: 198 72.93 - 91.16: 11 Dihedral angle restraints: 15595 sinusoidal: 8553 harmonic: 7042 Sorted by residual: dihedral pdb=" CA PRO A 909 " pdb=" C PRO A 909 " pdb=" N VAL A 910 " pdb=" CA VAL A 910 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA TYR A 596 " pdb=" C TYR A 596 " pdb=" N HIS A 597 " pdb=" CA HIS A 597 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA TYR D 596 " pdb=" C TYR D 596 " pdb=" N HIS D 597 " pdb=" CA HIS D 597 " ideal model delta harmonic sigma weight residual 180.00 156.19 23.81 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 15592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1409 0.070 - 0.140: 805 0.140 - 0.210: 262 0.210 - 0.280: 68 0.280 - 0.350: 19 Chirality restraints: 2563 Sorted by residual: chirality pdb=" CA ASP A 769 " pdb=" N ASP A 769 " pdb=" C ASP A 769 " pdb=" CB ASP A 769 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA ASP D 769 " pdb=" N ASP D 769 " pdb=" C ASP D 769 " pdb=" CB ASP D 769 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA ARG D 965 " pdb=" N ARG D 965 " pdb=" C ARG D 965 " pdb=" CB ARG D 965 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 2560 not shown) Planarity restraints: 4849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT F 8 " -0.240 2.00e-02 2.50e+03 1.48e-01 6.57e+02 pdb=" N1 DT F 8 " -0.085 2.00e-02 2.50e+03 pdb=" C2 DT F 8 " 0.040 2.00e-02 2.50e+03 pdb=" O2 DT F 8 " 0.282 2.00e-02 2.50e+03 pdb=" N3 DT F 8 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT F 8 " -0.097 2.00e-02 2.50e+03 pdb=" O4 DT F 8 " -0.218 2.00e-02 2.50e+03 pdb=" C5 DT F 8 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT F 8 " 0.230 2.00e-02 2.50e+03 pdb=" C6 DT F 8 " -0.020 2.00e-02 2.50e+03 pdb=" H3 DT F 8 " 0.030 2.00e-02 2.50e+03 pdb=" H6 DT F 8 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 185 " 0.246 9.50e-02 1.11e+02 1.67e-01 4.83e+02 pdb=" NE ARG A 185 " 0.072 2.00e-02 2.50e+03 pdb=" CZ ARG A 185 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 185 " -0.126 2.00e-02 2.50e+03 pdb=" NH2 ARG A 185 " -0.051 2.00e-02 2.50e+03 pdb="HH11 ARG A 185 " -0.131 2.00e-02 2.50e+03 pdb="HH12 ARG A 185 " 0.327 2.00e-02 2.50e+03 pdb="HH21 ARG A 185 " 0.113 2.00e-02 2.50e+03 pdb="HH22 ARG A 185 " -0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 185 " -0.215 9.50e-02 1.11e+02 1.45e-01 3.64e+02 pdb=" NE ARG D 185 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG D 185 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG D 185 " 0.112 2.00e-02 2.50e+03 pdb=" NH2 ARG D 185 " 0.055 2.00e-02 2.50e+03 pdb="HH11 ARG D 185 " 0.100 2.00e-02 2.50e+03 pdb="HH12 ARG D 185 " -0.280 2.00e-02 2.50e+03 pdb="HH21 ARG D 185 " -0.114 2.00e-02 2.50e+03 pdb="HH22 ARG D 185 " 0.145 2.00e-02 2.50e+03 ... (remaining 4846 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.89: 858 1.89 - 2.57: 26565 2.57 - 3.24: 103860 3.24 - 3.92: 143423 3.92 - 4.60: 211291 Nonbonded interactions: 485997 Sorted by model distance: nonbonded pdb=" HH TYR A 423 " pdb=" HG CYS A 611 " model vdw 1.210 2.270 nonbonded pdb=" OP1 DT F 8 " pdb=" HZ1CLYS D 721 " model vdw 1.385 2.450 nonbonded pdb=" HE ARG A 419 " pdb=" HG CYS A 611 " model vdw 1.470 2.270 nonbonded pdb=" HG CYS A 453 " pdb=" H LEU A 455 " model vdw 1.508 2.270 nonbonded pdb=" HG CYS A 464 " pdb=" H ASN A 466 " model vdw 1.516 2.270 ... (remaining 485992 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 9 through 299 or resid 301 through 720 or resid 722 throug \ h 2000)) selection = (chain 'D' and (resid 9 through 299 or resid 301 through 720 or resid 722 throug \ h 2000)) } ncs_group { reference = chain 'B' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 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: 3.320 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: 0.230 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 47.850 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 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 : 0.014 0.321 16861 Z= 0.822 Angle : 1.829 8.645 22996 Z= 1.252 Chirality : 0.096 0.350 2563 Planarity : 0.018 0.246 2916 Dihedral : 13.074 91.163 6211 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 0.