Starting phenix.real_space_refine on Mon Jul 6 20:33:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n9q_49176/07_2026/9n9q_49176.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n9q_49176/07_2026/9n9q_49176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n9q_49176/07_2026/9n9q_49176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n9q_49176/07_2026/9n9q_49176.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n9q_49176/07_2026/9n9q_49176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n9q_49176/07_2026/9n9q_49176.map" } resolution = 2.88 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= 0.035 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 1 6.06 5 P 197 5.49 5 Mg 1 5.21 5 S 132 5.16 5 C 23433 2.51 5 N 6591 2.21 5 O 7673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38028 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3016 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 357} Chain: "B" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2860 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 338} Chain breaks: 1 Chain: "C" Number of atoms: 2181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2181 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 256} Chain: "D" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1843 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain: "E" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1843 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain: "F" Number of atoms: 10052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 10052 Classifications: {'peptide': 1269} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1217} Chain: "G" Number of atoms: 11228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1432, 11228 Classifications: {'peptide': 1432} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1374} Chain: "H" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 885 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "a" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 853 Classifications: {'DNA': 42} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 41} Chain breaks: 2 Chain: "b" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1448 Classifications: {'DNA': 70} Link IDs: {'rna3p': 69} Chain: "c" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1817 Classifications: {'RNA': 85} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 44, 'rna3p_pyr': 35} Link IDs: {'rna2p': 6, 'rna3p': 78} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22324 SG CYS G 66 73.468 116.239 48.225 1.00 83.55 S ATOM 22335 SG CYS G 68 75.019 117.172 45.061 1.00 83.44 S ATOM 22447 SG CYS G 81 71.103 116.386 45.445 1.00 76.64 S ATOM 22472 SG CYS G 84 73.483 113.677 45.207 1.00 92.86 S Time building chain proxies: 7.32, per 1000 atoms: 0.19 Number of scatterers: 38028 At special positions: 0 Unit cell: (168.51, 218.652, 170.976, 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 1 29.99 S 132 16.00 P 197 15.00 Mg 1 11.99 O 7673 8.00 N 6591 7.00 C 23433 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS G 825 " - pdb=" SG CYS G 899 " distance=2.03 Simple disulfide: pdb=" SG CYS G 825 " - pdb=" SG CYS G 909 " distance=2.03 Simple disulfide: pdb=" SG CYS G 899 " - pdb=" SG CYS G 909 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G1502 " pdb="ZN ZN G1502 " - pdb=" SG CYS G 66 " pdb="ZN ZN G1502 " - pdb=" SG CYS G 81 " pdb="ZN ZN G1502 " - pdb=" SG CYS G 68 " pdb="ZN ZN G1502 " - pdb=" SG CYS G 84 " Number of angles added : 6 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7928 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 58 sheets defined 43.7% alpha, 17.7% beta 70 base pairs and 134 stacking pairs defined. Time for finding SS restraints: 5.52 Creating SS restraints... Processing helix chain 'A' and resid 20 through 64 removed outlier: 3.602A pdb=" N LYS A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLN A 52 " --> pdb=" O HIS A 48 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 97 removed outlier: 4.758A pdb=" N ARG A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 126 removed outlier: 3.995A pdb=" N LEU A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 117 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLN A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 178 through 187 removed outlier: 3.551A pdb=" N LEU A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 184 " --> pdb=" O MET A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 270 removed outlier: 3.523A pdb=" N TYR A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ARG A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.578A pdb=" N LYS A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 289 removed outlier: 3.529A pdb=" N LYS A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 315 Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 343 through 357 removed outlier: 3.693A pdb=" N LEU A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 