Starting phenix.real_space_refine on Sun Dec 21 22:26:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pxe_13700/12_2025/7pxe_13700.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pxe_13700/12_2025/7pxe_13700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pxe_13700/12_2025/7pxe_13700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pxe_13700/12_2025/7pxe_13700.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pxe_13700/12_2025/7pxe_13700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pxe_13700/12_2025/7pxe_13700.map" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 8 9.91 5 K 4 8.98 5 P 16 5.49 5 Mg 4 5.21 5 S 192 5.16 5 C 18724 2.51 5 N 4604 2.21 5 O 5376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28928 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7023 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 5 Chain: "A" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 178 Unusual residues: {' K': 4, ' CA': 2, ' MG': 1, '6PL': 4, 'CLR': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'6PL:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Restraints were copied for chains: B, C, D Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" K K A1209 " occ=0.25 residue: pdb=" K K A1210 " occ=0.25 residue: pdb=" K K A1211 " occ=0.50 residue: pdb=" K K A1212 " occ=0.50 Time building chain proxies: 7.87, per 1000 atoms: 0.27 Number of scatterers: 28928 At special positions: 0 Unit cell: (165.9, 165.9, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 8 19.99 K 4 19.00 S 192 16.00 P 16 15.00 Mg 4 11.99 O 5376 8.00 N 4604 7.00 C 18724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.4 seconds 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6696 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 24 sheets defined 56.8% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 48 through 77 removed outlier: 3.739A pdb=" N PHE A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 123 through 149 Processing helix chain 'A' and resid 162 through 186 removed outlier: 3.886A pdb=" N GLN A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 194 removed outlier: 3.715A pdb=" N LEU A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 203 removed outlier: 3.643A pdb=" N PHE A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 215 removed outlier: 3.722A pdb=" N SER A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 244 through 275 Processing helix chain 'A' and resid 287 through 300 Processing helix chain 'A' and resid 311 through 341 removed outlier: 3.516A pdb=" N PHE A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 366 through 378 Processing helix chain 'A' and resid 398 through 408 Processing helix chain 'A' and resid 421 through 428 Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 446 through 465 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 479 through 485 removed outlier: 3.980A pdb=" N LEU A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 514 removed outlier: 3.751A pdb=" N LEU A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 525 removed outlier: 3.831A pdb=" N PHE A 525 " --> pdb=" O MET A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 548 Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'A' and resid 564 through 575 Processing helix chain 'A' and resid 617 through 626 removed outlier: 3.934A pdb=" N VAL A 621 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG A 623 " --> pdb=" O ASP A 619 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TRP A 625 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 796 No H-bonds generated for 'chain 'A' and resid 794 through 796' Processing helix chain 'A' and resid 800 through 806 Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 834 through 837 removed outlier: 3.814A pdb=" N ALA A 837 " --> pdb=" O PRO A 834 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 834 through 837' Processing helix chain 'A' and resid 853 through 861 removed outlier: 3.838A pdb=" N ARG A 859 " --> pdb=" O ASP A 855 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 860 " --> pdb=" O TYR A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 864 No H-bonds generated for 'chain 'A' and resid 862 through 864' Processing helix chain 'A' and resid 879 through 886 Processing helix chain 'A' and resid 887 through 891 Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 911 through 923 Processing helix chain 'A' and resid 960 through 964 removed outlier: 3.814A pdb=" N ASN A 963 " --> pdb=" O TYR A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 979 removed outlier: 3.975A pdb=" N GLN A 977 " --> pdb=" O GLY A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 993 Processing helix chain 'A' and resid 994 through 999 Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.602A pdb=" N VAL A1007 " --> pdb=" O ALA A1004 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A1009 " --> pdb=" O SER A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1018 Processing helix chain 'A' and resid 1018 through 1030 removed outlier: 4.044A pdb=" N LEU A1022 " --> pdb=" O ASN A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1044 removed outlier: 4.226A pdb=" N GLY A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1061 Processing helix chain 'A' and resid 1075 through 1082 removed outlier: 4.010A pdb=" N GLY A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A1080 " --> pdb=" O ALA A1076 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS A1081 " --> pdb=" O GLN A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1096 Processing helix chain 'B' and resid 48 through 77 removed outlier: 3.739A pdb=" N PHE B 52 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 123 through 149 Processing helix chain 'B' and resid 162 through 186 removed outlier: 3.886A pdb=" N GLN B 166 " --> pdb=" O ASN B 162 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 194 removed outlier: 3.715A pdb=" N LEU B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.643A pdb=" N PHE B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 215 removed outlier: 3.722A pdb=" N SER B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 231 through 239 Processing helix chain 'B' and resid 244 through 275 Processing helix chain 'B' and resid 287 through 300 Processing helix chain 'B' and resid 311 through 341 removed outlier: 3.516A pdb=" N PHE B 320 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ALA B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Proline residue: B 334 - end of helix Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 398 through 408 Processing helix chain 'B' and resid 421 through 428 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 446 through 465 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 479 through 485 removed outlier: 3.980A pdb=" N LEU B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 514 removed outlier: 3.750A pdb=" N LEU B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 525 removed outlier: 3.831A pdb=" N PHE B 525 " --> pdb=" O MET B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 548 Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 564 through 575 Processing helix chain 'B' and resid 617 through 626 removed outlier: 3.934A pdb=" N VAL B 621 " --> pdb=" O SER B 617 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG B 623 " --> pdb=" O ASP B 619 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TRP B 625 " --> pdb=" O VAL B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 796 No H-bonds generated for 'chain 'B' and resid 794 through 796' Processing helix chain 'B' and resid 800 through 806 Processing helix chain 'B' and resid 828 through 833 Processing helix chain 'B' and resid 834 through 837 removed outlier: 3.814A pdb=" N ALA B 837 " --> pdb=" O PRO B 834 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 834 through 837' Processing helix chain 'B' and resid 853 through 861 removed outlier: 3.838A pdb=" N ARG B 859 " --> pdb=" O ASP B 855 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 860 " --> pdb=" O TYR B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 864 No H-bonds generated for 'chain 'B' and resid 862 through 864' Processing helix chain 'B' and resid 879 through 886 Processing helix chain 'B' and resid 887 through 891 Processing helix chain 'B' and resid 906 through 910 Processing helix chain 'B' and resid 911 through 923 Processing helix chain 'B' and resid 960 through 964 removed outlier: 3.814A pdb=" N ASN B 963 " --> pdb=" O TYR B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 979 removed outlier: 3.975A pdb=" N GLN B 977 " --> pdb=" O GLY B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 993 Processing helix chain 'B' and resid 994 through 999 Processing helix chain 'B' and resid 1004 through 1009 removed outlier: 3.602A pdb=" N VAL B1007 " --> pdb=" O ALA B1004 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B1009 " --> pdb=" O SER B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1018 Processing helix chain 'B' and resid 1018 through 1030 removed outlier: 4.044A pdb=" N LEU B1022 " --> pdb=" O ASN B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1044 removed outlier: 4.225A pdb=" N GLY B1044 " --> pdb=" O ILE B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1061 Processing helix chain 'B' and resid 1075 through 1082 removed outlier: 4.010A pdb=" N GLY B1079 " --> pdb=" O LEU B1075 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B1080 " --> pdb=" O ALA B1076 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS B1081 " --> pdb=" O GLN B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1083 through 1096 Processing helix chain 'C' and resid 48 through 77 removed outlier: 3.738A pdb=" N PHE C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 123 through 149 Processing helix chain 'C' and resid 162 through 186 removed outlier: 3.887A pdb=" N GLN C 166 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 194 removed outlier: 3.714A pdb=" N LEU C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 203 removed outlier: 3.643A pdb=" N PHE C 203 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 215 removed outlier: 3.722A pdb=" N SER C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 244 through 275 Processing helix chain 'C' and resid 287 through 300 Processing helix chain 'C' and resid 311 through 341 removed outlier: 3.516A pdb=" N PHE C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Proline residue: C 334 - end of helix Processing helix chain 'C' and resid 366 through 378 Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 421 through 428 Processing helix chain 'C' and resid 429 through 433 Processing helix chain 'C' and resid 446 through 465 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 479 through 485 removed outlier: 3.980A pdb=" N LEU C 483 " --> pdb=" O ASN C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 514 removed outlier: 3.750A pdb=" N LEU C 513 " --> pdb=" O ALA C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 525 removed outlier: 3.831A pdb=" N PHE C 525 " --> pdb=" O MET C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 548 Processing helix chain 'C' and resid 557 through 561 Processing helix chain 'C' and resid 564 through 575 Processing helix chain 'C' and resid 617 through 626 removed outlier: 3.933A pdb=" N VAL C 621 " --> pdb=" O SER C 617 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG C 623 " --> pdb=" O ASP C 619 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA C 624 " --> pdb=" O GLU C 620 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TRP C 625 " --> pdb=" O VAL C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 796 No H-bonds generated for 'chain 'C' and resid 794 through 796' Processing helix chain 'C' and resid 800 through 806 Processing helix chain 'C' and resid 828 through 833 Processing helix chain 'C' and resid 834 through 837 removed outlier: 3.814A pdb=" N ALA C 837 " --> pdb=" O PRO C 834 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 834 through 837' Processing helix chain 'C' and resid 853 through 861 removed outlier: 3.838A pdb=" N ARG C 859 " --> pdb=" O ASP C 855 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 860 " --> pdb=" O TYR C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 864 No H-bonds generated for 'chain 'C' and resid 862 through 864' Processing helix chain 'C' and resid 879 through 886 Processing helix chain 'C' and resid 887 through 891 Processing helix chain 'C' and resid 906 through 910 Processing helix chain 'C' and resid 911 through 923 Processing helix chain 'C' and resid 960 through 964 removed outlier: 3.813A pdb=" N ASN C 963 " --> pdb=" O TYR C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 979 removed outlier: 3.975A pdb=" N GLN C 977 " --> pdb=" O GLY C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 993 Processing helix chain 'C' and resid 994 through 999 Processing helix chain 'C' and resid 1004 through 1009 removed outlier: 3.602A pdb=" N VAL C1007 " --> pdb=" O ALA C1004 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP C1009 " --> pdb=" O SER C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1018 Processing helix chain 'C' and resid 1018 through 1030 removed outlier: 4.044A pdb=" N LEU C1022 " --> pdb=" O ASN C1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1044 removed outlier: 4.225A pdb=" N GLY C1044 " --> pdb=" O ILE C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1057 through 1061 Processing helix chain 'C' and resid 1075 through 1082 removed outlier: 4.009A pdb=" N GLY C1079 " --> pdb=" O LEU C1075 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C1080 " --> pdb=" O ALA C1076 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS C1081 " --> pdb=" O GLN C1077 " (cutoff:3.500A) Processing helix chain 'C' and resid 1083 through 1096 Processing helix chain 'D' and resid 48 through 77 removed outlier: 3.739A pdb=" N PHE D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 123 through 149 Processing helix chain 'D' and resid 162 through 186 removed outlier: 3.887A pdb=" N GLN D 166 " --> pdb=" O ASN D 162 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 194 removed outlier: 3.714A pdb=" N LEU