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.16), residues: 2024 helix: -1.04 (0.14), residues: 940 sheet: 0.54 (0.35), residues: 180 loop : -0.36 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 185 TYR 0.120 0.023 TYR A 866 PHE 0.073 0.011 PHE D 157 TRP 0.110 0.020 TRP D 778 HIS 0.010 0.003 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.01312 (16855) covalent geometry : angle 1.82878 (22996) hydrogen bonds : bond 0.22268 ( 784) hydrogen bonds : angle 7.05628 ( 2333) metal coordination : bond 0.20408 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 480 MET cc_start: 0.9280 (mmp) cc_final: 0.9057 (mmm) REVERT: A 709 MET cc_start: 0.9524 (mmm) cc_final: 0.9320 (mmm) REVERT: D 400 ASN cc_start: 0.8964 (m-40) cc_final: 0.8721 (m110) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 1.8281 time to fit residues: 565.3734 Evaluate side-chains 209 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN B A 396 ASN A 430 GLN A 779 HIS A 845 GLN D 300 ASN A D 430 GLN D 533 ASN D 779 HIS D 845 GLN D 903 GLN E1084 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.095388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.063384 restraints weight = 98441.032| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.55 r_work: 0.2632 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2510 r_free = 0.2510 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 16861 Z= 0.184 Angle : 0.708 6.115 22996 Z= 0.395 Chirality : 0.045 0.148 2563 Planarity : 0.007 0.097 2916 Dihedral : 10.678 84.788 2503 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.64 % Allowed : 7.36 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.18), residues: 2024 helix: 0.39 (0.17), residues: 950 sheet: 0.30 (0.29), residues: 262 loop : -0.27 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 473 TYR 0.027 0.002 TYR A 527 PHE 0.024 0.002 PHE A 559 TRP 0.028 0.002 TRP A 528 HIS 0.006 0.002 HIS D 597 Details of bonding type rmsd covalent geometry : bond 0.00398 (16855) covalent geometry : angle 0.70782 (22996) hydrogen bonds : bond 0.07030 ( 784) hydrogen bonds : angle 5.34233 ( 2333) metal coordination : bond 0.00856 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 228 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 480 MET cc_start: 0.9210 (mmp) cc_final: 0.8943 (mmm) REVERT: A 501 ASP cc_start: 0.9126 (m-30) cc_final: 0.8864 (t0) REVERT: A 578 MET cc_start: 0.7973 (mmp) cc_final: 0.7713 (mmp) REVERT: A 689 LEU cc_start: 0.8356 (mm) cc_final: 0.8035 (mm) REVERT: D 133 LYS cc_start: 0.8422 (mmtm) cc_final: 0.8181 (mmtm) REVERT: D 229 ARG cc_start: 0.8306 (mtm180) cc_final: 0.7951 (mmp80) REVERT: D 400 ASN cc_start: 0.8596 (m-40) cc_final: 0.8382 (m-40) REVERT: D 480 MET cc_start: 0.9194 (mmp) cc_final: 0.8909 (mmm) REVERT: D 501 ASP cc_start: 0.9132 (m-30) cc_final: 0.8860 (t0) outliers start: 11 outliers final: 2 residues processed: 236 average time/residue: 1.7996 time to fit residues: 460.4205 Evaluate side-chains 196 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 194 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain E residue 1060 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 120 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 845 GLN D 845 GLN D 927 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.092902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.061627 restraints weight = 105015.444| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.55 r_work: 0.2602 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16861 Z= 0.203 Angle : 0.644 6.365 22996 Z= 0.354 Chirality : 0.045 0.143 2563 Planarity : 0.006 0.080 2916 Dihedral : 10.535 79.145 2503 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.70 % Allowed : 9.15 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.18), residues: 2024 helix: 0.79 (0.17), residues: 948 sheet: 0.16 (0.28), residues: 274 loop : -0.20 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 708 TYR 0.027 0.002 TYR D 527 PHE 0.017 0.002 PHE A 559 TRP 0.012 0.002 TRP A 778 HIS 0.005 0.001 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00492 (16855) covalent geometry : angle 0.64379 (22996) hydrogen bonds : bond 0.06471 ( 784) hydrogen bonds : angle 4.87764 ( 2333) metal coordination : bond 0.00780 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 218 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8514 (t70) cc_final: 0.8277 (t70) REVERT: A 457 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8687 (mt-10) REVERT: A 459 ARG cc_start: 0.8820 (mtm110) cc_final: 