Starting phenix.real_space_refine on Tue Aug 26 21:42:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ca7_45381/08_2025/9ca7_45381.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ca7_45381/08_2025/9ca7_45381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ca7_45381/08_2025/9ca7_45381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ca7_45381/08_2025/9ca7_45381.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ca7_45381/08_2025/9ca7_45381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ca7_45381/08_2025/9ca7_45381.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 260 5.49 5 Mg 5 5.21 5 S 178 5.16 5 C 25882 2.51 5 N 7551 2.21 5 O 8495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 42373 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 736, 6036 Classifications: {'peptide': 736} Link IDs: {'PTRANS': 48, 'TRANS': 687} Chain breaks: 3 Chain: "B" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1125 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 12, 'TRANS': 124} Chain breaks: 2 Chain: "C" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3226 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 378} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 831 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 8, 'TRANS': 96} Chain breaks: 1 Chain: "E" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3344 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 416} Chain breaks: 1 Chain: "F" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3395 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 11, 'TRANS': 426} Chain: "G" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3430 Classifications: {'peptide': 445} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 427} Chain: "H" Number of atoms: 3361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3361 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 10, 'TRANS': 421} Chain breaks: 1 Chain: "I" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3365 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 419} Chain breaks: 1 Chain: "J" Number of atoms: 3254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3254 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 10, 'TRANS': 407} Chain breaks: 2 Chain: "Q" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 742 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "R" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "S" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "T" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "U" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 740 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "V" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "W" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "X" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "Y" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2466 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Chain: "Z" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2495 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11021 SG CYS D 128 74.279 116.533 63.473 1.00 83.33 S ATOM 11040 SG CYS D 131 70.841 117.923 62.663 1.00 58.50 S ATOM 11180 SG CYS D 149 74.038 120.007 61.857 1.00100.42 S ATOM 10943 SG CYS D 117 71.808 108.912 55.541 1.00 66.45 S ATOM 10961 SG CYS D 120 72.142 106.690 52.469 1.00 71.06 S ATOM 11078 SG CYS D 136 74.337 106.109 55.408 1.00 80.64 S ATOM 11109 SG CYS D 140 74.864 109.264 53.336 1.00 77.95 S Time building chain proxies: 8.03, per 1000 atoms: 0.19 Number of scatterers: 42373 At special positions: 0 Unit cell: (166.05, 186.55, 161.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 178 16.00 P 260 15.00 Mg 5 11.99 O 8495 8.00 N 7551 7.00 C 25882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" NE2 HIS D 144 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 128 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 131 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 149 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 136 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 120 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 140 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 117 " Number of angles added : 9 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8792 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 43 sheets defined 52.5% alpha, 10.9% beta 121 base pairs and 212 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'A' and resid 223 through 252 removed outlier: 3.619A pdb=" N LYS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 635 Processing helix chain 'A' and resid 648 through 663 Processing helix chain 'A' and resid 675 through 690 removed outlier: 4.650A pdb=" N LEU A 680 " --> pdb=" O THR A 676 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASN A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 731 through 738 removed outlier: 3.791A pdb=" N ARG A 737 " --> pdb=" O GLN A 733 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 756 through 764 removed outlier: 4.580A pdb=" N ASN A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 793 removed outlier: 4.045A pdb=" N LEU A 785 " --> pdb=" O SER A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 807 removed outlier: 3.624A pdb=" N PHE A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 816 Processing helix chain 'A' and resid 822 through 834 removed outlier: 3.622A pdb=" N VAL A 826 " --> pdb=" O ASN A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 846 Processing helix chain 'A' and resid 862 through 876 Processing helix chain 'A' and resid 889 through 903 Processing helix chain 'A' and resid 904 through 907 Processing helix chain 'A' and resid 928 through 932 Processing helix chain 'A' and resid 936 through 940 Processing helix chain 'A' and resid 942 through 947 removed outlier: 3.848A pdb=" N ARG A 945 " --> pdb=" O ASP A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 952 Processing helix chain 'A' and resid 956 through 962 Processing helix chain 'A' and resid 962 through 968 removed outlier: 3.937A pdb=" N ARG A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'A' and resid 1886 through 1911 Processing helix chain 'A' and resid 1919 through 1927 Processing helix chain 'A' and resid 1945 through 1950 Processing helix chain 'A' and resid 1952 through 1958 Processing helix chain 'A' and resid 1961 through 1969 Processing helix chain 'A' and resid 1969 through 1977 removed outlier: 3.504A pdb=" N ILE A1977 " --> pdb=" O ILE A1973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1998 through 2015 Processing helix chain 'A' and resid 2016 through 2020 removed outlier: 3.564A pdb=" N ARG A2019 " --> pdb=" O PRO A2016 " (cutoff:3.500A) Proline residue: A2020 - end of helix No H-bonds generated for 'chain 'A' and resid 2016 through 2020' Processing helix chain 'A' and resid 2021 through 2030 Processing helix chain 'A' and resid 2035 through 2041 removed outlier: 4.366A pdb=" N GLN A2039 " --> pdb=" O LEU A2035 " (cutoff:3.500A) Processing helix chain 'A' and resid 2042 through 2059 Processing helix chain 'A' and resid 2068 through 2083 Processing helix chain 'A' and resid 2094 through 2108 removed outlier: 3.743A pdb=" N GLN A2099 " --> pdb=" O VAL A2095 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A2100 " --> pdb=" O GLU A2096 " (cutoff:3.500A) Processing helix chain 'A' and resid 2141 through 2154 removed outlier: 3.680A pdb=" N ASP A2145 " --> pdb=" O ASN A2141 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N CYS A2152 " --> pdb=" O ALA A2148 " (cutoff:3.500A) Processing helix chain 'A' and resid 2171 through 2191 removed outlier: 4.006A pdb=" N ASN A2175 " --> pdb=" O THR A2171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2197 through 2203 removed outlier: 3.958A pdb=" N PHE A2201 " --> pdb=" O THR A2197 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 202 Processing helix chain 'B' and resid 270 through 278 removed outlier: 3.515A pdb=" N PHE B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 331 Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 67 through 80 removed outlier: 3.725A pdb=" N GLN C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 127 through 139 Processing helix chain 'C' and resid 176 through 192 Processing helix chain 'C' and resid 198 through 210 Processing helix chain 'C' and resid 215 through 225 Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 272 through 283 removed outlier: 3.613A pdb=" N VAL C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 4.619A pdb=" N LEU C 281 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 293 through 305 removed outlier: 3.764A pdb=" N LEU C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 315 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 328 through 341 Processing helix chain 'C' and resid 357 through 369 Processing helix chain 'C' and resid 371 through 376 removed outlier: 3.626A pdb=" N MET C 375 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 394 removed outlier: 4.191A pdb=" N GLU C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N HIS C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU C 391 " --> pdb=" O HIS C 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 35 Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 137 through 148 Processing helix chain 'E' and resid 42 through 59 removed outlier: 3.712A pdb=" N LYS E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 88 Processing helix chain 'E' and resid 97 through 102 removed outlier: 3.685A pdb=" N VAL E 101 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR E 102 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 119 removed outlier: 3.517A pdb=" N ALA E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 183 Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 240 through 249 Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.540A pdb=" N MET E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 289 Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.802A pdb=" N ARG E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 356 Processing helix chain 'E' and resid 367 through 382 Processing helix chain 'E' and resid 387 through 400 Processing helix chain 'E' and resid 402 through 409 Processing helix chain 'E' and resid 409 through 420 Processing helix chain 'E' and resid 426 through 437 Processing helix chain 'E' and resid 439 through 450 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'F' and resid 106 through 109 Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 175 through 186 Processing helix chain 'F' and resid 244 through 253 removed outlier: 4.106A pdb=" N ARG F 253 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 263 removed outlier: 4.271A pdb=" N PHE F 261 " --> pdb=" O PHE F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 286 Processing helix chain 'F' and resid 301 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.699A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 378 Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.932A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'G' and resid 42 through 59 removed outlier: 3.692A pdb=" N LYS G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 88 Processing helix chain 'G' and resid 99 through 102 Processing helix chain 'G' and resid 107 through 119 Processing helix chain 'G' and resid 175 through 183 removed outlier: 4.176A pdb=" N SER G 179 " --> pdb=" O SER G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 210 No H-bonds generated for 'chain 'G' and resid 208 through 210' Processing helix chain 'G' and resid 240 through 249 Processing helix chain 'G' and resid 255 through 264 Processing helix chain 'G' and resid 272 through 289 Processing helix chain 'G' and resid 304 through 307 Processing helix chain 'G' and resid 308 through 320 removed outlier: 3.524A pdb=" N HIS G 316 " --> pdb=" O PHE G 312 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG G 317 " --> pdb=" O THR G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 356 Processing helix chain 'G' and resid 367 through 382 Processing helix chain 'G' and resid 387 through 400 Processing helix chain 'G' and resid 402 through 408 removed outlier: 3.501A pdb=" N SER G 406 " --> pdb=" O THR G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 421 Processing helix chain 'G' and resid 426 through 437 Processing helix chain 'G' and resid 439 through 450 Processing helix chain 'H' and resid 49 through 66 Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'H' and resid 106 through 109 Processing helix chain 'H' and resid 114 through 126 Processing helix chain 'H' and resid 175 through 185 Processing helix chain 'H' and resid 210 through 214 removed outlier: 3.908A pdb=" N ASP H 214 " --> pdb=" O ARG H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 251 Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing helix chain 'H' and resid 258 through 263 Processing helix chain 'H' and resid 269 through 286 Processing helix chain 'H' and resid 301 through 304 Processing helix chain 'H' and resid 305 through 316 removed outlier: 3.815A pdb=" N ARG H 314 " --> pdb=" O SER H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 352 Processing helix chain 'H' and resid 363 through 379 Processing helix chain 'H' and resid 383 through 397 Processing helix chain 'H' and resid 398 through 416 removed outlier: 3.814A pdb=" N THR H 407 " --> pdb=" O ILE H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 422 through 433 Processing helix chain 'H' and resid 435 through 446 Processing helix chain 'I' and resid 42 through 58 Processing helix chain 'I' and resid 75 through 88 Processing helix chain 'I' and resid 99 through 102 removed outlier: 3.840A pdb=" N TYR I 102 " --> pdb=" O SER I 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 99 through 102' Processing helix chain 'I' and resid 107 through 120 Processing helix chain 'I' and resid 175 through 183 removed outlier: 3.954A pdb=" N SER I 179 " --> pdb=" O SER I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 210 No H-bonds generated for 'chain 'I' and resid 208 through 210' Processing helix chain 'I' and resid 240 through 247 Processing helix chain 'I' and resid 255 through 264 removed outlier: 3.876A pdb=" N LEU I 263 " --> pdb=" O MET I 259 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET I 264 " --> pdb=" O MET I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 290 Processing helix chain 'I' and resid 303 through 307 Processing helix chain 'I' and resid 308 through 320 removed outlier: 3.592A pdb=" N ARG I 317 " --> pdb=" O THR I 313 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU I 320 " --> pdb=" O HIS I 316 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 356 Processing helix chain 'I' and resid 367 through 382 Processing helix chain 'I' and resid 387 through 401 Processing helix chain 'I' and resid 402 through 409 Processing helix chain 'I' and resid 409 through 421 Processing helix chain 'I' and resid 426 through 437 Processing helix chain 'I' and resid 439 through 450 Processing helix chain 'J' and resid 49 through 66 Processing helix chain 'J' and resid 82 through 94 Processing helix chain 'J' and resid 106 through 109 Processing helix chain 'J' and resid 114 through 125 Processing helix chain 'J' and resid 175 through 185 Processing helix chain 'J' and resid 244 through 251 Processing helix chain 'J' and resid 255 through 257 No H-bonds generated for 'chain 'J' and resid 255 through 257' Processing helix chain 'J' and resid 258 through 263 Processing helix chain 'J' and resid 269 through 286 Processing helix chain 'J' and resid 301 through 304 Processing helix chain 'J' and resid 305 through 316 removed outlier: 3.712A pdb=" N ARG J 314 " --> pdb=" O SER J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 347 through 352 Processing helix chain 'J' and resid 363 through 379 Processing helix chain 'J' and resid 383 through 397 Processing helix chain 'J' and resid 398 through 416 removed outlier: 4.160A pdb=" N THR J 407 " --> pdb=" O ILE J 403 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA J 408 " --> pdb=" O GLN J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 433 Processing helix chain 'J' and resid 435 through 446 Processing helix chain 'Q' and resid 16 through 22 Processing helix chain 'Q' and resid 26 through 37 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.252A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'R' and resid 37 through 49 Processing helix chain 'R' and resid 55 through 84 Processing helix chain 'R' and resid 90 through 102 Processing helix chain 'R' and resid 103 through 123 Processing helix chain 'S' and resid 16 through 22 Processing helix chain 'S' and resid 26 through 37 Processing helix chain 'S' and resid 45 through 73 removed outlier: 4.433A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 90 Processing helix chain 'S' and resid 90 through 97 Processing helix chain 'S' and resid 112 through 116 Processing helix chain 'T' and resid 37 through 49 Processing helix chain 'T' and resid 55 through 84 Processing helix chain 'T' and resid 90 through 102 Processing helix chain 'T' and resid 103 through 125 Processing helix chain 'U' and resid 46 through 57 Processing helix chain 'U' and resid 63 through 79 removed outlier: 4.039A pdb=" N ASP U 77 " --> pdb=" O GLU U 73 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE U 78 " --> pdb=" O ILE U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 114 Processing helix chain 'U' and resid 120 through 132 removed outlier: 3.553A pdb=" N ILE U 124 " --> pdb=" O MET U 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 24 through 29 removed outlier: 3.955A pdb=" N GLN V 27 " --> pdb=" O ASP V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 41 Processing helix chain 'V' and resid 49 through 76 removed outlier: 3.640A pdb=" N GLU V 53 " --> pdb=" O LEU V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 82 through 94 Processing helix chain 'W' and resid 44 through 57 Processing helix chain 'W' and resid 63 through 79 removed outlier: 4.124A pdb=" N ASP W 77 " --> pdb=" O GLU W 73 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE W 78 " --> pdb=" O ILE W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 113 Processing helix chain 'W' and resid 120 through 132 Processing helix chain 'X' and resid 24 through 29 removed outlier: 3.874A pdb=" N GLN X 27 " --> pdb=" O ASP X 24 " (cutoff:3.500A) Processing helix chain 'X' and resid 30 through 41 Processing helix chain 'X' and resid 49 through 76 removed outlier: 3.623A pdb=" N GLU X 53 " --> pdb=" O LEU X 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 695 through 697 removed outlier: 6.146A pdb=" N ARG A 741 " --> pdb=" O ARG A 769 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU A 771 " --> pdb=" O ARG A 741 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU A 743 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU A 773 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A 745 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY A 639 " --> pdb=" O ARG A 770 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG A 840 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 852 through 859 removed outlier: 6.055A pdb=" N LEU A2063 " --> pdb=" O VAL A2134 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL A2062 " --> pdb=" O PHE A2114 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU A2116 " --> pdb=" O VAL A2062 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE A2064 " --> pdb=" O LEU A2116 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A2117 " --> pdb=" O LEU A2089 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 916 through 917 removed outlier: 6.027A pdb=" N PHE A 916 " --> pdb=" O GLU A1984 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 922 through 924 Processing sheet with id=AA5, first strand: chain 'B' and resid 211 through 219 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 261 through 268 current: chain 'F' and resid 158 through 164 removed outlier: 4.352A pdb=" N GLY F 159 " --> pdb=" O LEU F 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 169 through 174 current: chain 'F' and resid 202 through 207 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 202 through 207 current: chain 'G' and resid 152 through 163 removed outlier: 3.799A pdb=" N GLY G 166 " --> pdb=" O THR G 163 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 166 through 172 current: chain 'G' and resid 200 through 206 removed outlier: 5.327A pdb=" N VAL G 221 " --> pdb=" O GLN G 203 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG G 205 " --> pdb=" O VAL G 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AA7, first strand: chain 'C' and resid 23 through 26 removed outlier: 4.441A pdb=" N ASN C 8 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR C 91 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N LEU C 123 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE C 93 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL C 125 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE C 95 " --> pdb=" O VAL C 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AB1, first strand: chain 'C' and resid 171 through 173 removed outlier: 8.472A pdb=" N VAL C 318 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE C 146 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR C 320 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL C 148 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 317 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 248 through 249 removed outlier: 3.537A pdb=" N PHE C 248 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 126 through 127 Processing sheet with id=AB4, first strand: chain 'E' and resid 93 through 96 removed outlier: 6.575A pdb=" N LEU E 299 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ALA E 330 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL E 301 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL E 66 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N SER E 331 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU E 68 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ALA E 65 " --> pdb=" O MET E 359 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE E 361 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU E 67 " --> pdb=" O ILE E 361 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 121 through 141 removed outlier: 6.190A pdb=" N GLY E 160 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU E 138 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE E 158 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N HIS E 156 " --> pdb=" O PRO E 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 167 through 172 current: chain 'E' and resid 199 through 206 removed outlier: 5.532A pdb=" N VAL E 221 " --> pdb=" O GLN E 203 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ARG E 205 " --> pdb=" O VAL E 221 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AB7, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.457A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY F 77 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR F 359 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ALA F 76 " --> pdb=" O THR F 359 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 332 through 334 Processing sheet with id=AC1, first strand: chain 'G' and resid 35 through 36 Processing sheet with id=AC2, first strand: chain 'G' and resid 93 through 97 removed outlier: 6.289A pdb=" N CYS G 94 " --> pdb=" O PHE G 300 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ASP G 302 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N MET G 96 " --> pdb=" O ASP G 302 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL G 66 " --> pdb=" O PHE G 329 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N SER G 331 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU G 68 " --> pdb=" O SER G 331 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ALA G 65 " --> pdb=" O MET G 359 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE G 361 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU G 67 " --> pdb=" O ILE G 361 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 336 through 337 Processing sheet with id=AC4, first strand: chain 'H' and resid 42 through 43 Processing sheet with id=AC5, first strand: chain 'H' and resid 100 through 104 removed outlier: 6.399A pdb=" N THR H 101 " --> pdb=" O PHE H 297 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP H 299 " --> pdb=" O THR H 101 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE H 103 " --> pdb=" O ASP H 299 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY H 77 " --> pdb=" O THR H 328 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA H 72 " --> pdb=" O LEU H 355 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL H 357 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU H 74 " --> pdb=" O VAL H 357 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR H 359 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA H 76 " --> pdb=" O THR H 359 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 127 through 148 removed outlier: 6.757A pdb=" N THR H 162 " --> pdb=" O VAL H 143 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE H 145 " --> pdb=" O LYS H 160 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS H 160 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE H 147 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL H 158 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY H 159 " --> pdb=" O LEU H 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 169 through 174 current: chain 'H' and resid 202 through 207 Processing sheet with id=AC7, first strand: chain 'H' and resid 333 through 334 Processing sheet with id=AC8, first strand: chain 'I' and resid 35 through 36 Processing sheet with id=AC9, first strand: chain 'I' and resid 93 through 97 removed outlier: 6.386A pdb=" N VAL I 66 " --> pdb=" O PHE I 329 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N SER I 331 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU I 68 " --> pdb=" O SER I 331 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA I 65 " --> pdb=" O MET I 359 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE I 361 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU I 67 " --> pdb=" O ILE I 361 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 121 through 141 removed outlier: 6.074A pdb=" N GLY I 160 " --> pdb=" O THR I 136 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU I 138 " --> pdb=" O ILE I 158 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE I 158 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS I 156 " --> pdb=" O PRO I 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 166 through 172 current: chain 'I' and resid 200 through 206 removed outlier: 5.357A pdb=" N VAL I 221 " --> pdb=" O GLN I 203 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ARG I 205 " --> pdb=" O VAL I 221 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 336 through 337 Processing sheet with id=AD3, first strand: chain 'J' and resid 42 through 43 Processing sheet with id=AD4, first strand: chain 'J' and resid 100 through 104 removed outlier: 6.393A pdb=" N THR J 101 " --> pdb=" O PHE J 297 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP J 299 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE J 103 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU J 296 " --> pdb=" O ILE J 325 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ALA J 327 " --> pdb=" O LEU J 296 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE J 298 " --> pdb=" O ALA J 327 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA J 72 " --> pdb=" O LEU J 355 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL J 357 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU J 74 " --> pdb=" O VAL J 357 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR J 359 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA J 76 " --> pdb=" O THR J 359 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 127 through 148 removed outlier: 6.712A pdb=" N THR J 162 " --> pdb=" O VAL J 143 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE J 145 " --> pdb=" O LYS J 160 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS J 160 " --> pdb=" O ILE J 145 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE J 147 " --> pdb=" O VAL J 158 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL J 158 " --> pdb=" O ILE J 147 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY J 159 " --> pdb=" O LEU J 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 169 through 174 current: chain 'J' and resid 201 through 207 Processing sheet with id=AD6, first strand: chain 'J' and resid 333 through 334 Processing sheet with id=AD7, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.051A pdb=" N ARG Q 42 " --> pdb=" O ILE R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'Q' and resid 77 through 78 Processing sheet with id=AD9, first strand: chain 'Q' and resid 100 through 102 removed outlier: 6.843A pdb=" N THR Q 101 " --> pdb=" O TYR V 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'S' and resid 42 through 43 removed outlier: 7.325A pdb=" N ARG S 42 " --> pdb=" O ILE T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'S' and resid 77 through 78 Processing sheet with id=AE3, first strand: chain 'S' and resid 100 through 102 removed outlier: 6.867A pdb=" N THR S 101 " --> pdb=" O TYR X 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'U' and resid 83 through 84 removed outlier: 7.120A pdb=" N ARG U 83 " --> pdb=" O VAL V 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'U' and resid 118 through 119 Processing sheet with id=AE6, first strand: chain 'W' and resid 83 through 84 removed outlier: 6.935A pdb=" N ARG W 83 " --> pdb=" O VAL X 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'W' and resid 118 through 119 1802 hydrogen bonds defined for protein. 5208 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 314 hydrogen bonds 628 hydrogen bond angles 0 basepair planarities 121 basepair parallelities 212 stacking parallelities Total time for adding SS restraints: 8.61 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 13911 1.36 - 1.51: 12550 1.51 - 1.65: 16818 1.65 - 1.80: 217 1.80 - 1.95: 76 Bond restraints: 43572 Sorted by residual: bond pdb=" CB THR X 30 " pdb=" CG2 THR X 30 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.18e+00 bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" C4 ADP H 501 " pdb=" C5 ADP H 501 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" C4 ADP I 501 " pdb=" C5 ADP I 501 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.63e+00 ... (remaining 43567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 59128 2.07 - 4.14: 647 4.14 - 6.22: 78 6.22 - 8.29: 12 8.29 - 10.36: 12 Bond angle restraints: 59877 Sorted by residual: angle pdb=" OP1 DA Y 50 " pdb=" P DA Y 50 " pdb=" OP2 DA Y 50 " ideal model delta sigma weight residual 120.00 109.64 10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" OP1 DA Z -41 " pdb=" P DA Z -41 " pdb=" OP2 DA Z -41 " ideal model delta sigma weight residual 120.00 109.72 10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" OP1 DC Z -40 " pdb=" P DC Z -40 " pdb=" OP2 DC Z -40 " ideal model delta sigma weight residual 120.00 109.78 10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" OP1 DC Z 70 " pdb=" P DC Z 70 " pdb=" OP2 DC Z 70 " ideal model delta sigma weight residual 120.00 110.43 9.57 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C1' ADP J 501 " pdb=" C2' ADP J 501 " pdb=" C3' ADP J 501 " ideal model delta sigma weight residual 111.00 101.52 9.48 3.00e+00 1.11e-01 9.99e+00 ... (remaining 59872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 24503 34.96 - 69.92: 1439 69.92 - 104.88: 61 104.88 - 139.84: 3 139.84 - 174.80: 8 Dihedral angle restraints: 26014 sinusoidal: 12403 harmonic: 13611 Sorted by residual: dihedral pdb=" O1B ADP J 501 " pdb=" O3A ADP J 501 " pdb=" PB ADP J 501 " pdb=" PA ADP J 501 " ideal model delta sinusoidal sigma weight residual -60.00 100.20 -160.20 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual 300.00 157.66 142.34 1 2.00e+01 2.50e-03 4.30e+01 dihedral pdb=" C5' ADP H 501 " pdb=" O5' ADP H 501 " pdb=" PA ADP H 501 " pdb=" O2A ADP H 501 " ideal model delta sinusoidal sigma weight residual 300.00 168.17 131.83 1 2.00e+01 2.50e-03 4.00e+01 ... (remaining 26011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 6254 0.076 - 0.153: 557 0.153 - 0.229: 14 0.229 - 0.306: 0 0.306 - 0.382: 4 Chirality restraints: 6829 Sorted by residual: chirality pdb=" P DA Y 50 " pdb=" OP1 DA Y 50 " pdb=" OP2 DA Y 50 " pdb=" O5' DA Y 50 " both_signs ideal model delta sigma weight residual True 2.35 -2.73 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" P DA Z -41 " pdb=" OP1 DA Z -41 " pdb=" OP2 DA Z -41 " pdb=" O5' DA Z -41 " both_signs ideal model delta sigma weight residual True 2.35 -2.72 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" P DC Z -40 " pdb=" OP1 DC Z -40 " pdb=" OP2 DC Z -40 " pdb=" O5' DC Z -40 " both_signs ideal model delta sigma weight residual True 2.35 -2.71 -0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 6826 not shown) Planarity restraints: 6809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT Z 9 " 0.028 2.00e-02 2.50e+03 2.36e-02 1.40e+01 pdb=" N1 DT Z 9 " -0.059 2.00e-02 2.50e+03 pdb=" C2 DT Z 9 " 0.034 2.00e-02 2.50e+03 pdb=" O2 DT Z 9 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DT Z 9 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DT Z 9 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT Z 9 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DT Z 9 " 0.005 2.00e-02 2.50e+03 pdb=" C7 DT Z 9 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT Z 9 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC Z 8 " 0.024 2.00e-02 2.50e+03 2.24e-02 1.13e+01 pdb=" N1 DC Z 8 " -0.057 2.00e-02 2.50e+03 pdb=" C2 DC Z 8 " 0.025 2.00e-02 2.50e+03 pdb=" O2 DC Z 8 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DC Z 8 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC Z 8 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC Z 8 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DC Z 8 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DC Z 8 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 213 " -0.251 9.50e-02 1.11e+02 1.14e-01 1.02e+01 pdb=" NE ARG H 213 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG H 213 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG H 213 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG H 213 " -0.000 2.00e-02 2.50e+03 ... (remaining 6806 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 114 2.52 - 3.11: 30376 3.11 - 3.71: 68231 3.71 - 4.30: 99045 4.30 - 4.90: 159517 Nonbonded interactions: 357283 Sorted by model distance: nonbonded pdb=" O1B ADP J 501 " pdb="MG MG J 502 " model vdw 1.921 2.170 nonbonded pdb=" O2G AGS A3301 " pdb="MG MG A3302 " model vdw 1.970 2.170 nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 1.979 2.170 nonbonded pdb=" O2B ADP H 501 " pdb="MG MG H 502 " model vdw 2.066 2.170 nonbonded pdb=" OG1 THR J 84 " pdb="MG MG J 502 " model vdw 2.089 2.170 ... (remaining 357278 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 'E' selection = (chain 'G' and (resid 13 through 142 or resid 154 through 501)) selection = (chain 'I' and (resid 13 through 142 or resid 154 through 501)) } ncs_group { reference = (chain 'F' and (resid 16 through 149 or resid 157 through 209 or resid 224 throu \ gh 502)) selection = (chain 'H' and (resid 16 through 149 or resid 157 through 209 or resid 224 throu \ gh 502)) selection = (chain 'J' and (resid 16 through 453 or resid 501 through 502)) } ncs_group { reference = chain 'Q' selection = (chain 'S' and resid 15 through 110) } ncs_group { reference = chain 'R' selection = (chain 'T' and resid 33 through 124) } ncs_group { reference = chain 'U' selection = (chain 'W' and resid 45 through 134) } ncs_group { reference = chain 'V' selection = (chain 'X' and resid 24 through 102) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 41.040 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 : 0.004 0.049 43580 Z= 0.163 Angle : 0.566 10.359 59886 Z= 0.303 Chirality : 0.042 0.382 6829 Planarity : 0.006 0.114 6809 Dihedral : 18.851 174.799 17222 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.12), residues: 4651 helix: 1.78 (0.11), residues: 2293 sheet: 0.78 (0.19), residues: 689 loop : 0.49 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG H 213 TYR 0.027 0.002 TYR C 99 PHE 0.017 0.001 PHE C 154 TRP 0.051 0.002 TRP A 712 HIS 0.008 0.001 HIS G 316 Details of bonding type rmsd covalent geometry : bond 0.00374 (43572) covalent geometry : angle 0.56556 (59877) hydrogen bonds : bond 0.13877 ( 2116) hydrogen bonds : angle 4.84113 ( 5836) metal coordination : bond 0.01395 ( 8) metal coordination : angle 1.75636 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1327 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 LYS cc_start: 0.8702 (tppt) cc_final: 0.8304 (tppt) REVERT: A 647 LEU cc_start: 0.8444 (mt) cc_final: 0.8240 (mt) REVERT: A 685 GLU cc_start: 0.8560 (mm-30) cc_final: 0.7794 (mm-30) REVERT: A 747 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8170 (mm-30) REVERT: A 781 SER cc_start: 0.8450 (t) cc_final: 0.8205 (p) REVERT: A 795 HIS cc_start: 0.8054 (p-80) cc_final: 0.7724 (p-80) REVERT: A 823 GLU cc_start: 0.8446 (tt0) cc_final: 0.7977 (tt0) REVERT: A 831 LYS cc_start: 0.9091 (mtmt) cc_final: 0.8874 (ttmm) REVERT: A 871 ASP cc_start: 0.8390 (t0) cc_final: 0.7998 (t0) REVERT: A 947 ASP cc_start: 0.8115 (t0) cc_final: 0.7902 (t70) REVERT: A 952 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7679 (mm-30) REVERT: A 974 LEU cc_start: 0.8099 (tp) cc_final: 0.7895 (tp) REVERT: A 975 LEU cc_start: 0.7707 (mt) cc_final: 0.7438 (mt) REVERT: A 976 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7411 (mt-10) REVERT: A 1897 ARG cc_start: 0.7944 (ttp-170) cc_final: 0.7735 (ttp-170) REVERT: A 1921 GLU cc_start: 0.8137 (mp0) cc_final: 0.7458 (mp0) REVERT: A 2097 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7715 (mm110) REVERT: A 2103 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8308 (mt-10) REVERT: B 216 SER cc_start: 0.8763 (t) cc_final: 0.8541 (t) REVERT: B 218 THR cc_start: 0.8396 (m) cc_final: 0.7996 (p) REVERT: C 18 SER cc_start: 0.8994 (p) cc_final: 0.8771 (t) REVERT: C 20 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8068 (mm-30) REVERT: C 21 ASN cc_start: 0.8395 (m-40) cc_final: 0.8166 (m-40) REVERT: C 28 CYS cc_start: 0.8698 (p) cc_final: 0.8449 (p) REVERT: C 41 THR cc_start: 0.8761 (m) cc_final: 0.8539 (t) REVERT: C 45 ILE cc_start: 0.8961 (tp) cc_final: 0.8684 (tp) REVERT: C 84 TYR cc_start: 0.8714 (m-80) cc_final: 0.8505 (m-10) REVERT: C 97 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7866 (mp0) REVERT: C 110 ASN cc_start: 0.8417 (m-40) cc_final: 0.8192 (m-40) REVERT: C 137 ARG cc_start: 0.8408 (tpp80) cc_final: 0.8195 (tpp80) REVERT: C 235 ASP cc_start: 0.8645 (m-30) cc_final: 0.8264 (m-30) REVERT: C 245 LYS cc_start: 0.8197 (mmpt) cc_final: 0.7565 (mmpt) REVERT: C 246 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7763 (mmmt) REVERT: C 366 ILE cc_start: 0.9107 (tt) cc_final: 0.8789 (tt) REVERT: C 371 ASP cc_start: 0.7739 (t0) cc_final: 0.7219 (t0) REVERT: C 379 ARG cc_start: 0.8353 (ttp-110) cc_final: 0.8025 (ttp80) REVERT: D 134 ARG cc_start: 0.8724 (mmm160) cc_final: 0.8510 (mmm160) REVERT: E 47 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7483 (mt-10) REVERT: E 60 LYS cc_start: 0.8487 (mtpp) cc_final: 0.8220 (mtpp) REVERT: E 129 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7391 (mt-10) REVERT: E 137 GLU cc_start: 0.7724 (tt0) cc_final: 0.7466 (tt0) REVERT: E 168 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7724 (ttmm) REVERT: E 183 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7299 (mm-30) REVERT: E 211 THR cc_start: 0.8511 (m) cc_final: 0.8203 (p) REVERT: E 220 TYR cc_start: 0.8594 (m-80) cc_final: 0.8235 (m-80) REVERT: E 229 HIS cc_start: 0.8536 (t70) cc_final: 0.8296 (t-90) REVERT: E 231 LYS cc_start: 0.8442 (mttp) cc_final: 0.8055 (mttp) REVERT: E 285 LYS cc_start: 0.8311 (ttmm) cc_final: 0.7973 (ttmm) REVERT: E 306 MET cc_start: 0.8050 (mmp) cc_final: 0.7815 (mmt) REVERT: E 370 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8045 (mt-10) REVERT: E 404 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7605 (mtt180) REVERT: E 435 GLU cc_start: 0.7618 (tt0) cc_final: 0.7411 (tt0) REVERT: F 90 MET cc_start: 0.8413 (mtp) cc_final: 0.8098 (mtp) REVERT: F 112 GLU cc_start: 0.7572 (tp30) cc_final: 0.7318 (tp30) REVERT: F 157 LYS cc_start: 0.7892 (mttp) cc_final: 0.7574 (mttm) REVERT: F 160 LYS cc_start: 0.8361 (ttpt) cc_final: 0.7852 (ttmm) REVERT: F 169 GLU cc_start: 0.7542 (tt0) cc_final: 0.7311 (tt0) REVERT: F 180 GLU cc_start: 0.7945 (mm-30) cc_final: 0.6882 (mm-30) REVERT: F 184 LYS cc_start: 0.7950 (mmtm) cc_final: 0.7452 (mmtm) REVERT: F 186 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7907 (mtpp) REVERT: F 188 GLN cc_start: 0.7905 (mt0) cc_final: 0.7405 (mt0) REVERT: F 191 ASP cc_start: 0.8008 (m-30) cc_final: 0.7738 (m-30) REVERT: F 201 LYS cc_start: 0.8252 (tttp) cc_final: 0.7867 (tttp) REVERT: F 234 LYS cc_start: 0.8186 (mttt) cc_final: 0.7916 (mttt) REVERT: F 235 ARG cc_start: 0.8241 (ttt90) cc_final: 0.7976 (ttt-90) REVERT: F 236 LYS cc_start: 0.8141 (mmtp) cc_final: 0.7822 (mmtp) REVERT: F 237 GLU cc_start: 0.7402 (tt0) cc_final: 0.7183 (tt0) REVERT: F 238 VAL cc_start: 0.8347 (t) cc_final: 0.7910 (p) REVERT: F 274 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7455 (mm-30) REVERT: F 333 THR cc_start: 0.8266 (m) cc_final: 0.8064 (t) REVERT: F 348 ILE cc_start: 0.8497 (tp) cc_final: 0.8269 (tp) REVERT: F 352 ASP cc_start: 0.7774 (m-30) cc_final: 0.7569 (m-30) REVERT: F 365 LYS cc_start: 0.8176 (pttt) cc_final: 0.7941 (pttt) REVERT: G 28 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7240 (mt-10) REVERT: G 54 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7419 (mm-30) REVERT: G 123 ARG cc_start: 0.8357 (ttm170) cc_final: 0.8078 (ttm170) REVERT: G 125 LYS cc_start: 0.8366 (mtmt) cc_final: 0.8150 (mtmm) REVERT: G 137 GLU cc_start: 0.7681 (tt0) cc_final: 0.7437 (tt0) REVERT: G 139 THR cc_start: 0.8455 (m) cc_final: 0.8197 (p) REVERT: G 214 ASP cc_start: 0.7879 (m-30) cc_final: 0.7610 (m-30) REVERT: G 235 ILE cc_start: 0.8627 (mp) cc_final: 0.8370 (mt) REVERT: G 259 MET cc_start: 0.7411 (mmt) cc_final: 0.7112 (mmt) REVERT: G 326 ILE cc_start: 0.8592 (mt) cc_final: 0.8298 (mm) REVERT: G 332 ASN cc_start: 0.8730 (p0) cc_final: 0.8507 (p0) REVERT: G 344 ILE cc_start: 0.8603 (mm) cc_final: 0.8388 (mt) REVERT: G 353 ASP cc_start: 0.7773 (m-30) cc_final: 0.7541 (m-30) REVERT: G 388 GLU cc_start: 0.7746 (tp30) cc_final: 0.7242 (mm-30) REVERT: G 392 ASN cc_start: 0.8605 (m-40) cc_final: 0.8069 (m110) REVERT: G 404 ARG cc_start: 0.7773 (mtt90) cc_final: 0.7517 (mtt-85) REVERT: G 418 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7866 (mtpp) REVERT: G 447 LEU cc_start: 0.8191 (mt) cc_final: 0.7914 (mp) REVERT: G 455 MET cc_start: 0.7286 (mmm) cc_final: 0.6948 (mmm) REVERT: H 112 GLU cc_start: 0.7396 (tt0) cc_final: 0.7191 (tt0) REVERT: H 127 ILE cc_start: 0.8735 (mt) cc_final: 0.8515 (mm) REVERT: H 136 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7409 (mt-10) REVERT: H 160 LYS cc_start: 0.8318 (mttt) cc_final: 0.8033 (mttt) REVERT: H 185 ASP cc_start: 0.7814 (m-30) cc_final: 0.7515 (m-30) REVERT: H 204 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8206 (mtmt) REVERT: H 211 ARG cc_start: 0.8484 (ttt180) cc_final: 0.8107 (mmm-85) REVERT: H 235 ARG cc_start: 0.8105 (mtt180) cc_final: 0.7728 (ttm110) REVERT: H 253 ARG cc_start: 0.8093 (ptm160) cc_final: 0.7813 (ptp90) REVERT: H 313 ASN cc_start: 0.8076 (m-40) cc_final: 0.7467 (m-40) REVERT: H 314 ARG cc_start: 0.7407 (mmt180) cc_final: 0.6871 (mmt180) REVERT: H 319 ASP cc_start: 0.7461 (p0) cc_final: 0.7188 (p0) REVERT: H 320 MET cc_start: 0.7755 (mmm) cc_final: 0.7536 (mmt) REVERT: H 342 SER cc_start: 0.8698 (m) cc_final: 0.8404 (t) REVERT: H 358 SER cc_start: 0.8511 (m) cc_final: 0.8086 (t) REVERT: H 369 GLN cc_start: 0.8081 (tp-100) cc_final: 0.7757 (tt0) REVERT: H 377 GLU cc_start: 0.7771 (tp30) cc_final: 0.7482 (tp30) REVERT: H 382 MET cc_start: 0.8511 (mtp) cc_final: 0.8258 (mtm) REVERT: H 385 ASP cc_start: 0.8208 (m-30) cc_final: 0.7991 (m-30) REVERT: H 436 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6614 (tm-30) REVERT: H 443 MET cc_start: 0.7941 (ttm) cc_final: 0.7634 (ttp) REVERT: I 27 ASP cc_start: 0.7490 (p0) cc_final: 0.7249 (p0) REVERT: I 28 GLU cc_start: 0.7696 (mp0) cc_final: 0.7096 (mp0) REVERT: I 64 ARG cc_start: 0.8322 (mmt-90) cc_final: 0.8089 (mmt-90) REVERT: I 90 LYS cc_start: 0.8224 (pttt) cc_final: 0.7945 (pttt) REVERT: I 123 ARG cc_start: 0.7926 (ttm110) cc_final: 0.7683 (ttm110) REVERT: I 125 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8267 (ttpp) REVERT: I 165 LYS cc_start: 0.8721 (mttm) cc_final: 0.8495 (mttm) REVERT: I 184 ARG cc_start: 0.7956 (mtt180) cc_final: 0.7733 (mtt180) REVERT: I 209 TYR cc_start: 0.8606 (m-80) cc_final: 0.8237 (m-80) REVERT: I 218 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7093 (tp30) REVERT: I 221 VAL cc_start: 0.8250 (t) cc_final: 0.8004 (m) REVERT: I 259 MET cc_start: 0.8059 (mtp) cc_final: 0.7654 (mtm) REVERT: I 285 LYS cc_start: 0.8254 (tttp) cc_final: 0.7999 (tttt) REVERT: I 286 TYR cc_start: 0.8316 (m-80) cc_final: 0.8091 (m-80) REVERT: I 376 LYS cc_start: 0.8346 (tptp) cc_final: 0.8090 (tptm) REVERT: I 400 LYS cc_start: 0.8159 (mtpp) cc_final: 0.7871 (mtmm) REVERT: I 408 GLN cc_start: 0.7871 (mt0) cc_final: 0.7431 (mt0) REVERT: I 418 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7618 (mtpt) REVERT: I 435 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6960 (mm-30) REVERT: I 445 LYS cc_start: 0.7875 (tppt) cc_final: 0.7202 (tppt) REVERT: J 117 GLU cc_start: 0.7856 (tp30) cc_final: 0.7311 (tp30) REVERT: J 136 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7552 (mt-10) REVERT: J 141 GLU cc_start: 0.7818 (tt0) cc_final: 0.7537 (tt0) REVERT: J 177 LYS cc_start: 0.8047 (mttp) cc_final: 0.7547 (mttp) REVERT: J 231 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7017 (mm-30) REVERT: J 236 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7755 (mtpt) REVERT: J 246 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7158 (mt-10) REVERT: J 271 GLU cc_start: 0.7816 (mp0) cc_final: 0.7592 (mp0) REVERT: J 299 ASP cc_start: 0.8208 (t0) cc_final: 0.7784 (t70) REVERT: J 377 GLU cc_start: 0.7827 (tp30) cc_final: 0.7575 (tp30) REVERT: J 384 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7840 (mm-30) REVERT: J 392 ARG cc_start: 0.7776 (ttp80) cc_final: 0.7354 (ttp80) REVERT: J 414 ARG cc_start: 0.7949 (mtp-110) cc_final: 0.7718 (mtp-110) REVERT: J 436 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6749 (tm-30) REVERT: J 437 SER cc_start: 0.8210 (t) cc_final: 0.7988 (m) REVERT: Q 17 ARG cc_start: 0.8676 (ttp-170) cc_final: 0.8471 (ttp80) REVERT: R 82 HIS cc_start: 0.8280 (t-90) cc_final: 0.8074 (t-90) REVERT: R 85 LYS cc_start: 0.8704 (mttp) cc_final: 0.8483 (mtmm) REVERT: R 116 LYS cc_start: 0.8844 (ttpp) cc_final: 0.8594 (ttpp) REVERT: S 20 ARG cc_start: 0.8539 (mtt-85) cc_final: 0.8204 (mtt-85) REVERT: S 95 LYS cc_start: 0.8907 (ttmt) cc_final: 0.8706 (ttmt) REVERT: T 62 MET cc_start: 0.8865 (mmm) cc_final: 0.8405 (mmm) REVERT: U 108 ASN cc_start: 0.8720 (t0) cc_final: 0.8480 (t0) REVERT: V 29 ILE cc_start: 0.9044 (mm) cc_final: 0.8806 (mm) REVERT: V 44 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8430 (mtmt) REVERT: W 40 ARG cc_start: 0.8811 (ttm-80) cc_final: 0.8414 (ttt-90) REVERT: W 63 ARG cc_start: 0.8332 (mmm-85) cc_final: 0.7896 (mmm-85) REVERT: W 83 ARG cc_start: 0.8361 (mtp180) cc_final: 0.8044 (mtp85) REVERT: W 117 VAL cc_start: 0.9037 (t) cc_final: 0.8713 (m) outliers start: 0 outliers final: 0 residues processed: 1327 average time/residue: 0.2666 time to fit residues: 534.6434 Evaluate side-chains 1210 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1210 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 0.8980 chunk 470 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 730 GLN A 768 GLN A 848 GLN A 892 ASN A2003 GLN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN C 272 ASN C 303 GLN C 387 HIS E 316 HIS E 380 GLN E 450 GLN ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN G 254 GLN G 380 GLN G 408 GLN ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 233 GLN I 289 GLN I 373 GLN I 380 GLN J 404 GLN R 84 ASN T 82 HIS V 27 GLN X 25 ASN X 27 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.102371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.087704 restraints weight = 64803.711| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.53 r_work: 0.2816 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43580 Z= 0.153 Angle : 0.535 7.302 59886 Z= 0.286 Chirality : 0.041 0.162 6829 Planarity : 0.004 0.053 6809 Dihedral : 20.932 173.473 7878 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.91 % Allowed : 7.76 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.12), residues: 4651 helix: 1.98 (0.11), residues: 2330 sheet: 0.62 (0.19), residues: 707 loop : 0.53 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 317 TYR 0.012 0.001 TYR I 192 PHE 0.017 0.001 PHE C 88 TRP 0.026 0.001 TRP A 712 HIS 0.008 0.001 HIS I 316 Details of bonding type rmsd covalent geometry : bond 0.00343 (43572) covalent geometry : angle 0.53455 (59877) hydrogen bonds : bond 0.04329 ( 2116) hydrogen bonds : angle 3.92289 ( 5836) metal coordination : bond 0.00818 ( 8) metal coordination : angle 1.56940 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1273 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 1236 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 ASP cc_start: 0.8769 (t70) cc_final: 0.8224 (m-30) REVERT: A 635 LYS cc_start: 0.8654 (tppt) cc_final: 0.8269 (tppt) REVERT: A 685 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7884 (mm-30) REVERT: A 747 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7996 (mm-30) REVERT: A 823 GLU cc_start: 0.8341 (tt0) cc_final: 0.7974 (tt0) REVERT: A 825 LEU cc_start: 0.9019 (tp) cc_final: 0.8778 (tp) REVERT: A 863 LYS cc_start: 0.8051 (tptp) cc_final: 0.7733 (tptp) REVERT: A 871 ASP cc_start: 0.8091 (t0) cc_final: 0.7685 (t0) REVERT: A 947 ASP cc_start: 0.7948 (t0) cc_final: 0.7691 (t70) REVERT: A 952 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7641 (mm-30) REVERT: A 961 ASP cc_start: 0.8067 (m-30) cc_final: 0.7864 (m-30) REVERT: A 975 LEU cc_start: 0.7772 (mt) cc_final: 0.7511 (mt) REVERT: A 976 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7443 (mt-10) REVERT: A 1897 ARG cc_start: 0.7834 (ttp-170) cc_final: 0.7634 (ttp-170) REVERT: A 1921 GLU cc_start: 0.8166 (mp0) cc_final: 0.7585 (mp0) REVERT: A 1956 HIS cc_start: 0.8153 (t70) cc_final: 0.7928 (t-90) REVERT: A 2009 GLN cc_start: 0.8013 (tt0) cc_final: 0.7724 (tt0) REVERT: A 2029 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7852 (ttp80) REVERT: A 2076 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7843 (mt-10) REVERT: A 2097 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7741 (mm-40) REVERT: A 2198 THR cc_start: 0.8477 (p) cc_final: 0.8259 (p) REVERT: B 179 THR cc_start: 0.8518 (p) cc_final: 0.8178 (t) REVERT: B 218 THR cc_start: 0.8316 (m) cc_final: 0.7947 (p) REVERT: C 18 SER cc_start: 0.8987 (p) cc_final: 0.8721 (t) REVERT: C 45 ILE cc_start: 0.9039 (tp) cc_final: 0.8827 (tp) REVERT: C 108 SER cc_start: 0.8857 (m) cc_final: 0.8419 (t) REVERT: C 221 ASP cc_start: 0.7968 (m-30) cc_final: 0.7593 (m-30) REVERT: C 235 ASP cc_start: 0.8560 (m-30) cc_final: 0.8356 (m-30) REVERT: C 245 LYS cc_start: 0.8023 (mmpt) cc_final: 0.7542 (mmpt) REVERT: C 246 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7811 (mmmt) REVERT: C 356 ILE cc_start: 0.9094 (mm) cc_final: 0.8805 (mt) REVERT: C 366 ILE cc_start: 0.9186 (tt) cc_final: 0.8900 (tt) REVERT: E 27 ASP cc_start: 0.7916 (p0) cc_final: 0.7682 (p0) REVERT: E 60 LYS cc_start: 0.8436 (mtpp) cc_final: 0.8213 (mtpp) REVERT: E 137 GLU cc_start: 0.7714 (tt0) cc_final: 0.7463 (tt0) REVERT: E 158 ILE cc_start: 0.8419 (mt) cc_final: 0.7846 (tp) REVERT: E 168 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7882 (tttm) REVERT: E 170 LEU cc_start: 0.8546 (mt) cc_final: 0.8312 (mp) REVERT: E 211 THR cc_start: 0.8430 (m) cc_final: 0.8173 (p) REVERT: E 220 TYR cc_start: 0.8525 (m-80) cc_final: 0.8060 (m-80) REVERT: E 229 HIS cc_start: 0.8532 (t70) cc_final: 0.8291 (t-90) REVERT: E 231 LYS cc_start: 0.8413 (mttp) cc_final: 0.8057 (mttm) REVERT: E 285 LYS cc_start: 0.8268 (ttmm) cc_final: 0.7983 (ttmm) REVERT: E 306 MET cc_start: 0.8241 (mmp) cc_final: 0.8018 (mmp) REVERT: E 323 ILE cc_start: 0.8627 (mt) cc_final: 0.8422 (mm) REVERT: E 435 GLU cc_start: 0.7627 (tt0) cc_final: 0.7408 (tt0) REVERT: F 112 GLU cc_start: 0.7493 (tp30) cc_final: 0.7262 (tp30) REVERT: F 160 LYS cc_start: 0.8287 (ttpt) cc_final: 0.7815 (ttmm) REVERT: F 169 GLU cc_start: 0.7529 (tt0) cc_final: 0.7298 (tt0) REVERT: F 174 LEU cc_start: 0.8381 (mt) cc_final: 0.8148 (mt) REVERT: F 177 LYS cc_start: 0.8120 (mttt) cc_final: 0.7889 (mttt) REVERT: F 180 GLU cc_start: 0.7929 (mm-30) cc_final: 0.6918 (mm-30) REVERT: F 184 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7440 (mmtm) REVERT: F 186 LYS cc_start: 0.8243 (mtpp) cc_final: 0.8005 (mtpp) REVERT: F 191 ASP cc_start: 0.8092 (m-30) cc_final: 0.7842 (m-30) REVERT: F 201 LYS cc_start: 0.8208 (tttp) cc_final: 0.7854 (tttp) REVERT: F 207 ARG cc_start: 0.8292 (mtp-110) cc_final: 0.7938 (mmm160) REVERT: F 234 LYS cc_start: 0.8368 (mttt) cc_final: 0.8139 (mttt) REVERT: F 235 ARG cc_start: 0.8176 (ttt90) cc_final: 0.7962 (ttt-90) REVERT: F 236 LYS cc_start: 0.8195 (mmtp) cc_final: 0.7903 (mmtp) REVERT: F 237 GLU cc_start: 0.7536 (tt0) cc_final: 0.7281 (tt0) REVERT: F 238 VAL cc_start: 0.8339 (t) cc_final: 0.7931 (p) REVERT: F 274 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7458 (mm-30) REVERT: F 348 ILE cc_start: 0.8325 (tp) cc_final: 0.8100 (tp) REVERT: F 352 ASP cc_start: 0.7760 (m-30) cc_final: 0.7509 (m-30) REVERT: F 369 GLN cc_start: 0.7976 (tp40) cc_final: 0.7754 (tt0) REVERT: G 123 ARG cc_start: 0.8402 (ttm170) cc_final: 0.8146 (ttm-80) REVERT: G 125 LYS cc_start: 0.8366 (mtmt) cc_final: 0.8128 (mtmm) REVERT: G 137 GLU cc_start: 0.8005 (tt0) cc_final: 0.7698 (tt0) REVERT: G 139 THR cc_start: 0.8362 (m) cc_final: 0.8100 (p) REVERT: G 214 ASP cc_start: 0.8000 (m-30) cc_final: 0.7603 (m-30) REVERT: G 225 LYS cc_start: 0.8303 (mmpt) cc_final: 0.8027 (mtpt) REVERT: G 235 ILE cc_start: 0.8601 (mp) cc_final: 0.8329 (mt) REVERT: G 326 ILE cc_start: 0.8575 (mt) cc_final: 0.8310 (mm) REVERT: G 339 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7919 (mtp85) REVERT: G 388 GLU cc_start: 0.7875 (tp30) cc_final: 0.7312 (mm-30) REVERT: G 392 ASN cc_start: 0.8663 (m-40) cc_final: 0.8176 (m110) REVERT: G 418 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7983 (mtpp) REVERT: G 455 MET cc_start: 0.7171 (mmm) cc_final: 0.6923 (mmm) REVERT: H 136 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7509 (mt-10) REVERT: H 181 SER cc_start: 0.7954 (t) cc_final: 0.7444 (m) REVERT: H 184 LYS cc_start: 0.7994 (ttpt) cc_final: 0.7655 (ttpt) REVERT: H 204 LYS cc_start: 0.8290 (mtpt) cc_final: 0.8060 (mtmt) REVERT: H 211 ARG cc_start: 0.8623 (ttt180) cc_final: 0.8121 (mmm-85) REVERT: H 235 ARG cc_start: 0.8096 (mtt180) cc_final: 0.7738 (ttm110) REVERT: H 253 ARG cc_start: 0.8132 (ptm160) cc_final: 0.7785 (ptp90) REVERT: H 313 ASN cc_start: 0.8005 (m-40) cc_final: 0.7489 (m-40) REVERT: H 314 ARG cc_start: 0.7171 (mmt180) cc_final: 0.6714 (mmt180) REVERT: H 319 ASP cc_start: 0.7577 (p0) cc_final: 0.7314 (p0) REVERT: H 342 SER cc_start: 0.8722 (m) cc_final: 0.8438 (t) REVERT: H 358 SER cc_start: 0.8427 (m) cc_final: 0.8036 (t) REVERT: H 369 GLN cc_start: 0.8114 (tp-100) cc_final: 0.7832 (tt0) REVERT: H 377 GLU