D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 203 removed outlier: 3.643A pdb=" N PHE D 203 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 215 removed outlier: 3.722A pdb=" N SER D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 231 through 239 Processing helix chain 'D' and resid 244 through 275 Processing helix chain 'D' and resid 287 through 300 Processing helix chain 'D' and resid 311 through 341 removed outlier: 3.516A pdb=" N PHE D 320 " --> pdb=" O THR D 316 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA D 327 " --> pdb=" O LEU D 323 " (cutoff:3.500A) Proline residue: D 334 - end of helix Processing helix chain 'D' and resid 366 through 378 Processing helix chain 'D' and resid 398 through 408 Processing helix chain 'D' and resid 421 through 428 Processing helix chain 'D' and resid 429 through 433 Processing helix chain 'D' and resid 446 through 465 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 479 through 485 removed outlier: 3.980A pdb=" N LEU D 483 " --> pdb=" O ASN D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 514 removed outlier: 3.751A pdb=" N LEU D 513 " --> pdb=" O ALA D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 525 removed outlier: 3.830A pdb=" N PHE D 525 " --> pdb=" O MET D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 548 Processing helix chain 'D' and resid 557 through 561 Processing helix chain 'D' and resid 564 through 575 Processing helix chain 'D' and resid 617 through 626 removed outlier: 3.933A pdb=" N VAL D 621 " --> pdb=" O SER D 617 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG D 623 " --> pdb=" O ASP D 619 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA D 624 " --> pdb=" O GLU D 620 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TRP D 625 " --> pdb=" O VAL D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 796 No H-bonds generated for 'chain 'D' and resid 794 through 796' Processing helix chain 'D' and resid 800 through 806 Processing helix chain 'D' and resid 828 through 833 Processing helix chain 'D' and resid 834 through 837 removed outlier: 3.814A pdb=" N ALA D 837 " --> pdb=" O PRO D 834 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 834 through 837' Processing helix chain 'D' and resid 853 through 861 removed outlier: 3.837A pdb=" N ARG D 859 " --> pdb=" O ASP D 855 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 860 " --> pdb=" O TYR D 856 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 864 No H-bonds generated for 'chain 'D' and resid 862 through 864' Processing helix chain 'D' and resid 879 through 886 Processing helix chain 'D' and resid 887 through 891 Processing helix chain 'D' and resid 906 through 910 Processing helix chain 'D' and resid 911 through 923 Processing helix chain 'D' and resid 960 through 964 removed outlier: 3.813A pdb=" N ASN D 963 " --> pdb=" O TYR D 960 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 979 removed outlier: 3.975A pdb=" N GLN D 977 " --> pdb=" O GLY D 974 " (cutoff:3.500A) Processing helix chain 'D' and resid 990 through 993 Processing helix chain 'D' and resid 994 through 999 Processing helix chain 'D' and resid 1004 through 1009 removed outlier: 3.602A pdb=" N VAL D1007 " --> pdb=" O ALA D1004 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP D1009 " --> pdb=" O SER D1006 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1018 Processing helix chain 'D' and resid 1018 through 1030 removed outlier: 4.044A pdb=" N LEU D1022 " --> pdb=" O ASN D1018 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1044 removed outlier: 4.226A pdb=" N GLY D1044 " --> pdb=" O ILE D1040 " (cutoff:3.500A) Processing helix chain 'D' and resid 1057 through 1061 Processing helix chain 'D' and resid 1075 through 1082 removed outlier: 4.009A pdb=" N GLY D1079 " --> pdb=" O LEU D1075 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU D1080 " --> pdb=" O ALA D1076 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS D1081 " --> pdb=" O GLN D1077 " (cutoff:3.500A) Processing helix chain 'D' and resid 1083 through 1096 Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 156 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 416 removed outlier: 4.568A pdb=" N GLY A 363 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N HIS A 358 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N LEU A 437 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL A 360 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU A 439 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS A 362 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N CYS A 436 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLN A 473 " --> pdb=" O CYS A 436 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL A 438 " --> pdb=" O GLN A 473 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 550 through 555 removed outlier: 4.456A pdb=" N GLN A 610 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 582 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE A 614 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU A 580 " --> pdb=" O ILE A 614 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 780 through 781 removed outlier: 4.340A pdb=" N TYR A 780 " --> pdb=" O GLY A1050 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 799 removed outlier: 4.009A pdb=" N ASN A 874 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A 848 " --> pdb=" O SER A 871 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU A 873 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 850 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N CYS A 894 " --> pdb=" O ILE A 967 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLU A 969 " --> pdb=" O CYS A 894 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE A 896 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE A1003 " --> pdb=" O MET A 966 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR A 968 " --> pdb=" O PHE A1003 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1064 through 1069 removed outlier: 3.707A pdb=" N GLY A1101 " --> pdb=" O PHE A1137 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU A1139 " --> pdb=" O CYS A1099 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS A1099 " --> pdb=" O LEU A1139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 154 through 156 Processing sheet with id=AA8, first strand: chain 'B' and resid 412 through 416 removed outlier: 4.568A pdb=" N GLY B 363 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N HIS B 358 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N LEU B 437 " --> pdb=" O HIS B 358 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL B 360 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU B 439 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS B 362 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N CYS B 436 " --> pdb=" O ILE B 471 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLN B 473 " --> pdb=" O CYS B 436 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL B 438 " --> pdb=" O GLN B 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 550 through 555 removed outlier: 4.455A pdb=" N GLN B 610 