0.8539 (mtm-85) REVERT: A 499 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8886 (mt-10) REVERT: A 528 TRP cc_start: 0.8335 (t-100) cc_final: 0.8058 (t60) REVERT: A 561 LYS cc_start: 0.8205 (tptt) cc_final: 0.7788 (ttmm) REVERT: D 133 LYS cc_start: 0.8415 (mmtm) cc_final: 0.8136 (mmtm) REVERT: D 229 ARG cc_start: 0.8411 (mtm180) cc_final: 0.7971 (mmp80) REVERT: D 499 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.8841 (mt-10) REVERT: D 548 LYS cc_start: 0.8471 (ttmm) cc_final: 0.8144 (ttmt) REVERT: D 864 ARG cc_start: 0.8758 (tmm-80) cc_final: 0.8437 (tmm-80) outliers start: 12 outliers final: 1 residues processed: 227 average time/residue: 1.7667 time to fit residues: 435.2472 Evaluate side-chains 207 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 204 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain E residue 1058 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 142 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 205 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 845 GLN D 845 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.092663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.060997 restraints weight = 110250.305| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.62 r_work: 0.2602 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16861 Z= 0.210 Angle : 0.618 5.335 22996 Z= 0.339 Chirality : 0.045 0.142 2563 Planarity : 0.006 0.080 2916 Dihedral : 10.493 75.621 2503 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.16 % Allowed : 9.91 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.19), residues: 2024 helix: 0.92 (0.17), residues: 948 sheet: 0.08 (0.28), residues: 274 loop : -0.17 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 718 TYR 0.028 0.002 TYR D 527 PHE 0.018 0.002 PHE E1070 TRP 0.016 0.002 TRP D 528 HIS 0.004 0.001 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00511 (16855) covalent geometry : angle 0.61804 (22996) hydrogen bonds : bond 0.06227 ( 784) hydrogen bonds : angle 4.67984 ( 2333) metal coordination : bond 0.00599 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8479 (t70) cc_final: 0.8242 (m-30) REVERT: A 459 ARG cc_start: 0.8848 (mtm110) cc_final: 0.8475 (mtp180) REVERT: A 499 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8888 (mt-10) REVERT: A 501 ASP cc_start: 0.9244 (OUTLIER) cc_final: 0.8786 (t0) REVERT: A 528 TRP cc_start: 0.8386 (t-100) cc_final: 0.8085 (t60) REVERT: A 561 LYS cc_start: 0.8248 (tptt) cc_final: 0.7830 (ttmm) REVERT: A 576 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7126 (mp10) REVERT: A 787 VAL cc_start: 0.8311 (t) cc_final: 0.7958 (p) REVERT: B 1004 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7611 (mp10) REVERT: D 122 ASP cc_start: 0.8449 (t70) cc_final: 0.8137 (m-30) REVERT: D 133 LYS cc_start: 0.8452 (mmtm) cc_final: 0.8182 (mmtm) REVERT: D 229 ARG cc_start: 0.8485 (mtm180) cc_final: 0.8063 (mmt-90) REVERT: D 501 ASP cc_start: 0.9272 (OUTLIER) cc_final: 0.8820 (t0) REVERT: D 548 LYS cc_start: 0.8531 (ttmm) cc_final: 0.8240 (ttmt) REVERT: D 746 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.6926 (mpt90) REVERT: D 787 VAL cc_start: 0.8293 (t) cc_final: 0.7914 (p) outliers start: 20 outliers final: 5 residues processed: 219 average time/residue: 1.9820 time to fit residues: 471.0232 Evaluate side-chains 209 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain B residue 1004 GLN Chi-restraints excluded: chain B residue 1058 SER Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 679 LYS Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain E residue 1001 ILE Chi-restraints excluded: chain E residue 1058 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 21 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 845 GLN D 845 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.092125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.060710 restraints weight = 104370.598| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.55 r_work: 0.2569 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2471 r_free = 0.2471 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2471 r_free = 0.2471 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16861 Z= 0.230 Angle : 0.622 5.837 22996 Z= 0.339 Chirality : 0.045 0.141 2563 Planarity : 0.006 0.084 2916 Dihedral : 10.467 73.763 2503 