Starting phenix.real_space_refine on Tue Aug 26 10:05:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yo1_33978/08_2025/7yo1_33978.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yo1_33978/08_2025/7yo1_33978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yo1_33978/08_2025/7yo1_33978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yo1_33978/08_2025/7yo1_33978.map" model { file = "/net/cci-nas-00/data/ceres_data/7yo1_33978/08_2025/7yo1_33978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yo1_33978/08_2025/7yo1_33978.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 Mg 4 5.21 5 S 228 5.16 5 C 23144 2.51 5 N 6044 2.21 5 O 6372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35800 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 879, 7006 Classifications: {'peptide': 879} Link IDs: {'PTRANS': 27, 'TRANS': 851} Chain breaks: 5 Chain: "B" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1941 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 23, 'TRANS': 239} Chain: "C" Number of atoms: 7006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 879, 7006 Classifications: {'peptide': 879} Link IDs: {'PTRANS': 27, 'TRANS': 851} Chain breaks: 5 Chain: "D" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1941 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 23, 'TRANS': 239} Chain: "E" Number of atoms: 7006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 879, 7006 Classifications: {'peptide': 879} Link IDs: {'PTRANS': 27, 'TRANS': 851} Chain breaks: 5 Chain: "F" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1941 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 23, 'TRANS': 239} Chain: "G" Number of atoms: 7006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 879, 7006 Classifications: {'peptide': 879} Link IDs: {'PTRANS': 27, 'TRANS': 851} Chain breaks: 5 Chain: "H" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1941 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 23, 'TRANS': 239} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 3, ' MG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.04, per 1000 atoms: 0.25 Number of scatterers: 35800 At special positions: 0 Unit cell: (160.356, 162.348, 178.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 228 16.00 Mg 4 11.99 O 6372 8.00 N 6044 7.00 C 23144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 57 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 49 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 57 " distance=2.03 Simple disulfide: pdb=" SG CYS D 205 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 47 " - pdb=" SG CYS F 57 " distance=2.04 Simple disulfide: pdb=" SG CYS F 205 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 49 " distance=2.03 Simple disulfide: pdb=" SG CYS H 47 " - pdb=" SG CYS H 57 " distance=2.03 Simple disulfide: pdb=" SG CYS H 205 " - pdb=" SG CYS H 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8592 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 33 sheets defined 50.0% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 removed outlier: 4.319A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 94 through 106 Processing helix chain 'A' and resid 109 through 136 removed outlier: 3.571A pdb=" N ASN A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 171 removed outlier: 4.094A pdb=" N GLN A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 180 through 188 removed outlier: 3.674A pdb=" N ASP A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 200 Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 229 through 259 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 328 removed outlier: 4.318A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLY A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.989A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 548 Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 699 through 704 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 733 through 739 removed outlier: 3.784A pdb=" N LEU A 737 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 767 removed outlier: 4.266A pdb=" N ARG A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 785 through 792 Processing helix chain 'A' and resid 818 through 829 Processing helix chain 'A' and resid 872 through 876 removed outlier: 3.891A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 891 removed outlier: 3.757A pdb=" N VAL A 888 " --> pdb=" O ASP A 885 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 916 through 920 Processing helix chain 'A' and resid 921 through 930 removed outlier: 4.342A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 942 removed outlier: 4.256A pdb=" N LEU A 934 " --> pdb=" O ASN A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 965 through 973 removed outlier: 3.616A pdb=" N ASP A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 993 removed outlier: 4.353A pdb=" N ASP A 992 " --> pdb=" O ASP A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1008 Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.699A pdb=" N LEU B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 189 removed outlier: 3.691A pdb=" N LEU B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 219 removed outlier: 4.476A pdb=" N LEU B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 266 removed outlier: 3.764A pdb=" N VAL B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 301 Processing helix chain 'C' and resid 21 through 48 removed outlier: 3.887A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 106 Processing helix chain 'C' and resid 109 through 135 Processing helix chain 'C' and resid 147 through 171 removed outlier: 4.048A pdb=" N GLN C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 removed outlier: 3.540A pdb=" N LEU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 188 Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 207 through 215 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 229 through 259 removed outlier: 3.535A pdb=" N SER C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 328 removed outlier: 3.758A pdb=" N LEU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Proline residue: C 320 - end of helix removed outlier: 3.676A pdb=" N ASN C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'C' and resid 462 through 471 removed outlier: 3.685A pdb=" N ASN C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.636A pdb=" N GLU C 479 " --> pdb=" O ASN C 476 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY C 480 " --> pdb=" O TRP C 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 476 through 480' Processing helix chain 'C' and resid 486 through 500 Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 523 through 533 removed outlier: 4.194A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 548 Processing helix chain 'C' and resid 549 through 561 Processing helix chain 'C' and resid 601 through 608 removed outlier: 4.188A pdb=" N VAL C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 704 removed outlier: 3.744A pdb=" N VAL C 703 " --> pdb=" O GLU C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 759 through 764 Processing helix chain 'C' and resid 765 through 770 removed outlier: 4.875A pdb=" N GLU C 768 " --> pdb=" O ARG C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 793 through 797 removed outlier: 3.791A pdb=" N CYS C 797 " --> pdb=" O ILE C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 829 Processing helix chain 'C' and resid 872 through 876 removed outlier: 3.792A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 891 removed outlier: 3.830A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 905 Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 920 through 930 removed outlier: 4.259A pdb=" N MET C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 942 removed outlier: 3.806A pdb=" N LEU C 934 " --> pdb=" O ASN C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 956 Processing helix chain 'C' and resid 965 through 972 Processing helix chain 'C' and resid 987 through 991 Processing helix chain 'C' and resid 995 through 1007 Processing helix chain 'D' and resid 89 through 94 removed outlier: 4.400A pdb=" N GLY D 93 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 159 through 164 Processing helix chain 'D' and resid 183 through 190 removed outlier: 4.148A pdb=" N LEU D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 209 through 219 Processing helix chain 'D' and resid 220 through 228 removed outlier: 5.132A pdb=" N GLU D 225 " --> pdb=" O PRO D 222 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA D 226 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 301 removed outlier: 3.603A pdb=" N TYR D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR D 267 " --> pdb=" O ALA D 263 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLY D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Proline residue: D 270 - end of helix removed outlier: 3.705A pdb=" N ARG D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 48 removed outlier: 3.681A