54 Processing helix chain 'B' and resid 55 through 58 Processing helix chain 'B' and resid 84 through 96 removed outlier: 4.147A pdb=" N THR B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 125 removed outlier: 3.939A pdb=" N LEU B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLN B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 248 through 272 removed outlier: 4.580A pdb=" N ARG B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 315 removed outlier: 5.812A pdb=" N ALA B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL B 286 " --> pdb=" O LYS B 282 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER B 294 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.848A pdb=" N LYS B 354 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 356 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 12 Processing helix chain 'C' and resid 13 through 36 removed outlier: 4.226A pdb=" N LEU C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ARG C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER C 27 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP C 35 " --> pdb=" O ILE C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 56 Processing helix chain 'C' and resid 57 through 60 removed outlier: 3.957A pdb=" N LEU C 60 " --> pdb=" O ARG C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 62 through 81 removed outlier: 3.509A pdb=" N ILE C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 101 through 106 removed outlier: 3.717A pdb=" N TYR C 105 " --> pdb=" O ASN C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 135 removed outlier: 3.910A pdb=" N ASP C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 139 through 150 Processing helix chain 'C' and resid 155 through 164 Processing helix chain 'C' and resid 166 through 197 removed outlier: 4.284A pdb=" N GLY C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN C 189 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLY C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 235 through 260 Processing helix chain 'D' and resid 32 through 46 removed outlier: 3.727A pdb=" N THR D 36 " --> pdb=" O GLY D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 84 Processing helix chain 'D' and resid 113 through 119 removed outlier: 4.203A pdb=" N LYS D 117 " --> pdb=" O ASP D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 209 through 227 removed outlier: 3.848A pdb=" N LEU D 227 " --> pdb=" O HIS D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 231 removed outlier: 6.667A pdb=" N GLU D 231 " --> pdb=" O PHE D 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 228 through 231' Processing helix chain 'E' and resid 32 through 48 removed outlier: 3.929A pdb=" N THR E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 84 Processing helix chain 'E' and resid 113 through 116 Processing helix chain 'E' and resid 154 through 158 Processing helix chain 'E' and resid 209 through 227 removed outlier: 3.925A pdb=" N LEU E 227 " --> pdb=" O HIS E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 231 removed outlier: 6.256A pdb=" N GLU E 231 " --> pdb=" O PHE E 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 228 through 231' Processing helix chain 'F' and resid 24 through 32 removed outlier: 4.417A pdb=" N SER F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 55 Processing helix chain 'F' and resid 81 through 89 Processing helix chain 'F' and resid 199 through 208 removed outlier: 3.570A pdb=" N GLY F 208 " --> pdb=" O PHE F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 219 removed outlier: 3.993A pdb=" N PHE F 219 " --> pdb=" O ILE F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 235 Processing helix chain 'F' and resid 277 through 287 removed outlier: 3.503A pdb=" N ILE F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP F 282 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 304 removed outlier: 4.178A pdb=" N ASP F 303 " --> pdb=" O ASN F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 313 removed outlier: 4.003A pdb=" N HIS F 308 " --> pdb=" O TYR F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 332 removed outlier: 3.696A pdb=" N ALA F 322 " --> pdb=" O SER F 318 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 350 removed outlier: 4.022A pdb=" N ILE F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 370 Processing helix chain 'F' and resid 381 through 397 Processing helix chain 'F' and resid 415 through 442 Processing helix chain 'F' and resid 455 through 469 removed outlier: 4.139A pdb=" N VAL F 461 " --> pdb=" O THR F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 487 Processing helix chain 'F' and resid 504 through 509 removed outlier: 3.891A pdb=" N ARG F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 515 removed outlier: 3.776A pdb=" N TYR F 515 " --> pdb=" O TYR F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 573 removed outlier: 3.603A pdb=" N GLU F 573 " --> pdb=" O ALA