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.16 % Allowed : 10.02 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.19), residues: 2024 helix: 0.95 (0.17), residues: 950 sheet: -0.02 (0.28), residues: 276 loop : -0.21 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 664 TYR 0.026 0.002 TYR D 527 PHE 0.016 0.002 PHE A 559 TRP 0.019 0.002 TRP D 528 HIS 0.004 0.001 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00565 (16855) covalent geometry : angle 0.62236 (22996) hydrogen bonds : bond 0.06303 ( 784) hydrogen bonds : angle 4.63062 ( 2333) metal coordination : bond 0.00739 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8480 (t70) cc_final: 0.8199 (m-30) REVERT: A 459 ARG cc_start: 0.8831 (mtm110) cc_final: 0.8485 (mtp180) REVERT: A 499 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8875 (mt-10) REVERT: A 528 TRP cc_start: 0.8383 (t-100) cc_final: 0.8046 (t60) REVERT: A 561 LYS cc_start: 0.8198 (tptt) cc_final: 0.7806 (ttmm) REVERT: A 576 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6765 (mp10) REVERT: A 787 VAL cc_start: 0.8288 (t) cc_final: 0.7935 (p) REVERT: D 122 ASP cc_start: 0.8419 (t70) cc_final: 0.8098 (m-30) REVERT: D 133 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8142 (mmtm) REVERT: D 229 ARG cc_start: 0.8450 (mtm180) cc_final: 0.8004 (mmt-90) REVERT: D 499 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8818 (mt-10) REVERT: D 548 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8189 (ttmt) REVERT: D 576 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7043 (mp10) REVERT: D 746 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6869 (mpt90) REVERT: D 787 VAL cc_start: 0.8276 (t) cc_final: 0.7904 (p) outliers start: 20 outliers final: 8 residues processed: 217 average time/residue: 1.7752 time to fit residues: 418.5503 Evaluate side-chains 213 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain B residue 1001 ILE Chi-restraints excluded: chain B residue 1058 SER Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain D residue 576 GLN Chi-restraints excluded: chain D residue 679 LYS Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 980 LYS Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1058 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN A 845 GLN D 736 GLN D 845 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.061690 restraints weight = 106627.459| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.58 r_work: 0.2589 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16861 Z= 0.165 Angle : 0.581 6.011 22996 Z= 0.315 Chirality : 0.042 0.140 2563 Planarity : 0.006 0.071 2916 Dihedral : 10.422 72.520 2503 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.93 % Allowed : 10.95 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.19), residues: 2024 helix: 1.13 (0.17), residues: 950 sheet: 0.07 (0.28), residues: 276 loop : -0.20 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 864 TYR 0.021 0.002 TYR D 527 PHE 0.016 0.001 PHE A 559 TRP 0.018 0.001 TRP D 528 HIS 0.004 0.001 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00396 (16855) covalent geometry : angle 0.58127 (22996) hydrogen bonds : bond 0.05551 ( 784) hydrogen bonds : angle 4.50608 ( 2333) metal coordination : bond 0.00392 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8430 (t70) cc_final: 0.8175 (m-30) REVERT: A 459 ARG cc_start: 0.8823 (mtm110) cc_final: 0.8602 (mtm180) REVERT: A 499 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8869 (mt-10) REVERT: A 528 TRP cc_start: 0.8380 (t-100) cc_final: 0.8084 (t60) REVERT: A 561 LYS cc_start: 0.8129 (tptt) cc_final: 0.7773 (ttmm) REVERT: A 576 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6739 (mp10) REVERT: A 711 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8885 (ttmt) REVERT: A 787 VAL cc_start: 0.8273 (t) cc_final: 0.7926 (p) REVERT: D 122 ASP cc_start: 0.8390 (t70) cc_final: 0.8084 (m-30) REVERT: D 133 LYS cc_start: 0.8445 (mmtm) cc_final: 0.8110 (mmtt) REVERT: D 229 ARG cc_start: 0.8445 (mtm180) cc_final: 0.7977 (mmt-90) REVERT: D 499 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8806 (mt-10) REVERT: D 548 LYS cc_start: 0.8503 (ttmm) cc_final: 0.8153 (ttmt) REVERT: D 576 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6797 (mp10) REVERT: D 746 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.6879 (mpt90) REVERT: D 787 VAL