pdb=" N LEU E 26 " --> pdb=" O TRP E 22 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY E 36 " --> pdb=" O THR E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 51 No H-bonds generated for 'chain 'E' and resid 49 through 51' Processing helix chain 'E' and resid 94 through 106 Processing helix chain 'E' and resid 109 through 135 Processing helix chain 'E' and resid 147 through 171 removed outlier: 4.350A pdb=" N GLN E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE E 152 " --> pdb=" O PHE E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 179 Processing helix chain 'E' and resid 180 through 188 Processing helix chain 'E' and resid 189 through 200 Processing helix chain 'E' and resid 206 through 215 removed outlier: 3.657A pdb=" N LEU E 209 " --> pdb=" O LEU E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 Processing helix chain 'E' and resid 229 through 259 removed outlier: 3.530A pdb=" N SER E 259 " --> pdb=" O LEU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 265 removed outlier: 3.758A pdb=" N ASN E 265 " --> pdb=" O PRO E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 286 removed outlier: 3.524A pdb=" N SER E 286 " --> pdb=" O MET E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 328 removed outlier: 4.064A pdb=" N LEU E 312 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA E 313 " --> pdb=" O LEU E 309 " (cutoff:3.500A) Proline residue: E 320 - end of helix Processing helix chain 'E' and resid 352 through 364 Processing helix chain 'E' and resid 384 through 394 Processing helix chain 'E' and resid 407 through 414 Processing helix chain 'E' and resid 415 through 419 Processing helix chain 'E' and resid 432 through 451 Processing helix chain 'E' and resid 462 through 471 Processing helix chain 'E' and resid 476 through 480 removed outlier: 3.851A pdb=" N GLU E 479 " --> pdb=" O ASN E 476 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY E 480 " --> pdb=" O TRP E 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 476 through 480' Processing helix chain 'E' and resid 486 through 500 Processing helix chain 'E' and resid 502 through 512 Processing helix chain 'E' and resid 523 through 533 removed outlier: 4.222A pdb=" N TYR E 527 " --> pdb=" O THR E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 548 removed outlier: 3.536A pdb=" N LEU E 548 " --> pdb=" O ALA E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 560 Processing helix chain 'E' and resid 601 through 610 removed outlier: 4.389A pdb=" N VAL E 605 " --> pdb=" O ASP E 601 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE E 609 " --> pdb=" O VAL E 605 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE E 610 " --> pdb=" O LYS E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 704 removed outlier: 3.913A pdb=" N VAL E 703 " --> pdb=" O GLU E 699 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 713 Processing helix chain 'E' and resid 734 through 739 Processing helix chain 'E' and resid 759 through 767 removed outlier: 4.343A pdb=" N ARG E 765 " --> pdb=" O GLU E 761 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU E 766 " --> pdb=" O TYR E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 770 No H-bonds generated for 'chain 'E' and resid 768 through 770' Processing helix chain 'E' and resid 785 through 792 Processing helix chain 'E' and resid 817 through 830 Processing helix chain 'E' and resid 872 through 876 removed outlier: 3.725A pdb=" N ASN E 875 " --> pdb=" O THR E 872 " (cutoff:3.500A) Processing helix chain 'E' and resid 884 through 891 removed outlier: 3.512A pdb=" N VAL E 888 " --> pdb=" O ASP E 885 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN E 889 " --> pdb=" O THR E 886 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 891 " --> pdb=" O VAL E 888 " (cutoff:3.500A) Processing helix chain 'E' and resid 902 through 905 Processing helix chain 'E' and resid 906 through 911 Processing helix chain 'E' and resid 918 through 920 No H-bonds generated for 'chain 'E' and resid 918 through 920' Processing helix chain 'E' and resid 921 through 930 removed outlier: 4.391A pdb=" N SER E 925 " --> pdb=" O ASP E 921 " (cutoff:3.500A) Processing helix chain 'E' and resid 930 through 942 removed outlier: 3.906A pdb=" N LEU E 934 " --> pdb=" O ASN E 930 " (cutoff:3.500A) Processing helix chain 'E' and resid 946 through 957 Processing helix chain 'E' and resid 965 through 973 removed outlier: 3.528A pdb=" N ASP E 973 " --> pdb=" O LEU E 969 " (cutoff:3.500A) Processing helix chain 'E' and resid 995 through 1006 Processing helix chain 'F' and resid 159 through 164 Processing helix chain 'F' and resid 183 through 190 removed outlier: 3.757A pdb=" N LEU F 187 " --> pdb=" O ALA F 183 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 219 removed outlier: 4.652A pdb=" N LEU F 212 " --> pdb=" O ALA F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 228 removed outlier: 3.503A pdb=" N THR F 228 " --> pdb=" O GLU F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 266 removed outlier: 3.713A pdb=" N VAL F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 301 Processing helix chain 'G' and resid 21 through 48 removed outlier: 3.681A pdb=" N PHE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY G 36 " --> pdb=" O THR G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 94 through 106 Processing helix chain 'G' and resid 109 through 136 removed outlier: 3.582A pdb=" N ASN G 136 " --> pdb=" O ILE G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 171 removed outlier: 4.004A pdb=" N GLN G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 179 Processing helix chain 'G' and resid 180 through 188 removed outlier: 3.579A pdb=" N ASP G 186 " --> pdb=" O ASN G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 200 Processing helix chain 'G' and resid 207 through 215 Processing helix chain 'G' and resid 216 through 224 Processing helix chain 'G' and resid 229 through 259 Processing helix chain 'G' and resid 261 through 265 Processing helix chain 'G' and resid 273 through 286 Processing helix chain 'G' and resid 298 through 327 removed outlier: 4.440A pdb=" N GLY G 310 " --> pdb=" O PHE G 306 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU G 312 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ALA G 313 " --> pdb=" O LEU G 309 " (cutoff:3.500A) Proline residue: G 320 - end of helix Processing helix chain 'G' and resid 352 through 364 Processing helix chain 'G' and resid 384 through 394 Processing helix chain 'G' and resid 407 through 414 Processing helix chain 'G' and resid 432 through 451 removed outlier: 3.770A pdb=" N GLU G 436 " --> pdb=" O ASP G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 471 Processing helix chain 'G' and resid 486 through 500 Processing helix chain 'G' and resid 502 through 511 Processing helix chain 'G' and resid 523 through 533 removed outlier: 3.855A pdb=" N TYR G 527 " --> pdb=" O THR G 523 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER G 533 " --> pdb=" O LEU G 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 542 through 548 Processing helix chain 'G' and resid 549 through 560 Processing helix chain 'G' and resid 601 through 607 removed outlier: 3.570A pdb=" N VAL G 605 " --> pdb=" O ASP G 601 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG G 607 " --> pdb=" O LYS G 603 " (cutoff:3.500A) Processing helix chain 'G' and resid 699 through 703 Processing helix chain 'G' and resid 706 through 713 Processing helix chain 'G' and resid 734 through 739 Processing helix chain 'G' and resid 759 through 767 removed outlier: 3.646A pdb=" N ARG G 765 " --> pdb=" O GLU G 761 " (cutoff:3.500A) Processing helix chain 'G' and resid 768 through 770 No H-bonds generated for 'chain 'G' and resid 768 through 770' Processing helix chain 'G' and resid 785 through 792 Processing helix chain 'G' and resid 812 through 816 Processing helix chain 'G' and resid 817 through 829 removed outlier: 3.820A pdb=" N ILE G 821 " --> pdb=" O ASP G 817 " (cutoff:3.500A) Processing helix chain 'G' and resid 872 through 876 removed outlier: 3.882A pdb=" N ASN G 875 " --> pdb=" O THR G 872 " (cutoff:3.500A) Processing helix chain 'G' and resid 884 through 891 removed outlier: 3.811A pdb=" N VAL G 888 " --> pdb=" O ASP G 885 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN G 889 " --> pdb=" O THR G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 902 through 905 Processing helix chain 'G' and resid 906 through 911 Processing helix chain 'G' and resid 918 through 921 removed outlier: 4.201A pdb=" N ASP G 921 " --> pdb=" O SER G 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 918 through 921' Processing helix chain 'G' and resid 922 through 930 Processing helix chain 'G' and resid 930 through 942 removed outlier: 3.854A pdb=" N LEU G 934 " --> pdb=" O ASN G 930 " (cutoff:3.500A) Processing helix chain 'G' and resid 946 through 956 Processing helix chain 'G' and resid 965 through 973 Processing helix chain 'G' and resid 987 through 991 Processing helix chain 'G' and resid 