F 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 569 through 573' Processing helix chain 'F' and resid 607 through 611 Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 631 through 635 Processing helix chain 'F' and resid 636 through 648 removed outlier: 3.780A pdb=" N ARG F 648 " --> pdb=" O SER F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 674 removed outlier: 4.151A pdb=" N ARG F 674 " --> pdb=" O ALA F 670 " (cutoff:3.500A) Processing helix chain 'F' and resid 700 through 707 Processing helix chain 'F' and resid 784 through 789 Processing helix chain 'F' and resid 860 through 871 Processing helix chain 'F' and resid 904 through 941 Processing helix chain 'F' and resid 965 through 970 removed outlier: 3.679A pdb=" N LEU F 969 " --> pdb=" O THR F 965 " (cutoff:3.500A) Processing helix chain 'F' and resid 986 through 1020 Processing helix chain 'F' and resid 1063 through 1067 Processing helix chain 'F' and resid 1083 through 1089 removed outlier: 4.419A pdb=" N SER F1087 " --> pdb=" O LEU F1083 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG F1088 " --> pdb=" O GLY F1084 " (cutoff:3.500A) Processing helix chain 'F' and resid 1091 through 1105 Processing helix chain 'F' and resid 1119 through 1130 Processing helix chain 'F' and resid 1133 through 1135 No H-bonds generated for 'chain 'F' and resid 1133 through 1135' Processing helix chain 'F' and resid 1166 through 1171 Processing helix chain 'F' and resid 1199 through 1210 Processing helix chain 'F' and resid 1211 through 1220 Processing helix chain 'F' and resid 1225 through 1239 removed outlier: 3.774A pdb=" N ALA F1230 " --> pdb=" O VAL F1226 " (cutoff:3.500A) Processing helix chain 'F' and resid 1248 through 1261 removed outlier: 3.559A pdb=" N ASN F1252 " --> pdb=" O PRO F1248 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 30 Processing helix chain 'G' and resid 73 through 77 Processing helix chain 'G' and resid 90 through 96 Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 118 through 125 Processing helix chain 'G' and resid 127 through 136 Processing helix chain 'G' and resid 163 through 174 Processing helix chain 'G' and resid 175 through 180 removed outlier: 3.891A pdb=" N GLN G 179 " --> pdb=" O PRO G 175 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR G 180 " --> pdb=" O SER G 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 175 through 180' Processing helix chain 'G' and resid 194 through 205 removed outlier: 3.959A pdb=" N LEU G 198 " --> pdb=" O GLY G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 220 Processing helix chain 'G' and resid 223 through 247 removed outlier: 3.670A pdb=" N VAL G 236 " --> pdb=" O LYS G 232 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP G 245 " --> pdb=" O ARG G 241 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN G 246 " --> pdb=" O GLU G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 253 Processing helix chain 'G' and resid 263 through 267 Processing helix chain 'G' and resid 273 through 275 No H-bonds generated for 'chain 'G' and resid 273 through 275' Processing helix chain 'G' and resid 280 through 302 removed outlier: 3.785A pdb=" N ASP G 284 " --> pdb=" O SER G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 325 Processing helix chain 'G' and resid 345 through 349 removed outlier: 3.720A pdb=" N LYS G 349 " --> pdb=" O ASP G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 359 Processing helix chain 'G' and resid 387 through 394 Processing helix chain 'G' and resid 394 through 405 Processing helix chain 'G' and resid 410 through 420 Processing helix chain 'G' and resid 422 through 434 removed outlier: 3.640A pdb=" N TRP G 426 " --> pdb=" O GLU G 422 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN G 431 " --> pdb=" O ASP G 427 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS G 434 " --> pdb=" O GLU G 430 " (cutoff:3.500A) Processing helix chain 'G' and resid 447 through 449 No H-bonds generated for 'chain 'G' and resid 447 through 449' Processing helix chain 'G' and resid 467 through 469 No H-bonds generated for 'chain 'G' and resid 467 through 469' Processing helix chain 'G' and resid 470 through 475 Processing helix chain 'G' and resid 490 through 500 Processing helix chain 'G' and resid 521 through 532 Processing helix chain 'G' and resid 551 through 561 removed outlier: 3.511A pdb=" N VAL G 555 " --> pdb=" O SER G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 592 through 599 Processing helix chain 'G' and resid 602 through 606 Processing helix chain 'G' and resid 613 through 628 Processing helix chain 'G' and resid 629 through 652 removed outlier: 3.552A pdb=" N GLY G 652 " --> pdb=" O ALA G 648 " (cutoff:3.500A) Processing helix chain 'G' and resid 665 through 687 Processing helix chain 'G' and resid 690 through 720 Processing helix chain 'G' and resid 721 through 724 Processing helix chain 'G' and resid 725 through 733 Processing helix chain 'G' and