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 582 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE B 614 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU B 580 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 780 through 781 removed outlier: 4.340A pdb=" N TYR B 780 " --> pdb=" O GLY B1050 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 798 through 799 removed outlier: 4.008A pdb=" N ASN B 874 " --> pdb=" O LEU B 799 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL B 848 " --> pdb=" O SER B 871 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU B 873 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE B 850 " --> pdb=" O LEU B 873 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS B 894 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLU B 969 " --> pdb=" O CYS B 894 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE B 896 " --> pdb=" O GLU B 969 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N PHE B1003 " --> pdb=" O MET B 966 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR B 968 " --> pdb=" O PHE B1003 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1064 through 1069 removed outlier: 3.707A pdb=" N GLY B1101 " --> pdb=" O PHE B1137 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B1139 " --> pdb=" O CYS B1099 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS B1099 " --> pdb=" O LEU B1139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB5, first strand: chain 'C' and resid 412 through 416 removed outlier: 4.569A pdb=" N GLY C 363 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N HIS C 358 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N LEU C 437 " --> pdb=" O HIS C 358 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL C 360 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU C 439 " --> pdb=" O VAL C 360 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS C 362 " --> pdb=" O LEU C 439 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N CYS C 436 " --> pdb=" O ILE C 471 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLN C 473 " --> pdb=" O CYS C 436 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL C 438 " --> pdb=" O GLN C 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 550 through 555 removed outlier: 4.456A pdb=" N GLN C 610 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA C 582 " --> pdb=" O PHE C 612 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE C 614 " --> pdb=" O LEU C 580 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU C 580 " --> pdb=" O ILE C 614 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 780 through 781 removed outlier: 4.339A pdb=" N TYR C 780 " --> pdb=" O GLY C1050 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 798 through 799 removed outlier: 4.008A pdb=" N ASN C 874 " --> pdb=" O LEU C 799 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL C 848 " --> pdb=" O SER C 871 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU C 873 " --> pdb=" O VAL C 848 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 850 " --> pdb=" O LEU C 873 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS C 894 " --> pdb=" O ILE C 967 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLU C 969 " --> pdb=" O CYS C 894 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE C 896 " --> pdb=" O GLU C 969 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N PHE C1003 " --> pdb=" O MET C 966 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR C 968 " --> pdb=" O PHE C1003 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1064 through 1069 removed outlier: 3.707A pdb=" N GLY C1101 " --> pdb=" O PHE C1137 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU C1139 " --> pdb=" O CYS C1099 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS C1099 " --> pdb=" O LEU C1139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 154 through 156 Processing sheet with id=AC2, first strand: chain 'D' and resid 412 through 416 removed outlier: 4.568A pdb=" N GLY D 363 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N HIS D 358 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N LEU D 437 " --> pdb=" O HIS D 358 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL D 360 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU D 439 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS D 362 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N CYS D 436 " --> pdb=" O ILE D 471 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLN D 473 " --> pdb=" O CYS D 436 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL D 438 " --> pdb=" O GLN D 473 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 550 through 555 removed outlier: 4.457A pdb=" N GLN D 610 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D 582 " --> pdb=" O PHE D 612 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE D 614 " --> pdb=" O LEU D 580 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU D 580 " --> pdb=" O ILE D 614 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 780 through 781 removed outlier: 4.340A pdb=" N TYR D 780 " --> pdb=" O GLY D1050 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 798 through 799 removed outlier: 4.009A pdb=" N ASN D 874 " --> pdb=" O LEU D 799 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL D 848 " --> pdb=" O SER D 871 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU D 873 " --> pdb=" O VAL D 848 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE D 850 " --> pdb=" O LEU D 873 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N CYS D 894 " --> pdb=" O ILE D 967 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLU D 969 " --> pdb=" O CYS D 894 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ILE D 896 " --> pdb=" O GLU D 969 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N PHE D1003 " --> pdb=" O MET D 966 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR D 968 " --> pdb=" O PHE D1003 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1064 through 1069 removed outlier: 3.706A pdb=" N GLY D1101 " --> pdb=" O PHE D1137 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU D1139 " --> pdb=" O CYS D1099 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS D1099 " --> pdb=" O LEU D1139 " (cutoff:3.500A) 1408 hydrogen bonds defined for protein. 