995 through 1007 removed outlier: 3.567A pdb=" N LEU G 999 " --> pdb=" O CYS G 995 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 164 removed outlier: 3.549A pdb=" N LEU H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 removed outlier: 3.609A pdb=" N LEU H 187 " --> pdb=" O ALA H 183 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 209 through 219 Processing helix chain 'H' and resid 258 through 266 removed outlier: 4.169A pdb=" N VAL H 264 " --> pdb=" O ARG H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 302 removed outlier: 3.508A pdb=" N ARG H 296 " --> pdb=" O ALA H 292 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU H 297 " --> pdb=" O ARG H 293 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU H 302 " --> pdb=" O ARG H 298 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 402 removed outlier: 6.959A pdb=" N LYS A 343 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL A 376 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE A 345 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU A 378 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A 347 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 540 removed outlier: 3.559A pdb=" N LEU A 564 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 686 through 687 removed outlier: 4.181A pdb=" N TYR A 686 " --> pdb=" O GLY A 962 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 776 through 779 removed outlier: 6.406A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N HIS A 718 " --> pdb=" O CYS A 797 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET A 799 " --> pdb=" O HIS A 718 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILE A 879 " --> pdb=" O ASP A 798 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 975 through 981 removed outlier: 3.524A pdb=" N LEU A1048 " --> pdb=" O TYR A1015 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.523A pdb=" N ASP B 101 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA B 151 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 175 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 139 through 140 Processing sheet with id=AA9, first strand: chain 'C' and resid 398 through 402 removed outlier: 8.238A pdb=" N GLU C 399 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE C 375 " --> pdb=" O GLU C 399 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N TYR C 401 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE C 377 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA C 421 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C 459 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE C 456 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR C 458 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 535 through 540 removed outlier: 3.991A pdb=" N LEU C 564 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 686 through 687 removed outlier: 4.178A pdb=" N TYR C 686 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 776 through 779 removed outlier: 6.326A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 974 through 981 removed outlier: 3.983A pdb=" N ARG C 974 " --> pdb=" O PHE C1055 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 6.574A pdb=" N LEU D 100 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N SER D 127 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU D 102 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU D 124 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA D 151 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU D 126 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 231 through 232 Processing sheet with id=AB7, first strand: chain 'E' and resid 139 through 141 Processing sheet with id=AB8, first strand: chain 'E' and resid 398 through 401 removed outlier: 7.084A pdb=" N LYS E 343 " --> pdb=" O GLU E 374 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL E 376 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE E 345 " --> pdb=" O VAL E 376 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU E 378 " --> pdb=" O ILE E 345 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL E 347 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N HIS E 344 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N LEU E 423 " --> pdb=" O HIS E 344 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL E 346 " --> pdb=" O LEU E 423 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE E 456 " --> pdb=" O ASP E 482 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE E 484 " --> pdb=" O ILE E 456 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR E 458 " --> pdb=" O ILE E 484 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 535 through 540 removed outlier: 3.690A pdb=" N LEU E 564 " --> pdb=" O ILE E 598 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 686 through 687 removed outlier: 4.426A pdb=" N TYR E 686 " --> pdb=" O GLY E 962 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 776 through 780 removed outlier: 6.194A pdb=" N ILE E 754 " --> pdb=" O SER E 777 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU E 779 " --> pdb=" O ILE E 754 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE E 756 " --> pdb=" O LEU E 779 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N HIS E 718 " --> pdb=" O CYS E 797 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET E 799 " --> pdb=" O HIS E 718 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE E 879 " --> pdb=" O ASP E 798 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N CYS E 800 " --> pdb=" O ILE E 879 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLU E 881 " --> pdb=" O CYS E 800 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE E 802 " --> pdb=" O GLU E 881 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 974 through 981 removed outlier: 3.504A pdb=" N LEU E1048 " --> pdb=" O TYR E1015 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLY E1013 " --> pdb=" O PHE E1050 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU E1052 " --> pdb=" O CYS E1011 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N CYS E1011 " --> pdb=" O LEU E1052 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 77 through 79 removed outlier: 6.395A pdb=" N LEU F 78 " --> pdb=" O ARG F 103 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU F 102 " --> pdb=" O ASP F 125 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 85 through 86 removed outlier: 3.555A pdb=" N LEU F 86 " --> pdb=" O SER F 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 150 through 151 Processing sheet with id=AC7, first strand: chain 'F' and resid 203 through 204 removed outlier: 6.095A pdb=" N TRP F 203 " --> pdb=" O VAL F 232 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER F 240 " --> pdb=" O CYS F 231 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 139 through 140 Processing sheet with id=AC9, first strand: chain 'G' and resid 398 through 402 removed outlier: 4.614A pdb=" N GLY G 349 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N HIS G 344 " --> pdb=" O ALA G 421 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N LEU G 423 " --> pdb=" O HIS G 344 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL G 346 " --> pdb=" O LEU G 423 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU G 425 " --> pdb=" O VAL G 346 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS G 348 " --> pdb=" O LEU G 425 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN G 459 " --> pdb=" O ILE G 424 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE G 456 " --> pdb=" O ASP G 482 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE G 484 " --> pdb=" O ILE G 456 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR G 458 " --> pdb=" O ILE G 484 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 535 through 540 removed outlier: 3.654A pdb=" N LEU G 564 " --> pdb=" O ILE G 598 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 776 through 780 removed outlier: 7.111A pdb=" N HIS G 718 " --> pdb=" O ASP G 798 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N CYS G 800 " --> pdb=" O HIS G 718 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL G 720 " --> pdb=" O CYS G 800 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE G 802 " --> pdb=" O VAL G 720 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS G 722 " --> pdb=" O ILE G 802 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N SER G 804 " --> pdb=" O CYS G 722 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE G 724 " --> pdb=" O SER G 804 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE G 879 " --> pdb=" O ASP G 798 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS G 800 " --> pdb=" O ILE G 879 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLU G 881 " --> pdb=" O CYS G 800 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE G 802 " --> pdb=" O GLU G 881 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 975 through 981 removed outlier: 3.787A pdb=" N LEU G1048 " --> pdb=" O TYR G1015 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY G1013 " --> pdb=" O PHE G1050 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 76 through 79 removed outlier: 3.556A pdb=" N SER H 127 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA H 151 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU H 148 " --> pdb=" O SER H 173 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLN H 175 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU H 150 " --> pdb=" O GLN H 175 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU H 172 " --> pdb=" O HIS H 197 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ARG H 199 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU H 174 " --> pdb=" O ARG H 199 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 85 through 86 removed outlier: 4.147A pdb=" N LEU H 86 " --> pdb=" O SER H 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'H' and resid 203 through 204 removed outlier: 6.308A pdb=" N TRP H 203 " --> pdb=" O VAL H 232 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER H 240 " --> pdb=" O CYS H 231 " (cutoff:3.500A) 1621 hydrogen bonds defined for protein. 