resid 738 through 747 Processing helix chain 'G' and resid 779 through 800 removed outlier: 3.915A pdb=" N HIS G 788 " --> pdb=" O PHE G 784 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY G 789 " --> pdb=" O ILE G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 801 through 816 Processing helix chain 'G' and resid 845 through 851 Processing helix chain 'G' and resid 876 through 885 Processing helix chain 'G' and resid 895 through 899 removed outlier: 3.599A pdb=" N CYS G 899 " --> pdb=" O PRO G 896 " (cutoff:3.500A) Processing helix chain 'G' and resid 907 through 911 Processing helix chain 'G' and resid 925 through 936 Processing helix chain 'G' and resid 939 through 949 removed outlier: 6.037A pdb=" N THR G 945 " --> pdb=" O LEU G 941 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N PHE G 946 " --> pdb=" O THR G 942 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS G 947 " --> pdb=" O LEU G 943 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL G 948 " --> pdb=" O ARG G 944 " (cutoff:3.500A) Processing helix chain 'G' and resid 1136 through 1139 Processing helix chain 'G' and resid 1140 through 1149 Processing helix chain 'G' and resid 1218 through 1227 Processing helix chain 'G' and resid 1227 through 1245 removed outlier: 3.791A pdb=" N VAL G1242 " --> pdb=" O GLU G1238 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR G1243 " --> pdb=" O VAL G1239 " (cutoff:3.500A) Processing helix chain 'G' and resid 1251 through 1262 removed outlier: 4.250A pdb=" N PHE G1255 " --> pdb=" O ASN G1251 " (cutoff:3.500A) Processing helix chain 'G' and resid 1284 through 1295 Processing helix chain 'G' and resid 1317 through 1330 Processing helix chain 'G' and resid 1351 through 1358 Processing helix chain 'G' and resid 1361 through 1367 Processing helix chain 'G' and resid 1370 through 1382 Processing helix chain 'G' and resid 1389 through 1397 removed outlier: 3.639A pdb=" N ASN G1393 " --> pdb=" O GLY G1389 " (cutoff:3.500A) Processing helix chain 'G' and resid 1402 through 1410 removed outlier: 4.033A pdb=" N MET G1406 " --> pdb=" O GLY G1403 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG G1407 " --> pdb=" O THR G1404 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASP G1408 " --> pdb=" O GLY G1405 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP G1410 " --> pdb=" O ARG G1407 " (cutoff:3.500A) Processing helix chain 'G' and resid 1417 through 1432 Processing helix chain 'H' and resid 17 through 22 Processing helix chain 'H' and resid 27 through 57 removed outlier: 3.910A pdb=" N GLU H 56 " --> pdb=" O GLU H 52 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 Processing helix chain 'H' and resid 85 through 96 Processing helix chain 'H' and resid 104 through 108 Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141 removed outlier: 4.052A pdb=" N ILE A 204 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 212 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN A 13 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE A 158 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA A 157 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TYR A 151 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N CYS A 159 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 149 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 147 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 139 through 141 removed outlier: 4.599A pdb=" N LYS A 191 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 71 removed outlier: 6.423A pdb=" N LYS A 68 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU A 80 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ALA A 70 " --> pdb=" O LEU A 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 246 removed outlier: 7.715A pdb=" N ALA A 317 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL A 223 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 319 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 13 Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 13 Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 246 removed outlier: 3.920A pdb=" N ILE B 235 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ALA B 225 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 93 through 95 Processing sheet with id=AB1, first strand: chain 'C' and resid 108 through 109 Processing sheet with id=AB2, first strand: chain 'D' and resid 177 through 189 removed outlier: 6.879A pdb=" N VAL D 189 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N THR D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU D 198 " --> pdb=" O ARG D 27 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ARG D 27 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE D 200 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLU D 25 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE D 202 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS D 23 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR D 204 " --> pdb=" O GLU D 21 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLU D 21 " --> pdb=" O THR D 204 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP D 16 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLU D 25 " --> pdb=" O MET D 14 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N MET D 14 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ARG D 27 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL D 12 " --> pdb=" O ARG D 27 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL D 12 " --> pdb=" O THR E 234 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 98 through 105 removed outlier: 7.566A pdb=" N ASN D 141 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE D 59 " --> pdb=" O ASN D 141 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU D 143 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL D 57 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL D 145 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 53 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 88 through 90 Processing sheet with id=AB5, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AB6, first strand: chain 'D' and resid 152 through 153 Processing sheet with id=AB7, first strand: chain 'D' and resid 233 through 234 removed outlier: 6.838A pdb=" N THR D 234 " --> pdb=" O MET E 14 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ASP E 16 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL E 12 " --> pdb=" O ARG E 27 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ARG E 27 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N MET E 14 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU E 25 " --> pdb=" O MET E 14 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 16 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU E 196 " --> pdb=" O PRO E 28 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N THR E 193 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL E 189 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 98 through 104 removed outlier: 7.416A pdb=" N ASN E 141 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE E 59 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU E 143 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL E 57 " --> pdb=" O GLU E 143 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL E 145 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 88 through 90 Processing sheet with id=AC1, first strand: chain 'E' and resid 109 through 111 Processing sheet with id=AC2, first strand: chain 'E' and resid 152 through 153 Processing sheet with id=AC3, first strand: chain 'F' and resid 9 through 10 removed outlier: 6.499A pdb=" N VAL F 9 " --> pdb=" O GLY F1111 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 59 through 60 removed outlier: 5.247A pdb=" N LEU F 68 " --> pdb=" O TYR F 103 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N TYR F 103 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE F 70 " --> pdb=" O LYS F 101 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS F 101 " --> pdb=" O PHE F 70 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP F 72 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA F 98 " --> pdb=" O TYR F 120 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N TYR F 120 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU F 100 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASP F 118 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU F 102 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL F 116 " --> pdb=" O LEU F 102 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 133 through 135 Processing sheet with id=AC6, first strand: chain 'F' and resid 411 through 414 removed outlier: 3.626A pdb=" N SER F 144 " --> pdb=" O ARG F 489 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 151 through 158 removed outlier: 4.401A pdb=" N TYR F 166 " --> pdb=" O THR F 182 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE F 178 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU F 179 " --> pdb=" O TYR F 191 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 174 through 175 Processing sheet with id=AC9, first strand: chain 'F' and resid 222 through 226 Processing sheet with id=AD1, first strand: chain 'F' and resid 244 through 253 removed outlier: 6.575A pdb=" N VAL F 244 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP F 248 " --> pdb=" O ARG F 265 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 540 through 541 Processing sheet with id=AD3, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AD4, first strand: chain 'F' and resid 595 through 596 Processing sheet with id=AD5, first strand: chain 'F' and resid 712 through 716 removed outlier: 6.770A pdb=" N LYS F 692 " --> pdb=" O VAL F 688 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL F 688 " --> pdb=" O LYS F 692 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR F 694 " --> pdb=" O GLU F 686 