Starting phenix.real_space_refine on Wed Jun 25 20:35:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pxh_13703/06_2025/7pxh_13703.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pxh_13703/06_2025/7pxh_13703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pxh_13703/06_2025/7pxh_13703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pxh_13703/06_2025/7pxh_13703.map" model { file = "/net/cci-nas-00/data/ceres_data/7pxh_13703/06_2025/7pxh_13703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pxh_13703/06_2025/7pxh_13703.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 8 9.91 5 K 6 8.98 5 P 16 5.49 5 Mg 4 5.21 5 S 192 5.16 5 C 18824 2.51 5 N 4610 2.21 5 O 5262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28922 Number of models: 1 Model: "" Number of chains: 8 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: "B" 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: "C" 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: "D" 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: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 191 Unusual residues: {' K': 5, ' CA': 2, ' MG': 1, '6PL': 4, 'CLR': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 51 Chain: "B" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 266 Unusual residues: {' CA': 2, ' MG': 1, '6PL': 4, '8I2': 1, 'CLR': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 51 Chain: "C" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 187 Unusual residues: {' K': 1, ' CA': 2, ' MG': 1, '6PL': 4, 'CLR': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 51 Chain: "D" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 186 Unusual residues: {' CA': 2, ' MG': 1, '6PL': 4, 'CLR': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 51 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" K K A1209 " occ=0.50 residue: pdb=" K K A1210 " occ=0.50 residue: pdb=" K K A1211 " occ=0.50 residue: pdb=" K K A1212 " occ=0.50 residue: pdb=" K K A1213 " occ=0.25 residue: pdb=" K K C1209 " occ=0.25 Time building chain proxies: 17.72, per 1000 atoms: 0.61 Number of scatterers: 28922 At special positions: 0 Unit cell: (165.9, 165.9, 128.8, 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 6 19.00 S 192 16.00 P 16 15.00 Mg 4 11.99 O 5262 8.00 N 4610 7.00 C 18824 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.94 Conformation dependent library (CDL) restraints added in 3.8 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: 182 helices and 24 sheets defined 56.1% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 48 through 77 removed outlier: 3.859A pdb=" N PHE A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.867A pdb=" N ASP A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 149 removed outlier: 3.762A pdb=" N ILE A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 186 removed outlier: 4.012A pdb=" N GLN A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 195 through 203 removed outlier: 3.699A pdb=" N PHE A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 215 removed outlier: 3.817A pdb=" N SER A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.641A pdb=" N ARG A 225 " --> pdb=" O ARG A 222 " (cutoff:3.500A) 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 331 removed outlier: 3.514A pdb=" N PHE A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 341 removed outlier: 3.775A pdb=" N ASP A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) 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 429 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: 3.888A pdb=" N LEU A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 514 removed outlier: 3.588A pdb=" N LEU A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 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 627 removed outlier: 3.628A pdb=" N VAL A 621 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A 623 " --> pdb=" O ASP A 619 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALA A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 4.293A 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 807 removed outlier: 3.567A pdb=" N THR A 807 " --> pdb=" O GLN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 834 through 837 removed outlier: 3.859A 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: 3.846A pdb=" N ARG A 859 " --> pdb=" O ASP A 855 " (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 removed outlier: 3.579A pdb=" N LEU A 883 " --> pdb=" O SER A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 911 through 924 Processing helix chain 'A' and resid 960 through 964 removed outlier: 3.518A pdb=" N ASN A 963 " --> pdb=" O TYR A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 979 removed outlier: 3.647A pdb=" N ASN A 975 " --> pdb=" O ASN A 972 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 976 " --> pdb=" O ASP A 973 " (cutoff:3.500A) removed outlier: 4.251A 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 1006 through 1009 removed outlier: 3.580A pdb=" N ASP A1009 " --> pdb=" O SER A1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1006 through 1009' Processing helix chain 'A' and resid 1010 through 1018 Processing helix chain 'A' and resid 1018 through 1030 removed outlier: 4.114A pdb=" N LEU A1022 " --> pdb=" O ASN A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1044 removed outlier: 3.667A pdb=" N GLU A1038 " --> pdb=" O THR A1034 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1061 Processing helix chain 'A' and resid 1076 through 1081 removed outlier: 4.095A pdb=" N GLU A1080 " --> pdb=" O ALA A1076 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N CYS A1081 " --> pdb=" O GLN A1077 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1076 through 1081' Processing helix chain 'A' and resid 1083 through 1096 Processing helix chain 'B' and resid 48 through 77 removed outlier: 3.859A pdb=" N PHE B 52 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.866A pdb=" N ASP B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 149 removed outlier: 3.761A pdb=" N ILE B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 186 removed outlier: 4.012A pdb=" N GLN B 166 " --> pdb=" O ASN B 162 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 195 Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.699A pdb=" N PHE B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 215 removed outlier: 3.817A pdb=" N SER B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 removed outlier: 3.641A pdb=" N ARG B 225 " --> pdb=" O ARG B 222 " (cutoff:3.500A) 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 331 removed outlier: 3.514A pdb=" N PHE B 320 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 341 removed outlier: 3.775A pdb=" N ASP B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) 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 429 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: 3.888A pdb=" N LEU B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 514 removed outlier: 3.586A pdb=" N LEU B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 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 627 removed outlier: 3.628A pdb=" N VAL B 621 " --> pdb=" O SER B 617 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG B 623 " --> pdb=" O ASP B 619 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALA B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 4.292A 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 807 removed outlier: 3.567A pdb=" N THR B 807 " --> pdb=" O GLN B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 833 Processing helix chain 'B' and resid 834 through 837 removed outlier: 3.860A 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: 3.846A pdb=" N ARG B 859 " --> pdb=" O ASP B 855 " (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 removed outlier: 3.580A pdb=" N LEU B 883 " --> pdb=" O SER B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 910 Processing helix chain 'B' and resid 911 through 924 Processing helix chain 'B' and resid 960 through 964 removed outlier: 3.518A pdb=" N ASN B 963 " --> pdb=" O