4590 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: 8.58 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6585 1.33 - 1.45: 9161 1.45 - 1.57: 20549 1.57 - 1.69: 1 1.69 - 1.82: 320 Bond restraints: 36616 Sorted by residual: bond pdb=" N LEU F 166 " pdb=" CA LEU F 166 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.10e-03 1.21e+04 1.69e+01 bond pdb=" N VAL B 46 " pdb=" CA VAL B 46 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.13e+01 bond pdb=" N ILE E 810 " pdb=" CA ILE E 810 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.11e-02 8.12e+03 1.07e+01 bond pdb=" N LEU G 499 " pdb=" CA LEU G 499 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.18e-02 7.18e+03 1.01e+01 bond pdb=" N GLN E 19 " pdb=" CA GLN E 19 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.22e-02 6.72e+03 9.57e+00 ... (remaining 36611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 49200 2.61 - 5.23: 534 5.23 - 7.84: 34 7.84 - 10.45: 2 10.45 - 13.07: 2 Bond angle restraints: 49772 Sorted by residual: angle pdb=" N PRO B 220 " pdb=" CA PRO B 220 " pdb=" C PRO B 220 " ideal model delta sigma weight residual 110.95 97.88 13.07 1.62e+00 3.81e-01 6.51e+01 angle pdb=" N ILE C 732 " pdb=" CA ILE C 732 " pdb=" C ILE C 732 " ideal model delta sigma weight residual 109.21 98.71 10.50 1.36e+00 5.41e-01 5.96e+01 angle pdb=" N ILE A 732 " pdb=" CA ILE A 732 " pdb=" C ILE A 732 " ideal model delta sigma weight residual 109.58 101.14 8.44 1.29e+00 6.01e-01 4.28e+01 angle pdb=" CA LYS A 228 " pdb=" C LYS A 228 " pdb=" O LYS A 228 " ideal model delta sigma weight residual 121.40 114.61 6.79 1.13e+00 7.83e-01 3.61e+01 angle pdb=" N LYS A 228 " pdb=" CA LYS A 228 " pdb=" C LYS A 228 " ideal model delta sigma weight residual 109.24 100.44 8.80 1.51e+00 4.39e-01 3.40e+01 ... (remaining 49767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 19579 18.00 - 35.99: 1782 35.99 - 53.99: 303 53.99 - 71.98: 49 71.98 - 89.98: 17 Dihedral angle restraints: 21730 sinusoidal: 8466 harmonic: 13264 Sorted by residual: dihedral pdb=" CB CYS D 205 " pdb=" SG CYS D 205 " pdb=" SG CYS D 231 " pdb=" CB CYS D 231 " ideal model delta sinusoidal sigma weight residual -86.00 -174.50 88.50 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS H 205 " pdb=" SG CYS H 205 " pdb=" SG CYS H 231 " pdb=" CB CYS H 231 " ideal model delta sinusoidal sigma weight residual -86.00 -174.17 88.17 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" CB CYS H 47 " pdb=" SG CYS H 47 " pdb=" SG CYS H 57 " pdb=" CB CYS H 57 " ideal model delta sinusoidal sigma weight residual -86.00 -163.78 77.78 1 1.00e+01 1.00e-02 7.57e+01 ... (remaining 21727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 5415 0.092 - 0.184: 305 0.184 - 0.276: 18 0.276 - 0.368: 4 0.368 - 0.460: 2 Chirality restraints: 5744 Sorted by residual: chirality pdb=" CA ILE C 732 " pdb=" N ILE C 732 " pdb=" C ILE C 732 " pdb=" CB ILE C 732 " both_signs ideal model delta sigma weight residual False 2.43 2.89 -0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" CA ILE A 732 " pdb=" N ILE A 732 " pdb=" C ILE A 732 " pdb=" CB ILE A 732 " both_signs ideal model delta sigma weight residual False 2.43 2.86 -0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CA LYS A 228 " pdb=" N LYS A 228 " pdb=" C LYS A 228 " pdb=" CB LYS A 228 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 5741 not shown) Planarity restraints: 6284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS H 219 " -0.084 5.00e-02 4.00e+02 1.28e-01 2.61e+01 pdb=" N PRO H 220 " 0.221 5.00e-02 4.00e+02 pdb=" CA PRO H 220 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO H 220 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER F 58 " 0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C SER F 58 " -0.075 2.00e-02 2.50e+03 pdb=" O SER F 58 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA F 59 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 164 " -0.021 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C GLY B 164 " 0.072 2.00e-02 2.50e+03 pdb=" O GLY B 164 " -0.027 2.00e-02 2.50e+03 pdb=" N ALA B 165 " -0.023 2.00e-02 2.50e+03 ... (remaining 6281 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 264 2.60 - 3.18: 30205 3.18 - 3.75: 55254 3.75 - 4.33: 75543 4.33 - 4.90: 126522 Nonbonded interactions: 287788 Sorted by model distance: nonbonded pdb=" OE1 GLN H 255 " pdb=" NH2 ARG H 260 " model vdw 2.028 3.120 nonbonded pdb=" OG1 THR A 284 " pdb=" OH TYR C 290 " model vdw 2.129 3.040 nonbonded pdb=" NH1 ARG E 742 " pdb=" O PRO E 774 " model vdw 2.173 3.120 nonbonded pdb=" OH TYR A 290 " pdb=" OG1 THR G 284 " model vdw 2.176 3.040 nonbonded pdb=" OG1 THR C 284 " pdb=" OH TYR E 290 " model vdw 2.179 3.040 ... (remaining 287783 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 13 through 1102) selection = (chain 'C' and resid 13 through 1102) selection = (chain 'E' and resid 13 through 1102) selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 35.960 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 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:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 36626 Z= 0.208 Angle : 0.599 13.068 49792 Z= 0.353 Chirality : 0.045 0.460 5744 Planarity : 0.004 0.128 6284 Dihedral : 13.733 89.976 13108 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.53 % Favored : 97.23 % Rotamer: Outliers : 0.49 % Allowed : 0.75 % Favored : 98.76 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.12), residues: 4512 helix: 1.24 (0.12), residues: 2004 sheet: -0.33 (0.23), residues: 524 loop : -0.41 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 296 TYR 0.029 0.001 TYR A1015 PHE 0.020 0.001 PHE A 511 TRP 0.018 0.001 TRP D 116 HIS 0.003 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00336 (36616) covalent geometry : angle 0.59904 (49772) SS BOND : bond 0.00324 ( 10) SS BOND : angle 0.90262 ( 20) hydrogen bonds : bond 0.16712 ( 1621) hydrogen bonds : angle 5.82360 ( 4590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 605 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9254 (tp) cc_final: 0.8947 (tp) REVERT: A 228 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7055 (mtpt) REVERT: A 706 THR cc_start: 0.8110 (m) cc_final: 0.7903 (m) REVERT: A 735 ARG cc_start: 0.8612 (tmm-80) cc_final: 0.8261 (ttm-80) REVERT: A 798 ASP cc_start: 0.7740 (m-30) cc_final: 0.7537 (m-30) REVERT: B 298 ARG cc_start: 0.5348 (tpt-90) cc_final: 0.4352 (mmm160) REVERT: C 603 LYS cc_start: 0.8324 (mmmt) cc_final: 0.7759 (mppt) REVERT: D 303 ARG cc_start: 0.1999 (ttt-90) cc_final: 0.1635 (ttt90) REVERT: E 282 MET cc_start: 0.8731 (tpt) cc_final: 0.8471 (tpp) REVERT: E 453 LYS cc_start: 0.7611 (tppt) cc_final: 0.7406 (tmmt) REVERT: G 555 GLU cc_start: 0.7287 (pt0) cc_final: 0.7072 (pt0) outliers start: 19 outliers final: 6 residues processed: 620 average time/residue: 0.2225 time to fit residues: 229.0188 Evaluate side-chains 509 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 502 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 811 ASP Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain H residue 169 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 222 GLN A 268 ASN A 270 GLN A 884 ASN A 887 ASN B 153 ASN B 197 HIS C 225 ASN C 771 HIS C 967 GLN C 979 GLN D 153 ASN D 175 GLN E 225 ASN E 409 HIS E 736 ASN F 122 GLN G 884 ASN H 130 GLN H 153 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.155807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.114544 restraints weight = 44395.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.110846 restraints weight = 57790.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.113268 restraints weight = 59553.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.113386 restraints weight = 35723.