cc_start: 0.7835 (tp30) cc_final: 0.7571 (tp30) REVERT: H 381 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7885 (mm-30) REVERT: H 382 MET cc_start: 0.8415 (mtp) cc_final: 0.8210 (mtm) REVERT: H 436 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6503 (tm-30) REVERT: H 443 MET cc_start: 0.7855 (ttm) cc_final: 0.7565 (ttp) REVERT: I 27 ASP cc_start: 0.7656 (p0) cc_final: 0.7387 (p0) REVERT: I 28 GLU cc_start: 0.7558 (mp0) cc_final: 0.7049 (mp0) REVERT: I 125 LYS cc_start: 0.8523 (ttpp) cc_final: 0.8194 (ttpp) REVERT: I 137 GLU cc_start: 0.7664 (tt0) cc_final: 0.7304 (tt0) REVERT: I 165 LYS cc_start: 0.8669 (mttm) cc_final: 0.8441 (mttp) REVERT: I 184 ARG cc_start: 0.7771 (mtt180) cc_final: 0.7551 (mtt180) REVERT: I 209 TYR cc_start: 0.8527 (m-80) cc_final: 0.8069 (m-80) REVERT: I 251 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7401 (mm-40) REVERT: I 259 MET cc_start: 0.7824 (mtp) cc_final: 0.7351 (mtm) REVERT: I 369 GLN cc_start: 0.7931 (mp10) cc_final: 0.7597 (mp10) REVERT: I 400 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7905 (mtmm) REVERT: I 402 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7793 (m) REVERT: I 408 GLN cc_start: 0.7663 (mt0) cc_final: 0.7326 (mt0) REVERT: I 418 LYS cc_start: 0.8043 (ttmm) cc_final: 0.7748 (mtpt) REVERT: I 435 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7129 (mm-30) REVERT: I 445 LYS cc_start: 0.7937 (tppt) cc_final: 0.7321 (tppt) REVERT: J 20 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7133 (mm-30) REVERT: J 86 ILE cc_start: 0.8207 (mm) cc_final: 0.7990 (mt) REVERT: J 136 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7471 (mt-10) REVERT: J 141 GLU cc_start: 0.7797 (tt0) cc_final: 0.7538 (tt0) REVERT: J 236 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7955 (mtpt) REVERT: J 271 GLU cc_start: 0.7773 (mp0) cc_final: 0.7399 (mp0) REVERT: J 299 ASP cc_start: 0.8221 (t0) cc_final: 0.7821 (t70) REVERT: J 377 GLU cc_start: 0.7830 (tp30) cc_final: 0.7597 (tp30) REVERT: J 384 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7841 (mm-30) REVERT: J 392 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7374 (ttp80) REVERT: J 414 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.7708 (mtp-110) REVERT: R 82 HIS cc_start: 0.8294 (t-90) cc_final: 0.8088 (t-90) REVERT: R 88 THR cc_start: 0.8682 (t) cc_final: 0.8274 (p) REVERT: R 116 LYS cc_start: 0.8809 (ttpp) cc_final: 0.8589 (ttpp) REVERT: T 42 TYR cc_start: 0.8470 (t80) cc_final: 0.8228 (t80) REVERT: T 62 MET cc_start: 0.8941 (mmm) cc_final: 0.8495 (mmm) REVERT: U 60 LEU cc_start: 0.8621 (mt) cc_final: 0.8396 (mt) REVERT: V 29 ILE cc_start: 0.9047 (mm) cc_final: 0.8818 (mm) REVERT: W 40 ARG cc_start: 0.8710 (ttm-80) cc_final: 0.8326 (ttt-90) REVERT: W 83 ARG cc_start: 0.8357 (mtp180) cc_final: 0.8131 (mtp85) REVERT: W 118 THR cc_start: 0.9149 (m) cc_final: 0.8888 (p) outliers start: 37 outliers final: 23 residues processed: 1250 average time/residue: 0.2645 time to fit residues: 496.8641 Evaluate side-chains 1221 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 1197 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 272 ASN Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 201 LYS Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 339 SER Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 391 optimal weight: 0.9980 chunk 231 optimal weight: 0.9980 chunk 337 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 483 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 199 optimal weight: 0.1980 chunk 357 optimal weight: 1.9990 chunk 401 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 291 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 768 GLN A 892 ASN A1906 GLN A2007 GLN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN C 303 GLN D 91 GLN E 380 GLN F 404 GLN G 408 GLN G 420 ASN ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 GLN I 289 GLN I 380 GLN J 404 GLN V 27 GLN V 93 GLN X 25 ASN X 27 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.083821 restraints weight = 64850.320| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.58 r_work: 0.2757 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 43580 Z= 0.165 Angle : 0.524 6.965 59886 Z= 0.280 Chirality : 0.041 0.158 6829 Planarity : 0.004 0.054 6809 Dihedral : 20.896 173.611 7878 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.41 % Allowed : 10.30 % Favored : 88.29 % 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: 1.85 (0.12), residues: 4651 helix: 2.02 (0.11), residues: 2328 sheet: 0.57 (0.19), residues: 703 loop : 0.50 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 64 TYR 0.018 0.001 TYR X 88 PHE 0.014 0.001 PHE E 177 TRP 0.020 0.001 TRP A 712 HIS 0.008 0.001 HIS I 316 Details of bonding type rmsd covalent geometry : bond 0.00378 (43572) covalent geometry : angle 0.52400 (59877) hydrogen bonds : bond 0.04093 ( 2116) hydrogen bonds : angle 3.78313 ( 5836) metal coordination : bond 0.01044 ( 8) metal coordination : angle 1.58364 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 1205 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 627 ASP cc_start: 0.8777 (t70) cc_final: 0.8267 (m-30) REVERT: A 685 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7945 (mm-30) REVERT: A 716 ASN cc_start: 0.8154 (t0) cc_final: 0.7777 (t0) REVERT: A 823 GLU cc_start: 0.8311 (tt0) cc_final: 0.7978 (tt0) REVERT: A 825 LEU cc_start: 0.9049 (tp) cc_final: 0.8818 (tp) REVERT: A 863 LYS cc_start: 0.8059 (tptp) cc_final: 0.7719 (tptp) REVERT: A 871 ASP cc_start: 0.8137 (t0) cc_final: 0.7871 (t70) REVERT: A 947 ASP cc_start: 0.7987 (t0) cc_final: 0.7719 (t70) REVERT: A 952 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7605 (mm-30) REVERT: A 961 ASP cc_start: 0.8000 (m-30) cc_final: 0.7724 (m-30) REVERT: A 975 LEU cc_start: 0.7757 (mt) cc_final: 0.7489 (mt) REVERT: A 976 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7380 (mt-10) REVERT: A 1897 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7626 (ttp-170) REVERT: A 1921 GLU cc_start: 0.8185 (mp0) cc_final: 0.7808 (mp0) REVERT: A 1953 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7685 (mt-10) REVERT: A 1956 HIS cc_start: 0.8226 (t70) cc_final: 0.8008 (t-90) REVERT: A 2009 GLN cc_start: 0.8039 (tt0) cc_final: 0.7554 (tt0) REVERT: A 2097 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7745 (mm-40) REVERT: A 2198 THR cc_start: 0.8474 (p) cc_final: 0.8243 (p) REVERT: C 18 SER cc_start: 0.8994 (p) cc_final: 0.8705 (t) REVERT: C 108 SER cc_start: 0.8777 (m) cc_final: 0.8360 (t) REVERT: C 221 ASP cc_start: 0.8018 (m-30) cc_final: 0.7615 (m-30) REVERT: C 245 LYS cc_start: 0.8154 (mmpt) cc_final: 0.7681 (mmpt) REVERT: C 246 LYS cc_start: 0.8191 (mmmt) cc_final: 0.7775 (mmmt) REVERT: C 307 GLU cc_start: 0.8114 (pm20) cc_final: 0.7459 (pm20) REVERT: C 356 ILE cc_start: 0.9060 (mm) cc_final: 0.8797 (mt) REVERT: C 366 ILE cc_start: 0.9130 (tt) cc_final: 0.8886 (tt) REVERT: E 60 LYS cc_start: 0.8425 (mtpp) cc_final: 0.8202 (mtpp) REVERT: E 137 GLU cc_start: 0.7797 (tt0) cc_final: 0.7535 (tt0) REVERT: E 168 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7954 (ttmt) REVERT: E 211 THR cc_start: 0.8431 (m) cc_final: 0.8175 (p) REVERT: E 218 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7345 (mm-30) REVERT: E 220 TYR cc_start: 0.8502 (m-80) cc_final: 0.8280 (m-80) REVERT: E 231 LYS cc_start: 0.8342 (mttp) cc_final: 0.8070 (mttm) REVERT: E 285 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7992 (ttmm) REVERT: E 306 MET cc_start: 0.8265 (mmp) cc_final: 0.8054 (mmp) REVERT: E 323 ILE cc_start: 0.8580 (mt) cc_final: 0.8361 (mm) REVERT: E 435 GLU cc_start: 0.7660 (tt0) cc_final: 0.7408 (tt0) REVERT: E 455 MET cc_start: 0.7646 (mmm) cc_final: 0.7145 (mmm) REVERT: F 112 GLU cc_start: 0.7541 (tp30) cc_final: 0.7291 (tp30) REVERT: F 136 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7342 (mt-10) REVERT: F 160 LYS cc_start: 0.8335 (ttpt) cc_final: 0.7837 (ttmm) REVERT: F 169 GLU cc_start: 0.7592 (tt0) cc_final: 0.7353 (tt0) REVERT: F 174 LEU cc_start: 0.8345 (mt) cc_final: 0.8115 (mt) REVERT: F 180 GLU cc_start: 0.7938 (mm-30) cc_final: 0.6958 (mm-30) REVERT: F 184 LYS cc_start: 0.7942 (mmtm) cc_final: 0.7443 (mmtm) REVERT: F 186 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7975 (mtpp) REVERT: F 188 GLN cc_start: 0.8126 (mt0) cc_final: 0.7681 (mt0) REVERT: F 191 ASP cc_start: 0.8162 (m-30) cc_final: 0.7855 (m-30) REVERT: F 201 LYS cc_start: 0.8225 (tttp) cc_final: 0.7845 (tttp) REVERT: F 207 ARG cc_start: 0.8236 (mtp-110) cc_final: 0.7866 (mmm160) REVERT: F 234 LYS cc_start: 0.8350 (mttt) cc_final: 0.8106 (mttt) REVERT: F 235 ARG cc_start: 0.8182 (ttt90) cc_final: 0.7948 (ttt-90) REVERT: F 236 LYS cc_start: 0.8163 (mmtp) cc_final: 0.7840 (mmtp) REVERT: F 237 GLU cc_start: 0.7523 (tt0) cc_final: 0.7265 (tt0) REVERT: F 238 VAL cc_start: 0.8315 (t) cc_final: 0.7913 (p) REVERT: F 274 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7523 (mm-30) REVERT: F 348 ILE cc_start: 0.8290 (tp) cc_final: 0.8052 (tp) REVERT: F 352 ASP cc_start: 0.7763 (m-30) cc_final: 0.7506 (m-30) REVERT: G 123 ARG cc_start: 0.8392 (ttm170) cc_final: 0.8097 (ttm-80) REVERT: G 125 LYS cc_start: 0.8373 (mtmt) cc_final: 0.8112 (mtmm) REVERT: G 137 GLU cc_start: 0.7962 (tt0) cc_final: 0.7587 (tt0) REVERT: G 139 THR cc_start: 0.8329 (m) cc_final: 0.8095 (p) REVERT: G 214 ASP cc_start: 0.7957 (m-30) cc_final: 0.7536 (m-30) REVERT: G 225 LYS cc_start: 0.8265 (mmpt) cc_final: 0.8012 (mtpt) REVERT: G 235 ILE cc_start: 0.8600 (mp) cc_final: 0.8343 (mt) REVERT: G 326 ILE cc_start: 0.8512 (mt) cc_final: 0.8235 (mm) REVERT: G 353 ASP cc_start: 0.7829 (m-30) cc_final: 0.7593 (m-30) REVERT: G 388 GLU cc_start: 0.7857 (tp30) cc_final: 0.7263 (mm-30) REVERT: G 392 ASN cc_start: 0.8621 (m-40) cc_final: 0.8130 (m110) REVERT: G 418 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7923 (mtpp) REVERT: G 435 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7318 (mp0) REVERT: G 447 LEU cc_start: 0.8247 (mt) cc_final: 0.7934 (mp) REVERT: G 455 MET cc_start: 0.7158 (mmm) cc_final: 0.6950 (mmm) REVERT: H 136 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7527 (mt-10) REVERT: H 181 SER cc_start: 0.7789 (t) cc_final: 0.7236 (m) REVERT: H 204 LYS cc_start: 0.8314 (mtpt) cc_final: 0.8055 (mtmt) REVERT: H 211 ARG cc_start: 0.8542 (ttt180) cc_final: 0.8034 (mmm-85) REVERT: H 235 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7744 (ttm110) REVERT: H 248 ASP cc_start: 0.7454 (m-30) cc_final: 0.7215 (m-30) REVERT: H 313 ASN cc_start: 0.8106 (m-40) cc_final: 0.7559 (m-40) REVERT: H 314 ARG cc_start: 0.7186 (mmt180) cc_final: 0.6723 (mmt180) REVERT: H 342 SER cc_start: 0.8723 (m) cc_final: 0.8436 (t) REVERT: H 358 SER cc_start: 0.8463 (m) cc_final: 0.8081 (t) REVERT: H 369 GLN cc_start: 0.8095 (tp-100) cc_final: 0.7817 (tt0) REVERT: H 377 GLU cc_start: 0.7834 (tp30) cc_final: 0.7551 (tp30) REVERT: H 381 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7856 (mm-30) REVERT: H 382 MET cc_start: 0.8432 (mtp) cc_final: 0.8217 (mtm) REVERT: H 436 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6463 (tm-30) REVERT: H 443 MET cc_start: 0.7792 (ttm) cc_final: 0.7519 (ttp) REVERT: I 28 GLU cc_start: 0.7627 (mp0) cc_final: 0.7146 (mp0) REVERT: I 90 LYS cc_start: 0.8291 (pttt) cc_final: 0.8007 (pttt) REVERT: I 125 LYS cc_start: 0.8545 (ttpp) cc_final: 0.8211 (ttpp) REVERT: I 137 GLU cc_start: 0.7713 (tt0) cc_final: 0.7342 (tt0) REVERT: I 165 LYS cc_start: 0.8682 (mttm) cc_final: 0.8464 (mttp) REVERT: I 184 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7501 (mtt180) REVERT: I 209 TYR cc_start: 0.8528 (m-80) cc_final: 0.8078 (m-80) REVERT: I 251 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7472 (mm-40) REVERT: I 259 MET cc_start: 0.7745 (mtp) cc_final: 0.7088 (mtp) REVERT: I 369 GLN cc_start: 0.7887 (mp10) cc_final: 0.7516 (mp10) REVERT: I 400 LYS cc_start: 0.8148 (mtpp) cc_final: 0.7866 (mtmm) REVERT: I 408 GLN cc_start: 0.7655 (mt0) cc_final: 0.7317 (mt0) REVERT: I 418 LYS cc_start: 0.8124 (ttmm) cc_final: 0.7777 (mtpt) REVERT: I 435 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7135 (mm-30) REVERT: I 445 LYS cc_start: 0.7939 (tppt) cc_final: 0.7301 (tppt) REVERT: J 20 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7203 (mm-30) REVERT: J 86 ILE cc_start: 0.8138 (mm) cc_final: 0.7900 (mt) REVERT: J 134 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7462 (mt-10) REVERT: J 136 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7496 (mt-10) REVERT: J 141 GLU cc_start: 0.7844 (tt0) cc_final: 0.7593 (tt0) REVERT: J 169 GLU cc_start: 0.7687 (tt0) cc_final: 0.7379 (tm-30) REVERT: J 236 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7889 (mtpt) REVERT: J 271 GLU cc_start: 0.7841 (mp0) cc_final: 0.7601 (mp0) REVERT: J 299 ASP cc_start: 0.8235 (t0) cc_final: 0.7844 (t70) REVERT: J 377 GLU cc_start: 0.7793 (tp30) cc_final: 0.7564 (tp30) REVERT: J 392 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7376 (ttp80) REVERT: J 414 ARG cc_start: 0.7922 (mtp-110) cc_final: 0.7684 (mtp-110) REVERT: R 88 THR cc_start: 0.8670 (t) cc_final: 0.8325 (p) REVERT: R 93 GLU cc_start: 0.8161 (mp0) cc_final: 0.7947 (mp0) REVERT: R 116 LYS cc_start: 0.8835 (ttpp) cc_final: 0.8613 (ttpp) REVERT: T 42 TYR cc_start: 0.8484 (t80) cc_final: 0.8223 (t80) REVERT: T 62 MET cc_start: 0.8934 (mmm) cc_final: 0.8477 (mmm) REVERT: U 60 LEU cc_start: 0.8629 (mt) cc_final: 0.8368 (mt) REVERT: U 131 ARG cc_start: 0.8747 (mtp85) cc_final: 0.8484 (mtp85) REVERT: W 40 ARG cc_start: 0.8719 (ttm-80) cc_final: 0.8323 (ttt-90) REVERT: W 83 ARG cc_start: 0.8340 (mtp180) cc_final: 0.8090 (mtp85) REVERT: W 118 THR cc_start: 0.9161 (m) cc_final: 0.8895 (p) REVERT: X 84 MET cc_start: 0.8437 (mmm) cc_final: 0.8193 (tpp) REVERT: X 88 TYR cc_start: 0.8750 (m-80) cc_final: 0.8101 (m-80) REVERT: X 91 LYS cc_start: 0.9043 (ttmm) cc_final: 0.8825 (ttmm) outliers start: 57 outliers final: 38 residues processed: 1222 average time/residue: 0.2683 time to fit residues: 493.5100 Evaluate side-chains 1226 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 1188 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 1909 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 365 LYS Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 288 LYS Chi-restraints excluded: chain J residue 339 SER Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 290 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 357 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 384 optimal weight: 0.5980 chunk 292 optimal weight: 2.9990 chunk 358 optimal weight: 0.9980 chunk 360 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 892 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN D 91 GLN E 229 HIS E 380 GLN F 146 GLN G 316 HIS G 369 GLN G 420 ASN ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 GLN I 289 GLN I 380 GLN J 404 GLN V 27 GLN X 25 ASN X 27 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.099375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.084521 restraints weight = 65188.104| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.56 r_work: 0.2756 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 43580 Z= 0.173 Angle : 0.524 6.917 59886 Z= 0.279 Chirality : 0.041 0.161 6829 Planarity : 0.004 0.056 6809 Dihedral : 20.881 173.727 7878 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.80 % Allowed : 11.17 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.12), residues: 4651 helix: 2.01 (0.11), residues: 2338 sheet: 0.46 (0.19), residues: 694 loop : 0.43 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 71 TYR 0.016 0.001 TYR C 236 PHE 0.012 0.001 PHE C 154 TRP 0.022 0.001 TRP A 682 HIS 0.008 0.001 HIS I 316 Details of bonding type rmsd covalent geometry : bond 0.00398 (43572) covalent geometry : angle 0.52344 (59877) hydrogen bonds : bond 0.03977 ( 2116) hydrogen bonds : angle 3.70999 ( 5836) metal coordination : bond 0.01176 ( 8) metal coordination : angle 1.63722 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1283 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 1210 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 ASP cc_start: 0.8812 (t70) cc_final: 0.8264 (m-30) REVERT: A 685 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7771 (mm-30) REVERT: A 716 ASN cc_start: 0.8187 (t0) cc_final: 0.7784 (t0) REVERT: A 746 ASP cc_start: 0.7581 (t0) cc_final: 0.7287 (t70) REVERT: A 823 GLU cc_start: 0.8324 (tt0) cc_final: 0.8049 (tt0) REVERT: A 825 LEU cc_start: 0.9059 (tp) cc_final: 0.8825 (tp) REVERT: A 863 LYS cc_start: 0.8052 (tptp) cc_final: 0.7715 (tptp) REVERT: A 871 ASP cc_start: 0.8179 (t0) cc_final: 0.7782 (t0) REVERT: A 947 ASP cc_start: 0.7995 (t0) cc_final: 0.7735 (t70) REVERT: A 952 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7600 (mm-30) REVERT: A 961 ASP cc_start: 0.7954 (m-30) cc_final: 0.7680 (m-30) REVERT: A 975 LEU cc_start: 0.7726 (mt) cc_final: 0.7451 (mt) REVERT: A 976 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7352 (mt-10) REVERT: A 1897 ARG cc_start: 0.7813 (ttp-170) cc_final: 0.7601 (ttp-170) REVERT: A 1921 GLU cc_start: 0.8156 (mp0) cc_final: 0.7781 (mp0) REVERT: A 1953 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7685 (mt-10) REVERT: A 1956 HIS cc_start: 0.8241 (t70) cc_final: 0.8038 (t-90) REVERT: A 2009 GLN cc_start: 0.7982 (tt0) cc_final: 0.7459 (tt0) REVERT: A 2097 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7795 (mm-40) REVERT: A 2126 ASN cc_start: 0.8159 (t0) cc_final: 0.7953 (t0) REVERT: A 2198 THR cc_start: 0.8498 (p) cc_final: 0.8270 (p) REVERT: B 263 ARG cc_start: 0.8215 (mtp85) cc_final: 0.8012 (mtp85) REVERT: C 18 SER cc_start: 0.8988 (p) cc_final: 0.8701 (t) REVERT: C 108 SER cc_start: 0.8764 (m) cc_final: 0.8340 (t) REVERT: C 109 MET cc_start: 0.8923 (tpp) cc_final: 0.8481 (mtp) REVERT: C 111 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8127 (tt0) REVERT: C 189 SER cc_start: 0.8399 (p) cc_final: 0.8103 (m) REVERT: C 221 ASP cc_start: 0.8028 (m-30) cc_final: 0.7620 (m-30) REVERT: C 245 LYS cc_start: 0.8181 (mmpt) cc_final: 0.7702 (mmpt) REVERT: C 246 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7784 (mmmt) REVERT: C 307 GLU cc_start: 0.7890 (pm20) cc_final: 0.7567 (pm20) REVERT: C 366 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8913 (tt) REVERT: C 383 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7596 (mm-30) REVERT: C 393 LYS cc_start: 0.8539 (tppp) cc_final: 0.8279 (mttm) REVERT: E 60 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8190 (mtpp) REVERT: E 137 GLU cc_start: 0.7765 (tt0) cc_final: 0.7471 (tt0) REVERT: E 168 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7823 (tttm) REVERT: E 211 THR cc_start: 0.8459 (m) cc_final: 0.8182 (p) REVERT: E 218 