TYR B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 979 removed outlier: 3.646A pdb=" N ASN B 975 " --> pdb=" O ASN B 972 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 976 " --> pdb=" O ASP B 973 " (cutoff:3.500A) removed outlier: 4.251A 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 1006 through 1009 removed outlier: 3.581A pdb=" N ASP B1009 " --> pdb=" O SER B1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1006 through 1009' Processing helix chain 'B' and resid 1010 through 1018 Processing helix chain 'B' and resid 1018 through 1030 removed outlier: 4.115A pdb=" N LEU B1022 " --> pdb=" O ASN B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1044 removed outlier: 3.667A pdb=" N GLU B1038 " --> pdb=" O THR B1034 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY B1044 " --> pdb=" O ILE B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1061 Processing helix chain 'B' and resid 1076 through 1081 removed outlier: 4.096A pdb=" N GLU B1080 " --> pdb=" O ALA B1076 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N CYS B1081 " --> pdb=" O GLN B1077 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1076 through 1081' Processing helix chain 'B' and resid 1083 through 1096 Processing helix chain 'C' and resid 48 through 77 removed outlier: 3.711A pdb=" N PHE C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 71 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.787A pdb=" N ASP C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 148 removed outlier: 3.775A pdb=" N ILE C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 186 removed outlier: 4.038A pdb=" N GLN C 166 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 194 removed outlier: 3.517A pdb=" N LEU C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 203 removed outlier: 3.583A pdb=" N ASP C 201 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 215 removed outlier: 3.715A pdb=" N TYR C 213 " --> pdb=" O PHE C 209 " (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: 3.551A pdb=" N LEU C 323 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 324 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 4.734A 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 removed outlier: 3.507A pdb=" N HIS C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 421 through 429 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: 3.843A pdb=" N LEU C 483 " --> pdb=" O ASN C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 514 removed outlier: 3.628A pdb=" N LEU C 513 " --> pdb=" O ALA C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 524 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 622 removed outlier: 3.602A pdb=" N VAL C 621 " --> pdb=" O SER C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 627 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 807 removed outlier: 3.576A pdb=" N THR C 807 " --> pdb=" O GLN C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 833 removed outlier: 3.686A pdb=" N VAL C 832 " --> pdb=" O LEU C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 837 removed outlier: 3.663A 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: 3.806A pdb=" N ARG C 859 " --> pdb=" O ASP C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 886 removed outlier: 3.525A pdb=" N LEU C 883 " --> pdb=" O SER C 879 " (cutoff:3.500A) 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 924 Processing helix chain 'C' and resid 960 through 964 Processing helix chain 'C' and resid 972 through 979 removed outlier: 3.613A pdb=" N ASN C 975 " --> pdb=" O ASN C 972 " (cutoff:3.500A) removed outlier: 3.957A 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 1006 through 1009 removed outlier: 3.698A pdb=" N ASP C1009 " --> pdb=" O SER C1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1006 through 1009' Processing helix chain 'C' and resid 1010 through 1018 Processing helix chain 'C' and resid 1018 through 1030 removed outlier: 4.095A pdb=" N LEU C1022 " --> pdb=" O ASN C1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1044 removed outlier: 3.742A pdb=" N GLU C1038 " --> pdb=" O THR C1034 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C1039 " --> pdb=" O PRO C1035 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY C1044 " --> pdb=" O ILE C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1053 through 1058 Processing helix chain 'C' and resid 1059 through 1061 No H-bonds generated for 'chain 'C' and resid 1059 through 1061' Processing helix chain 'C' and resid 1076 through 1081 removed outlier: 4.159A pdb=" N GLU C1080 " --> pdb=" O ALA C1076 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N CYS C1081 " --> pdb=" O GLN C1077 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1076 through 1081' Processing helix chain 'C' and resid 1083 through 1095 Processing helix chain 'D' and resid 48 through 77 removed outlier: 3.712A pdb=" N PHE D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG D 71 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.786A pdb=" N ASP D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 148 removed outlier: 3.776A pdb=" N ILE D 128 " --> pdb=" O THR D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 186 removed outlier: 4.039A pdb=" N GLN D 166 " --> pdb=" O ASN D 162 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 194 removed outlier: 3.517A pdb=" N LEU D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 203 removed outlier: 3.584A pdb=" N ASP D 201 " --> pdb=" O TYR D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 215 removed outlier: 3.716A pdb=" N TYR D 213 " --> pdb=" O PHE D 209 " (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: 3.552A pdb=" N LEU D 323 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 324 " --> pdb=" O PHE D 320 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 4.735A 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 removed outlier: 3.508A pdb=" N HIS D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 408 Processing helix chain 'D' and resid 421 through 429 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: 3.842A pdb=" N LEU D 483 " --> pdb=" O ASN D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 514 removed outlier: 3.628A pdb=" N LEU D 513 " --> pdb=" O ALA D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 524 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 622 removed outlier: 3.601A pdb=" N VAL D 621 " --> pdb=" O SER D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 627 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 807 removed outlier: 3.576A pdb=" N THR D 807 " --> pdb=" O GLN D 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 828 through 833 removed outlier: 3.687A pdb=" N VAL D 832 " --> pdb=" O LEU D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 837 removed outlier: 3.662A 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: 3.806A pdb=" N ARG D 859 " --> pdb=" O ASP D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 879 through 886 removed outlier: 3.525A pdb=" N LEU D 883 " --> pdb=" O SER D 879 " (cutoff:3.500A) 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 924 Processing helix chain 'D' and resid 960 through 964 Processing helix chain 'D' and resid 972 through 979 removed outlier: 3.612A pdb=" N ASN D 975 " --> pdb=" O ASN D 972 " (cutoff:3.500A) removed outlier: 3.957A 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 1006 through 1009 removed outlier: 3.697A pdb=" N ASP D1009 " --> pdb=" O SER D1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1006 through 1009' Processing helix chain 'D' and resid 1010 through 1018 Processing helix chain 'D' and resid 1018 through 1030 removed outlier: 4.095A pdb=" N LEU D1022 " --> pdb=" O ASN D1018 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1044 removed outlier: 3.742A pdb=" N GLU D1038 " --> pdb=" O THR D1034 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D1039 " --> pdb=" O PRO D1035 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY D1044 " --> pdb=" O ILE D1040 " (cutoff:3.500A) Processing helix chain 'D' and resid 1053 