cc_start: 0.8268 (t) cc_final: 0.7903 (p) outliers start: 16 outliers final: 10 residues processed: 211 average time/residue: 1.7902 time to fit residues: 411.8372 Evaluate side-chains 220 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain B residue 1001 ILE Chi-restraints excluded: chain B residue 1058 SER Chi-restraints excluded: chain B residue 1068 ARG Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain D residue 561 LYS Chi-restraints excluded: chain D residue 576 GLN Chi-restraints excluded: chain D residue 679 LYS Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain E residue 1054 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 203 optimal weight: 4.9990 chunk 191 optimal weight: 0.1980 chunk 117 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 158 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 HIS A 845 GLN D 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.062601 restraints weight = 110931.692| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.62 r_work: 0.2643 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2519 r_free = 0.2519 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2519 r_free = 0.2519 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16861 Z= 0.127 Angle : 0.549 6.666 22996 Z= 0.293 Chirality : 0.041 0.143 2563 Planarity : 0.005 0.054 2916 Dihedral : 10.359 72.383 2503 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.58 % Allowed : 11.36 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.19), residues: 2024 helix: 1.29 (0.18), residues: 962 sheet: 0.18 (0.29), residues: 276 loop : -0.23 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 864 TYR 0.018 0.002 TYR A 527 PHE 0.017 0.001 PHE A 559 TRP 0.019 0.001 TRP D 528 HIS 0.004 0.001 HIS A 554 Details of bonding type rmsd covalent geometry : bond 0.00301 (16855) covalent geometry : angle 0.54926 (22996) hydrogen bonds : bond 0.04696 ( 784) hydrogen bonds : angle 4.34020 ( 2333) metal coordination : bond 0.00242 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8416 (t70) cc_final: 0.8146 (m-30) REVERT: A 229 ARG cc_start: 0.8423 (mtm180) cc_final: 0.7983 (mmt-90) REVERT: A 459 ARG cc_start: 0.8823 (mtm110) cc_final: 0.8620 (mtm180) REVERT: A 528 TRP cc_start: 0.8392 (t-100) cc_final: 0.8102 (t60) REVERT: A 576 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6723 (mp10) REVERT: A 711 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8838 (ttmt) REVERT: A 787 VAL cc_start: 0.8403 (t) cc_final: 0.8063 (p) REVERT: B 1061 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7188 (pp20) REVERT: B 1063 THR cc_start: 0.7874 (m) cc_final: 0.7573 (t) REVERT: D 122 ASP cc_start: 0.8383 (t70) cc_final: 0.8088 (m-30) REVERT: D 133 LYS cc_start: 0.8476 (mmtm) cc_final: 0.8180 (mmtt) REVERT: D 229 ARG cc_start: 0.8420 (mtm180) cc_final: 0.7994 (mmt-90) REVERT: D 548 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8174 (ttmt) REVERT: D 551 LYS cc_start: 0.8510 (tmtm) cc_final: 0.8295 (tmtm) REVERT: D 576 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.6798 (mp10) REVERT: D 746 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.6839 (mpt90) REVERT: D 787 VAL cc_start: 0.8318 (t) cc_final: 0.7967 (p) outliers start: 10 outliers final: 4 residues processed: 208 average time/residue: 1.9521 time to fit residues: 442.0190 Evaluate side-chains 204 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain D residue 576 GLN Chi-restraints excluded: chain D residue 679 LYS Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 980 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 111 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 182 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN A 845 GLN D 554 HIS D 736 GLN D 845 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.093624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.062173 restraints weight = 103397.096| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.55 r_work: 0.2634 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2512 r_free = 0.2512 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16861 Z= 0.148 Angle : 0.557 6.291 22996 Z= 0.298 Chirality : 0.042 0.141 2563 Planarity : 0.005 0.062 2916 Dihedral : 10.354 72.126 2503 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.81 % Allowed : 11.30 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.19), residues: 