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.114503 restraints weight = 33002.481| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36626 Z= 0.140 Angle : 0.529 8.044 49792 Z= 0.265 Chirality : 0.040 0.167 5744 Planarity : 0.004 0.091 6284 Dihedral : 3.830 59.964 4926 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.48 % Favored : 97.43 % Rotamer: Outliers : 1.31 % Allowed : 7.67 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.12), residues: 4512 helix: 1.14 (0.11), residues: 2109 sheet: -0.20 (0.25), residues: 464 loop : -0.48 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 413 TYR 0.023 0.001 TYR A1015 PHE 0.028 0.001 PHE A1055 TRP 0.020 0.001 TRP H 215 HIS 0.006 0.001 HIS F 219 Details of bonding type rmsd covalent geometry : bond 0.00326 (36616) covalent geometry : angle 0.52851 (49772) SS BOND : bond 0.00157 ( 10) SS BOND : angle 0.87260 ( 20) hydrogen bonds : bond 0.04780 ( 1621) hydrogen bonds : angle 4.60800 ( 4590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 540 time to evaluate : 1.489 Fit side-chains REVERT: A 161 LEU cc_start: 0.9337 (tp) cc_final: 0.9007 (tp) REVERT: A 735 ARG cc_start: 0.8122 (tmm-80) cc_final: 0.7894 (ptm-80) REVERT: A 798 ASP cc_start: 0.7717 (m-30) cc_final: 0.7461 (m-30) REVERT: B 298 ARG cc_start: 0.5310 (tpt-90) cc_final: 0.4333 (mmm160) REVERT: C 967 GLN cc_start: 0.7447 (mm110) cc_final: 0.6737 (mt0) REVERT: D 303 ARG cc_start: 0.2235 (ttt-90) cc_final: 0.1830 (ttt90) REVERT: E 324 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7460 (tm-30) REVERT: G 798 ASP cc_start: 0.8007 (m-30) cc_final: 0.7767 (m-30) outliers start: 51 outliers final: 39 residues processed: 565 average time/residue: 0.2255 time to fit residues: 209.6092 Evaluate side-chains 548 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 509 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 782 THR Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 992 ASP Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 811 ASP Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 983 LEU Chi-restraints excluded: chain F residue 47 CYS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 317 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 728 SER Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 784 LEU Chi-restraints excluded: chain G residue 881 GLU Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 169 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 422 optimal weight: 0.9980 chunk 425 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 346 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 chunk 404 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 318 optimal weight: 20.0000 chunk 174 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 268 ASN A 365 HIS A 884 ASN B 98 GLN B 130 GLN B 153 ASN B 197 HIS D 153 ASN E 225 ASN H 153 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.155351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.114067 restraints weight = 44352.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.109765 restraints weight = 63648.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.111782 restraints weight = 60916.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.112787 restraints weight = 38535.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.113210 restraints weight = 34018.857| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36626 Z= 0.127 Angle : 0.500 7.794 49792 Z= 0.251 Chirality : 0.039 0.167 5744 Planarity : 0.004 0.070 6284 Dihedral : 3.703 55.909 4922 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.22 % Favored : 97.70 % Rotamer: Outliers : 1.75 % Allowed : 10.48 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.12), residues: 4512 helix: 1.26 (0.11), residues: 2077 sheet: -0.24 (0.25), residues: 474 loop : -0.40 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 960 TYR 0.027 0.001 TYR E 904 PHE 0.021 0.001 PHE C 511 TRP 0.021 0.001 TRP H 215 HIS 0.004 0.001 HIS E 771 Details of bonding type rmsd covalent geometry : bond 0.00300 (36616) covalent geometry : angle 0.49976 (49772) SS BOND : bond 0.00121 ( 10) SS BOND : angle 0.73279 ( 20) hydrogen bonds : bond 0.04221 ( 1621) hydrogen bonds : angle 4.32476 ( 4590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 525 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8600 (t80) cc_final: 0.8332 (t80) REVERT: A 161 LEU cc_start: 0.9359 (tp) cc_final: 0.9016 (tp) REVERT: A 268 ASN cc_start: 0.7344 (t0) cc_final: 0.6890 (p0) REVERT: B 298 ARG cc_start: 0.5332 (tpt-90) cc_final: 0.4321 (mmm160) REVERT: D 97 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6977 (mp) REVERT: G 603 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8212 (mmtp) REVERT: G 798 ASP cc_start: 0.7943 (m-30) cc_final: 0.7733 (m-30) REVERT: H 212 LEU cc_start: 0.6981 (tp) cc_final: 0.6578 (pp) outliers start: 68 outliers final: 47 residues processed: 563 average time/residue: 0.2203 time to fit residues: 206.0389 Evaluate side-chains 545 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 497 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 992 ASP Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 759 SER Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 983 LEU Chi-restraints excluded: chain E residue 1010 LEU Chi-restraints excluded: chain F residue 47 CYS Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 317 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 728 SER Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 881 GLU Chi-restraints excluded: chain G residue 884 ASN Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 169 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 206 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 324 optimal weight: 2.9990 chunk 416 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 146 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 371 optimal weight: 4.9990 chunk 154 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 884 ASN B 98 GLN B 153 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.154440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.112668 restraints weight = 44174.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.109348 restraints weight = 57113.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.111478 restraints weight = 61213.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.111845 restraints weight = 35831.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.114237 restraints weight = 32637.794| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36626 Z= 0.131 Angle : 0.497 6.986 49792 Z= 0.249 Chirality : 0.039 0.167 5744 Planarity : 0.004 0.057 6284 Dihedral : 3.651 53.783 4916 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.66 % Favored : 97.30 % Rotamer: Outliers : 1.98 % Allowed : 12.54 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.12), residues: 4512 helix: 1.26 (0.11), residues: 2077 sheet: -0.26 (0.25), residues: 474 loop : -0.39 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 960 TYR 0.026 0.001 TYR A 198 PHE 0.020 0.001 PHE G 144 TRP 0.019 0.001 TRP E 22 HIS 0.004 0.001 HIS E 771 Details of bonding type rmsd covalent geometry : bond 0.00315 (36616) covalent geometry : angle 0.49688 (49772) SS BOND : bond 0.00115 ( 10) SS BOND : angle 0.64267 ( 20) hydrogen bonds : bond 0.04111 ( 1621) hydrogen bonds : angle 4.20778 ( 4590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 513 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9342 (tp) cc_final: 0.9008 (tp) REVERT: A 905 LEU cc_start: 0.8831 (mt) cc_final: 0.8512 (mt) REVERT: B 298 ARG cc_start: 0.5276 (tpt-90) cc_final: 0.4254 (mmm160) REVERT: C 744 SER cc_start: 0.9097 (m) cc_final: 0.8779 (m) REVERT: C 967 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6681 (mt0) REVERT: C 983 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7334 (pp) REVERT: C 984 ASP cc_start: 0.6553 (m-30) cc_final: 0.6312 (m-30) REVERT: D 97 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6983 (mp) REVERT: G 603 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8266 (mmtp) REVERT: G 798 ASP cc_start: 0.7985 (m-30) cc_final: 0.7765 (m-30) outliers start: 77 outliers final: 59 residues processed: 557 average time/residue: 0.2229 time to fit residues: 205.0941 Evaluate side-chains 553 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 492 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 992 ASP Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 755 VAL Chi-restraints excluded: chain E residue 759 SER Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 983 LEU Chi-restraints excluded: chain E residue 1010 LEU Chi-restraints excluded: chain F residue 47 CYS Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 317 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 728 SER Chi-restraints excluded: chain G residue 765 ARG Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 884 ASN Chi-restraints excluded: chain G residue 990 LEU Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 229 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 347 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 430 optimal weight: 8.9990 chunk 365 optimal weight: 0.6980 chunk 248 optimal weight: 0.7980 chunk 400 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 294 optimal weight: 2.9990 chunk 312 optimal weight: 0.0060 chunk 262 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 157 ASN A 268 ASN B 98 GLN B 153 ASN D 153 ASN G 449 ASN H 153 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.156411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.114267 restraints weight = 44195.