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 721 through 722 Processing sheet with id=AD7, first strand: chain 'F' and resid 731 through 733 Processing sheet with id=AD8, first strand: chain 'F' and resid 753 through 754 Processing sheet with id=AD9, first strand: chain 'F' and resid 1137 through 1138 removed outlier: 6.971A pdb=" N ILE F 780 " --> pdb=" O ARG F1060 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL F1062 " --> pdb=" O ILE F 780 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE F 782 " --> pdb=" O VAL F1062 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR F1154 " --> pdb=" O PHE F 768 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 810 through 811 removed outlier: 3.557A pdb=" N THR F 807 " --> pdb=" O GLY F 810 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP F 806 " --> pdb=" O ILE F1028 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE F1028 " --> pdb=" O ASP F 806 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP F 894 " --> pdb=" O TYR F1035 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA F1037 " --> pdb=" O VAL F 892 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N VAL F 892 " --> pdb=" O ALA F1037 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LYS F1039 " --> pdb=" O GLY F 890 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLY F 890 " --> pdb=" O LYS F1039 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 846 through 848 removed outlier: 6.824A pdb=" N LEU F 882 " --> pdb=" O LEU F 847 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 851 through 853 Processing sheet with id=AE4, first strand: chain 'F' and resid 949 through 950 removed outlier: 3.790A pdb=" N VAL F 949 " --> pdb=" O LEU F 958 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU F 958 " --> pdb=" O VAL F 949 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'F' and resid 1172 through 1174 Processing sheet with id=AE6, first strand: chain 'F' and resid 1197 through 1198 Processing sheet with id=AE7, first strand: chain 'F' and resid 1266 through 1268 Processing sheet with id=AE8, first strand: chain 'G' and resid 99 through 108 removed outlier: 6.496A pdb=" N LYS G 257 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 10.513A pdb=" N VAL G 105 " --> pdb=" O ILE G 255 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N ILE G 255 " --> pdb=" O VAL G 105 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 161 through 162 removed outlier: 6.754A pdb=" N ILE G 190 " --> pdb=" O ILE G 143 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 548 through 549 Processing sheet with id=AF2, first strand: chain 'G' and resid 820 through 822 Processing sheet with id=AF3, first strand: chain 'G' and resid 831 through 833 Processing sheet with id=AF4, first strand: chain 'G' and resid 836 through 838 removed outlier: 6.701A pdb=" N LEU G 836 " --> pdb=" O VAL G 843 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 859 through 860 Processing sheet with id=AF6, first strand: chain 'G' and resid 960 through 962 removed outlier: 4.355A pdb=" N ASP G 988 " --> pdb=" O LEU G1019 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 1007 through 1012 Processing sheet with id=AF8, first strand: chain 'G' and resid 1040 through 1044 removed outlier: 6.332A pdb=" N GLY G1041 " --> pdb=" O LYS G1126 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS G1126 " --> pdb=" O GLY G1041 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE G1043 " --> pdb=" O LEU G1124 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS G1075 " --> pdb=" O LEU G1110 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 1098 through 1103 Processing sheet with id=AG1, first strand: chain 'G' and resid 1187 through 1193 removed outlier: 3.847A pdb=" N ASP G1204 " --> pdb=" O VAL G1166 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 1281 through 1283 removed outlier: 6.413A pdb=" N THR G1344 " --> pdb=" O GLN G1269 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 1314 through 1316 removed outlier: 7.007A pdb=" N THR G1336 " --> pdb=" O GLU G1301 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 1412 through 1416 1592 hydrogen bonds defined for protein. 4494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 172 hydrogen bonds 332 hydrogen bond angles 0 basepair planarities 70 basepair parallelities 134 stacking parallelities Total time for adding SS restraints: 12.90 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12013 1.34 - 1.47: 9479 1.47 - 1.59: 17064 1.59 - 1.72: 306 1.72 - 1.85: 234 Bond restraints: 39096 Sorted by residual: bond pdb=" C3' DA b -16 " pdb=" C2' DA b -16 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DA b -25 " pdb=" C2' DA b -25 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.96e+00 bond pdb=" C3' DT b -55 " pdb=" C2' DT b -55 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.49e+00 bond pdb=" C3' DA b -15 " pdb=" C2' DA b -15 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.15e+00 