2024 helix: 1.36 (0.18), residues: 950 sheet: 0.17 (0.29), residues: 276 loop : -0.16 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 864 TYR 0.020 0.002 TYR A 527 PHE 0.016 0.001 PHE A 559 TRP 0.020 0.001 TRP D 528 HIS 0.005 0.001 HIS D 554 Details of bonding type rmsd covalent geometry : bond 0.00357 (16855) covalent geometry : angle 0.55716 (22996) hydrogen bonds : bond 0.04983 ( 784) hydrogen bonds : angle 4.35256 ( 2333) metal coordination : bond 0.00338 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8419 (t70) cc_final: 0.8136 (m-30) REVERT: A 229 ARG cc_start: 0.8418 (mtm180) cc_final: 0.7974 (mmt-90) REVERT: A 459 ARG cc_start: 0.8833 (mtm110) cc_final: 0.8624 (mtm180) REVERT: A 528 TRP cc_start: 0.8392 (t-100) cc_final: 0.8091 (t60) REVERT: A 711 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8856 (ttmt) REVERT: A 787 VAL cc_start: 0.8354 (t) cc_final: 0.8015 (p) REVERT: B 1063 THR cc_start: 0.7873 (m) cc_final: 0.7603 (t) REVERT: D 122 ASP cc_start: 0.8392 (t70) cc_final: 0.8073 (m-30) REVERT: D 133 LYS cc_start: 0.8481 (mmtm) cc_final: 0.8232 (mmtm) REVERT: D 229 ARG cc_start: 0.8430 (mtm180) cc_final: 0.7996 (mmt-90) REVERT: D 548 LYS cc_start: 0.8522 (ttmm) cc_final: 0.8193 (ttmt) REVERT: D 551 LYS cc_start: 0.8533 (tmtm) cc_final: 0.8312 (tmtm) REVERT: D 746 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.6891 (mpt90) REVERT: D 787 VAL cc_start: 0.8314 (t) cc_final: 0.7967 (p) outliers start: 14 outliers final: 9 residues processed: 207 average time/residue: 1.8306 time to fit residues: 412.7816 Evaluate side-chains 219 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain D residue 561 LYS Chi-restraints excluded: chain D residue 576 GLN Chi-restraints excluded: chain D residue 679 LYS Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 980 LYS Chi-restraints excluded: chain E residue 1054 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 59 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 HIS D 845 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.092379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.061857 restraints weight = 111318.941| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 2.54 r_work: 0.2607 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2485 r_free = 0.2485 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2485 r_free = 0.2485 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16861 Z= 0.203 Angle : 0.592 6.583 22996 Z= 0.320 Chirality : 0.044 0.139 2563 Planarity : 0.006 0.075 2916 Dihedral : 10.401 72.185 2503 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.70 % Allowed : 11.59 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.19), residues: 2024 helix: 1.24 (0.18), residues: 950 sheet: 0.07 (0.29), residues: 262 loop : -0.25 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 718 TYR 0.023 0.002 TYR A 527 PHE 0.015 0.002 PHE A 559 TRP 0.024 0.002 TRP D 528 HIS 0.007 0.001 HIS A 554 Details of bonding type rmsd covalent geometry : bond 0.00498 (16855) covalent geometry : angle 0.59229 (22996) hydrogen bonds : bond 0.05740 ( 784) hydrogen bonds : angle 4.43130 ( 2333) metal coordination : bond 0.00504 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8454 (t70) cc_final: 0.8192 (m-30) REVERT: A 459 ARG cc_start: 0.8850 (mtm110) cc_final: 0.8647 (mtm180) REVERT: A 528 TRP cc_start: 0.8418 (t-100) cc_final: 0.8120 (t60) REVERT: A 561 LYS cc_start: 0.8194 (tptt) cc_final: 0.7821 (ttmm) REVERT: A 711 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8885 (ttmt) REVERT: A 787 VAL cc_start: 0.8347 (t) cc_final: 0.8009 (p) REVERT: A 928 GLN cc_start: 0.8560 (mt0) cc_final: 0.8307 (mt0) REVERT: B 1063 THR cc_start: 0.7885 (m) cc_final: 0.7628 (t) REVERT: D 122 ASP cc_start: 0.8422 (t70) cc_final: 0.8093 (m-30) REVERT: D 133 LYS cc_start: 0.8523 (mmtm) cc_final: 0.8212 (mmtt) REVERT: D 229 ARG cc_start: 0.8498 (mtm180) cc_final: 0.8033 (mmt-90) REVERT: D 499 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.8806 (mt-10) REVERT: D 548 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8234 (ttmt) REVERT: D 554 HIS cc_start: 0.8069 (t-90) cc_final: 0.7869 (t-170) REVERT: D 787 VAL cc_start: 0.8325 (t) cc_final: 0.7980 (p) outliers start: 12 outliers final: 7 residues processed: 215 average time/residue: 1.7593 time to fit residues: 411.3663 Evaluate