through 1058 Processing helix chain 'D' and resid 1059 through 1061 No H-bonds generated for 'chain 'D' and resid 1059 through 1061' Processing helix chain 'D' and resid 1076 through 1081 removed outlier: 4.158A pdb=" N GLU D1080 " --> pdb=" O ALA D1076 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N CYS D1081 " --> pdb=" O GLN D1077 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1076 through 1081' Processing helix chain 'D' and resid 1083 through 1095 Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 416 removed outlier: 8.572A pdb=" N GLU A 413 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL A 389 " --> pdb=" O GLU A 413 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE A 415 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE A 391 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ARG A 357 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL A 390 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 359 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU A 392 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL A 361 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N HIS A 358 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N LEU A 437 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 360 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 550 through 555 removed outlier: 4.479A pdb=" N GLN A 610 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 582 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE A 614 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.346A 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: 4.535A 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: 6.511A pdb=" N VAL A 848 " --> pdb=" O SER A 871 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU A 873 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE A 850 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL A 813 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL A 851 " --> pdb=" O VAL A 813 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 815 " --> pdb=" O VAL A 851 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS A 894 " --> pdb=" O ILE A 967 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLU A 969 " --> pdb=" O CYS A 894 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE A 896 " --> pdb=" O GLU A 969 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1064 through 1069 removed outlier: 6.572A pdb=" N GLN A1135 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A1102 " --> pdb=" O GLN A1135 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE A1137 " --> pdb=" O ILE A1100 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A1098 " --> pdb=" O LEU A1139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AA8, first strand: chain 'B' and resid 412 through 416 removed outlier: 8.571A pdb=" N GLU B 413 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 389 " --> pdb=" O GLU B 413 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE B 415 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE B 391 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG B 357 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL B 390 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE B 359 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU B 392 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 361 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N HIS B 358 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N LEU B 437 " --> pdb=" O HIS B 358 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 360 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 550 through 555 removed outlier: 4.479A pdb=" N GLN B 610 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B 582 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE B 614 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 6.345A 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: 4.534A 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: 6.511A pdb=" N VAL B 848 " --> pdb=" O SER B 871 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU B 873 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE B 850 " --> pdb=" O LEU B 873 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL B 813 " --> pdb=" O VAL B 849 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL B 851 " --> pdb=" O VAL B 813 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 815 " --> pdb=" O VAL B 851 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N CYS B 894 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLU B 969 " --> pdb=" O CYS B 894 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE B 896 " --> pdb=" O GLU B 969 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1064 through 1069 removed outlier: 6.571A pdb=" N GLN B1135 " --> pdb=" O LEU B1102 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B1102 " --> pdb=" O GLN B1135 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE B1137 " --> pdb=" O ILE B1100 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B1098 " --> pdb=" O LEU B1139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB5, first strand: chain 'C' and resid 412 through 416 removed outlier: 6.196A pdb=" N VAL C 389 " --> pdb=" O GLU C 413 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE C 415 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE C 391 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N HIS C 358 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N LEU C 437 " --> pdb=" O HIS C 358 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL C 360 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 550 through 555 removed outlier: 3.574A pdb=" N ALA C 615 " --> pdb=" O GLU C 550 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN C 610 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 582 " --> pdb=" O PHE C 612 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE C 614 " --> pdb=" O LEU C 580 " (cutoff:3.500A) removed outlier: 6.307A 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: 4.520A 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: 6.527A pdb=" N VAL C 848 " --> pdb=" O SER C 871 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU C 873 " --> pdb=" O VAL C 848 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE C 850 " --> pdb=" O LEU C 873 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL C 813 " --> pdb=" O VAL C 849 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL C 851 " --> pdb=" O VAL C 813 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 815 " --> pdb=" O VAL C 851 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N CYS C 894 " --> pdb=" O ILE C 967 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLU C 969 " --> pdb=" O CYS C 894 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE C 896 " --> pdb=" O GLU C 969 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1064 through 1069 removed outlier: 6.485A pdb=" N GLN C1135 " --> pdb=" O LEU C1102 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU C1102 " --> pdb=" O GLN C1135 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE C1137 " --> pdb=" O ILE C1100 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C1104 " --> pdb=" O TYR C1119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AC2, first strand: chain 'D' and resid 412 through 416 removed outlier: 6.196A pdb=" N VAL D 389 " --> pdb=" O GLU D 413 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N PHE D 415 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE D 391 " --> pdb=" O PHE D 415 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N HIS D 358 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N LEU D 437 " --> pdb=" O HIS D 358 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL D 360 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS D 436 " --> pdb=" O ILE D 471 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLN D 473 " --> pdb=" O CYS D 436 " (cutoff:3.500A) removed outlier: 7.379A 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: 3.574A pdb=" N ALA D 615 " --> pdb=" O GLU D 550 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN D 610 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA D 582 " --> pdb=" O PHE D 612 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE D 614 " --> pdb=" O LEU D 580 " (cutoff:3.500A) removed outlier: 6.307A 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: 4.520A 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: 6.527A pdb=" N VAL D 848 " --> pdb=" O SER D 871 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU D 873 " --> pdb=" O VAL D 848 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE D 850 " --> pdb=" O LEU D 873 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL D 813 " --> pdb=" O VAL D 849 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL D 851 " --> pdb=" O VAL D 813 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL D 815 " --> pdb=" O VAL D 851 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS D 894 " --> pdb=" O ILE D 967 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLU D 969 " --> pdb=" O CYS D 894 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE D 896 " --> pdb=" O GLU D 969 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1064 through 1069 removed outlier: 6.485A pdb=" N GLN D1135 " --> pdb=" O LEU D1102 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU D1102 " --> pdb=" O GLN D1135 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE D1137 " --> pdb=" O ILE D1100 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG D1104 " --> pdb=" O TYR D1119 " (cutoff:3.500A) 1330 hydrogen bonds defined for protein. 3702 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: 14.10 Time building geometry restraints manager: 8.80 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: 4588 1.31 - 1.43: 7716 1.43 - 1.56: 16868 1.56 - 1.68: 68 1.68 - 1.81: 296 Bond restraints: 29536 Sorted by residual: bond pdb=" C11 6PL B1207 " pdb=" O3 6PL B1207 " ideal model delta sigma weight residual 1.327 1.444 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" C11 6PL D1206 " pdb=" O3 6PL D1206 " ideal model delta sigma weight residual 1.327 1.444 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C11 6PL A1205 " pdb=" O3 6PL A1205 " ideal model delta sigma weight residual 1.327 1.444 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C11 6PL B1205 " pdb=" O3 6PL B1205 " ideal model delta sigma weight residual 1.327 1.444 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C11 6PL D1204 " pdb=" O3 6PL D1204 " ideal model delta sigma weight residual 1.327 1.444 -0.117 2.00e-02 2.50e+03 3.39e+01 ... (remaining 29531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 39470 3.22 - 6.44: 445 6.44 - 9.65: 53 9.65 - 12.87: 18 12.87 - 16.09: 16 Bond angle restraints: 40002 Sorted by residual: angle pdb=" O3P 6PL A1205 " pdb=" P 6PL A1205 " pdb=" O4P 6PL A1205 " ideal model delta sigma weight residual 93.65 109.74 -16.09 3.00e+00 1.11e-01 2.88e+01 angle pdb=" O3P 6PL B1205 " pdb=" P 6PL B1205 " pdb=" O4P 6PL B1205 " ideal model delta sigma weight residual 93.65 109.72 -16.07 3.00e+00 1.11e-01 2.87e+01 angle pdb=" O3P 6PL D1206 " pdb=" P 6PL D1206 " pdb=" O4P 6PL D1206 " ideal model delta sigma weight residual 93.65 109.50 -15.85 3.00e+00 1.11e-01 2.79e+01 angle pdb=" O3P 6PL A1206 " pdb=" P 6PL A1206 " pdb=" O4P 6PL A1206 " ideal model delta sigma weight residual 93.65 109.45 -15.80 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O3P 6PL C1206 " pdb=" P 6PL C1206 " pdb=" O4P 6PL C1206 " ideal model delta sigma weight residual 93.65 109.45 -15.80 3.00e+00 1.11e-01 2.77e+01 ... (remaining 39997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 16247 17.57 - 35.14: 1268 35.14 - 52.70: 295 52.70 - 70.27: 104 70.27 - 87.84: 22 Dihedral angle restraints: 17936 sinusoidal: 7596 harmonic: 10340 Sorted by residual: dihedral pdb=" CG ARG D1060 " pdb=" CD ARG D1060 " pdb=" NE ARG D1060 " pdb=" CZ ARG D1060 " ideal model delta sinusoidal sigma weight residual 180.00 -135.27 -44.73 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG C1060 " pdb=" CD ARG C1060 " pdb=" NE ARG C1060 " pdb=" CZ ARG C1060 " ideal model delta sinusoidal sigma weight residual 180.00 -135.28 -44.72 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA GLU A 969 " pdb=" C GLU A 969 " pdb=" N LEU A 970 " pdb=" CA LEU A 970 " ideal model delta harmonic sigma weight residual -180.00 -163.90 -16.10 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 17933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4103 0.066 - 0.131: 391 0.131 - 0.197: 9 0.197 - 0.262: 20 0.262 - 0.328: 5 Chirality restraints: 4528 Sorted by residual: 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 -2.65 0.33 2.00e-01 2.50e+01 2.69e+00 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 2.68e+00 chirality pdb=" C14 CLR C1208 " pdb=" C13 CLR C1208 " pdb=" C15 CLR C1208 " pdb=" C8 CLR C1208 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 4525 not shown) Planarity restraints: 4946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 206 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO B 207 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 206 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.35e+00 pdb=" N PRO A 207 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 276 " 0.046 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO D 277 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 277 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 277 " 0.039 5.00e-02 4.00e+02 ... (remaining 4943 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 504 2.69 - 3.30: 32083 3.30 - 3.92: 55222 3.92 - 4.53: 75823 4.53 - 5.14: 116275 Nonbonded interactions: 279907 Sorted by model distance: nonbonded pdb=" O ASN D 523 " pdb="MG MG D1203 " model vdw 2.079 2.170 nonbonded pdb=" O ASN C 523 " pdb="MG MG C1203 " model vdw 2.080 2.170 nonbonded pdb=" O MET C 549 " pdb="MG MG C1203 " model vdw 2.120 2.170 nonbonded pdb=" O MET D 549 " pdb="MG MG D1203 " model vdw 2.120 2.170 nonbonded pdb=" OH TYR A 477 " pdb=" OE1 GLU A1038 " model vdw 2.225 3.040 ... (remaining 279902 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 1145 or resid 1201 through 1208)) selection = (chain 'B' and (resid 44 through 1145 or resid 1201 through 1208)) selection = (chain 'C' and (resid 44 through 1145 or resid 1201 through 1208)) 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: 5.440 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: 1.550 Check model and map are aligned: 0.210 Set scattering table: 0.290 Process input model: 71.430 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 0.006 0.117 29538 Z= 0.281 Angle : 0.788 16.090 40002 Z= 0.314 Chirality : 0.042 0.328 4528 Planarity : 0.004 0.077 4946 Dihedral : 14.202 87.839 11240 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.45 % Allowed : 0.45 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 3492 helix: 0.54 (0.13), residues: 1656 sheet: 0.81 (0.25), residues: 476 loop : 0.49 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 539 HIS 0.005 0.000 HIS D 372 PHE 0.007 0.001 PHE C 174 TYR 0.014 0.001 TYR B 197 ARG 0.006 0.000 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.26964 ( 1330) hydrogen bonds : angle 7.02290 ( 3702) covalent geometry : bond 0.00560 (29536) covalent geometry : angle 0.78751 (40002) Misc. bond : bond 0.00029 ( 2) *********************** 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 439 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 425 time to evaluate : 3.164 Fit side-chains REVERT: A 255 SER cc_start: 0.9060 (m) cc_final: 0.8849 (m) REVERT: C 50 TRP cc_start: 0.8103 (p-90) cc_final: 0.7848 (p90) REVERT: D 571 LEU cc_start: 0.9206 (tt) cc_final: 0.8966 (tm) REVERT: D 1106 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7459 (ttp80) outliers start: 14 outliers final: 0 residues processed: 429 average time/residue: 1.2256 time to fit residues: 629.9879 Evaluate side-chains 321 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 179 optimal weight: 40.0000 chunk 142 optimal weight: 0.9980 chunk 275 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 167 optimal weight: 