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.110507 restraints weight = 57073.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.113071 restraints weight = 58767.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.113040 restraints weight = 36315.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.113800 restraints weight = 33625.371| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36626 Z= 0.097 Angle : 0.475 10.398 49792 Z= 0.236 Chirality : 0.038 0.153 5744 Planarity : 0.004 0.051 6284 Dihedral : 3.525 50.627 4916 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.08 % Favored : 97.87 % Rotamer: Outliers : 1.67 % Allowed : 14.08 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.13), residues: 4512 helix: 1.45 (0.12), residues: 2057 sheet: -0.20 (0.25), residues: 470 loop : -0.33 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 578 TYR 0.025 0.001 TYR A 198 PHE 0.020 0.001 PHE E 511 TRP 0.021 0.001 TRP E 22 HIS 0.002 0.000 HIS C 344 Details of bonding type rmsd covalent geometry : bond 0.00219 (36616) covalent geometry : angle 0.47529 (49772) SS BOND : bond 0.00118 ( 10) SS BOND : angle 0.63004 ( 20) hydrogen bonds : bond 0.03620 ( 1621) hydrogen bonds : angle 4.05455 ( 4590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 534 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9350 (tp) cc_final: 0.9017 (tp) REVERT: A 268 ASN cc_start: 0.7251 (t0) cc_final: 0.6842 (p0) REVERT: B 230 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6859 (mp) REVERT: B 298 ARG cc_start: 0.5162 (tpt-90) cc_final: 0.4161 (mmm160) REVERT: C 744 SER cc_start: 0.9076 (m) cc_final: 0.8804 (m) REVERT: C 967 GLN cc_start: 0.7336 (mm-40) cc_final: 0.6676 (mt0) REVERT: C 983 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7225 (pp) REVERT: C 984 ASP cc_start: 0.6523 (m-30) cc_final: 0.6295 (m-30) REVERT: C 1042 GLU cc_start: 0.6712 (tp30) cc_final: 0.6433 (mm-30) REVERT: D 97 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6889 (mp) REVERT: G 21 MET cc_start: 0.6907 (mtm) cc_final: 0.6480 (mtm) REVERT: G 314 MET cc_start: 0.8441 (ttp) cc_final: 0.8092 (ttp) REVERT: G 798 ASP cc_start: 0.7850 (m-30) cc_final: 0.7626 (m-30) REVERT: H 84 ARG cc_start: 0.6823 (tpt90) cc_final: 0.5994 (mmm160) REVERT: H 291 ARG cc_start: 0.7384 (mmt90) cc_final: 0.7079 (mmt-90) outliers start: 65 outliers final: 45 residues processed: 573 average time/residue: 0.2198 time to fit residues: 209.3627 Evaluate side-chains 548 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 500 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 405 VAL Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 965 THR Chi-restraints excluded: chain E residue 983 LEU Chi-restraints excluded: chain E residue 1010 LEU Chi-restraints excluded: chain F residue 47 CYS Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 728 SER Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 884 ASN Chi-restraints excluded: chain G residue 990 LEU Chi-restraints excluded: chain H residue 169 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 368 optimal weight: 0.9980 chunk 29 optimal weight: 0.0970 chunk 213 optimal weight: 10.0000 chunk 431 optimal weight: 5.9990 chunk 429 optimal weight: 8.9990 chunk 72 optimal weight: 0.0070 chunk 339 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 433 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 overall best weight: 2.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 365 HIS B 153 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.152860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.110835 restraints weight = 44485.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.107171 restraints weight = 56307.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.109437 restraints weight = 61897.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.109982 restraints weight = 34869.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.112404 restraints weight = 31188.447| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36626 Z= 0.165 Angle : 0.528 9.553 49792 Z= 0.262 Chirality : 0.040 0.170 5744 Planarity : 0.004 0.050 6284 Dihedral : 3.675 48.909 4916 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.84 % Favored : 97.07 % Rotamer: Outliers : 2.52 % Allowed : 13.95 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.12), residues: 4512 helix: 1.23 (0.11), residues: 2081 sheet: -0.29 (0.24), residues: 474 loop : -0.38 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 74 TYR 0.024 0.001 TYR A 198 PHE 0.018 0.002 PHE C 511 TRP 0.022 0.001 TRP E 22 HIS 0.006 0.001 HIS E 771 Details of bonding type rmsd covalent geometry : bond 0.00405 (36616) covalent geometry : angle 0.52824 (49772) SS BOND : bond 0.00122 ( 10) SS BOND : angle 0.60178 ( 20) hydrogen bonds : bond 0.04346 ( 1621) hydrogen bonds : angle 4.21586 ( 4590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 517 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9328 (tp) cc_final: 0.8996 (tp) REVERT: A 268 ASN cc_start: 0.7320 (t0) cc_final: 0.6813 (p0) REVERT: A 905 LEU cc_start: 0.8835 (mt) cc_final: 0.8505 (mt) REVERT: B 230 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7014 (mp) REVERT: B 298 ARG cc_start: 0.5139 (tpt-90) cc_final: 0.4109 (mmm160) REVERT: C 744 SER cc_start: 0.9150 (m) cc_final: 0.8849 (m) REVERT: C 983 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7321 (pp) REVERT: C 984 ASP cc_start: 0.6495 (m-30) cc_final: 0.6257 (m-30) REVERT: D 76 LEU cc_start: 0.7435 (mt) cc_final: 0.7229 (tp) REVERT: D 97 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6645 (mp) REVERT: E 917 VAL cc_start: 0.9420 (OUTLIER) cc_final: 0.9195 (t) REVERT: E 1054 GLN cc_start: 0.7624 (pt0) cc_final: 0.7318 (pt0) REVERT: G 21 MET cc_start: 0.6886 (mtm) cc_final: 0.6493 (mtm) REVERT: G 815 LEU cc_start: 0.4332 (OUTLIER) cc_final: 0.3882 (pp) REVERT: G 960 ARG cc_start: 0.7186 (ttp-170) cc_final: 0.6764 (ttm-80) REVERT: H 76 LEU cc_start: 0.7323 (tt) cc_final: 0.7019 (tt) REVERT: H 84 ARG cc_start: 0.7028 (tpt90) cc_final: 0.6074 (mmm160) outliers start: 98 outliers final: 73 residues processed: 577 average time/residue: 0.2219 time to fit residues: 212.3110 Evaluate side-chains 578 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 500 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 992 ASP Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 405 VAL Chi-restraints excluded: chain E residue 759 SER Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 922 SER Chi-restraints excluded: chain E residue 965 THR Chi-restraints excluded: chain E residue 983 LEU Chi-restraints excluded: chain E residue 1010 LEU Chi-restraints excluded: chain E residue 1033 VAL Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 317 SER Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 728 SER Chi-restraints excluded: chain G residue 765 ARG Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 815 LEU Chi-restraints excluded: chain G residue 884 ASN Chi-restraints excluded: chain G residue 990 LEU Chi-restraints excluded: chain G residue 1010 LEU Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 229 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 265 optimal weight: 2.9990 chunk 108 optimal weight: 0.0370 chunk 145 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 253 optimal weight: 2.9990 chunk 349 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 429 optimal weight: 7.9990 chunk 166 optimal weight: 0.0970 chunk 342 optimal weight: 2.9990 chunk 397 optimal weight: 4.9990 overall best weight: 1.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 365 HIS B 153 ASN C 268 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN G 449 ASN H 153 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.152748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.111385 restraints weight = 44551.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.109037 restraints weight = 55772.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.110118 restraints weight = 63631.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.110815 restraints weight = 35023.