side-chains 214 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 205 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain D residue 576 GLN Chi-restraints excluded: chain D residue 679 LYS Chi-restraints excluded: chain E residue 1054 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 40 optimal weight: 1.9990 chunk 192 optimal weight: 0.0170 chunk 158 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 HIS A 845 GLN D 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.093772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.062258 restraints weight = 107315.718| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.59 r_work: 0.2636 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2513 r_free = 0.2513 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2513 r_free = 0.2513 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16861 Z= 0.131 Angle : 0.556 6.507 22996 Z= 0.297 Chirality : 0.041 0.144 2563 Planarity : 0.005 0.058 2916 Dihedral : 10.366 73.081 2503 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.58 % Allowed : 11.88 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.19), residues: 2024 helix: 1.34 (0.18), residues: 962 sheet: 0.16 (0.30), residues: 262 loop : -0.30 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 864 TYR 0.018 0.002 TYR A 527 PHE 0.016 0.001 PHE A 559 TRP 0.025 0.001 TRP D 528 HIS 0.003 0.001 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00309 (16855) covalent geometry : angle 0.55649 (22996) hydrogen bonds : bond 0.04833 ( 784) hydrogen bonds : angle 4.31981 ( 2333) metal coordination : bond 0.00239 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8416 (t70) cc_final: 0.8129 (m-30) REVERT: A 229 ARG cc_start: 0.8405 (mtm180) cc_final: 0.7940 (mmt-90) REVERT: A 528 TRP cc_start: 0.8411 (t-100) cc_final: 0.8101 (t60) REVERT: A 711 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8841 (ttmt) REVERT: A 787 VAL cc_start: 0.8379 (t) cc_final: 0.8036 (p) REVERT: A 928 GLN cc_start: 0.8531 (mt0) cc_final: 0.8276 (mt0) REVERT: B 1063 THR cc_start: 0.7883 (m) cc_final: 0.7623 (t) REVERT: D 122 ASP cc_start: 0.8386 (t70) cc_final: 0.8070 (m-30) REVERT: D 133 LYS cc_start: 0.8506 (mmtm) cc_final: 0.8211 (mmtt) REVERT: D 229 ARG cc_start: 0.8411 (mtm180) cc_final: 0.7981 (mmt-90) REVERT: D 548 LYS cc_start: 0.8536 (ttmm) cc_final: 0.8212 (ttmt) REVERT: D 551 LYS cc_start: 0.8541 (tmtm) cc_final: 0.8323 (tmtm) REVERT: D 787 VAL cc_start: 0.8290 (t) cc_final: 0.7939 (p) outliers start: 10 outliers final: 8 residues processed: 215 average time/residue: 1.7508 time to fit residues: 409.5343 Evaluate side-chains 216 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 207 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 980 LYS Chi-restraints excluded: chain D residue 576 GLN Chi-restraints excluded: chain D residue 679 LYS Chi-restraints excluded: chain D residue 738 SER Chi-restraints excluded: chain E residue 1054 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 190 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 13 optimal weight: 0.0030 chunk 150 optimal weight: 0.6980 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 554 HIS D 845 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.093966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.063699 restraints weight = 99702.716| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.44 r_work: 0.2648 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16861 Z= 0.139 Angle : 0.555 6.528 22996 Z= 0.296 Chirality : 0.041 0.142 2563 Planarity : 0.005 0.061 2916 Dihedral : 10.355 73.747 2503 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.52 % Allowed : 12.17 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.19), residues: 2024 helix: 1.42 (0.18), residues: 950 sheet: 0.18 (0.30), residues: 262 loop : -0.19 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 864 TYR 0.019 0.002 TYR A 527 PHE 0.016 0.001 PHE A 559 TRP 0.026 0.001 TRP D 528 HIS 0.005 0.001 HIS D 554 Details of bonding type rmsd covalent geometry : bond 0.00333 (16855) covalent geometry : angle 0.55489 (22996) hydrogen bonds : bond 0.04845 ( 784) hydrogen bonds : angle 4.30060 ( 2333) metal coordination : bond 0.00288 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17019.50 seconds wall clock time: 287 minutes 12.84 seconds (17232.84 seconds total)