10.0000 chunk 205 optimal weight: 0.8980 chunk 319 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN C 445 GLN D 122 GLN D 445 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.080564 restraints weight = 38787.608| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.61 r_work: 0.2790 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29538 Z= 0.164 Angle : 0.544 7.439 40002 Z= 0.283 Chirality : 0.042 0.288 4528 Planarity : 0.004 0.068 4946 Dihedral : 10.635 77.299 4724 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.91 % Allowed : 8.49 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.14), residues: 3492 helix: 0.82 (0.12), residues: 1688 sheet: 0.74 (0.25), residues: 468 loop : 0.52 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 289 HIS 0.005 0.001 HIS C 372 PHE 0.032 0.002 PHE B 134 TYR 0.017 0.002 TYR D1016 ARG 0.002 0.000 ARG C 859 Details of bonding type rmsd hydrogen bonds : bond 0.05355 ( 1330) hydrogen bonds : angle 4.66862 ( 3702) covalent geometry : bond 0.00378 (29536) covalent geometry : angle 0.54426 (40002) Misc. bond : bond 0.00028 ( 2) *********************** 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 402 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 343 time to evaluate : 3.526 Fit side-chains REVERT: A 388 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: A 911 ASP cc_start: 0.8327 (m-30) cc_final: 0.7981 (m-30) REVERT: B 388 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: C 122 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: C 191 TRP cc_start: 0.8373 (m100) cc_final: 0.7921 (m-90) REVERT: C 331 SER cc_start: 0.8482 (m) cc_final: 0.8216 (p) REVERT: D 571 LEU cc_start: 0.9140 (tt) cc_final: 0.8882 (tm) REVERT: D 800 ASP cc_start: 0.8211 (m-30) cc_final: 0.7854 (m-30) REVERT: D 990 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8318 (mm-30) REVERT: D 1106 ARG cc_start: 0.8541 (ttp80) cc_final: 0.7992 (ttp80) outliers start: 59 outliers final: 34 residues processed: 369 average time/residue: 1.2120 time to fit residues: 538.8734 Evaluate side-chains 341 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 304 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 551 MET Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 551 MET Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 912 LYS Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 802 ASN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain C residue 1034 THR Chi-restraints excluded: chain D residue 114 TRP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 1034 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 223 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 243 optimal weight: 0.0970 chunk 113 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 102 optimal weight: 0.0170 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 347 optimal weight: 2.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 372 HIS C 445 GLN D 122 GLN D 372 HIS D 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.079507 restraints weight = 38781.881| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.60 r_work: 0.2770 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29538 Z= 0.125 Angle : 0.476 6.813 40002 Z= 0.244 Chirality : 0.040 0.297 4528 Planarity : 0.004 0.063 4946 Dihedral : 10.265 77.795 4724 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.78 % Allowed : 10.30 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.14), residues: 3492 helix: 1.11 (0.13), residues: 1692 sheet: 0.85 (0.26), residues: 420 loop : 0.59 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 114 HIS 0.006 0.001 HIS C 372 PHE 0.014 0.001 PHE A 525 TYR 0.016 0.001 TYR D 213 ARG 0.005 0.000 ARG C 829 Details of bonding type rmsd hydrogen bonds : bond 0.04836 ( 1330) hydrogen bonds : angle 4.29138 ( 3702) covalent geometry : bond 0.00282 (29536) covalent geometry : angle 0.47626 (40002) Misc. bond : bond 0.00021 ( 2) *********************** 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 372 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 317 time to evaluate : 3.482 Fit side-chains REVERT: A 368 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8326 (mp0) REVERT: B 285 ARG cc_start: 0.8638 (tpp-160) cc_final: 0.8422 (tpp-160) REVERT: B 368 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8440 (mp0) REVERT: B 388 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: C 191 TRP cc_start: 0.8310 (m100) cc_final: 0.7885 (m-90) REVERT: C 550 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.7962 (pt0) REVERT: D 113 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7262 (t70) REVERT: D 550 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.7951 (pt0) REVERT: D 571 LEU cc_start: 0.9119 (tt) cc_final: 0.8864 (tm) REVERT: D 800 ASP cc_start: 0.8201 (m-30) cc_final: 0.7834 (m-30) REVERT: D 990 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8365 (mm-30) REVERT: D 1055 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8255 (tm-30) REVERT: D 1106 ARG cc_start: 0.8610 (ttp80) cc_final: 0.7997 (ttp80) outliers start: 55 outliers final: 21 residues processed: 344 average time/residue: 1.3299 time to fit residues: 548.6507 Evaluate side-chains 328 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 303 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 802 ASN Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 1034 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 129 optimal weight: 3.9990 chunk 312 optimal weight: 3.9990 chunk 299 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 349 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 288 optimal weight: 0.6980 chunk 294 optimal weight: 0.8980 chunk 208 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS C 372 HIS C 445 GLN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 HIS D 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.079491 restraints weight = 38866.783| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.61 r_work: 0.2770 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 29538 Z= 0.113 Angle : 0.458 7.588 40002 Z= 0.234 Chirality : 0.040 0.285 4528 Planarity : 0.004 0.062 4946 Dihedral : 10.034 77.028 4724 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.16 % Allowed : 10.66 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.14), residues: 3492 helix: 1.23 (0.13), residues: 1688 sheet: 0.83 (0.26), residues: 420 loop : 0.62 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 114 HIS 0.006 0.001 HIS C 372 PHE 0.014 0.001 PHE A 525 TYR 0.011 0.001 TYR D1016 ARG 0.003 0.000 ARG D 829 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 1330) hydrogen bonds : angle 4.14098 ( 3702) covalent geometry : bond 0.00255 (29536) covalent geometry : angle 0.45839 (40002) Misc. bond : bond 0.00012 ( 2) *********************** 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 383 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 316 time to evaluate : 3.228 Fit side-chains REVERT: A 279 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8600 (t70) REVERT: A 368 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8372 (mp0) REVERT: A 911 ASP cc_start: 0.8327 (m-30) cc_final: 0.7981 (m-30) REVERT: B 147 ASP cc_start: 0.8344 (t0) cc_final: 0.8122 (t0) REVERT: B 285 ARG cc_start: 0.8620 (tpp-160) cc_final: 0.8384 (tpp-160) REVERT: B 368 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8430 (mp0) REVERT: C 113 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7228 (t70) REVERT: C 331 SER cc_start: 0.8448 (m) cc_final: 0.8043 (p) REVERT: C 550 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.7606 (pm20) REVERT: D 113 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7167 (t70) REVERT: D 550 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.7986 (pt0) REVERT: D 800 ASP cc_start: 0.8204 (m-30) cc_final: 0.7828 (m-30) REVERT: D 990 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8338 (mt-10) REVERT: D 1055 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8282 (tm-30) REVERT: D 1106 ARG cc_start: 0.8621 (ttp80) cc_final: 0.8000 (ttp80) outliers start: 