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.113376 restraints weight = 30168.920| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36626 Z= 0.150 Angle : 0.521 9.640 49792 Z= 0.259 Chirality : 0.040 0.171 5744 Planarity : 0.004 0.054 6284 Dihedral : 3.704 46.429 4916 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % Rotamer: Outliers : 2.60 % Allowed : 14.57 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.12), residues: 4512 helix: 1.12 (0.11), residues: 2103 sheet: -0.38 (0.24), residues: 472 loop : -0.51 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 976 TYR 0.017 0.001 TYR A 198 PHE 0.017 0.001 PHE E 511 TRP 0.024 0.001 TRP E 22 HIS 0.004 0.001 HIS E 771 Details of bonding type rmsd covalent geometry : bond 0.00365 (36616) covalent geometry : angle 0.52136 (49772) SS BOND : bond 0.00122 ( 10) SS BOND : angle 0.67349 ( 20) hydrogen bonds : bond 0.04225 ( 1621) hydrogen bonds : angle 4.21390 ( 4590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 505 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: A 142 GLN cc_start: 0.5117 (tp-100) cc_final: 0.4899 (tp-100) REVERT: A 161 LEU cc_start: 0.9329 (tp) cc_final: 0.9010 (tp) REVERT: A 176 TRP cc_start: 0.8829 (m100) cc_final: 0.8586 (m100) REVERT: A 268 ASN cc_start: 0.7346 (t0) cc_final: 0.6821 (p0) REVERT: A 905 LEU cc_start: 0.8847 (mt) cc_final: 0.8514 (mt) REVERT: B 230 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7006 (mp) REVERT: B 298 ARG cc_start: 0.5068 (tpt-90) cc_final: 0.4049 (mmm160) REVERT: C 478 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8443 (mtmm) REVERT: C 744 SER cc_start: 0.9147 (m) cc_final: 0.8849 (m) REVERT: C 967 GLN cc_start: 0.7301 (mm-40) cc_final: 0.6605 (mt0) REVERT: C 983 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7366 (pp) REVERT: C 984 ASP cc_start: 0.6396 (m-30) cc_final: 0.6195 (m-30) REVERT: D 97 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6581 (mp) REVERT: E 917 VAL cc_start: 0.9425 (OUTLIER) cc_final: 0.9192 (t) REVERT: G 21 MET cc_start: 0.6883 (mtm) cc_final: 0.6496 (mtm) REVERT: G 314 MET cc_start: 0.8553 (ttp) cc_final: 0.8210 (ttp) REVERT: G 815 LEU cc_start: 0.4488 (OUTLIER) cc_final: 0.4015 (pp) REVERT: G 960 ARG cc_start: 0.7211 (ttp-170) cc_final: 0.6808 (ttm-80) REVERT: H 76 LEU cc_start: 0.7376 (tt) cc_final: 0.7031 (tt) REVERT: H 84 ARG cc_start: 0.7081 (tpt90) cc_final: 0.6160 (mmm160) REVERT: H 291 ARG cc_start: 0.7458 (mmt90) cc_final: 0.7145 (mmt-90) outliers start: 101 outliers final: 74 residues processed: 570 average time/residue: 0.2232 time to fit residues: 211.1665 Evaluate side-chains 566 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 487 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 405 VAL Chi-restraints excluded: chain E residue 759 SER Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 922 SER Chi-restraints excluded: chain E residue 965 THR Chi-restraints excluded: chain E residue 983 LEU Chi-restraints excluded: chain E residue 1010 LEU Chi-restraints excluded: chain E residue 1033 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 267 GLN Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 317 SER Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 727 VAL Chi-restraints excluded: chain G residue 728 SER Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain G residue 765 ARG Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 815 LEU Chi-restraints excluded: chain G residue 884 ASN Chi-restraints excluded: chain G residue 990 LEU Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 229 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 149 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 445 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 395 optimal weight: 0.9990 chunk 260 optimal weight: 5.9990 chunk 289 optimal weight: 0.7980 chunk 396 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 321 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 365 HIS B 81 ASN B 153 ASN C 268 ASN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.154758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.112182 restraints weight = 44159.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.107901 restraints weight = 54447.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.110849 restraints weight = 56376.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.110769 restraints weight = 34383.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.112174 restraints weight = 31220.150| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36626 Z= 0.120 Angle : 0.506 9.437 49792 Z= 0.250 Chirality : 0.039 0.157 5744 Planarity : 0.004 0.057 6284 Dihedral : 3.585 22.263 4912 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.73 % Favored : 97.19 % Rotamer: Outliers : 2.19 % Allowed : 15.53 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.12), residues: 4512 helix: 1.28 (0.11), residues: 2075 sheet: -0.39 (0.24), residues: 472 loop : -0.40 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 976 TYR 0.024 0.001 TYR A 198 PHE 0.020 0.001 PHE C 511 TRP 0.025 0.001 TRP E 22 HIS 0.003 0.001 HIS E 771 Details of bonding type rmsd covalent geometry : bond 0.00284 (36616) covalent geometry : angle 0.50546 (49772) SS BOND : bond 0.00107 ( 10) SS BOND : angle 0.60992 ( 20) hydrogen bonds : bond 0.03935 ( 1621) hydrogen bonds : angle 4.13082 ( 4590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 496 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9323 (tp) cc_final: 0.9008 (tp) REVERT: A 176 TRP cc_start: 0.8802 (m100) cc_final: 0.8566 (m100) REVERT: A 268 ASN cc_start: 0.7409 (t0) cc_final: 0.6839 (p0) REVERT: A 513 MET cc_start: 0.7854 (tpp) cc_final: 0.7579 (tpt) REVERT: A 905 LEU cc_start: 0.8818 (mt) cc_final: 0.8498 (mt) REVERT: A 930 ASN cc_start: 0.7882 (p0) cc_final: 0.7649 (p0) REVERT: B 230 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7047 (mp) REVERT: B 298 ARG cc_start: 0.5054 (tpt-90) cc_final: 0.4027 (mmm160) REVERT: C 744 SER cc_start: 0.9141 (m) cc_final: 0.8843 (m) REVERT: C 983 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7282 (pp) REVERT: C 984 ASP cc_start: 0.6466 (m-30) cc_final: 0.6252 (m-30) REVERT: D 97 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6531 (mp) REVERT: E 815 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6411 (mt) REVERT: E 917 VAL cc_start: 0.9415 (OUTLIER) cc_final: 0.9185 (t) REVERT: G 314 MET cc_start: 0.8466 (ttp) cc_final: 0.8112 (ttp) REVERT: G 815 LEU cc_start: 0.4601 (OUTLIER) cc_final: 0.4146 (pp) REVERT: G 960 ARG cc_start: 0.7200 (ttp-170) cc_final: 0.6807 (ttm-80) REVERT: H 76 LEU cc_start: 0.7539 (tt) cc_final: 0.7252 (tt) REVERT: H 84 ARG cc_start: 0.7272 (tpt90) cc_final: 0.6236 (mmm160) outliers start: 85 outliers final: 65 residues processed: 551 average time/residue: 0.2235 time to fit residues: 203.9589 Evaluate side-chains 559 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 488 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 782 THR Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 405 VAL Chi-restraints excluded: chain E residue 759 SER Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 905 LEU Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 922 SER Chi-restraints excluded: chain E residue 983 LEU Chi-restraints excluded: chain E residue 1010 LEU Chi-restraints excluded: chain E residue 1033 VAL Chi-restraints excluded: chain F residue 47 CYS Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 728 SER Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain G residue 765 ARG Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 815 LEU Chi-restraints excluded: chain G residue 884 ASN Chi-restraints excluded: chain G residue 964 SER Chi-restraints excluded: chain G residue 990 LEU Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 229 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 83 optimal weight: 7.9990 chunk 435 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 345 optimal weight: 0.6980 chunk 265 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 348 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 235 optimal weight: 0.0270 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 365 HIS B 81 ASN B 153 ASN C 268 ASN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN H 153 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.154294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.112581 restraints weight = 44324.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.108781 restraints weight = 55736.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.111108 restraints weight = 59585.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.111769 restraints weight = 34570.