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7295 (tp30) REVERT: E 220 TYR cc_start: 0.8504 (m-80) cc_final: 0.8271 (m-80) REVERT: E 229 HIS cc_start: 0.8647 (t70) cc_final: 0.8439 (t-90) REVERT: E 231 LYS cc_start: 0.8352 (mttp) cc_final: 0.8105 (mttm) REVERT: E 285 LYS cc_start: 0.8267 (ttmm) cc_final: 0.7973 (ttmm) REVERT: E 323 ILE cc_start: 0.8564 (mt) cc_final: 0.8326 (mm) REVERT: E 435 GLU cc_start: 0.7676 (tt0) cc_final: 0.7411 (tt0) REVERT: F 112 GLU cc_start: 0.7535 (tp30) cc_final: 0.7283 (tp30) REVERT: F 136 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7292 (mt-10) REVERT: F 160 LYS cc_start: 0.8371 (ttpt) cc_final: 0.7976 (ttmm) REVERT: F 169 GLU cc_start: 0.7605 (tt0) cc_final: 0.7344 (tt0) REVERT: F 174 LEU cc_start: 0.8324 (mt) cc_final: 0.8080 (mt) REVERT: F 177 LYS cc_start: 0.8065 (mttt) cc_final: 0.7776 (mttt) REVERT: F 180 GLU cc_start: 0.7924 (mm-30) cc_final: 0.6941 (mm-30) REVERT: F 184 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7441 (mmtm) REVERT: F 186 LYS cc_start: 0.8205 (mtpp) cc_final: 0.7983 (mtpp) REVERT: F 188 GLN cc_start: 0.8103 (mt0) cc_final: 0.7685 (mt0) REVERT: F 191 ASP cc_start: 0.8180 (m-30) cc_final: 0.7793 (m-30) REVERT: F 201 LYS cc_start: 0.8217 (tttp) cc_final: 0.7834 (tttp) REVERT: F 234 LYS cc_start: 0.8347 (mttt) cc_final: 0.8124 (mttt) REVERT: F 236 LYS cc_start: 0.8129 (mmtp) cc_final: 0.7850 (mmtp) REVERT: F 237 GLU cc_start: 0.7532 (tt0) cc_final: 0.7272 (tt0) REVERT: F 238 VAL cc_start: 0.8314 (t) cc_final: 0.7909 (p) REVERT: F 274 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7536 (mm-30) REVERT: F 348 ILE cc_start: 0.8268 (tp) cc_final: 0.8048 (tp) REVERT: F 352 ASP cc_start: 0.7741 (m-30) cc_final: 0.7491 (m-30) REVERT: G 123 ARG cc_start: 0.8387 (ttm170) cc_final: 0.8080 (ttm-80) REVERT: G 125 LYS cc_start: 0.8372 (mtmt) cc_final: 0.8113 (mtmm) REVERT: G 137 GLU cc_start: 0.7966 (tt0) cc_final: 0.7594 (tt0) REVERT: G 139 THR cc_start: 0.8285 (m) cc_final: 0.8046 (p) REVERT: G 214 ASP cc_start: 0.7940 (m-30) cc_final: 0.7518 (m-30) REVERT: G 225 LYS cc_start: 0.8263 (mmpt) cc_final: 0.8012 (mtpp) REVERT: G 320 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7142 (mp0) REVERT: G 326 ILE cc_start: 0.8519 (mt) cc_final: 0.8236 (mm) REVERT: G 353 ASP cc_start: 0.7849 (m-30) cc_final: 0.7582 (m-30) REVERT: G 388 GLU cc_start: 0.7894 (tp30) cc_final: 0.7269 (mm-30) REVERT: G 392 ASN cc_start: 0.8608 (m-40) cc_final: 0.8083 (m110) REVERT: G 418 LYS cc_start: 0.8133 (mtpt) cc_final: 0.7887 (mtpp) REVERT: G 435 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7296 (mp0) REVERT: G 447 LEU cc_start: 0.8234 (mt) cc_final: 0.7912 (mp) REVERT: H 117 GLU cc_start: 0.8152 (tp30) cc_final: 0.7863 (tp30) REVERT: H 136 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7538 (mt-10) REVERT: H 184 LYS cc_start: 0.8004 (ttpt) cc_final: 0.7680 (ttpt) REVERT: H 204 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8100 (mtmt) REVERT: H 235 ARG cc_start: 0.8162 (mtt180) cc_final: 0.7805 (ttm110) REVERT: H 248 ASP cc_start: 0.7428 (m-30) cc_final: 0.7190 (m-30) REVERT: H 253 ARG cc_start: 0.8195 (ptm160) cc_final: 0.7811 (ptp90) REVERT: H 313 ASN cc_start: 0.8097 (m-40) cc_final: 0.7602 (m-40) REVERT: H 314 ARG cc_start: 0.7194 (mmt180) cc_final: 0.6759 (mmt180) REVERT: H 342 SER cc_start: 0.8730 (m) cc_final: 0.8403 (t) REVERT: H 358 SER cc_start: 0.8483 (m) cc_final: 0.8092 (t) REVERT: H 369 GLN cc_start: 0.8111 (tp-100) cc_final: 0.7823 (tt0) REVERT: H 377 GLU cc_start: 0.7815 (tp30) cc_final: 0.7561 (tp30) REVERT: H 381 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7870 (mm-30) REVERT: H 382 MET cc_start: 0.8444 (mtp) cc_final: 0.8234 (mtm) REVERT: H 436 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6444 (tm-30) REVERT: H 443 MET cc_start: 0.7765 (ttm) cc_final: 0.7478 (ttp) REVERT: I 28 GLU cc_start: 0.7627 (mp0) cc_final: 0.7136 (mp0) REVERT: I 90 LYS cc_start: 0.8293 (pttt) cc_final: 0.7995 (pttt) REVERT: I 125 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8203 (ttpp) REVERT: I 137 GLU cc_start: 0.7644 (tt0) cc_final: 0.7288 (tt0) REVERT: I 165 LYS cc_start: 0.8672 (mttm) cc_final: 0.8443 (mttp) REVERT: I 184 ARG cc_start: 0.7849 (mtt180) cc_final: 0.7486 (mtt180) REVERT: I 209 TYR cc_start: 0.8539 (m-80) cc_final: 0.8112 (m-80) REVERT: I 251 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7455 (mm-40) REVERT: I 259 MET cc_start: 0.7740 (mtp) cc_final: 0.7068 (mtp) REVERT: I 369 GLN cc_start: 0.7893 (mp10) cc_final: 0.7524 (mp10) REVERT: I 400 LYS cc_start: 0.8164 (mtpp) cc_final: 0.7873 (mtmm) REVERT: I 408 GLN cc_start: 0.7693 (mt0) cc_final: 0.7263 (mt0) REVERT: I 418 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7774 (mtpt) REVERT: I 435 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7121 (mm-30) REVERT: I 445 LYS cc_start: 0.7828 (tppt) cc_final: 0.7198 (tppt) REVERT: J 20 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7191 (mm-30) REVERT: J 71 ARG cc_start: 0.8125 (mmt90) cc_final: 0.7894 (mmt90) REVERT: J 86 ILE cc_start: 0.8114 (mm) cc_final: 0.7880 (mt) REVERT: J 134 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7493 (mt-10) REVERT: J 136 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7543 (mt-10) REVERT: J 141 GLU cc_start: 0.7845 (tt0) cc_final: 0.7578 (tt0) REVERT: J 169 GLU cc_start: 0.7701 (tt0) cc_final: 0.7377 (tm-30) REVERT: J 236 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7895 (mtpt) REVERT: J 271 GLU cc_start: 0.7836 (mp0) cc_final: 0.7600 (mp0) REVERT: J 299 ASP cc_start: 0.8247 (t0) cc_final: 0.7851 (t70) REVERT: J 377 GLU cc_start: 0.7786 (tp30) cc_final: 0.7570 (tp30) REVERT: J 392 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7338 (ttp80) REVERT: J 414 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7705 (mtp-110) REVERT: R 88 THR cc_start: 0.8682 (t) cc_final: 0.8369 (p) REVERT: R 93 GLU cc_start: 0.8172 (mp0) cc_final: 0.7963 (mp0) REVERT: R 116 LYS cc_start: 0.8831 (ttpp) cc_final: 0.8603 (ttpp) REVERT: T 42 TYR cc_start: 0.8489 (t80) cc_final: 0.8223 (t80) REVERT: T 62 MET cc_start: 0.8919 (mmm) cc_final: 0.8440 (mmm) REVERT: W 40 ARG cc_start: 0.8710 (ttm-80) cc_final: 0.8324 (ttt-90) REVERT: W 83 ARG cc_start: 0.8372 (mtp180) cc_final: 0.8113 (mtp85) REVERT: W 118 THR cc_start: 0.9172 (m) cc_final: 0.8890 (p) REVERT: X 84 MET cc_start: 0.8477 (mmm) cc_final: 0.8269 (mmm) outliers start: 73 outliers final: 51 residues processed: 1235 average time/residue: 0.2766 time to fit residues: 515.1856 Evaluate side-chains 1238 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 1186 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 1895 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 365 LYS Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 164 LYS Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 303 GLU Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain I residue 406 SER Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 234 LYS Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 288 LYS Chi-restraints excluded: chain J residue 339 SER Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 93 GLN Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 175 optimal weight: 1.9990 chunk 332 optimal weight: 1.9990 chunk 415 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 293 optimal weight: 0.5980 chunk 307 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 260 optimal weight: 0.5980 chunk 184 optimal weight: 0.9990 chunk 474 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 875 GLN A 892 ASN C 110 ASN C 303 GLN D 91 GLN E 380 GLN F 146 GLN ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 422 GLN I 236 GLN I 289 GLN ** I 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 380 GLN J 404 GLN V 27 GLN X 25 ASN X 27 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.084771 restraints weight = 64986.454| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.61 r_work: 0.2758 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 43580 Z= 0.168 Angle : 0.524 8.034 59886 Z= 0.278 Chirality : 0.041 0.158 6829 Planarity : 0.004 0.057 6809 Dihedral : 20.868 173.612 7878 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.68 % Allowed : 12.43 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.12), residues: 4651 helix: 2.02 (0.11), residues: 2338 sheet: 0.49 (0.20), residues: 681 loop : 0.41 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 71 TYR 0.016 0.001 TYR E 209 PHE 0.009 0.001 PHE Q 25 TRP 0.017 0.001 TRP A 712 HIS 0.010 0.001 HIS I 316 Details of bonding type rmsd covalent geometry : bond 0.00386 (43572) covalent geometry : angle 0.52348 (59877) hydrogen bonds : bond 0.03889 ( 2116) hydrogen bonds : angle 3.66928 ( 5836) metal coordination : bond 0.01195 ( 8) metal coordination : angle 1.70374 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 1185 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 ASP cc_start: 0.8792 (t70) cc_final: 0.8306 (m-30) REVERT: A 685 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7807 (mm-30) REVERT: A 716 ASN cc_start: 0.8209 (t0) cc_final: 0.7809 (t0) REVERT: A 823 GLU cc_start: 0.8318 (tt0) cc_final: 0.8061 (tt0) REVERT: A 825 LEU cc_start: 0.9038 (tp) cc_final: 0.8800 (tp) REVERT: A 863 LYS cc_start: 0.8060 (tptp) cc_final: 0.7730 (tptp) REVERT: A 871 ASP cc_start: 0.8161 (t0) cc_final: 0.7872 (t70) REVERT: A 947 ASP cc_start: 0.7997 (t0) cc_final: 0.7745 (t0) REVERT: A 952 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7625 (mm-30) REVERT: A 961 ASP cc_start: 0.7948 (m-30) cc_final: 0.7666 (m-30) REVERT: A 975 LEU cc_start: 0.7777 (mt) cc_final: 0.7509 (mt) REVERT: A 1897 ARG cc_start: 0.7855 (ttp-170) cc_final: 0.7648 (ttp-170) REVERT: A 1906 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8111 (mm110) REVERT: A 1921 GLU cc_start: 0.8166 (mp0) cc_final: 0.7786 (mp0) REVERT: A 1953 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7736 (mt-10) REVERT: A 2068 MET cc_start: 0.8634 (mtt) cc_final: 0.8396 (mtm) REVERT: A 2097 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7831 (mm-40) REVERT: A 2198 THR cc_start: 0.8538 (p) cc_final: 0.8322 (p) REVERT: B 133 MET cc_start: 0.6727 (mmm) cc_final: 0.6413 (mmm) REVERT: C 1 MET cc_start: 0.5385 (tmm) cc_final: 0.4978 (tmm) REVERT: C 18 SER cc_start: 0.8985 (p) cc_final: 0.8683 (t) REVERT: C 47 GLU cc_start: 0.7774 (tp30) cc_final: 0.7441 (mm-30) REVERT: C 90 ASP cc_start: 0.8313 (t0) cc_final: 0.7805 (t0) REVERT: C 108 SER cc_start: 0.8759 (m) cc_final: 0.8352 (t) REVERT: C 111 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8143 (tt0) REVERT: C 189 SER cc_start: 0.8389 (p) cc_final: 0.8099 (m) REVERT: C 221 ASP cc_start: 0.8048 (m-30) cc_final: 0.7633 (m-30) REVERT: C 245 LYS cc_start: 0.8153 (mmpt) cc_final: 0.7689 (mmpt) REVERT: C 246 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7799 (mmmt) REVERT: C 366 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8873 (tt) REVERT: C 383 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7636 (mm-30) REVERT: C 393 LYS cc_start: 0.8517 (tppp) cc_final: 0.8239 (mttm) REVERT: E 60 LYS cc_start: 0.8437 (mtpp) cc_final: 0.8212 (mtpp) REVERT: E 137 GLU cc_start: 0.7773 (tt0) cc_final: 0.7533 (tt0) REVERT: E 168 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7940 (ttmt) REVERT: E 211 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8245 (p) REVERT: E 218 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7504 (tp30) REVERT: E 220 TYR cc_start: 0.8510 (m-80) cc_final: 0.7966 (m-80) REVERT: E 229 HIS cc_start: 0.8646 (t70) cc_final: 0.8355 (t70) REVERT: E 231 LYS cc_start: 0.8336 (mttp) cc_final: 0.8123 (mttm) REVERT: E 285 LYS cc_start: 0.8300 (ttmm) cc_final: 0.8003 (ttmm) REVERT: E 323 ILE cc_start: 0.8586 (mt) cc_final: 0.8351 (mm) REVERT: E 435 GLU cc_start: 0.7687 (tt0) cc_final: 0.7428 (tt0) REVERT: F 112 GLU cc_start: 0.7556 (tp30) cc_final: 0.7309 (tp30) REVERT: F 136 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7283 (mt-10) REVERT: F 137 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7924 (tp) REVERT: F 160 LYS cc_start: 0.8402 (ttpt) cc_final: 0.7974 (ttmm) REVERT: F 169 GLU cc_start: 0.7598 (tt0) cc_final: 0.7346 (tt0) REVERT: F 177 LYS cc_start: 0.8166 (mttt) cc_final: 0.7947 (mttt) REVERT: F 180 GLU cc_start: 0.7953 (mm-30) cc_final: 0.6970 (mm-30) REVERT: F 184 LYS cc_start: 0.7959 (mmtm) cc_final: 0.7470 (mmtm) REVERT: F 186 LYS cc_start: 0.8236 (mtpp) cc_final: 0.8017 (mtpp) REVERT: F 188 GLN cc_start: 0.8141 (mt0) cc_final: 0.7673 (mt0) REVERT: F 191 ASP cc_start: 0.8170 (m-30) cc_final: 0.7806 (m-30) REVERT: F 201 LYS cc_start: 0.8250 (tttp) cc_final: 0.7880 (tttp) REVERT: F 234 LYS cc_start: 0.8385 (mttt) cc_final: 0.8165 (mttt) REVERT: F 236 LYS cc_start: 0.8160 (mmtp) cc_final: 0.7892 (mmtp) REVERT: F 237 GLU cc_start: 0.7492 (tt0) cc_final: 0.7237 (tt0) REVERT: F 238 VAL cc_start: 0.8335 (t) cc_final: 0.7934 (p) REVERT: F 274 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7531 (mm-30) REVERT: F 348 ILE cc_start: 0.8286 (tp) cc_final: 0.8055 (tp) REVERT: F 352 ASP cc_start: 0.7749 (m-30) cc_final: 0.7488 (m-30) REVERT: G 123 ARG cc_start: 0.8391 (ttm170) cc_final: 0.8100 (ttm-80) REVERT: G 125 LYS cc_start: 0.8381 (mtmt) cc_final: 0.8133 (mttp) REVERT: G 137 GLU cc_start: 0.7960 (tt0) cc_final: 0.7610 (tt0) REVERT: G 139 THR cc_start: 0.8301 (m) cc_final: 0.8031 (p) REVERT: G 142 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7419 (mm-30) REVERT: G 214 ASP cc_start: 0.7932 (m-30) cc_final: 0.7519 (m-30) REVERT: G 225 LYS cc_start: 0.8304 (mmpt) cc_final: 0.8069 (mtpp) REVERT: G 320 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7120 (mp0) REVERT: G 326 ILE cc_start: 0.8511 (mt) cc_final: 0.8243 (mm) REVERT: G 353 ASP cc_start: 0.7862 (m-30) cc_final: 0.7586 (m-30) REVERT: G 388 GLU cc_start: 0.7915 (tp30) cc_final: 0.7298 (mm-30) REVERT: G 392 ASN cc_start: 0.8635 (m-40) cc_final: 0.8136 (m110) REVERT: G 418 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7927 (mtpp) REVERT: G 435 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7335 (mp0) REVERT: G 447 LEU cc_start: 0.8232 (mt) cc_final: 0.7919 (mp) REVERT: H 136 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7561 (mt-10) REVERT: H 185 ASP cc_start: 0.7854 (m-30) cc_final: 0.7623 (m-30) REVERT: H 204 LYS cc_start: 0.8366 (mtpt) cc_final: 0.8121 (mtmt) REVERT: H 211 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8197 (mmm-85) REVERT: H 235 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7843 (ttm110) REVERT: H 248 ASP cc_start: 0.7455 (m-30) cc_final: 0.7242 (m-30) REVERT: H 253 ARG cc_start: 0.8224 (ptm160) cc_final: 0.7854 (ptp90) REVERT: H 313 ASN cc_start: 0.8164 (m-40) cc_final: 0.7655 (m-40) REVERT: H 314 ARG cc_start: 0.7200 (mmt180) cc_final: 0.6786 (mmt180) REVERT: H 342 SER cc_start: 0.8747 (m) cc_final: 0.8418 (t) REVERT: H 358 SER cc_start: 0.8464 (m) cc_final: 0.8072 (t) REVERT: H 369 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7862 (tt0) REVERT: H 382 MET cc_start: 0.8447 (mtp) cc_final: 0.8231 (mtm) REVERT: H 436 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6494 (tm-30) REVERT: H 443 MET cc_start: 0.7788 (ttm) cc_final: 0.7508 (ttp) REVERT: I 28 GLU cc_start: 0.7644 (mp0) cc_final: 0.7153 (mp0) REVERT: I 125 LYS cc_start: 0.8557 (ttpp) cc_final: 0.8233 (ttpp) REVERT: I 137 GLU cc_start: 0.7651 (tt0) cc_final: 0.7318 (tt0) REVERT: I 139 THR cc_start: 0.8344 (m) cc_final: 0.8040 (p) REVERT: I 165 LYS cc_start: 0.8652 (mttm) cc_final: 0.8423 (mttp) REVERT: I 184 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7513 (mtt180) REVERT: I 209 TYR cc_start: 0.8552 (m-80) cc_final: 0.8141 (m-80) REVERT: I 251 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7466 (mm-40) REVERT: I 259 MET cc_start: 0.7742 (mtp) cc_final: 0.7297 (mtm) REVERT: I 353 ASP cc_start: 0.7441 (m-30) cc_final: 0.7231 (m-30) REVERT: I 369 GLN cc_start: 0.7907 (mp10) cc_final: 0.7577 (mp10) REVERT: I 389 GLU cc_start: 0.8018 (pt0) cc_final: 0.7705 (tt0) REVERT: I 400 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7890 (mtmm) REVERT: I 408 GLN cc_start: 0.7708 (mt0) cc_final: 0.7268 (mt0) REVERT: I 418 LYS cc_start: 0.8181 (ttmm) cc_final: 0.7797 (mtpt) REVERT: I 435 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7189 (mm-30) REVERT: I 445 LYS cc_start: 0.7881 (tppt) cc_final: 0.7251 (tppt) REVERT: J 20 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7234 (mm-30) REVERT: J 71 ARG cc_start: 0.8129 (mmt90) cc_final: 0.7895 (mmt90) REVERT: J 86 ILE cc_start: 0.8163 (mm) cc_final: 0.7915 (mt) REVERT: J 134 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7542 (mt-10) REVERT: J 136 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7578 (mt-10) REVERT: J 141 GLU cc_start: 0.7816 (tt0) cc_final: 0.7551 (tt0) REVERT: J 169 GLU cc_start: 0.7696 (tt0) cc_final: 0.7394 (tm-30) REVERT: J 236 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7927 (mtpt) REVERT: J 271 GLU cc_start: 0.7829 (mp0) cc_final: 0.7457 (mp0) REVERT: J 299 ASP cc_start: 0.8279 (t0) cc_final: 0.7883 (t70) REVERT: J 377 GLU cc_start: 0.7812 (tp30) cc_final: 0.7597 (tp30) REVERT: J 392 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7390 (ttp80) REVERT: J 414 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.7711 (mtp-110) REVERT: R 83 TYR cc_start: 0.7788 (m-10) cc_final: 0.7556 (m-10) REVERT: R 88 THR cc_start: 0.8702 (t) cc_final: 0.8398 (p) REVERT: R 93 GLU cc_start: 0.8148 (mp0) cc_final: 0.7942 (mp0) REVERT: R 116 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8611 (ttpp) REVERT: T 42 TYR cc_start: 0.8487 (t80) cc_final: 0.8243 (t80) REVERT: T 62 MET cc_start: 0.8922 (mmm) cc_final: 0.8473 (mmm) REVERT: W 40 ARG cc_start: 0.8709 (ttm-80) cc_final: 0.8341 (ttt-90) REVERT: W 83 ARG cc_start: 0.8365 (mtp180) cc_final: 0.8116 (mtp180) REVERT: W 118 THR cc_start: 0.9174 (m) cc_final: 0.8895 (p) outliers start: 68 outliers final: 49 residues processed: 1209 average time/residue: 0.2705 time to fit residues: 493.6876 Evaluate side-chains 1229 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 1176 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 1895 ARG Chi-restraints excluded: chain A residue 1909 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 365 LYS Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 164 LYS Chi-restraints excluded: chain H residue 211 ARG Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 303 GLU Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 339 SER Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 86 optimal weight: 5.9990 chunk 262 optimal weight: 0.2980 chunk 295 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 292 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 chunk 404 optimal weight: 0.5980 chunk 