3876 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.57 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4576 1.31 - 1.43: 7861 1.43 - 1.56: 16631 1.56 - 1.69: 40 1.69 - 1.81: 296 Bond restraints: 29404 Sorted by residual: bond pdb=" C11 6PL C1206 " pdb=" O3 6PL C1206 " ideal model delta sigma weight residual 1.327 1.444 -0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" C11 6PL B1206 " pdb=" O3 6PL B1206 " ideal model delta sigma weight residual 1.327 1.443 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C11 6PL D1206 " pdb=" O3 6PL D1206 " ideal model delta sigma weight residual 1.327 1.443 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C11 6PL A1206 " pdb=" O3 6PL A1206 " ideal model delta sigma weight residual 1.327 1.443 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C11 6PL B1205 " pdb=" O3 6PL B1205 " ideal model delta sigma weight residual 1.327 1.443 -0.116 2.00e-02 2.50e+03 3.38e+01 ... (remaining 29399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 39376 3.18 - 6.36: 384 6.36 - 9.53: 40 9.53 - 12.71: 16 12.71 - 15.89: 16 Bond angle restraints: 39832 Sorted by residual: angle pdb=" O3P 6PL D1207 " pdb=" P 6PL D1207 " pdb=" O4P 6PL D1207 " ideal model delta sigma weight residual 93.65 109.54 -15.89 3.00e+00 1.11e-01 2.80e+01 angle pdb=" O3P 6PL C1207 " pdb=" P 6PL C1207 " pdb=" O4P 6PL C1207 " ideal model delta sigma weight residual 93.65 109.54 -15.89 3.00e+00 1.11e-01 2.80e+01 angle pdb=" O3P 6PL B1207 " pdb=" P 6PL B1207 " pdb=" O4P 6PL B1207 " ideal model delta sigma weight residual 93.65 109.51 -15.86 3.00e+00 1.11e-01 2.79e+01 angle pdb=" O3P 6PL A1207 " pdb=" P 6PL A1207 " pdb=" O4P 6PL A1207 " ideal model delta sigma weight residual 93.65 109.49 -15.84 3.00e+00 1.11e-01 2.79e+01 angle pdb=" O3P 6PL C1205 " pdb=" P 6PL C1205 " pdb=" O4P 6PL C1205 " ideal model delta sigma weight residual 93.65 109.43 -15.78 3.00e+00 1.11e-01 2.77e+01 ... (remaining 39827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 15354 17.54 - 35.07: 1681 35.07 - 52.61: 609 52.61 - 70.15: 100 70.15 - 87.69: 20 Dihedral angle restraints: 17764 sinusoidal: 7424 harmonic: 10340 Sorted by residual: dihedral pdb=" CG ARG B 623 " pdb=" CD ARG B 623 " pdb=" NE ARG B 623 " pdb=" CZ ARG B 623 " ideal model delta sinusoidal sigma weight residual 90.00 133.90 -43.90 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG A 623 " pdb=" CD ARG A 623 " pdb=" NE ARG A 623 " pdb=" CZ ARG A 623 " ideal model delta sinusoidal sigma weight residual 90.00 133.90 -43.90 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG C 623 " pdb=" CD ARG C 623 " pdb=" NE ARG C 623 " pdb=" CZ ARG C 623 " ideal model delta sinusoidal sigma weight residual 90.00 133.89 -43.89 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 17761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4083 0.066 - 0.132: 408 0.132 - 0.198: 4 0.198 - 0.264: 21 0.264 - 0.329: 4 Chirality restraints: 4520 Sorted by residual: chirality pdb=" C14 CLR A1208 " pdb=" C13 CLR A1208 " pdb=" C15 CLR A1208 " pdb=" C8 CLR A1208 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C14 CLR B1208 " pdb=" C13 CLR B1208 " pdb=" C15 CLR B1208 " pdb=" C8 CLR B1208 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C14 CLR D1208 " pdb=" C13 CLR D1208 " pdb=" C15 CLR D1208 " pdb=" C8 CLR D1208 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 4517 not shown) Planarity restraints: 4932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 206 " 0.024 5.00e-02 4.00e+02 3.52e-02 1.99e+00 pdb=" N PRO B 207 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 206 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO D 207 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 207 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 207 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 206 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO C 207 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 207 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 207 " 0.020 5.00e-02 4.00e+02 ... (remaining 4929 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.75: 3115 2.75 - 3.35: 32285 3.35 - 3.94: 55302 3.94 - 4.54: 78175 4.54 - 5.14: 114165 Nonbonded interactions: 283042 Sorted by model distance: nonbonded pdb=" OH TYR A 304 " pdb=" OG1 THR C 298 " model vdw 2.151 3.040 nonbonded pdb=" O ALA D 526 " pdb="MG MG D1203 " model vdw 2.280 2.170 nonbonded pdb=" O ALA A 526 " pdb="MG MG A1203 " model vdw 2.281 2.170 nonbonded pdb=" O ALA B 526 " pdb="MG MG B1203 " model vdw 2.281 2.170 nonbonded pdb=" O ALA C 526 " pdb="MG MG C1203 " model vdw 2.281 2.170 ... (remaining 283037 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 44 through 1208) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.25 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: 8.380 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: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 29.550 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 29404 Z= 0.265 Angle : 0.730 15.888 39832 Z= 0.287 Chirality : 0.042 0.329 4520 Planarity : 0.003 0.035 4932 Dihedral : 16.772 87.686 11068 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.94 % Allowed : 19.93 % Favored : 78.13 % 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 are not related in a simple way. whole: 1.17 (0.14), residues: 3492 helix: 0.81 (0.12), residues: 1716 sheet: 1.22 (0.26), residues: 420 loop : 0.85 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 382 TYR 0.006 0.001 TYR C 346 PHE 0.011 0.001 PHE D 525 TRP 0.005 0.001 TRP B 861 HIS 0.003 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00533 (29404) covalent geometry : angle 0.73011 (39832) hydrogen bonds : bond 0.24823 ( 1408) hydrogen bonds : angle 6.54114 ( 3876) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 254 time to evaluate : 1.163 Fit side-chains REVERT: B 388 GLU cc_start: 0.8022 (pt0) cc_final: 0.7819 (pt0) outliers start: 60 outliers final: 32 residues processed: 290 average time/residue: 0.6257 time to fit residues: 214.8848 Evaluate side-chains 267 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 1036 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN B 802 ASN C 122 GLN D 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.114571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.077904 restraints weight = 41617.337| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.54 r_work: 0.2836 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29404 Z= 0.127 Angle : 0.479 5.949 39832 Z= 0.258 Chirality : 0.040 0.132 4520 Planarity : 0.004 0.040 4932 Dihedral : 9.284 67.506 4600 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.04 % Allowed : 17.99 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.14), residues: 3492 helix: 1.28 (0.12), residues: 1744 sheet: 1.07 (0.26), residues: 420 loop : 0.91 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 407 TYR 0.014 0.001 TYR A1016 PHE 0.015 0.001 PHE C 321 TRP 0.007 0.001 TRP A 289 HIS 0.002 0.001 HIS C 478 Details of bonding type rmsd covalent geometry : bond 0.00257 (29404) covalent geometry : angle 0.47893 (39832) hydrogen bonds : bond 0.05936 ( 1408) hydrogen bonds : angle 4.82053 ( 3876) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 273 time to evaluate : 1.156 Fit side-chains REVERT: C 468 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8818 (mm) REVERT: D 1140 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8795 (mtm) outliers start: 94 outliers final: 37 residues processed: 338 average time/residue: 0.6385 time to fit residues: 255.1850 Evaluate side-chains 279 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 240 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 967 ILE Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 973 ASP Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 833 MET Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 833 MET Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 973 ASP Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1140 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 132 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 301 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 231 optimal weight: 7.9990 chunk 179 optimal weight: 20.