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.114080 restraints weight = 30792.237| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36626 Z= 0.118 Angle : 0.506 9.253 49792 Z= 0.251 Chirality : 0.039 0.156 5744 Planarity : 0.004 0.056 6284 Dihedral : 3.540 16.901 4912 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % Rotamer: Outliers : 2.21 % Allowed : 15.60 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.12), residues: 4512 helix: 1.31 (0.12), residues: 2073 sheet: -0.31 (0.24), residues: 482 loop : -0.39 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 291 TYR 0.020 0.001 TYR A 198 PHE 0.017 0.001 PHE E 511 TRP 0.029 0.001 TRP E 22 HIS 0.003 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00279 (36616) covalent geometry : angle 0.50626 (49772) SS BOND : bond 0.00102 ( 10) SS BOND : angle 0.60501 ( 20) hydrogen bonds : bond 0.03872 ( 1621) hydrogen bonds : angle 4.09501 ( 4590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 496 time to evaluate : 1.670 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9337 (tp) cc_final: 0.9013 (tp) REVERT: A 176 TRP cc_start: 0.8795 (m100) cc_final: 0.8557 (m100) REVERT: A 268 ASN cc_start: 0.7424 (t0) cc_final: 0.6864 (p0) REVERT: A 930 ASN cc_start: 0.7805 (p0) cc_final: 0.7570 (p0) REVERT: B 230 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7045 (mp) REVERT: B 298 ARG cc_start: 0.4975 (tpt-90) cc_final: 0.3959 (mmm160) REVERT: C 744 SER cc_start: 0.9161 (m) cc_final: 0.8863 (m) REVERT: C 967 GLN cc_start: 0.7324 (mm-40) cc_final: 0.6646 (mt0) REVERT: C 983 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7291 (pp) REVERT: E 815 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6387 (mt) REVERT: E 917 VAL cc_start: 0.9417 (OUTLIER) cc_final: 0.9191 (t) REVERT: G 314 MET cc_start: 0.8484 (ttp) cc_final: 0.8135 (ttp) REVERT: G 815 LEU cc_start: 0.4610 (OUTLIER) cc_final: 0.4118 (pp) REVERT: G 960 ARG cc_start: 0.7210 (ttp-170) cc_final: 0.6859 (ttm-80) REVERT: H 76 LEU cc_start: 0.7518 (tt) cc_final: 0.7219 (tt) REVERT: H 84 ARG cc_start: 0.7260 (tpt90) cc_final: 0.6405 (mmm160) REVERT: H 291 ARG cc_start: 0.7428 (mmt90) cc_final: 0.7191 (mmt-90) outliers start: 86 outliers final: 75 residues processed: 553 average time/residue: 0.2213 time to fit residues: 203.3679 Evaluate side-chains 574 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 494 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 771 HIS Chi-restraints excluded: chain C residue 782 THR Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 992 ASP Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 405 VAL Chi-restraints excluded: chain E residue 755 VAL Chi-restraints excluded: chain E residue 759 SER Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 905 LEU Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 983 LEU Chi-restraints excluded: chain E residue 1010 LEU Chi-restraints excluded: chain E residue 1033 VAL Chi-restraints excluded: chain E residue 1054 GLN Chi-restraints excluded: chain F residue 47 CYS Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 267 GLN Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 727 VAL Chi-restraints excluded: chain G residue 728 SER Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain G residue 765 ARG Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 815 LEU Chi-restraints excluded: chain G residue 881 GLU Chi-restraints excluded: chain G residue 884 ASN Chi-restraints excluded: chain G residue 990 LEU Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 229 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 31 optimal weight: 0.9990 chunk 429 optimal weight: 8.9990 chunk 272 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 370 optimal weight: 4.9990 chunk 417 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 409 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 157 ASN B 81 ASN B 153 ASN C 268 ASN C 476 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN H 153 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.154049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.112372 restraints weight = 44417.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.109240 restraints weight = 55487.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.111360 restraints weight = 59360.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.111731 restraints weight = 34721.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.113997 restraints weight = 31838.081| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36626 Z= 0.122 Angle : 0.509 9.141 49792 Z= 0.252 Chirality : 0.039 0.155 5744 Planarity : 0.004 0.056 6284 Dihedral : 3.544 16.890 4912 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.79 % Favored : 97.16 % Rotamer: Outliers : 2.34 % Allowed : 15.50 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.12), residues: 4512 helix: 1.32 (0.12), residues: 2073 sheet: -0.35 (0.24), residues: 474 loop : -0.41 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 976 TYR 0.019 0.001 TYR A 198 PHE 0.017 0.001 PHE E 511 TRP 0.029 0.001 TRP E 22 HIS 0.003 0.001 HIS E 771 Details of bonding type rmsd covalent geometry : bond 0.00292 (36616) covalent geometry : angle 0.50892 (49772) SS BOND : bond 0.00100 ( 10) SS BOND : angle 0.60973 ( 20) hydrogen bonds : bond 0.03883 ( 1621) hydrogen bonds : angle 4.09328 ( 4590) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 502 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9341 (tp) cc_final: 0.9018 (tp) REVERT: A 268 ASN cc_start: 0.7440 (t0) cc_final: 0.6869 (p0) REVERT: A 930 ASN cc_start: 0.7810 (p0) cc_final: 0.7571 (p0) REVERT: B 230 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7003 (mp) REVERT: B 298 ARG cc_start: 0.5113 (tpt-90) cc_final: 0.4029 (mmm160) REVERT: C 744 SER cc_start: 0.9186 (m) cc_final: 0.8898 (m) REVERT: C 967 GLN cc_start: 0.7273 (mm-40) cc_final: 0.6561 (mt0) REVERT: E 815 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6352 (mt) REVERT: E 917 VAL cc_start: 0.9413 (OUTLIER) cc_final: 0.9202 (t) REVERT: G 314 MET cc_start: 0.8472 (ttp) cc_final: 0.8126 (ttp) REVERT: G 815 LEU cc_start: 0.4602 (OUTLIER) cc_final: 0.4106 (pp) REVERT: G 960 ARG cc_start: 0.7193 (ttp-170) cc_final: 0.6857 (ttm-80) REVERT: H 76 LEU cc_start: 0.7497 (tt) cc_final: 0.7192 (tt) REVERT: H 84 ARG cc_start: 0.7210 (tpt90) cc_final: 0.6428 (mmm160) outliers start: 91 outliers final: 78 residues processed: 560 average time/residue: 0.2180 time to fit residues: 203.3488 Evaluate side-chains 577 residues out of total 3884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 495 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 829 SER Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 782 THR Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain C residue 992 ASP Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 405 VAL Chi-restraints excluded: chain E residue 755 VAL Chi-restraints excluded: chain E residue 759 SER Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 879 ILE Chi-restraints excluded: chain E residue 905 LEU Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 983 LEU Chi-restraints excluded: chain E residue 1010 LEU Chi-restraints excluded: chain E residue 1033 VAL Chi-restraints excluded: chain E residue 1054 GLN Chi-restraints excluded: chain F residue 47 CYS Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 84 ARG Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 727 VAL Chi-restraints excluded: chain G residue 728 SER Chi-restraints excluded: chain G residue 739 MET Chi-restraints excluded: chain G residue 765 ARG Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 815 LEU Chi-restraints excluded: chain G residue 884 ASN Chi-restraints excluded: chain G residue 964 SER Chi-restraints excluded: chain G residue 990 LEU Chi-restraints excluded: chain G residue 1029 THR Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 229 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 93 optimal weight: 0.9980 chunk 257 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 418 optimal weight: 5.9990 chunk 262 optimal weight: 0.8980 chunk 329 optimal weight: 0.2980 chunk 239 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 156 optimal weight: 0.1980 chunk 276 optimal weight: 0.5980 chunk 344 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 153 ASN C 254 HIS C 268 ASN ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 449 ASN H 153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.156237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.114994 restraints weight = 44038.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.111652 restraints weight = 62711.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.113604 restraints weight = 60078.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.114377 restraints weight = 38100.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.114790 restraints weight = 35018.967| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 36626 Z= 0.097 Angle : 0.497 13.033 49792 Z= 0.244 Chirality : 0.039 0.154 5744 Planarity : 0.004 0.058 6284 Dihedral : 3.457 16.953 4912 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.50 % Favored : 97.45 % Rotamer: Outliers : 1.60 % Allowed : 16.43 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.13), residues: 4512 helix: 1.50 (0.12), residues: 2045 sheet: -0.21 (0.24), residues: 478 loop : -0.33 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 291 TYR 0.031 0.001 TYR A 198 PHE 0.020 0.001 PHE E 511 TRP 0.028 0.001 TRP E 22 HIS 0.009 0.000 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00217 (36616) covalent geometry : angle 0.49697 (49772) SS BOND : bond 0.00086 ( 10) SS BOND : angle 0.62081 ( 20) hydrogen bonds : bond 0.03504 ( 1621) hydrogen bonds : angle 3.99102 ( 4590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6461.91 seconds wall clock time: 112 minutes 38.50 seconds (6758.50 seconds total)