285 optimal weight: 0.9990 chunk 266 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 875 GLN A 892 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN E 380 GLN F 146 GLN F 422 GLN ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 404 GLN V 27 GLN X 25 ASN X 27 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.087973 restraints weight = 64042.453| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.57 r_work: 0.2766 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43580 Z= 0.140 Angle : 0.513 9.450 59886 Z= 0.272 Chirality : 0.040 0.180 6829 Planarity : 0.004 0.054 6809 Dihedral : 20.843 173.261 7878 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.73 % Allowed : 12.95 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.12), residues: 4651 helix: 2.06 (0.11), residues: 2341 sheet: 0.49 (0.20), residues: 680 loop : 0.42 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 317 TYR 0.017 0.001 TYR R 83 PHE 0.009 0.001 PHE R 70 TRP 0.012 0.001 TRP A 786 HIS 0.010 0.001 HIS I 316 Details of bonding type rmsd covalent geometry : bond 0.00317 (43572) covalent geometry : angle 0.51290 (59877) hydrogen bonds : bond 0.03688 ( 2116) hydrogen bonds : angle 3.61019 ( 5836) metal coordination : bond 0.00976 ( 8) metal coordination : angle 1.74914 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 1190 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 ASP cc_start: 0.8785 (t70) cc_final: 0.8287 (m-30) REVERT: A 685 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7799 (mm-30) REVERT: A 716 ASN cc_start: 0.8204 (t0) cc_final: 0.7807 (t0) REVERT: A 823 GLU cc_start: 0.8319 (tt0) cc_final: 0.8092 (tt0) REVERT: A 825 LEU cc_start: 0.9039 (tp) cc_final: 0.8804 (tp) REVERT: A 863 LYS cc_start: 0.8043 (tptp) cc_final: 0.7718 (tptp) REVERT: A 871 ASP cc_start: 0.8122 (t0) cc_final: 0.7814 (t70) REVERT: A 947 ASP cc_start: 0.8036 (t0) cc_final: 0.7763 (t0) REVERT: A 952 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7502 (mm-30) REVERT: A 961 ASP cc_start: 0.7894 (m-30) cc_final: 0.7614 (m-30) REVERT: A 975 LEU cc_start: 0.7779 (mt) cc_final: 0.7507 (mt) REVERT: A 1921 GLU cc_start: 0.8157 (mp0) cc_final: 0.7588 (mp0) REVERT: A 1953 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7679 (mt-10) REVERT: A 2009 GLN cc_start: 0.7964 (tt0) cc_final: 0.7530 (tt0) REVERT: A 2068 MET cc_start: 0.8592 (mtt) cc_final: 0.8382 (mtm) REVERT: A 2097 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7844 (mm-40) REVERT: A 2198 THR cc_start: 0.8526 (p) cc_final: 0.8299 (p) REVERT: B 133 MET cc_start: 0.6689 (mmm) cc_final: 0.6361 (mmm) REVERT: B 215 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7958 (t-170) REVERT: C 1 MET cc_start: 0.5365 (tmm) cc_final: 0.4942 (tmm) REVERT: C 47 GLU cc_start: 0.7751 (tp30) cc_final: 0.7520 (mm-30) REVERT: C 90 ASP cc_start: 0.8305 (t0) cc_final: 0.7663 (t0) REVERT: C 108 SER cc_start: 0.8702 (m) cc_final: 0.8300 (t) REVERT: C 189 SER cc_start: 0.8386 (p) cc_final: 0.8105 (m) REVERT: C 221 ASP cc_start: 0.8014 (m-30) cc_final: 0.7594 (m-30) REVERT: C 224 LYS cc_start: 0.8496 (tttp) cc_final: 0.8291 (ttmm) REVERT: C 245 LYS cc_start: 0.8149 (mmpt) cc_final: 0.7753 (mmpt) REVERT: C 246 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7781 (mmmt) REVERT: C 366 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8831 (tt) REVERT: C 378 THR cc_start: 0.8641 (p) cc_final: 0.8423 (p) REVERT: E 60 LYS cc_start: 0.8416 (mtpp) cc_final: 0.8186 (mtpp) REVERT: E 90 LYS cc_start: 0.8257 (tttt) cc_final: 0.8021 (tttt) REVERT: E 137 GLU cc_start: 0.7757 (tt0) cc_final: 0.7506 (tt0) REVERT: E 162 LYS cc_start: 0.8544 (ptmt) cc_final: 0.8344 (ptpt) REVERT: E 168 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7933 (ttmt) REVERT: E 211 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8240 (p) REVERT: E 218 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7513 (tp30) REVERT: E 220 TYR cc_start: 0.8485 (m-80) cc_final: 0.7991 (m-80) REVERT: E 229 HIS cc_start: 0.8612 (t70) cc_final: 0.8318 (t70) REVERT: E 285 LYS cc_start: 0.8265 (ttmm) cc_final: 0.7987 (ttmm) REVERT: E 323 ILE cc_start: 0.8562 (mt) cc_final: 0.8356 (mm) REVERT: E 435 GLU cc_start: 0.7675 (tt0) cc_final: 0.7404 (tt0) REVERT: F 112 GLU cc_start: 0.7568 (tp30) cc_final: 0.7313 (tp30) REVERT: F 136 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7286 (mt-10) REVERT: F 160 LYS cc_start: 0.8385 (ttpt) cc_final: 0.7937 (ttmm) REVERT: F 169 GLU cc_start: 0.7609 (tt0) cc_final: 0.7344 (tt0) REVERT: F 180 GLU cc_start: 0.7940 (mm-30) cc_final: 0.6920 (mm-30) REVERT: F 181 SER cc_start: 0.8543 (m) cc_final: 0.8227 (t) REVERT: F 184 LYS cc_start: 0.7936 (mmtm) cc_final: 0.7447 (mmtm) REVERT: F 186 LYS cc_start: 0.8222 (mtpp) cc_final: 0.8015 (mtpp) REVERT: F 201 LYS cc_start: 0.8244 (tttp) cc_final: 0.7895 (tttp) REVERT: F 234 LYS cc_start: 0.8402 (mttt) cc_final: 0.8140 (mttt) REVERT: F 236 LYS cc_start: 0.8153 (mmtp) cc_final: 0.7874 (mmtp) REVERT: F 237 GLU cc_start: 0.7468 (tt0) cc_final: 0.7219 (tt0) REVERT: F 238 VAL cc_start: 0.8359 (t) cc_final: 0.7971 (p) REVERT: F 274 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7516 (mm-30) REVERT: F 348 ILE cc_start: 0.8254 (tp) cc_final: 0.8021 (tp) REVERT: F 352 ASP cc_start: 0.7738 (m-30) cc_final: 0.7477 (m-30) REVERT: G 123 ARG cc_start: 0.8379 (ttm170) cc_final: 0.8091 (ttm-80) REVERT: G 125 LYS cc_start: 0.8366 (mtmt) cc_final: 0.8097 (mttp) REVERT: G 137 GLU cc_start: 0.7956 (tt0) cc_final: 0.7595 (tt0) REVERT: G 139 THR cc_start: 0.8261 (m) cc_final: 0.8058 (p) REVERT: G 142 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7376 (mm-30) REVERT: G 214 ASP cc_start: 0.7942 (m-30) cc_final: 0.7522 (m-30) REVERT: G 225 LYS cc_start: 0.8297 (mmpt) cc_final: 0.8072 (mtpp) REVERT: G 320 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7065 (mp0) REVERT: G 326 ILE cc_start: 0.8503 (mt) cc_final: 0.8233 (mm) REVERT: G 353 ASP cc_start: 0.7851 (m-30) cc_final: 0.7571 (m-30) REVERT: G 388 GLU cc_start: 0.7925 (tp30) cc_final: 0.7282 (mm-30) REVERT: G 392 ASN cc_start: 0.8637 (m-40) cc_final: 0.8122 (m110) REVERT: G 418 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7911 (mtpp) REVERT: G 435 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7318 (mp0) REVERT: G 447 LEU cc_start: 0.8229 (mt) cc_final: 0.7883 (mp) REVERT: H 136 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7574 (mm-30) REVERT: H 181 SER cc_start: 0.7806 (t) cc_final: 0.7271 (p) REVERT: H 185 ASP cc_start: 0.7850 (m-30) cc_final: 0.7593 (m-30) REVERT: H 204 LYS cc_start: 0.8351 (mtpt) cc_final: 0.8074 (mtmt) REVERT: H 211 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8058 (mmm-85) REVERT: H 235 ARG cc_start: 0.8166 (mtt180) cc_final: 0.7786 (ttm110) REVERT: H 248 ASP cc_start: 0.7426 (m-30) cc_final: 0.7204 (m-30) REVERT: H 313 ASN cc_start: 0.8145 (m-40) cc_final: 0.7667 (m-40) REVERT: H 314 ARG cc_start: 0.7227 (mmt180) cc_final: 0.6810 (mmt180) REVERT: H 342 SER cc_start: 0.8726 (m) cc_final: 0.8398 (t) REVERT: H 358 SER cc_start: 0.8468 (m) cc_final: 0.8080 (t) REVERT: H 369 GLN cc_start: 0.8119 (tp-100) cc_final: 0.7816 (mt0) REVERT: H 382 MET cc_start: 0.8439 (mtp) cc_final: 0.8234 (mtm) REVERT: H 436 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6479 (tm-30) REVERT: H 443 MET cc_start: 0.7755 (ttm) cc_final: 0.7456 (ttp) REVERT: I 28 GLU cc_start: 0.7624 (mp0) cc_final: 0.7135 (mp0) REVERT: I 125 LYS cc_start: 0.8541 (ttpp) cc_final: 0.8213 (ttpp) REVERT: I 137 GLU cc_start: 0.7666 (tt0) cc_final: 0.7328 (tt0) REVERT: I 139 THR cc_start: 0.8309 (m) cc_final: 0.8028 (p) REVERT: I 165 LYS cc_start: 0.8634 (mttm) cc_final: 0.8412 (mttp) REVERT: I 184 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7501 (mtt180) REVERT: I 209 TYR cc_start: 0.8549 (m-80) cc_final: 0.8152 (m-80) REVERT: I 251 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7426 (mm-40) REVERT: I 259 MET cc_start: 0.7738 (mtp) cc_final: 0.7298 (mtp) REVERT: I 369 GLN cc_start: 0.7890 (mp10) cc_final: 0.7561 (mp10) REVERT: I 389 GLU cc_start: 0.7988 (pt0) cc_final: 0.7676 (tt0) REVERT: I 400 LYS cc_start: 0.8119 (mtpp) cc_final: 0.7856 (mtmm) REVERT: I 408 GLN cc_start: 0.7705 (mt0) cc_final: 0.7241 (mt0) REVERT: I 418 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7821 (mtpt) REVERT: I 435 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7267 (mm-30) REVERT: I 445 LYS cc_start: 0.7851 (tppt) cc_final: 0.7217 (tppt) REVERT: J 18 ARG cc_start: 0.7322 (mtp85) cc_final: 0.7091 (mtp85) REVERT: J 20 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7200 (mm-30) REVERT: J 71 ARG cc_start: 0.8121 (mmt90) cc_final: 0.7866 (mmt90) REVERT: J 86 ILE cc_start: 0.8131 (mm) cc_final: 0.7877 (mt) REVERT: J 133 GLU cc_start: 0.7966 (pt0) cc_final: 0.7726 (pt0) REVERT: J 134 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7517 (mt-10) REVERT: J 136 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7553 (mt-10) REVERT: J 141 GLU cc_start: 0.7789 (tt0) cc_final: 0.7531 (tt0) REVERT: J 169 GLU cc_start: 0.7706 (tt0) cc_final: 0.7390 (tm-30) REVERT: J 236 LYS cc_start: 0.8228 (mtpt) cc_final: 0.7935 (mtpt) REVERT: J 271 GLU cc_start: 0.7798 (mp0) cc_final: 0.7420 (mp0) REVERT: J 285 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7560 (mm-30) REVERT: J 299 ASP cc_start: 0.8273 (t0) cc_final: 0.7878 (t70) REVERT: J 377 GLU cc_start: 0.7798 (tp30) cc_final: 0.7575 (tp30) REVERT: J 392 ARG cc_start: 0.7782 (ttp80) cc_final: 0.7361 (ttp80) REVERT: J 404 GLN cc_start: 0.7621 (mt0) cc_final: 0.7329 (mt0) REVERT: J 414 ARG cc_start: 0.7879 (mtp-110) cc_final: 0.7647 (mtp-110) REVERT: R 88 THR cc_start: 0.8701 (t) cc_final: 0.8404 (p) REVERT: R 93 GLU cc_start: 0.8157 (mp0) cc_final: 0.7916 (mp0) REVERT: R 116 LYS cc_start: 0.8829 (ttpp) cc_final: 0.8606 (ttpp) REVERT: T 42 TYR cc_start: 0.8483 (t80) cc_final: 0.8207 (t80) REVERT: T 62 MET cc_start: 0.8942 (mmm) cc_final: 0.8481 (mmm) REVERT: U 90 MET cc_start: 0.8712 (mmm) cc_final: 0.8443 (mmm) REVERT: W 40 ARG cc_start: 0.8691 (ttm-80) cc_final: 0.8320 (ttt-90) REVERT: W 118 THR cc_start: 0.9169 (m) cc_final: 0.8904 (p) REVERT: X 80 THR cc_start: 0.8773 (t) cc_final: 0.8536 (p) REVERT: X 84 MET cc_start: 0.8338 (mmm) cc_final: 0.8091 (tpp) REVERT: X 88 TYR cc_start: 0.8680 (m-10) cc_final: 0.8009 (m-80) outliers start: 70 outliers final: 55 residues processed: 1214 average time/residue: 0.2777 time to fit residues: 508.5326 Evaluate side-chains 1226 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 1167 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 851 LYS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1895 ARG Chi-restraints excluded: chain A residue 1909 GLU Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 342 SER Chi-restraints excluded: chain F residue 365 LYS Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 164 LYS Chi-restraints excluded: chain H residue 211 ARG Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 303 GLU Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 288 LYS Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 339 SER Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 77 LYS Chi-restraints excluded: chain X residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 449 optimal weight: 4.9990 chunk 320 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 283 optimal weight: 0.1980 chunk 115 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 481 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 334 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 303 GLN E 380 GLN F 146 GLN F 188 GLN F 341 GLN ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 GLN S 38 ASN V 27 GLN X 25 ASN X 27 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.099013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.083974 restraints weight = 64900.183| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.60 r_work: 0.2760 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 43580 Z= 0.199 Angle : 0.539 10.397 59886 Z= 0.285 Chirality : 0.042 0.170 6829 Planarity : 0.004 0.064 6809 Dihedral : 20.871 173.829 7878 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.08 % Allowed : 13.19 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.12), residues: 4651 helix: 2.00 (0.11), residues: 2342 sheet: 0.46 (0.20), residues: 671 loop : 0.39 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 317 TYR 0.016 0.001 TYR E 209 PHE 0.011 0.001 PHE E 177 TRP 0.027 0.001 TRP A 682 HIS 0.008 0.001 HIS I 316 Details of bonding type rmsd covalent geometry : bond 0.00463 (43572) covalent geometry : angle 0.53820 (59877) hydrogen bonds : bond 0.04019 ( 2116) hydrogen bonds : angle 3.66605 ( 5836) metal coordination : bond 0.01584 ( 8) metal coordination : angle 1.58594 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 1187 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 627 ASP cc_start: 0.8807 (t70) cc_final: 0.8326 (m-30) REVERT: A 685 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7799 (mm-30) REVERT: A 716 ASN cc_start: 0.8250 (t0) cc_final: 0.7911 (t0) REVERT: A 825 LEU cc_start: 0.9072 (tp) cc_final: 0.8836 (tp) REVERT: A 863 LYS cc_start: 0.8080 (tptp) cc_final: 0.7763 (tptp) REVERT: A 871 ASP cc_start: 0.8155 (t0) cc_final: 0.7845 (t70) REVERT: A 947 ASP cc_start: 0.7995 (t0) cc_final: 0.7754 (t70) REVERT: A 952 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7642 (mm-30) REVERT: A 961 ASP cc_start: 0.7920 (m-30) cc_final: 0.7635 (m-30) REVERT: A 976 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7313 (mt-10) REVERT: A 1906 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8118 (mm110) REVERT: A 1921 GLU cc_start: 0.8153 (mp0) cc_final: 0.7777 (mp0) REVERT: A 2009 GLN cc_start: 0.7988 (tt0) cc_final: 0.7627 (tt0) REVERT: A 2097 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7891 (mm-40) REVERT: B 133 MET cc_start: 0.6717 (mmm) cc_final: 0.6390 (mmm) REVERT: B 215 HIS cc_start: 0.8304 (OUTLIER) cc_final: 0.8035 (t-170) REVERT: B 264 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8253 (p) REVERT: C 1 MET cc_start: 0.5366 (tmm) cc_final: 0.4974 (tmm) REVERT: C 90 ASP cc_start: 0.8326 (t0) cc_final: 0.7690 (t0) REVERT: C 108 SER cc_start: 0.8744 (m) cc_final: 0.8343 (t) REVERT: C 109 MET cc_start: 0.8853 (tpp) cc_final: 0.8482 (ttt) REVERT: C 189 SER cc_start: 0.8392 (p) cc_final: 0.8104 (m) REVERT: C 221 ASP cc_start: 0.8040 (m-30) cc_final: 0.7625 (m-30) REVERT: C 245 LYS cc_start: 0.8161 (mmpt) cc_final: 0.7792 (mmpt) REVERT: C 246 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7819 (mmmt) REVERT: C 366 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8833 (tt) REVERT: E 60 LYS cc_start: 0.8425 (mtpp) cc_final: 0.8207 (mtpp) REVERT: E 90 LYS cc_start: 0.8269 (tttt) cc_final: 0.8051 (tttt) REVERT: E 137 GLU cc_start: 0.7794 (tt0) cc_final: 0.7535 (tt0) REVERT: E 162 LYS cc_start: 0.8523 (ptmt) cc_final: 0.8308 (ptpt) REVERT: E 168 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7959 (ttmt) REVERT: E 211 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8258 (p) REVERT: E 218 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7544 (tp30) REVERT: E 220 TYR cc_start: 0.8502 (m-80) cc_final: 0.7966 (m-80) REVERT: E 229 HIS cc_start: 0.8639 (t70) cc_final: 0.8413 (t70) REVERT: E 285 LYS cc_start: 0.8298 (ttmm) cc_final: 0.7997 (ttmm) REVERT: E 435 GLU cc_start: 0.7696 (tt0) cc_final: 0.7413 (tt0) REVERT: F 112 GLU cc_start: 0.7588 (tp30) cc_final: 0.7333 (tp30) REVERT: F 136 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7228 (mt-10) REVERT: F 160 LYS cc_start: 0.8402 (ttpt) cc_final: 0.7970 (ttmm) REVERT: F 169 GLU cc_start: 0.7606 (tt0) cc_final: 0.7347 (tt0) REVERT: F 180 GLU cc_start: 0.7945 (mm-30) cc_final: 0.6937 (mm-30) REVERT: F 184 LYS cc_start: 0.7933 (mmtm) cc_final: 0.7478 (mmtm) REVERT: F 186 LYS cc_start: 0.8258 (mtpp) cc_final: 0.8046 (mtpp) REVERT: F 201 LYS cc_start: 0.8248 (tttp) cc_final: 0.7888 (tttp) REVERT: F 236 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7922 (mmtp) REVERT: F 237 GLU cc_start: 0.7497 (tt0) cc_final: 0.7249 (tt0) REVERT: F 238 VAL cc_start: 0.8335 (t) cc_final: 0.7937 (p) REVERT: F 274 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7520 (mm-30) REVERT: F 348 ILE cc_start: 0.8291 (tp) cc_final: 0.8062 (tp) REVERT: F 352 ASP cc_start: 0.7773 (m-30) cc_final: 0.7517 (m-30) REVERT: F 414 ARG cc_start: 0.7276 (mtm180) cc_final: 0.7017 (mtm110) REVERT: G 59 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8521 (mtmm) REVERT: G 90 LYS cc_start: 0.8294 (tptm) cc_final: 0.8014 (tptm) REVERT: G 123 ARG cc_start: 0.8379 (ttm170) cc_final: 0.7999 (ttm-80) REVERT: G 125 LYS cc_start: 0.8374 (mtmt) cc_final: 0.8122 (mttp) REVERT: G 137 GLU cc_start: 0.7971 (tt0) cc_final: 0.7620 (tt0) REVERT: G 139 THR cc_start: 0.8333 (m) cc_final: 0.8108 (p) REVERT: G 142 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7408 (mm-30) REVERT: G 214 ASP cc_start: 0.7952 (m-30) cc_final: 0.7516 (m-30) REVERT: G 225 LYS cc_start: 0.8307 (mmpt) cc_final: 0.8084 (mtpp) REVERT: G 320 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7145 (mp0) REVERT: G 326 ILE cc_start: 0.8528 (mt) cc_final: 0.8256 (mm) REVERT: G 353 ASP cc_start: 0.7804 (m-30) cc_final: 0.7565 (m-30) REVERT: G 388 GLU cc_start: 0.7949 (tp30) cc_final: 0.7298 (mm-30) REVERT: G 392 ASN cc_start: 0.8662 (m-40) cc_final: 0.8126 (m110) REVERT: G 404 ARG cc_start: 0.7720 (mtt90) cc_final: 0.7513 (mtt-85) REVERT: G 418 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7921 (mtpp) REVERT: G 435 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7339 (mp0) REVERT: G 447 LEU cc_start: 0.8240 (mt) cc_final: 0.7911 (mp) REVERT: H 136 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7532 (mt-10) REVERT: H 185 ASP cc_start: 0.7859 (m-30) cc_final: 0.7608 (m-30) REVERT: H 204 LYS cc_start: 0.8385 (mtpt) cc_final: 0.8132 (mtmt) REVERT: H 211 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.8166 (mmm-85) REVERT: H 235 ARG cc_start: 0.8224 (mtt180) cc_final: 0.7849 (ttm110) REVERT: H 248 ASP cc_start: 0.7480 (m-30) cc_final: 0.7275 (m-30) REVERT: H 253 ARG cc_start: 0.8224 (ptm160) cc_final: 0.7847 (ptp90) REVERT: H 313 ASN cc_start: 0.8156 (m-40) cc_final: 0.7652 (m-40) REVERT: H 314 ARG cc_start: 0.7183 (mmt180) cc_final: 0.6773 (mmt180) REVERT: H 342 SER cc_start: 0.8777 (m) cc_final: 0.8431 (t) REVERT: H 358 SER cc_start: 0.8478 (m) cc_final: 0.8084 (t) REVERT: H 369 GLN cc_start: 0.8145 (tp-100) cc_final: 0.7867 (tt0) REVERT: H 382 MET cc_start: 0.8500 (mtp) cc_final: 0.8284 (mtm) REVERT: H 436 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6510 (tm-30) REVERT: H 443 MET cc_start: 0.7773 (ttm) cc_final: 0.7493 (ttp) REVERT: I 28 GLU cc_start: 0.7615 (mp0) cc_final: 0.7141 (mp0) REVERT: I 125 LYS cc_start: 0.8551 (ttpp) cc_final: 0.8230 (ttpp) REVERT: I 137 GLU cc_start: 0.7658 (tt0) cc_final: 0.7342 (tt0) REVERT: I 139 THR cc_start: 0.8353 (m) cc_final: 0.8051 (p) REVERT: I 165 LYS cc_start: 0.8643 (mttm) cc_final: 0.8419 (mttp) REVERT: I 184 ARG cc_start: 0.7866 (mtt180) cc_final: 0.7510 (mtt180) REVERT: I 209 TYR cc_start: 0.8602 (m-80) cc_final: 0.8173 (m-80) REVERT: I 251 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7445 (mm-40) REVERT: I 259 MET cc_start: 0.7772 (mtp) cc_final: 0.7386 (mtp) REVERT: I 369 GLN cc_start: 0.7908 (mp10) cc_final: 0.7574 (mp10) REVERT: I 389 GLU cc_start: 0.7993 (pt0) cc_final: 0.7714 (tt0) REVERT: I 400 LYS cc_start: 0.8146 (mtpp) cc_final: 0.7873 (mtmm) REVERT: I 408 GLN cc_start: 0.7716 (mt0) cc_final: 0.7290 (mt0) REVERT: I 418 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7838 (mtpt) REVERT: I 435 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7299 (mm-30) REVERT: I 445 LYS cc_start: 0.7886 (tppt) cc_final: 0.7255 (tppt) REVERT: J 20 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7311 (mm-30) REVERT: J 71 ARG cc_start: 0.8156 (mmt90) cc_final: 0.7941 (mmt90) REVERT: J 86 ILE cc_start: 0.8167 (mm) cc_final: 0.7925 (mt) REVERT: J 134 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7532 (mt-10) REVERT: J 136 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7543 (mt-10) REVERT: J 141 GLU cc_start: 0.7812 (tt0) cc_final: 0.7554 (tt0) REVERT: J 169 GLU cc_start: 0.7701 (tt0) cc_final: 0.7429 (tm-30) REVERT: J 236 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7913 (mtpt) REVERT: J 271 GLU cc_start: 0.7797 (mp0) cc_final: 0.7428 (mp0) REVERT: J 299 ASP cc_start: 0.8288 (t0) cc_final: 0.7899 (t70) REVERT: J 377 GLU cc_start: 0.7821 (tp30) cc_final: 0.7602 (tp30) REVERT: J 392 ARG cc_start: 0.7817 (ttp80) cc_final: 0.7398 (ttp80) REVERT: J 414 ARG cc_start: 0.7890 (mtp-110) cc_final: 0.7667 (mtp-110) REVERT: R 88 THR cc_start: 0.8706 (t) cc_final: 0.8404 (p) REVERT: R 93 GLU cc_start: 0.8157 (mp0) cc_final: 0.7951 (mp0) REVERT: R 116 LYS cc_start: 0.8845 (ttpp) cc_final: 0.8624 (ttpp) REVERT: T 42 TYR cc_start: 0.8499 (t80) cc_final: 0.8278 (t80) REVERT: T 62 MET cc_start: 0.8959 (mmm) cc_final: 0.8495 (mmm) REVERT: U 90 MET cc_start: 0.8760 (mmm) cc_final: 0.8489 (mmm) REVERT: W 40 ARG cc_start: 0.8705 (ttm-80) cc_final: 0.8346 (ttt-90) REVERT: X 80 THR cc_start: 0.8805 (t) cc_final: 0.8567 (p) REVERT: X 84 MET cc_start: 0.8459 (mmm) cc_final: 0.8229 (tpp) REVERT: X 88 TYR cc_start: 0.8667 (m-10) cc_final: 0.8035 (m-80) outliers start: 84 outliers final: 65 residues processed: 1222 average time/residue: 0.2553 time to fit residues: 473.0578 Evaluate side-chains 1236 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 1167 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1895 ARG Chi-restraints excluded: chain A residue 1909 GLU Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 342 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 365 LYS Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 164 LYS Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 417 LYS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 353 ASP Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 234 LYS Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 288 LYS Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 339 SER Chi-restraints excluded: chain J residue 437 SER Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 253 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 411 optimal weight: 0.7980 chunk 297 optimal weight: 0.1980 chunk 303 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 181 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 198 optimal weight: 0.0970 chunk 458 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN E 380 GLN F 146 GLN F 188 GLN F 341 GLN ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 404 GLN V 27 GLN X 25 ASN X 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.099964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.085041 restraints weight = 65081.754| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.56 r_work: 0.2810 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 43580 Z= 0.130 Angle : 0.516 10.758 59886 Z= 0.273 Chirality : 0.040 0.152 6829 Planarity : 0.004 0.055 6809 Dihedral : 20.829 172.976 7878 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.61 % Allowed : 14.23 % Favored : 84.16 % 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: 1.85 (0.12), residues: 4651 helix: 2.08 (0.11), residues: 2343 sheet: 0.49 (0.20), residues: 670 loop : 0.42 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 81 TYR 0.016 0.001 TYR E 131 PHE 0.010 0.001 PHE R 70 TRP 0.023 0.001 TRP A 682 HIS 0.011 0.001 HIS I 316 Details of bonding type rmsd covalent geometry : bond 0.00292 (43572) covalent geometry : angle 0.51512 (59877) hydrogen bonds : bond 0.03594 ( 2116) hydrogen bonds : angle 3.57824 ( 5836) metal coordination : bond 0.00955 ( 8) metal coordination : angle 1.76759 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 1168 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 ASP cc_start: 0.8768 (t70) cc_final: 0.8294 (m-30) REVERT: A 685 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8209 (tp30) REVERT: A 716 ASN cc_start: 0.8193 (t0) cc_final: 0.7852 (t0) REVERT: A 825 LEU cc_start: 0.9040 (tp) cc_final: 0.8808 (tp) REVERT: A 863 LYS cc_start: 0.8008 (tptp) cc_final: 0.7687 (tptp) REVERT: A 871 ASP cc_start: 0.8115 (t0) cc_final: 0.7803 (t70) REVERT: A 947 ASP cc_start: 0.8008 (t0) cc_final: 0.7742 (t0) REVERT: A 1906 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8097 (mm110) REVERT: A 2009 GLN cc_start: 0.7986 (tt0) cc_final: 0.7555 (tt0) REVERT: A 2013 GLU cc_start: 0.8011 (tp30) cc_final: 0.7629 (tp30) REVERT: A 2198 THR cc_start: 0.8556 (p) cc_final: 0.8345 (p) REVERT: B 133 MET cc_start: 0.6660 (mmm) cc_final: 0.6338 (mmm) REVERT: B 215 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7991 (t-170) REVERT: C 1 MET cc_start: 0.5276 (tmm) cc_final: 0.4928 (tmm) REVERT: C 90 ASP cc_start: 0.8272 (t0) cc_final: 0.7642 (t0) REVERT: C 108 SER cc_start: 0.8782 (m) cc_final: 0.8396 (t) REVERT: C 109 MET cc_start: 0.8876 (tpp) cc_final: 0.8606 (ttt) REVERT: C 189 SER cc_start: 0.8348 (p) cc_final: 0.8054 (m) REVERT: C 221 ASP cc_start: 0.7985 (m-30) cc_final: 0.7565 (m-30) REVERT: C 245 LYS cc_start: 0.8110 (mmpt) cc_final: 0.7682 (mmpt) REVERT: C 246 LYS cc_start: 0.8141 (mmmt) cc_final: 0.7799 (mmmt) REVERT: C 366 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8833 (tt) REVERT: C 382 TYR cc_start: 0.8398 (t80) cc_final: 0.8134 (t80) REVERT: C 393 LYS cc_start: 0.8526 (tppp) cc_final: 0.8246 (mttm) REVERT: E 60 LYS cc_start: 0.8415 (mtpp) cc_final: 0.8197 (mtpp) REVERT: E 90 LYS cc_start: 0.8264 (tttt) cc_final: 0.8044 (tttt) REVERT: E 137 GLU cc_start: 0.7774 (tt0) cc_final: 0.7528 (tt0) REVERT: E 162 LYS cc_start: 0.8521 (ptmt) cc_final: 0.8310 (ptpt) REVERT: E 168 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7969 (ttmt) REVERT: E 211 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8243 (p) REVERT: E 218 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7484 (tp30) REVERT: E 229 HIS cc_start: 0.8625 (t70) cc_final: 0.8386 (t70) REVERT: E 249 ARG cc_start: 0.7511 (mmt-90) cc_final: 0.7310 (mmt-90) REVERT: E 285 LYS cc_start: 0.8290 (ttmm) cc_final: 0.8008 (ttmm) REVERT: E 435 GLU cc_start: 0.7683 (tt0) cc_final: 0.7409 (tt0) REVERT: F 112 GLU cc_start: 0.7583 (tp30) cc_final: 0.7322 (tp30) REVERT: F 136 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7239 (mt-10) REVERT: F 160 LYS cc_start: 0.8324 (ttpt) cc_final: 0.7981 (ttmm) REVERT: F 169 GLU cc_start: 0.7580 (tt0) cc_final: 0.7338 (tt0) REVERT: F 174 LEU cc_start: 0.8237 (mt) cc_final: 0.8036 (mt) REVERT: F 180 GLU cc_start: 0.7939 (mm-30) cc_final: 0.6952 (mm-30) REVERT: F 184 LYS cc_start: 0.7936 (mmtm) cc_final: 0.7460 (mmtm) REVERT: F 201 LYS cc_start: 0.8257 (tttp) cc_final: 0.7885 (tttp) REVERT: F 236 LYS cc_start: 0.8187 (mmtp) cc_final: 0.7947 (mmtp) REVERT: F 237 GLU cc_start: 0.7462 (tt0) cc_final: 0.7210 (tt0) REVERT: F 238 VAL cc_start: 0.8385 (t) cc_final: 0.8002 (p) REVERT: F 274 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7468 (mm-30) REVERT: F 348 ILE cc_start: 0.8274 (tp) cc_final: 0.8031 (tp) REVERT: F 352 ASP cc_start: 0.7755 (m-30) cc_final: 0.7491 (m-30) REVERT: F 414 ARG cc_start: 0.7258 (mtm180) cc_final: 0.6949 (mtm110) REVERT: G 59 LYS cc_start: 0.8763 (mtpt) cc_final: 0.8516 (mtmm) REVERT: G 123 ARG cc_start: 0.8389 (ttm170) cc_final: 0.8124 (ttm-80) REVERT: G 137 GLU cc_start: 0.7932 (tt0) cc_final: 0.7589 (tt0) REVERT: G 142 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7391 (mm-30) REVERT: G 214 ASP cc_start: 0.7936 (m-30) cc_final: 0.7555 (m-30) REVERT: G 225 LYS cc_start: 0.8312 (mmpt) cc_final: 0.8095 (mtpp) REVERT: G 227 ASP cc_start: 0.7589 (t70) cc_final: 0.7328 (t0) REVERT: G 326 ILE cc_start: 0.8529 (mt) cc_final: 0.8269 (mm) REVERT: G 353 ASP cc_start: 0.7812 (m-30) cc_final: 0.7561 (m-30) REVERT: G 388 GLU cc_start: 0.7950 (tp30) cc_final: 0.7306 (mm-30) REVERT: G 392 ASN cc_start: 0.8665 (m-40) cc_final: 0.8121 (m110) REVERT: G 418 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7953 (mtpp) REVERT: G 435 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7296 (mp0) REVERT: G 447 LEU cc_start: 0.8249 (mt) cc_final: 0.7909 (mp) REVERT: H 136 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7582 (mm-30) REVERT: H 139 GLU cc_start: 0.7935 (tt0) cc_final: 0.7593 (tt0) REVERT: H 185 ASP cc_start: 0.7801 (m-30) cc_final: 0.7533 (m-30) REVERT: H 204 LYS cc_start: 0.8350 (mtpt) cc_final: 0.8099 (mtmt) REVERT: H 211 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8235 (mmm-85) REVERT: H 235 ARG cc_start: 0.8187 (mtt180) cc_final: 0.7816 (ttm110) REVERT: H 253 ARG cc_start: 0.8198 (ptm160) cc_final: 0.7831 (ptp90) REVERT: H 313 ASN cc_start: 0.8157 (m-40) cc_final: 0.7697 (m-40) REVERT: H 314 ARG cc_start: 0.7157 (mmt180) cc_final: 0.6782 (mmt180) REVERT: H 342 SER cc_start: 0.8748 (m) cc_final: 0.8429 (t) REVERT: H 358 SER cc_start: 0.8435 (m) cc_final: 0.8051 (t) REVERT: H 369 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7829 (mt0) REVERT: H 382 MET cc_start: 0.8426 (mtp) cc_final: 0.8219 (mtm) REVERT: H 436 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6553 (tm-30) REVERT: H 443 MET cc_start: 0.7751 (ttm) cc_final: 0.7447 (ttp) REVERT: I 28 GLU cc_start: 0.7583 (mp0) cc_final: 0.7109 (mp0) REVERT: I 125 LYS cc_start: 0.8554 (ttpp) cc_final: 0.8242 (ttpp) REVERT: I 137 GLU cc_start: 0.7640 (tt0) cc_final: 0.7326 (tt0) REVERT: I 139 THR cc_start: 0.8309 (m) cc_final: 0.8034 (p) REVERT: I 165 LYS cc_start: 0.8608 (mttm) cc_final: 0.8394 (mttp) REVERT: I 184 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7455 (mtt180) REVERT: I 209 TYR cc_start: 0.8543 (m-80) cc_final: 0.8170 (m-80) REVERT: I 251 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7408 (mm-40) REVERT: I 259 MET cc_start: 0.7759 (mtp) cc_final: 0.7204 (mtp) REVERT: I 369 GLN cc_start: 0.7915 (mp10) cc_final: 0.7606 (mp10) REVERT: I 388 GLU cc_start: 0.7984 (tp30) cc_final: 0.7720 (tp30) REVERT: I 389 GLU cc_start: 0.7909 (pt0) cc_final: 0.7630 (tt0) REVERT: I 392 ASN cc_start: 0.8480 (m110) cc_final: 0.8080 (m110) REVERT: I 400 LYS cc_start: 0.8129 (mtpp) cc_final: 0.7877 (mtmm) REVERT: I 408 GLN cc_start: 0.7709 (mt0) cc_final: 0.7271 (mt0) REVERT: I 418 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7837 (mtpt) REVERT: I 445 LYS cc_start: 0.7910 (tppt) cc_final: 0.7289 (tppt) REVERT: J 20 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7278 (mm-30) REVERT: J 71 ARG cc_start: 0.8139 (mmt90) cc_final: 0.7925 (mmt90) REVERT: J 86 ILE cc_start: 0.8158 (mm) cc_final: 0.7902 (mt) REVERT: J 133 GLU cc_start: 0.7943 (pt0) cc_final: 0.7717 (pt0) REVERT: J 134 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7530 (mt-10) REVERT: J 136 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7511 (mt-10) REVERT: J 141 GLU cc_start: 0.7795 (tt0) cc_final: 0.7542 (tt0) REVERT: J 169 GLU cc_start: 0.7661 (tt0) cc_final: 0.7400 (tm-30) REVERT: J 236 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7954 (mtpt) REVERT: J 271 GLU cc_start: 0.7781 (mp0) cc_final: 0.7413 (mp0) REVERT: J 285 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7549 (mm-30) REVERT: J 299 ASP cc_start: 0.8281 (t0) cc_final: 0.7902 (t70) REVERT: J 377 GLU cc_start: 0.7828 (tp30) cc_final: 0.7598 (tp30) REVERT: J 392 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7401 (ttp80) REVERT: J 404 GLN cc_start: 0.7637 (mt0) cc_final: 0.7327 (mt0) REVERT: J 414 ARG cc_start: 0.7876 (mtp-110) cc_final: 0.7654 (mtp-110) REVERT: R 88 THR cc_start: 0.8711 (t) cc_final: 0.8412 (p) REVERT: R 93 GLU cc_start: 0.8168 (mp0) cc_final: 0.7933 (mp0) REVERT: R 116 LYS cc_start: 0.8814 (ttpp) cc_final: 0.8600 (ttpp) REVERT: T 42 TYR cc_start: 0.8460 (t80) cc_final: 0.8205 (t80) REVERT: T 62 MET cc_start: 0.8952 (mmm) cc_final: 0.8518 (mmm) REVERT: U 69 ARG cc_start: 0.8938 (mtm110) cc_final: 0.8660 (ttm110) REVERT: U 90 MET cc_start: 0.8715 (mmm) cc_final: 0.8491 (mmm) REVERT: W 40 ARG cc_start: 0.8684 (ttm-80) cc_final: 0.8331 (ttt-90) REVERT: W 118 THR cc_start: 0.9175 (m) cc_final: 0.8925 (p) REVERT: X 80 THR cc_start: 0.8799 (t) cc_final: 0.8558 (p) REVERT: X 88 TYR cc_start: 0.8640 (m-10) cc_final: 0.8068 (m-80) outliers start: 65 outliers final: 52 residues processed: 1193 average time/residue: 0.2577 time to fit residues: 462.8960 Evaluate side-chains 1210 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 1154 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1895 ARG Chi-restraints excluded: chain A residue 1909 GLU Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 342 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 365 LYS Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 164 LYS Chi-restraints excluded: chain H residue 211 ARG Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 353 ASP Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 288 LYS Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 437 SER Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 115 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 459 optimal weight: 2.9990 chunk 362 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 345 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN E 380 GLN F 146 GLN F 188 GLN ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 27 GLN X 25 ASN X 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.098658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.083712 restraints weight = 65299.105| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.58 r_work: 0.2760 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 43580 Z= 0.169 Angle : 0.540 11.463 59886 Z= 0.284 Chirality : 0.041 0.156 6829 Planarity : 0.004 0.057 6809 Dihedral : 20.825 173.195 7878 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.61 % Allowed : 14.80 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.12), residues: 4651 helix: 2.04 (0.11), residues: 2339 sheet: 0.48 (0.20), residues: 663 loop : 0.40 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 317 TYR 0.019 0.001 TYR A 698 PHE 0.010 0.001 PHE C 372 TRP 0.013 0.001 TRP A 712 HIS 0.014 0.001 HIS I 316 Details of bonding type rmsd covalent geometry : bond 0.00390 (43572) covalent geometry : angle 0.53987 (59877) hydrogen bonds : bond 0.03787 ( 2116) hydrogen bonds : angle 3.61310 ( 5836) metal coordination : bond 0.01310 ( 8) metal coordination : angle 1.57757 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 1162 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 627 ASP cc_start: 0.8784 (t70) cc_final: 0.8308 (m-30) REVERT: A 635 LYS cc_start: 0.8657 (tppt) cc_final: 0.8251 (tppt) REVERT: A 716 ASN cc_start: 0.8253 (t0) cc_final: 0.7924 (t0) REVERT: A 825 LEU cc_start: 0.9080 (tp) cc_final: 0.8839 (tp) REVERT: A 863 LYS cc_start: 0.8045 (tptp) cc_final: 0.7720 (tptp) REVERT: A 871 ASP cc_start: 0.8152 (t0) cc_final: 0.7842 (t70) REVERT: A 947 ASP cc_start: 0.8040 (t0) cc_final: 0.7790 (t0) REVERT: A 1906 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8080 (mm110) REVERT: A 2009 GLN cc_start: 0.7984 (tt0) cc_final: 0.7593 (tt0) REVERT: A 2013 GLU cc_start: 0.8018 (tp30) cc_final: 0.7657 (tp30) REVERT: A 2068 MET cc_start: 0.8672 (mtt) cc_final: 0.8409 (mtm) REVERT: A 2071 MET cc_start: 0.8656 (tpp) cc_final: 0.8315 (tpt) REVERT: B 215 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.7973 (t-170) REVERT: C 1 MET cc_start: 0.5339 (tmm) cc_final: 0.4986 (tmm) REVERT: C 90 ASP cc_start: 0.8340 (t0) cc_final: 0.7719 (t0) REVERT: C 108 SER cc_start: 0.8771 (m) cc_final: 0.8360 (t) REVERT: C 189 SER cc_start: 0.8395 (p) cc_final: 0.8104 (m) REVERT: C 221 ASP cc_start: 0.8035 (m-30) cc_final: 0.7606 (m-30) REVERT: C 245 LYS cc_start: 0.8157 (mmpt) cc_final: 0.7777 (mmpt) REVERT: C 246 LYS cc_start: 0.8171 (mmmt) cc_final: 0.7802 (mmmt) REVERT: C 308 GLU cc_start: 0.8052 (mp0) cc_final: 0.7723 (mp0) REVERT: C 366 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8826 (tt) REVERT: E 60 LYS cc_start: 0.8421 (mtpp) cc_final: 0.8207 (mtpp) REVERT: E 90 LYS cc_start: 0.8298 (tttt) cc_final: 0.8076 (tttt) REVERT: E 137 GLU cc_start: 0.7786 (tt0) cc_final: 0.7536 (tt0) REVERT: E 162 LYS cc_start: 0.8514 (ptmt) cc_final: 0.8288 (ptpt) REVERT: E 168 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7960 (ttmt) REVERT: E 181 GLN cc_start: 0.7969 (mt0) cc_final: 0.7638 (mt0) REVERT: E 211 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8100 (p) REVERT: E 218 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7510 (tp30) REVERT: E 229 HIS cc_start: 0.8634 (t70) cc_final: 0.8408 (t70) REVERT: E 249 ARG cc_start: 0.7574 (mmt-90) cc_final: 0.7274 (mmt-90) REVERT: E 285 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7949 (ttmm) REVERT: E 435 GLU cc_start: 0.7706 (tt0) cc_final: 0.7416 (tt0) REVERT: F 112 GLU cc_start: 0.7610 (tp30) cc_final: 0.7317 (tp30) REVERT: F 136 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7140 (mt-10) REVERT: F 160 LYS cc_start: 0.8281 (ttpt) cc_final: 0.7918 (ttmm) REVERT: F 169 GLU cc_start: 0.7618 (tt0) cc_final: 0.7356 (tt0) REVERT: F 180 GLU cc_start: 0.7952 (mm-30) cc_final: 0.6942 (mm-30) REVERT: F 184 LYS cc_start: 0.7953 (mmtm) cc_final: 0.7447 (mmtm) REVERT: F 201 LYS cc_start: 0.8218 (tttp) cc_final: 0.7842 (tttp) REVERT: F 236 LYS cc_start: 0.8159 (mmtp) cc_final: 0.7893 (mmtp) REVERT: F 237 GLU cc_start: 0.7458 (tt0) cc_final: 0.7204 (tt0) REVERT: F 238 VAL cc_start: 0.8352 (t) cc_final: 0.7960 (p) REVERT: F 274 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7494 (mm-30) REVERT: F 348 ILE cc_start: 0.8272 (tp) cc_final: 0.8037 (tp) REVERT: F 352 ASP cc_start: 0.7770 (m-30) cc_final: 0.7509 (m-30) REVERT: F 369 GLN cc_start: 0.7977 (tp40) cc_final: 0.7707 (tp40) REVERT: F 414 ARG cc_start: 0.7274 (mtm180) cc_final: 0.6926 (mtm110) REVERT: G 90 LYS cc_start: 0.8305 (tptm) cc_final: 0.8045 (tptm) REVERT: G 123 ARG cc_start: 0.8372 (ttm170) cc_final: 0.7996 (ttm-80) REVERT: G 125 LYS cc_start: 0.8336 (mttp) cc_final: 0.8100 (mttp) REVERT: G 137 GLU cc_start: 0.7954 (tt0) cc_final: 0.7558 (tm-30) REVERT: G 142 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7374 (mm-30) REVERT: G 214 ASP cc_start: 0.7955 (m-30) cc_final: 0.7551 (m-30) REVERT: G 225 LYS cc_start: 0.8307 (mmpt) cc_final: 0.8082 (mtpp) REVERT: G 320 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7110 (mp0) REVERT: G 326 ILE cc_start: 0.8504 (mt) cc_final: 0.8229 (mm) REVERT: G 353 ASP cc_start: 0.7791 (m-30) cc_final: 0.7555 (m-30) REVERT: G 371 MET cc_start: 0.8447 (mtt) cc_final: 0.8205 (mtp) REVERT: G 388 GLU cc_start: 0.7947 (tp30) cc_final: 0.7286 (mm-30) REVERT: G 392 ASN cc_start: 0.8617 (m-40) cc_final: 0.8100 (m110) REVERT: G 418 LYS cc_start: 0.8167 (mtpt) cc_final: 0.7933 (mtpp) REVERT: G 435 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7324 (mp0) REVERT: G 447 LEU cc_start: 0.8216 (mt) cc_final: 0.7893 (mp) REVERT: H 136 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7587 (mm-30) REVERT: H 139 GLU cc_start: 0.7955 (tt0) cc_final: 0.7638 (tt0) REVERT: H 185 ASP cc_start: 0.7821 (m-30) cc_final: 0.7573 (m-30) REVERT: H 204 LYS cc_start: 0.8364 (mtpt) cc_final: 0.8107 (mtmt) REVERT: H 211 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8234 (mmm-85) REVERT: H 235 ARG cc_start: 0.8208 (mtt180) cc_final: 0.7824 (ttm110) REVERT: H 253 ARG cc_start: 0.8216 (ptm160) cc_final: 0.7837 (ptp90) REVERT: H 313 ASN cc_start: 0.8146 (m-40) cc_final: 0.7649 (m-40) REVERT: H 314 ARG cc_start: 0.7176 (mmt180) cc_final: 0.6763 (mmt180) REVERT: H 358 SER cc_start: 0.8461 (m) cc_final: 0.8079 (t) REVERT: H 369 GLN cc_start: 0.8121 (tp-100) cc_final: 0.7830 (mt0) REVERT: H 382 MET cc_start: 0.8490 (mtp) cc_final: 0.8278 (mtm) REVERT: H 436 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6509 (tm-30) REVERT: H 443 MET cc_start: 0.7751 (ttm) cc_final: 0.7469 (ttp) REVERT: I 28 GLU cc_start: 0.7612 (mp0) cc_final: 0.7138 (mp0) REVERT: I 125 LYS cc_start: 0.8543 (ttpp) cc_final: 0.8227 (ttpp) REVERT: I 137 GLU cc_start: 0.7648 (tt0) cc_final: 0.7312 (tt0) REVERT: I 139 THR cc_start: 0.8311 (m) cc_final: 0.8038 (p) REVERT: I 165 LYS cc_start: 0.8639 (mttm) cc_final: 0.8419 (mttp) REVERT: I 184 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7491 (mtt180) REVERT: I 209 TYR cc_start: 0.8585 (m-80) cc_final: 0.8236 (m-80) REVERT: I 251 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7412 (mm-40) REVERT: I 259 MET cc_start: 0.7730 (mtp) cc_final: 0.7262 (mtp) REVERT: I 369 GLN cc_start: 0.7901 (mp10) cc_final: 0.7565 (mp10) REVERT: I 389 GLU cc_start: 0.7984 (pt0) cc_final: 0.7690 (tt0) REVERT: I 400 LYS cc_start: 0.8129 (mtpp) cc_final: 0.7867 (mtmm) REVERT: I 408 GLN cc_start: 0.7694 (mt0) cc_final: 0.7255 (mt0) REVERT: I 418 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7827 (mtpt) REVERT: I 435 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7224 (mm-30) REVERT: I 445 LYS cc_start: 0.7885 (tppt) cc_final: 0.7253 (tppt) REVERT: J 20 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7425 (mm-30) REVERT: J 71 ARG cc_start: 0.8148 (mmt90) cc_final: 0.7924 (mmt90) REVERT: J 86 ILE cc_start: 0.8133 (mm) cc_final: 0.7885 (mt) REVERT: J 133 GLU cc_start: 0.7954 (pt0) cc_final: 0.7705 (pt0) REVERT: J 134 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7528 (mt-10) REVERT: J 136 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7537 (mt-10) REVERT: J 141 GLU cc_start: 0.7802 (tt0) cc_final: 0.7539 (tt0) REVERT: J 169 GLU cc_start: 0.7703 (tt0) cc_final: 0.7416 (tm-30) REVERT: J 236 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7922 (mtpt) REVERT: J 246 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7306 (mt-10) REVERT: J 271 GLU cc_start: 0.7751 (mp0) cc_final: 0.7389 (mp0) REVERT: J 285 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7569 (mm-30) REVERT: J 299 ASP cc_start: 0.8277 (t0) cc_final: 0.7890 (t70) REVERT: J 377 GLU cc_start: 0.7804 (tp30) cc_final: 0.7593 (tp30) REVERT: J 392 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7385 (ttp80) REVERT: J 404 GLN cc_start: 0.7619 (mt0) cc_final: 0.7329 (mt0) REVERT: J 414 ARG cc_start: 0.7891 (mtp-110) cc_final: 0.7673 (mtp-110) REVERT: R 88 THR cc_start: 0.8712 (t) cc_final: 0.8425 (p) REVERT: R 93 GLU cc_start: 0.8196 (mp0) cc_final: 0.7968 (mp0) REVERT: R 116 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8612 (ttpp) REVERT: T 42 TYR cc_start: 0.8470 (t80) cc_final: 0.8213 (t80) REVERT: T 62 MET cc_start: 0.8949 (mmm) cc_final: 0.8495 (mmm) REVERT: U 69 ARG cc_start: 0.8928 (mtm110) cc_final: 0.8650 (ttm110) REVERT: U 90 MET cc_start: 0.8713 (mmm) cc_final: 0.8502 (mmm) REVERT: W 40 ARG cc_start: 0.8701 (ttm-80) cc_final: 0.8336 (ttt-90) REVERT: W 118 THR cc_start: 0.9177 (m) cc_final: 0.8898 (p) REVERT: X 80 THR cc_start: 0.8817 (t) cc_final: 0.8566 (p) REVERT: X 88 TYR cc_start: 0.8654 (m-10) cc_final: 0.8209 (m-80) outliers start: 65 outliers final: 57 residues processed: 1189 average time/residue: 0.2722 time to fit residues: 488.0614 Evaluate side-chains 1214 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 1153 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 800 HIS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1895 ARG Chi-restraints excluded: chain A residue 1909 GLU Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 342 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 365 LYS Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 164 LYS Chi-restraints excluded: chain H residue 211 ARG Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 353 ASP Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 288 LYS Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 437 SER Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 340 optimal weight: 0.0470 chunk 44 optimal weight: 0.2980 chunk 133 optimal weight: 0.8980 chunk 239 optimal weight: 0.0970 chunk 4 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 324 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 286 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 267 optimal weight: 4.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN D 91 GLN E 380 GLN F 146 GLN F 188 GLN ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 27 GLN X 25 ASN X 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.100367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.085358 restraints weight = 64697.143| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.58 r_work: 0.2788 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43580 Z= 0.121 Angle : 0.521 10.223 59886 Z= 0.275 Chirality : 0.039 0.154 6829 Planarity : 0.004 0.054 6809 Dihedral : 20.769 172.935 7878 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.36 % Allowed : 15.12 % 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: 1.88 (0.13), residues: 4651 helix: 2.11 (0.11), residues: 2336 sheet: 0.51 (0.20), residues: 671 loop : 0.42 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 615 TYR 0.026 0.001 TYR C 382 PHE 0.011 0.001 PHE C 394 TRP 0.013 0.001 TRP A 786 HIS 0.013 0.001 HIS I 316 Details of bonding type rmsd covalent geometry : bond 0.00270 (43572) covalent geometry : angle 0.52043 (59877) hydrogen bonds : bond 0.03439 ( 2116) hydrogen bonds : angle 3.52275 ( 5836) metal coordination : bond 0.00776 ( 8) metal coordination : angle 1.78862 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9302 Ramachandran restraints generated. 4651 Oldfield, 0 Emsley, 4651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 1150 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 ASP cc_start: 0.8756 (t70) cc_final: 0.8276 (m-30) REVERT: A 635 LYS cc_start: 0.8657 (tppt) cc_final: 0.8260 (tppt) REVERT: A 716 ASN cc_start: 0.8227 (t0) cc_final: 0.7900 (t0) REVERT: A 825 LEU cc_start: 0.9034 (tp) cc_final: 0.8790 (tp) REVERT: A 863 LYS cc_start: 0.8062 (tptp) cc_final: 0.7739 (tptp) REVERT: A 871 ASP cc_start: 0.8131 (t0) cc_final: 0.7810 (t70) REVERT: A 947 ASP cc_start: 0.8026 (t0) cc_final: 0.7768 (t0) REVERT: A 1906 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8115 (mm-40) REVERT: A 2009 GLN cc_start: 0.7955 (tt0) cc_final: 0.7619 (tt0) REVERT: A 2013 GLU cc_start: 0.8001 (tp30) cc_final: 0.7708 (tp30) REVERT: A 2030 THR cc_start: 0.8183 (t) cc_final: 0.7800 (m) REVERT: A 2068 MET cc_start: 0.8629 (mtt) cc_final: 0.8367 (mtm) REVERT: A 2198 THR cc_start: 0.8520 (p) cc_final: 0.8302 (p) REVERT: C 1 MET cc_start: 0.5315 (tmm) cc_final: 0.4962 (tmm) REVERT: C 90 ASP cc_start: 0.8366 (t0) cc_final: 0.7748 (t0) REVERT: C 108 SER cc_start: 0.8735 (m) cc_final: 0.8304 (t) REVERT: C 149 ASP cc_start: 0.8060 (t0) cc_final: 0.7771 (p0) REVERT: C 189 SER cc_start: 0.8363 (p) cc_final: 0.8068 (m) REVERT: C 245 LYS cc_start: 0.8165 (mmpt) cc_final: 0.7799 (mmpt) REVERT: C 246 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7788 (mmmt) REVERT: C 308 GLU cc_start: 0.7939 (mp0) cc_final: 0.7683 (mp0) REVERT: C 366 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8821 (tt) REVERT: C 379 ARG cc_start: 0.8701 (ttp80) cc_final: 0.8416 (ttp80) REVERT: D 148 ARG cc_start: 0.8705 (mtt-85) cc_final: 0.8447 (mtt180) REVERT: E 60 LYS cc_start: 0.8417 (mtpp) cc_final: 0.8195 (mtpp) REVERT: E 90 LYS cc_start: 0.8311 (tttt) cc_final: 0.8066 (tttt) REVERT: E 137 GLU cc_start: 0.7813 (tt0) cc_final: 0.7573 (tt0) REVERT: E 162 LYS cc_start: 0.8519 (ptmt) cc_final: 0.8297 (ptpt) REVERT: E 168 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7965 (ttmt) REVERT: E 211 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8112 (p) REVERT: E 229 HIS cc_start: 0.8599 (t70) cc_final: 0.8380 (t70) REVERT: E 249 ARG cc_start: 0.7615 (mmt-90) cc_final: 0.7304 (mmt-90) REVERT: E 285 LYS cc_start: 0.8130 (ttmm) cc_final: 0.7807 (ttmm) REVERT: E 435 GLU cc_start: 0.7745 (tt0) cc_final: 0.7468 (tt0) REVERT: F 112 GLU cc_start: 0.7660 (tp30) cc_final: 0.7344 (tp30) REVERT: F 136 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7126 (mt-10) REVERT: F 160 LYS cc_start: 0.8314 (ttpt) cc_final: 0.7907 (ttmm) REVERT: F 169 GLU cc_start: 0.7613 (tt0) cc_final: 0.7349 (tt0) REVERT: F 180 GLU cc_start: 0.7952 (mm-30) cc_final: 0.6876 (mm-30) REVERT: F 181 SER cc_start: 0.8521 (m) cc_final: 0.8189 (t) REVERT: F 184 LYS cc_start: 0.7973 (mmtm) cc_final: 0.7446 (mmtm) REVERT: F 192 VAL cc_start: 0.8783 (t) cc_final: 0.8582 (t) REVERT: F 201 LYS cc_start: 0.8216 (tttp) cc_final: 0.7863 (tttp) REVERT: F 233 GLN cc_start: 0.8200 (tt0) cc_final: 0.7595 (tt0) REVERT: F 236 LYS cc_start: 0.8160 (mmtp) cc_final: 0.7902 (mmtp) REVERT: F 237 GLU cc_start: 0.7449 (tt0) cc_final: 0.7205 (tt0) REVERT: F 238 VAL cc_start: 0.8360 (t) cc_final: 0.7973 (p) REVERT: F 274 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7471 (mm-30) REVERT: F 326 MET cc_start: 0.8272 (mtt) cc_final: 0.7978 (mtm) REVERT: F 348 ILE cc_start: 0.8247 (tp) cc_final: 0.8004 (tp) REVERT: F 352 ASP cc_start: 0.7750 (m-30) cc_final: 0.7496 (m-30) REVERT: F 414 ARG cc_start: 0.7271 (mtm180) cc_final: 0.6925 (mtm110) REVERT: G 125 LYS cc_start: 0.8337 (mttp) cc_final: 0.8103 (mttp) REVERT: G 137 GLU cc_start: 0.7970 (tt0) cc_final: 0.7619 (tm-30) REVERT: G 142 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7343 (mm-30) REVERT: G 214 ASP cc_start: 0.7888 (m-30) cc_final: 0.7537 (m-30) REVERT: G 225 LYS cc_start: 0.8293 (mmpt) cc_final: 0.8067 (mtpp) REVERT: G 320 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7087 (mp0) REVERT: G 353 ASP cc_start: 0.7806 (m-30) cc_final: 0.7562 (m-30) REVERT: G 388 GLU cc_start: 0.7934 (tp30) cc_final: 0.7286 (mm-30) REVERT: G 392 ASN cc_start: 0.8659 (m-40) cc_final: 0.8146 (m110) REVERT: G 418 LYS cc_start: 0.8251 (mtpt) cc_final: 0.8028 (mtpp) REVERT: G 435 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7271 (mp0) REVERT: G 447 LEU cc_start: 0.8211 (mt) cc_final: 0.7869 (mp) REVERT: H 136 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7526 (mm-30) REVERT: H 139 GLU cc_start: 0.7931 (tt0) cc_final: 0.7596 (tt0) REVERT: H 185 ASP cc_start: 0.7790 (m-30) cc_final: 0.7526 (m-30) REVERT: H 204 LYS cc_start: 0.8335 (mtpt) cc_final: 0.8105 (mtmt) REVERT: H 211 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8235 (mmm-85) REVERT: H 253 ARG cc_start: 0.8202 (ptm160) cc_final: 0.7820 (ptp90) REVERT: H 313 ASN cc_start: 0.8123 (m-40) cc_final: 0.7628 (m-40) REVERT: H 314 ARG cc_start: 0.7185 (mmt180) cc_final: 0.6793 (mmt180) REVERT: H 358 SER cc_start: 0.8444 (m) cc_final: 0.8066 (t) REVERT: H 369 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7784 (mt0) REVERT: H 415 LYS cc_start: 0.8551 (tptp) cc_final: 0.8294 (tppt) REVERT: H 436 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6602 (tm-30) REVERT: H 443 MET cc_start: 0.7722 (ttm) cc_final: 0.7454 (ttp) REVERT: I 28 GLU cc_start: 0.7583 (mp0) cc_final: 0.7157 (mp0) REVERT: I 125 LYS cc_start: 0.8555 (ttpp) cc_final: 0.8238 (ttpp) REVERT: I 137 GLU cc_start: 0.7655 (tt0) cc_final: 0.7324 (tt0) REVERT: I 139 THR cc_start: 0.8279 (m) cc_final: 0.8047 (p) REVERT: I 165 LYS cc_start: 0.8633 (mttm) cc_final: 0.8423 (mttp) REVERT: I 184 ARG cc_start: 0.7841 (mtt180) cc_final: 0.7469 (mtt180) REVERT: I 209 TYR cc_start: 0.8555 (m-80) cc_final: 0.8193 (m-80) REVERT: I 216 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7495 (tm-30) REVERT: I 251 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7365 (mm-40) REVERT: I 259 MET cc_start: 0.7704 (mtp) cc_final: 0.7253 (mtp) REVERT: I 286 TYR cc_start: 0.8226 (m-80) cc_final: 0.7993 (m-80) REVERT: I 369 GLN cc_start: 0.7881 (mp10) cc_final: 0.7494 (mp10) REVERT: I 389 GLU cc_start: 0.7895 (pt0) cc_final: 0.7637 (tt0) REVERT: I 400 LYS cc_start: 0.8067 (mtpp) cc_final: 0.7831 (mtmm) REVERT: I 408 GLN cc_start: 0.7699 (mt0) cc_final: 0.7244 (mt0) REVERT: I 418 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7823 (mtpt) REVERT: I 445 LYS cc_start: 0.7927 (tppt) cc_final: 0.7313 (tppt) REVERT: J 86 ILE cc_start: 0.8151 (mm) cc_final: 0.7890 (mt) REVERT: J 133 GLU cc_start: 0.7931 (pt0) cc_final: 0.7696 (pt0) REVERT: J 134 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7483 (mt-10) REVERT: J 136 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7621 (mt-10) REVERT: J 141 GLU cc_start: 0.7800 (tt0) cc_final: 0.7534 (tt0) REVERT: J 169 GLU cc_start: 0.7693 (tt0) cc_final: 0.7428 (tm-30) REVERT: J 236 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7911 (mtpt) REVERT: J 246 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7277 (mt-10) REVERT: J 271 GLU cc_start: 0.7724 (mp0) cc_final: 0.7346 (mp0) REVERT: J 277 ASN cc_start: 0.8611 (m-40) cc_final: 0.8351 (m-40) REVERT: J 285 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7580 (mm-30) REVERT: J 299 ASP cc_start: 0.8259 (t0) cc_final: 0.7893 (t70) REVERT: J 366 ASP cc_start: 0.7890 (m-30) cc_final: 0.7685 (m-30) REVERT: J 377 GLU cc_start: 0.7789 (tp30) cc_final: 0.7575 (tp30) REVERT: J 392 ARG cc_start: 0.7784 (ttp80) cc_final: 0.7373 (ttp80) REVERT: J 414 ARG cc_start: 0.7948 (mtp-110) cc_final: 0.7724 (mtp-110) REVERT: R 88 THR cc_start: 0.8711 (t) cc_final: 0.8431 (p) REVERT: R 93 GLU cc_start: 0.8179 (mp0) cc_final: 0.7935 (mp0) REVERT: R 116 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8614 (ttpp) REVERT: T 42 TYR cc_start: 0.8436 (t80) cc_final: 0.8159 (t80) REVERT: T 62 MET cc_start: 0.8953 (mmm) cc_final: 0.8535 (mmm) REVERT: T 101 LEU cc_start: 0.8998 (mt) cc_final: 0.8783 (mm) REVERT: U 69 ARG cc_start: 0.8947 (mtm110) cc_final: 0.8667 (ttm110) REVERT: W 40 ARG cc_start: 0.8680 (ttm-80) cc_final: 0.8330 (ttt-90) REVERT: W 83 ARG cc_start: 0.8421 (mtp180) cc_final: 0.8205 (mtp180) REVERT: W 118 THR cc_start: 0.9164 (m) cc_final: 0.8959 (p) REVERT: X 80 THR cc_start: 0.8798 (t) cc_final: 0.8556 (p) REVERT: X 84 MET cc_start: 0.8690 (tpp) cc_final: 0.8133 (mmm) REVERT: X 88 TYR cc_start: 0.8616 (m-10) cc_final: 0.8175 (m-80) outliers start: 55 outliers final: 44 residues processed: 1175 average time/residue: 0.2655 time to fit residues: 471.2983 Evaluate side-chains 1185 residues out of total 4047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 1137 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1909 GLU Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 342 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 365 LYS Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 164 LYS Chi-restraints excluded: chain H residue 211 ARG Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 353 ASP Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 437 SER Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain X residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 356 optimal weight: 4.9990 chunk 309 optimal weight: 0.0470 chunk 76 optimal weight: 0.8980 chunk 478 optimal weight: 1.9990 chunk 307 optimal weight: 0.7980 chunk 413 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 330 optimal weight: 0.6980 chunk 452 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 303 GLN ** E 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 GLN G 280 ASN ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 GLN I 289 GLN ** I 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 380 GLN V 27 GLN X 25 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.085076 restraints weight = 64962.413| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.59 r_work: 0.2778 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43580 Z= 0.132 Angle : 0.527 11.952 59886 Z= 0.277 Chirality : 0.040 0.162 6829 Planarity : 0.004 0.066 6809 Dihedral : 20.748 173.185 7878 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.28 % Allowed : 15.39 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.13), residues: 4651 helix: 2.11 (0.11), residues: 2336 sheet: 0.53 (0.20), residues: 663 loop : 0.43 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 317 TYR 0.024 0.001 TYR C 382 PHE 0.016 0.001 PHE C 372 TRP 0.012 0.001 TRP A 786 HIS 0.008 0.001 HIS I 316 Details of bonding type rmsd covalent geometry : bond 0.00299 (43572) covalent geometry : angle 0.52677 (59877) hydrogen bonds : bond 0.03509 ( 2116) hydrogen bonds : angle 3.52804 ( 5836) metal coordination : bond 0.00890 ( 8) metal coordination : angle 1.75380 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11850.82 seconds wall clock time: 202 minutes 39.56 seconds (12159.56 seconds total)