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN C 122 GLN D 122 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.110902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.073949 restraints weight = 41704.665| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.52 r_work: 0.2754 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 29404 Z= 0.201 Angle : 0.511 5.388 39832 Z= 0.269 Chirality : 0.043 0.153 4520 Planarity : 0.004 0.040 4932 Dihedral : 8.896 59.998 4572 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.75 % Allowed : 17.38 % Favored : 79.88 % 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 are not related in a simple way. whole: 1.42 (0.14), residues: 3492 helix: 1.26 (0.12), residues: 1744 sheet: 0.84 (0.26), residues: 420 loop : 0.77 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1026 TYR 0.017 0.001 TYR C1016 PHE 0.020 0.002 PHE A 525 TRP 0.010 0.001 TRP B 289 HIS 0.004 0.001 HIS C 478 Details of bonding type rmsd covalent geometry : bond 0.00477 (29404) covalent geometry : angle 0.51068 (39832) hydrogen bonds : bond 0.05659 ( 1408) hydrogen bonds : angle 4.58945 ( 3876) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 252 time to evaluate : 1.098 Fit side-chains REVERT: A 122 GLN cc_start: 0.8211 (mt0) cc_final: 0.7996 (mt0) REVERT: A 1140 MET cc_start: 0.9023 (mtp) cc_final: 0.8804 (mtm) REVERT: B 147 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7937 (t0) REVERT: B 867 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8856 (mm) REVERT: C 468 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8938 (mm) REVERT: D 551 MET cc_start: 0.9092 (ttp) cc_final: 0.8857 (tmm) REVERT: D 867 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8872 (mm) outliers start: 85 outliers final: 45 residues processed: 307 average time/residue: 0.6571 time to fit residues: 237.6542 Evaluate side-chains 290 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 122 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 334 optimal weight: 4.9990 chunk 339 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN C 122 GLN D 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.110513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.073765 restraints weight = 41590.743| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.50 r_work: 0.2750 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29404 Z= 0.182 Angle : 0.486 6.265 39832 Z= 0.258 Chirality : 0.042 0.136 4520 Planarity : 0.004 0.038 4932 Dihedral : 8.530 59.883 4572 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.75 % Allowed : 15.83 % Favored : 80.43 % 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 are not related in a simple way. whole: 1.37 (0.14), residues: 3492 helix: 1.27 (0.12), residues: 1748 sheet: 0.60 (0.25), residues: 420 loop : 0.76 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 829 TYR 0.016 0.001 TYR A1016 PHE 0.020 0.001 PHE D 525 TRP 0.010 0.001 TRP B 289 HIS 0.004 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00423 (29404) covalent geometry : angle 0.48576 (39832) hydrogen bonds : bond 0.05147 ( 1408) hydrogen bonds : angle 4.46052 ( 3876) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 248 time to evaluate : 1.084 Fit side-chains REVERT: A 122 GLN cc_start: 0.8234 (mt0) cc_final: 0.8018 (mt0) REVERT: A 147 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.7873 (t0) REVERT: B 122 GLN cc_start: 0.8222 (mt0) cc_final: 0.7999 (mt0) REVERT: B 147 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7937 (t0) REVERT: B 867 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8885 (mm) REVERT: C 122 GLN cc_start: 0.8180 (mt0) cc_final: 0.7964 (mt0) REVERT: D 147 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7956 (t0) REVERT: D 867 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8919 (mm) outliers start: 116 outliers final: 59 residues processed: 327 average time/residue: 0.6402 time to fit residues: 248.1111 Evaluate side-chains 302 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 238 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 153 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 267 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 303 optimal weight: 3.9990 chunk 348 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.075582 restraints weight = 41504.925| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.52 r_work: 0.2788 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29404 Z= 0.115 Angle : 0.442 7.289 39832 Z= 0.234 Chirality : 0.040 0.133 4520 Planarity : 0.003 0.038 4932 Dihedral : 8.088 59.039 4572 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.10 % Allowed : 16.86 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.14), residues: 3492 helix: 1.40 (0.13), residues: 1752 sheet: 0.61 (0.26), residues: 420 loop : 0.80 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 801 TYR 0.012 0.001 TYR A1016 PHE 0.015 0.001 PHE D 321 TRP 0.010 0.001 TRP D 289 HIS 0.003 0.001 HIS C 478 Details of bonding type rmsd covalent geometry : bond 0.00253 (29404) covalent geometry : angle 0.44210 (39832) hydrogen bonds : bond 0.04349 ( 1408) hydrogen bonds : angle 4.26285 ( 3876) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 260 time to evaluate : 1.122 Fit side-chains REVERT: A 122 GLN cc_start: 0.8197 (mt0) cc_final: 0.7940 (mt0) REVERT: A 801 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7945 (mtt90) REVERT: B 122 GLN cc_start: 0.8193 (mt0) cc_final: 0.7955 (mt0) REVERT: B 209 PHE cc_start: 0.7947 (m-10) cc_final: 0.7733 (m-10) REVERT: C 122 GLN cc_start: 0.8209 (mt0) cc_final: 0.7991 (mt0) REVERT: C 147 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7883 (t0) REVERT: C 209 PHE cc_start: 0.7906 (m-10) cc_final: 0.7678 (m-10) REVERT: D 147 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7920 (t0) REVERT: D 209 PHE cc_start: 0.7886 (m-10) cc_final: 0.7613 (m-10) REVERT: D 801 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7706 (mtt90) REVERT: D 867 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8817 (mm) outliers start: 96 outliers final: 56 residues processed: 328 average time/residue: 0.6620 time to fit residues: 256.1075 Evaluate side-chains 305 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 244 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 801 ARG Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 184 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 348 optimal weight: 0.1980 chunk 263 optimal weight: 2.9990 chunk 262 optimal weight: 7.9990 chunk 126 optimal weight: 0.5980 chunk 259 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 chunk 201 optimal weight: 0.8980 chunk 276 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.076785 restraints weight = 41502.406| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.50 r_work: 0.2811 