67 outliers final: 26 residues processed: 351 average time/residue: 1.1784 time to fit residues: 499.7985 Evaluate side-chains 330 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 299 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 802 ASN Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 1034 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 186 optimal weight: 3.9990 chunk 348 optimal weight: 4.9990 chunk 350 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 339 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS B 166 GLN C 372 HIS C 445 GLN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 HIS D 445 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.077131 restraints weight = 38540.865| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.60 r_work: 0.2728 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29538 Z= 0.162 Angle : 0.484 6.391 40002 Z= 0.249 Chirality : 0.042 0.275 4528 Planarity : 0.004 0.061 4946 Dihedral : 9.910 76.196 4724 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.16 % Allowed : 10.98 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.14), residues: 3492 helix: 1.11 (0.12), residues: 1724 sheet: 0.77 (0.25), residues: 420 loop : 0.53 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 289 HIS 0.007 0.001 HIS D 372 PHE 0.019 0.001 PHE B 525 TYR 0.014 0.001 TYR C1016 ARG 0.002 0.000 ARG B 222 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 1330) hydrogen bonds : angle 4.15360 ( 3702) covalent geometry : bond 0.00384 (29536) covalent geometry : angle 0.48425 (40002) Misc. bond : bond 0.00023 ( 2) *********************** 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 372 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 305 time to evaluate : 3.325 Fit side-chains REVERT: A 368 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8400 (mp0) REVERT: A 911 ASP cc_start: 0.8316 (m-30) cc_final: 0.7924 (m-30) REVERT: A 1048 ARG cc_start: 0.8602 (ttm170) cc_final: 0.8367 (mtp180) REVERT: B 147 ASP cc_start: 0.8361 (t0) cc_final: 0.8136 (t0) REVERT: B 191 TRP cc_start: 0.7904 (m-90) cc_final: 0.7008 (m-90) REVERT: B 285 ARG cc_start: 0.8615 (tpp-160) cc_final: 0.8369 (tpp-160) REVERT: B 368 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8455 (mp0) REVERT: B 1048 ARG cc_start: 0.8602 (ttm170) cc_final: 0.8347 (mtp180) REVERT: C 113 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7165 (t70) REVERT: C 127 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6864 (mtm180) REVERT: C 331 SER cc_start: 0.8393 (m) cc_final: 0.7956 (p) REVERT: C 337 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7225 (mp) REVERT: C 383 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7598 (mp0) REVERT: C 550 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.7733 (pm20) REVERT: C 862 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.7976 (tmmm) REVERT: C 1038 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8151 (mp0) REVERT: D 337 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7280 (mp) REVERT: D 550 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: D 800 ASP cc_start: 0.8249 (m-30) cc_final: 0.7865 (m-30) REVERT: D 969 GLU cc_start: 0.8709 (tt0) cc_final: 0.8493 (tt0) REVERT: D 990 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8395 (mt-10) REVERT: D 1055 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8218 (tm-30) REVERT: D 1106 ARG cc_start: 0.8744 (ttp80) cc_final: 0.8105 (ttp80) outliers start: 67 outliers final: 37 residues processed: 339 average time/residue: 1.2246 time to fit residues: 498.1052 Evaluate side-chains 342 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 298 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 862 LYS Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 1034 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 326 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS C 372 HIS ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 HIS D 445 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.077910 restraints weight = 38780.705| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.61 r_work: 0.2741 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 29538 Z= 0.126 Angle : 0.469 7.314 40002 Z= 0.239 Chirality : 0.040 0.277 4528 Planarity : 0.004 0.060 4946 Dihedral : 9.649 76.078 4724 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.23 % Allowed : 11.60 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.14), residues: 3492 helix: 1.16 (0.12), residues: 1724 sheet: 0.74 (0.25), residues: 420 loop : 0.54 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 289 HIS 0.007 0.001 HIS D 372 PHE 0.020 0.001 PHE D 174 TYR 0.016 0.001 TYR C 213 ARG 0.003 0.000 ARG B 222 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 1330) hydrogen bonds : angle 4.06553 ( 3702) covalent geometry : bond 0.00293 (29536) covalent geometry : angle 0.46853 (40002) Misc. bond : bond 0.00015 ( 2) *********************** 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 375 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 306 time to evaluate : 3.344 Fit side-chains REVERT: A 117 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7588 (mp0) REVERT: A 911 ASP cc_start: 0.8321 (m-30) cc_final: 0.7930 (m-30) REVERT: A 1048 ARG cc_start: 0.8593 (ttm170) cc_final: 0.8366 (mtp180) REVERT: B 117 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7613 (mt-10) REVERT: B 147 ASP cc_start: 0.8392 (t0) cc_final: 0.8167 (t0) REVERT: B 1048 ARG cc_start: 0.8600 (ttm170) cc_final: 0.8357 (mtp180) REVERT: C 113 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7128 (t70) REVERT: C 331 SER cc_start: 0.8388 (m) cc_final: 0.7950 (p) REVERT: C 337 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7163 (mp) REVERT: C 351 LYS cc_start: 0.8417 (tppt) cc_final: 0.8181 (tppt) REVERT: C 383 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7644 (mp0) REVERT: C 550 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.7613 (pm20) REVERT: C 862 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.7913 (tmmm) REVERT: C 969 GLU cc_start: 0.8724 (tt0) cc_final: 0.8504 (tt0) REVERT: C 1038 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8187 (mp0) REVERT: D 113 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.6944 (t70) REVERT: D 383 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7620 (mp0) REVERT: D 550 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: D 800 ASP cc_start: 0.8218 (m-30) cc_final: 0.7831 (m-30) REVERT: D 911 ASP cc_start: 0.8430 (m-30) cc_final: 0.7843 (m-30) REVERT: D 990 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8416 (mt-10) REVERT: D 1038 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8067 (mp0) REVERT: D 1055 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8244 (tm-30) REVERT: D 1106 ARG cc_start: 0.8759 (ttp80) cc_final: 0.8122 (ttp80) outliers start: 69 outliers final: 41 residues processed: 343 average time/residue: 1.2128 time to fit residues: 502.2530 Evaluate side-chains 341 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 294 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 802 ASN Chi-restraints excluded: chain C residue 862 LYS Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 1034 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 271 optimal weight: 4.9990 chunk 312 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS C 372 HIS ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 HIS D 445 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.077143 restraints weight = 38709.488| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.59 r_work: 0.2726 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 29538 Z= 0.147 Angle : 0.478 7.207 40002 Z= 0.245 Chirality : 0.041 0.273 4528 Planarity : 0.004 0.060 4946 Dihedral : 9.388 75.657 4724 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.13 % Allowed : 11.92 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.14), residues: 3492 helix: 1.15 (0.12), residues: 1724 sheet: 0.71 (0.25), residues: 420 loop : 0.55 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 159 HIS 0.007 0.001 HIS C 372 PHE 0.019 0.001 PHE B 525 TYR 0.016 0.001 TYR D 213 ARG 0.003 0.000 ARG B 222 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 1330) hydrogen bonds : angle 4.06519 ( 3702) covalent geometry : bond 0.00350 (29536) covalent geometry : angle 0.47848 (40002) Misc. bond : bond 0.00019 ( 2) *********************** 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 370 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 304 time to evaluate : 4.029 Fit side-chains REVERT: A 117 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7633 (mt-10) REVERT: A 147 ASP cc_start: 0.8305 (t0) cc_final: 0.8073 (t0) REVERT: A 255 SER cc_start: 0.9312 (OUTLIER) cc_final: 0.9108 (p) REVERT: A 384 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: A 911 ASP cc_start: 0.8357 (m-30) cc_final: 0.7948 (m-30) REVERT: A 990 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8222 (mm-30) REVERT: A 1048 ARG cc_start: 0.8592 (ttm170) cc_final: 0.8364 (mtp180) REVERT: B 117 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7597 (mt-10) REVERT: B 147 ASP cc_start: 0.8378 (t0) cc_final: 0.8170 (t0) REVERT: B 1048 ARG cc_start: 0.8586 (ttm170) cc_final: 0.8344 (mtp180) REVERT: C 113 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7133 (t70) REVERT: C 147 ASP cc_start: 0.7976 (t70) cc_final: 0.7487 (t0) REVERT: C 331 SER cc_start: 0.8364 (m) cc_final: 0.7918 (p) REVERT: C 337 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7174 (mp) REVERT: C 383 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7658 (mp0) REVERT: C 550 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: C 862 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.7911 (tmmm) REVERT: C 969 GLU cc_start: 0.8736 (tt0) cc_final: 0.8519 (tt0) REVERT: C 1038 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8170 (mp0) REVERT: D 113 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.6956 (t70) REVERT: D 147 ASP cc_start: 0.7990 (t70) cc_final: 0.7512 (t0) REVERT: D 383 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7665 (mp0) REVERT: D 398 ASP cc_start: 0.7843 (p0) cc_final: 0.7614 (p0) REVERT: D 550 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: D 800 ASP cc_start: 0.8206 (m-30) cc_final: 0.7827 (m-30) REVERT: D 911 ASP cc_start: 0.8470 (m-30) cc_final: 0.7865 (m-30) REVERT: D 990 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8407 (mt-10) REVERT: D 1038 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: D 1055 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8225 (tm-30) outliers start: 66 outliers final: 40 residues processed: 337 average time/residue: 1.5711 time to fit residues: 636.1683 Evaluate side-chains 349 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 300 time to evaluate : 3.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 862 LYS Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain C residue 1034 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 1034 THR Chi-restraints excluded: chain D residue 1038 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 64 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 309 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 78 optimal weight: 0.0770 chunk 139 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS B 372 HIS C 372 HIS ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 HIS D 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.119047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.078588 restraints weight = 38851.043| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.61 r_work: 0.2755 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 29538 Z= 0.108 Angle : 0.457 8.079 40002 Z= 0.234 Chirality : 0.040 0.273 4528 Planarity : 0.004 0.060 4946 Dihedral : 9.074 75.618 4724 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.74 % Allowed : 12.34 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.14), residues: 3492 helix: 1.25 (0.13), residues: 1724 sheet: 0.71 (0.25), residues: 420 loop : 0.63 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 289 HIS 0.007 0.001 HIS A 372 PHE 0.018 0.001 PHE D 174 TYR 0.017 0.001 TYR C 213 ARG 0.003 0.000 ARG B 222 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 1330) hydrogen bonds : angle 3.96597 ( 3702) covalent geometry : bond 0.00245 (29536) covalent geometry : angle 0.45710 (40002) Misc. bond : bond 0.00005 ( 2) *********************** 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 373 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 319 time to evaluate : 3.397 Fit side-chains revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8284 (t0) cc_final: 0.8082 (t0) REVERT: A 255 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.9107 (p) REVERT: A 911 ASP cc_start: 0.8335 (m-30) cc_final: 0.7941 (m-30) REVERT: A 990 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8123 (mm-30) REVERT: A 1048 ARG cc_start: 0.8588 (ttm170) cc_final: 0.8369 (mtp180) REVERT: B 1048 ARG cc_start: 0.8578 (ttm170) cc_final: 0.8351 (mtp180) REVERT: C 113 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7110 (t70) REVERT: C 147 ASP cc_start: 0.7935 (t70) cc_final: 0.7474 (t0) REVERT: C 331 SER cc_start: 0.8319 (m) cc_final: 0.7879 (p) REVERT: C 383 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7657 (mp0) REVERT: C 398 ASP cc_start: 0.7795 (p0) cc_final: 0.7591 (p0) REVERT: C 550 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.7690 (pm20) REVERT: C 862 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.7918 (tmmm) REVERT: C 969 GLU cc_start: 0.8734 (tt0) cc_final: 0.8523 (tt0) REVERT: C 1038 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8152 (mp0) REVERT: D 147 ASP cc_start: 0.7965 (t70) cc_final: 0.7513 (t0) REVERT: D 383 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7661 (mp0) REVERT: D 550 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: D 800 ASP cc_start: 0.8204 (m-30) cc_final: 0.7807 (m-30) REVERT: D 911 ASP cc_start: 0.8438 (m-30) cc_final: 0.7832 (m-30) REVERT: D 990 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8409 (mt-10) REVERT: D 1038 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: D 1055 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8174 (tm-30) outliers start: 54 outliers final: 37 residues processed: 350 average time/residue: 1.2065 time to fit residues: 509.6828 Evaluate side-chains 345 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 302 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 802 ASN Chi-restraints excluded: chain C residue 862 LYS Chi-restraints excluded: chain C residue 971 VAL Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 984 ASP Chi-restraints excluded: chain D residue 1038 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 113 optimal weight: 0.7980 chunk 320 optimal weight: 4.9990 chunk 328 optimal weight: 0.8980 chunk 147 optimal weight: 0.0060 chunk 306 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 338 optimal weight: 0.7980 chunk 330 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 342 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS B 372 HIS C 372 HIS ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN D 372 HIS D 445 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.078936 restraints weight = 38777.861| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.64 r_work: 0.2762 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29538 Z= 0.102 Angle : 0.458 8.489 40002 Z= 0.234 Chirality : 0.039 0.274 4528 Planarity : 0.004 0.060 4946 Dihedral : 8.873 75.550 4724 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.68 % Allowed : 12.73 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.14), residues: 3492 helix: 1.33 (0.13), residues: 1720 sheet: 0.73 (0.26), residues: 420 loop : 0.60 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 539 HIS 0.007 0.001 HIS A 372 PHE 0.016 0.001 PHE D 174 TYR 0.017 0.001 TYR D 213 ARG 0.004 0.000 ARG B 222 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 1330) hydrogen bonds : angle 3.91295 ( 3702) covalent geometry : bond 0.00227 (29536) covalent geometry : angle 0.45779 (40002) Misc. bond : bond 0.00003 ( 2) *********************** 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 365 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 313 time to evaluate : 3.402 Fit side-chains REVERT: A 117 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7509 (mp0) REVERT: A 147 ASP cc_start: 0.8258 (t0) cc_final: 0.8054 (t0) REVERT: A 255 SER cc_start: 0.9262 (OUTLIER) cc_final: 0.9059 (p) REVERT: A 388 GLU cc_start: 0.8595 (tt0) cc_final: 0.8038 (tm-30) REVERT: A 778 MET cc_start: 0.7236 (mmp) cc_final: 0.5564 (pmt) REVERT: A 911 ASP cc_start: 0.8325 (m-30) cc_final: 0.7886 (m-30) REVERT: A 990 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8068 (mm-30) REVERT: A 1048 ARG cc_start: 0.8518 (ttm170) cc_final: 0.8306 (mtp180) REVERT: B 1048 ARG cc_start: 0.8528 (ttm170) cc_final: 0.8308 (mtp180) REVERT: C 113 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7044 (t70) REVERT: C 147 ASP cc_start: 0.7892 (t70) cc_final: 0.7451 (t0) REVERT: C 331 SER cc_start: 0.8269 (m) cc_final: 0.7802 (p) REVERT: C 383 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7620 (mp0) REVERT: C 398 ASP cc_start: 0.7688 (p0) cc_final: 0.7480 (p0) REVERT: C 550 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7580 (pm20) REVERT: C 862 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.7896 (tmmm) REVERT: C 969 GLU cc_start: 0.8738 (tt0) cc_final: 0.8513 (tt0) REVERT: C 1038 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8120 (mp0) REVERT: D 147 ASP cc_start: 0.7899 (t70) cc_final: 0.7469 (t0) REVERT: D 383 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7627 (mp0) REVERT: D 550 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: D 800 ASP cc_start: 0.8124 (m-30) cc_final: 0.7725 (m-30) REVERT: D 911 ASP cc_start: 0.8401 (m-30) cc_final: 0.7742 (m-30) REVERT: D 990 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8337 (mt-10) REVERT: D 1038 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: D 1055 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8231 (tm-30) outliers start: 52 outliers final: 36 residues processed: 342 average time/residue: 1.5979 time to fit residues: 658.7153 Evaluate side-chains 346 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 304 time to evaluate : 3.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 802 ASN Chi-restraints excluded: chain C residue 862 LYS Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 971 VAL Chi-restraints excluded: chain D residue 984 ASP Chi-restraints excluded: chain D residue 1038 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 136 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 279 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 296 optimal weight: 0.0060 chunk 135 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 249 optimal weight: 0.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS B 372 HIS C 372 HIS ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 HIS D 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.078757 restraints weight = 38784.310| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.64 r_work: 0.2757 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29538 Z= 0.109 Angle : 0.458 7.710 40002 Z= 0.235 Chirality : 0.040 0.275 4528 Planarity : 0.004 0.059 4946 Dihedral : 8.772 75.351 4724 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.39 % Allowed : 13.08 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.14), residues: 3492 helix: 1.34 (0.13), residues: 1720 sheet: 0.74 (0.25), residues: 420 loop : 0.59 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 539 HIS 0.009 0.001 HIS A 372 PHE 0.016 0.001 PHE D 174 TYR 0.019 0.001 TYR C 213 ARG 0.005 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 1330) hydrogen bonds : angle 3.90713 ( 3702) covalent geometry : bond 0.00247 (29536) covalent geometry : angle 0.45762 (40002) Misc. bond : bond 0.00001 ( 2) ********************** 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 347 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 304 time to evaluate : 3.121 Fit side-chains REVERT: A 117 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7505 (mp0) REVERT: A 147 ASP cc_start: 0.8271 (t0) cc_final: 0.8069 (t0) REVERT: A 255 SER cc_start: 0.9262 (OUTLIER) cc_final: 0.9058 (p) REVERT: A 388 GLU cc_start: 0.8595 (tt0) cc_final: 0.8010 (tm-30) REVERT: A 778 MET cc_start: 0.7241 (mmp) cc_final: 0.5563 (pmt) REVERT: A 911 ASP cc_start: 0.8332 (m-30) cc_final: 0.7903 (m-30) REVERT: A 990 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8068 (mm-30) REVERT: A 1048 ARG cc_start: 0.8523 (ttm170) cc_final: 0.8311 (mtp180) REVERT: B 1048 ARG cc_start: 0.8528 (ttm170) cc_final: 0.8309 (mtp180) REVERT: C 113 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7013 (t70) REVERT: C 147 ASP cc_start: 0.7925 (t70) cc_final: 0.7489 (t0) REVERT: C 201 ASP cc_start: 0.8655 (m-30) cc_final: 0.8090 (m-30) REVERT: C 331 SER cc_start: 0.8260 (m) cc_final: 0.7779 (p) REVERT: C 383 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7650 (mp0) REVERT: C 550 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7551 (pm20) REVERT: C 862 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.7861 (tmmm) REVERT: C 913 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8427 (mt-10) REVERT: C 969 GLU cc_start: 0.8745 (tt0) cc_final: 0.8518 (tt0) REVERT: C 1038 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8113 (mp0) REVERT: D 147 ASP cc_start: 0.7926 (t70) cc_final: 0.7508 (t0) REVERT: D 383 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7636 (mp0) REVERT: D 550 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.7584 (pm20) REVERT: D 806 MET cc_start: 0.8506 (ppp) cc_final: 0.8108 (ptm) REVERT: D 911 ASP cc_start: 0.8406 (m-30) cc_final: 0.7753 (m-30) REVERT: D 990 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8344 (mt-10) REVERT: D 1038 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8058 (mp0) REVERT: D 1055 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8226 (tm-30) outliers start: 43 outliers final: 35 residues processed: 333 average time/residue: 1.2603 time to fit residues: 507.1349 Evaluate side-chains 343 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 303 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 971 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 971 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 550 GLU Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 802 ASN Chi-restraints excluded: chain C residue 862 LYS Chi-restraints excluded: chain C residue 984 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 550 GLU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 971 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 31 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 156 optimal weight: 0.4980 chunk 163 optimal weight: 0.0060 chunk 226 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS B 372 HIS C 372 HIS ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 HIS D 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.078979 restraints weight = 38718.674| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.64 r_work: 0.2763 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29538 Z= 0.102 Angle : 0.452 7.700 40002 Z= 0.232 Chirality : 0.039 0.274 4528 Planarity : 0.004 0.059 4946 Dihedral : 8.685 75.374 4724 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.65 % Allowed : 12.89 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.14), residues: 3492 helix: 1.36 (0.13), residues: 1720 sheet: 0.74 (0.26), residues: 420 loop : 0.58 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 191 HIS 0.009 0.001 HIS B 372 PHE 0.017 0.001 PHE D 174 TYR 0.019 0.001 TYR D 213 ARG 0.004 0.000 ARG B 222 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 1330) hydrogen bonds : angle 3.88888 ( 3702) covalent geometry : bond 0.00229 (29536) covalent geometry : angle 0.45151 (40002) Misc. bond : bond 0.00002 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27791.95 seconds wall clock time: 484 minutes 1.54 seconds (29041.54 seconds total)