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29404 Z= 0.101 Angle : 0.430 6.832 39832 Z= 0.226 Chirality : 0.039 0.133 4520 Planarity : 0.003 0.037 4932 Dihedral : 7.679 58.641 4572 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.10 % Allowed : 16.93 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.14), residues: 3492 helix: 1.54 (0.13), residues: 1748 sheet: 0.59 (0.26), residues: 420 loop : 0.85 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 222 TYR 0.010 0.001 TYR A1016 PHE 0.014 0.001 PHE A 321 TRP 0.008 0.001 TRP D 289 HIS 0.002 0.000 HIS C 478 Details of bonding type rmsd covalent geometry : bond 0.00217 (29404) covalent geometry : angle 0.43007 (39832) hydrogen bonds : bond 0.03975 ( 1408) hydrogen bonds : angle 4.14006 ( 3876) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 264 time to evaluate : 1.102 Fit side-chains REVERT: B 108 MET cc_start: 0.1986 (mmm) cc_final: 0.1755 (mmm) REVERT: B 209 PHE cc_start: 0.7922 (m-10) cc_final: 0.7714 (m-10) REVERT: B 801 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.8026 (mtt90) REVERT: C 209 PHE cc_start: 0.7852 (m-10) cc_final: 0.7623 (m-10) REVERT: D 209 PHE cc_start: 0.7837 (m-10) cc_final: 0.7602 (m-10) REVERT: D 801 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7760 (mtt90) outliers start: 96 outliers final: 57 residues processed: 330 average time/residue: 0.6071 time to fit residues: 238.6830 Evaluate side-chains 301 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 242 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 801 ARG Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 801 ARG Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 302 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 254 optimal weight: 0.9980 chunk 268 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 295 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 288 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN C 122 GLN D 122 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.111957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.075415 restraints weight = 41525.131| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.51 r_work: 0.2783 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 29404 Z= 0.131 Angle : 0.453 7.664 39832 Z= 0.237 Chirality : 0.040 0.134 4520 Planarity : 0.003 0.038 4932 Dihedral : 7.591 59.854 4572 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.94 % Allowed : 17.15 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.14), residues: 3492 helix: 1.51 (0.13), residues: 1752 sheet: 0.57 (0.26), residues: 420 loop : 0.82 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 801 TYR 0.014 0.001 TYR A1016 PHE 0.018 0.001 PHE D 525 TRP 0.007 0.001 TRP D 289 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00299 (29404) covalent geometry : angle 0.45314 (39832) hydrogen bonds : bond 0.04318 ( 1408) hydrogen bonds : angle 4.20438 ( 3876) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 248 time to evaluate : 1.354 Fit side-chains REVERT: A 147 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.7860 (t0) REVERT: A 536 MET cc_start: 0.6362 (ptt) cc_final: 0.6147 (ptp) REVERT: A 801 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.8008 (mtt90) REVERT: A 1036 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: B 108 MET cc_start: 0.2032 (mmm) cc_final: 0.1829 (mmm) REVERT: C 122 GLN cc_start: 0.8354 (mt0) cc_final: 0.8151 (mt0) REVERT: C 147 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7906 (t0) REVERT: C 209 PHE cc_start: 0.7901 (m-10) cc_final: 0.7659 (m-10) REVERT: D 147 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7900 (t0) REVERT: D 801 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7746 (mtt90) REVERT: D 1036 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8122 (mp0) outliers start: 91 outliers final: 56 residues processed: 310 average time/residue: 0.6371 time to fit residues: 234.1226 Evaluate side-chains 308 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 245 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 801 ARG Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 801 ARG Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 120 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 270 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN D 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.111985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.075638 restraints weight = 41602.788| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.50 r_work: 0.2787 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 29404 Z= 0.125 Angle : 0.449 6.994 39832 Z= 0.235 Chirality : 0.040 0.133 4520 Planarity : 0.003 0.037 4932 Dihedral : 7.449 58.362 4572 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.68 % Allowed : 17.31 % Favored : 80.01 % 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 are not related in a simple way. whole: 1.58 (0.14), residues: 3492 helix: 1.50 (0.13), residues: 1752 sheet: 0.55 (0.26), residues: 420 loop : 0.81 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 801 TYR 0.013 0.001 TYR A1016 PHE 0.017 0.001 PHE C 525 TRP 0.008 0.001 TRP D 289 HIS 0.003 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00284 (29404) covalent geometry : angle 0.44889 (39832) hydrogen bonds : bond 0.04226 ( 1408) hydrogen bonds : angle 4.18345 ( 3876) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 251 time to evaluate : 1.275 Fit side-chains REVERT: A 147 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.7864 (t0) REVERT: A 1036 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: B 108 MET cc_start: 0.1951 (mmm) cc_final: 0.1712 (mmm) REVERT: B 147 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.7973 (t0) REVERT: B 801 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.8067 (mtt90) REVERT: B 986 ASP cc_start: 0.8487 (t70) cc_final: 0.8232 (t0) REVERT: B 1036 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: C 122 GLN cc_start: 0.8416 (mt0) cc_final: 0.8173 (mt0) REVERT: C 147 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7904 (t0) REVERT: C 209 PHE cc_start: 0.7872 (m-10) cc_final: 0.7664 (m-10) REVERT: C 1036 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: D 147 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7888 (t0) REVERT: D 801 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7827 (mtt90) REVERT: D 867 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8813 (mm) REVERT: D 1036 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8132 (mp0) outliers start: 83 outliers final: 53 residues processed: 304 average time/residue: 0.6502 time to fit residues: 233.5001 Evaluate side-chains 312 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 248 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 801 ARG Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 801 ARG Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 201 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 286 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 315 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 158 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN D 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.112753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.076407 restraints weight = 41489.084| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.50 r_work: 0.2802 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 29404 Z= 0.109 Angle : 0.441 8.801 39832 Z= 0.230 Chirality : 0.040 0.133 4520 Planarity : 0.003 0.039 4932 Dihedral : 7.295 57.089 4572 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.33 % Allowed : 17.70 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.14), residues: 3492 helix: 1.55 (0.13), residues: 1748 sheet: 0.54 (0.26), residues: 420 loop : 0.84 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 801 TYR 0.011 0.001 TYR A1016 PHE 0.018 0.001 PHE C 525 TRP 0.008 0.001 TRP D 289 HIS 0.002 0.001 HIS D 478 Details of bonding type rmsd covalent geometry : bond 0.00241 (29404) covalent geometry : angle 0.44099 (39832) hydrogen bonds : bond 0.04004 ( 1408) hydrogen bonds : angle 4.12769 ( 3876) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 256 time to evaluate : 0.902 Fit side-chains REVERT: A 147 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7864 (t0) REVERT: A 986 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8265 (t0) REVERT: A 1036 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: B 108 MET cc_start: 0.1955 (mmm) cc_final: 0.1730 (mmm) REVERT: B 986 ASP cc_start: 0.8510 (t70) cc_final: 0.8244 (t0) REVERT: B 1036 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: B 1039 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.8000 (mt) REVERT: C 147 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7903 (t0) REVERT: C 209 PHE cc_start: 0.7862 (m-10) cc_final: 0.7642 (m-10) REVERT: C 1036 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: D 122 GLN cc_start: 0.8155 (mt0) cc_final: 0.7932 (mt0) REVERT: D 147 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7886 (t0) REVERT: D 531 LYS cc_start: 0.8184 (ptpp) cc_final: 0.7925 (pptt) REVERT: D 801 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7853 (mtt90) REVERT: D 1036 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8129 (mp0) outliers start: 72 outliers final: 52 residues processed: 306 average time/residue: 0.6555 time to fit residues: 235.6105 Evaluate side-chains 310 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 248 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 801 ARG Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 196 optimal weight: 0.0670 chunk 40 optimal weight: 1.9990 chunk 221 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN C 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.077118 restraints weight = 41310.433| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.51 r_work: 0.2817 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29404 Z= 0.099 Angle : 0.443 8.103 39832 Z= 0.231 Chirality : 0.039 0.131 4520 Planarity : 0.003 0.037 4932 Dihedral : 7.172 56.678 4572 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.07 % Allowed : 18.06 % Favored : 79.88 % 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 are not related in a simple way. whole: 1.68 (0.14), residues: 3492 helix: 1.59 (0.13), residues: 1752 sheet: 0.55 (0.26), residues: 420 loop : 0.87 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 801 TYR 0.010 0.001 TYR A1016 PHE 0.018 0.001 PHE C 525 TRP 0.008 0.001 TRP B 289 HIS 0.002 0.000 HIS C 478 Details of bonding type rmsd covalent geometry : bond 0.00215 (29404) covalent geometry : angle 0.44324 (39832) hydrogen bonds : bond 0.03796 ( 1408) hydrogen bonds : angle 4.06127 ( 3876) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 256 time to evaluate : 1.126 Fit side-chains REVERT: A 147 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7853 (t0) REVERT: A 986 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8262 (t0) REVERT: A 1036 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: B 108 MET cc_start: 0.1926 (mmm) cc_final: 0.1709 (mmm) REVERT: B 147 ASP cc_start: 0.8311 (t70) cc_final: 0.8019 (t0) REVERT: B 986 ASP cc_start: 0.8451 (t70) cc_final: 0.8188 (t0) REVERT: B 1036 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: C 122 GLN cc_start: 0.8380 (mt0) cc_final: 0.8170 (mt0) REVERT: C 147 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7936 (t0) REVERT: C 209 PHE cc_start: 0.7845 (m-10) cc_final: 0.7571 (m-10) REVERT: C 1036 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: D 122 GLN cc_start: 0.8151 (mt0) cc_final: 0.7937 (mt0) REVERT: D 147 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7850 (t0) REVERT: D 155 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6648 (ptm-80) REVERT: D 531 LYS cc_start: 0.8173 (ptpp) cc_final: 0.7919 (pptt) REVERT: D 801 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7839 (mtt90) REVERT: D 986 ASP cc_start: 0.8471 (t70) cc_final: 0.8179 (t0) REVERT: D 1036 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: D 1039 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7994 (mt) outliers start: 64 outliers final: 47 residues processed: 301 average time/residue: 0.6425 time to fit residues: 228.1962 Evaluate side-chains 305 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 247 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 1012 MET Chi-restraints excluded: chain B residue 1036 GLU Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 413 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1036 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 801 ARG Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1037 LEU Chi-restraints excluded: chain D residue 1039 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 5 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 333 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 317 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 192 optimal weight: 0.0170 chunk 89 optimal weight: 4.9990 overall best weight: 1.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.110555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.073928 restraints weight = 41690.134| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.51 r_work: 0.2754 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29404 Z= 0.187 Angle : 0.505 7.976 39832 Z= 0.263 Chirality : 0.042 0.136 4520 Planarity : 0.004 0.037 4932 Dihedral : 7.395 59.300 4572 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.13 % Allowed : 17.99 % Favored : 79.88 % 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 are not related in a simple way. whole: 1.50 (0.14), residues: 3492 helix: 1.41 (0.13), residues: 1752 sheet: 0.54 (0.25), residues: 420 loop : 0.79 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 801 TYR 0.018 0.001 TYR A1016 PHE 0.025 0.002 PHE A 525 TRP 0.009 0.001 TRP A 159 HIS 0.004 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00442 (29404) covalent geometry : angle 0.50454 (39832) hydrogen bonds : bond 0.04810 ( 1408) hydrogen bonds : angle 4.30911 ( 3876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14480.84 seconds wall clock time: 245 minutes 53.16 seconds (14753.16 seconds total)