bond pdb=" C3' DT b -23 " pdb=" C2' DT b -23 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.95e+00 ... (remaining 39091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 53233 2.66 - 5.31: 318 5.31 - 7.97: 29 7.97 - 10.62: 4 10.62 - 13.28: 3 Bond angle restraints: 53587 Sorted by residual: angle pdb=" C ARG B 340 " pdb=" CA ARG B 340 " pdb=" CB ARG B 340 " ideal model delta sigma weight residual 116.54 110.01 6.53 1.15e+00 7.56e-01 3.22e+01 angle pdb=" O4' DA a 56 " pdb=" C4' DA a 56 " pdb=" C3' DA a 56 " ideal model delta sigma weight residual 106.00 103.13 2.87 6.00e-01 2.78e+00 2.29e+01 angle pdb=" CA CYS G 825 " pdb=" CB CYS G 825 " pdb=" SG CYS G 825 " ideal model delta sigma weight residual 114.40 125.39 -10.99 2.30e+00 1.89e-01 2.28e+01 angle pdb=" C1' C c 13 " pdb=" N1 C c 13 " pdb=" C2 C c 13 " ideal model delta sigma weight residual 118.80 123.63 -4.83 1.10e+00 8.26e-01 1.93e+01 angle pdb=" N3 DT b -59 " pdb=" C4 DT b -59 " pdb=" O4 DT b -59 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 53582 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.67: 22215 34.67 - 69.34: 1470 69.34 - 104.01: 51 104.01 - 138.67: 2 138.67 - 173.34: 2 Dihedral angle restraints: 23740 sinusoidal: 11425 harmonic: 12315 Sorted by residual: dihedral pdb=" CB CYS G 825 " pdb=" SG CYS G 825 " pdb=" SG CYS G 909 " pdb=" CB CYS G 909 " ideal model delta sinusoidal sigma weight residual -86.00 -170.08 84.08 1 1.00e+01 1.00e-02 8.61e+01 dihedral pdb=" O4' C c 13 " pdb=" C1' C c 13 " pdb=" N1 C c 13 " pdb=" C2 C c 13 " ideal model delta sinusoidal sigma weight residual 200.00 30.60 169.40 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" CB CYS G 825 " pdb=" SG CYS G 825 " pdb=" SG CYS G 899 " pdb=" CB CYS G 899 " ideal model delta sinusoidal sigma weight residual -86.00 -148.99 62.99 1 1.00e+01 1.00e-02 5.24e+01 ... (remaining 23737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4469 0.043 - 0.087: 1167 0.087 - 0.130: 417 0.130 - 0.174: 19 0.174 - 0.217: 5 Chirality restraints: 6077 Sorted by residual: chirality pdb=" CA PRO B 234 " pdb=" N PRO B 234 " pdb=" C PRO B 234 " pdb=" CB PRO B 234 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB VAL A 46 " pdb=" CA VAL A 46 " pdb=" CG1 VAL A 46 " pdb=" CG2 VAL A 46 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C1' U c 75 " pdb=" O4' U c 75 " pdb=" C2' U c 75 " pdb=" N1 U c 75 " both_signs ideal model delta sigma weight residual False 2.45 2.25 0.19 2.00e-01 2.50e+01 9.34e-01 ... (remaining 6074 not shown) Planarity restraints: 6189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G c 28 " -0.039 2.00e-02 2.50e+03 1.61e-02 7.81e+00 pdb=" N9 G c 28 " 0.035 2.00e-02 2.50e+03 pdb=" C8 G c 28 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G c 28 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G c 28 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G c 28 " -0.008 2.00e-02 2.50e+03 pdb=" O6 G c 28 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G c 28 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G c 28 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G c 28 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G c 28 " 0.010 2.00e-02 2.50e+03 pdb=" C4 G c 28 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U c 75 " -0.029 2.00e-02 2.50e+03 1.63e-02 5.96e+00 pdb=" N1 U c 75 " 0.038 2.00e-02 2.50e+03 pdb=" C2 U c 75 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U c 75 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U c 75 " -0.007 2.00e-02 2.50e+03 pdb=" C4 U c 75 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U c 75 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U c 75 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U c 75 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 220 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO B 221 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 221 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 221 " -0.030 5.00e-02 4.00e+02 ... (remaining 6186 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 16 2.57 - 3.15: 28999 3.15 - 3.73: 60152 3.73 - 4.32: 84468 4.32 - 4.90: 136801 Nonbonded interactions: 310436 Sorted by model distance: nonbonded pdb=" OD1 ASP G 481 " pdb="MG MG G1501 " model vdw 1.986 2.170 nonbonded pdb=" OD1 ASP G 477 " pdb="MG MG G1501 " model vdw 2.010 2.170 nonbonded pdb=" OD1 ASP G 479 " pdb="MG MG G1501 " model vdw 2.018 2.170 nonbonded pdb=" O ASP B 22 " pdb=" OE1 GLU B 26 " model vdw 2.339 3.040 nonbonded pdb=" N GLU B 250 " pdb=" OE1 GLU B 250 " model vdw 2.457 3.120 ... (remaining 310431 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 63 or resid 83 through 365)) selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 5.010 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: 0.040 Extract box with map and model: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 46.150 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 39103 Z= 0.226 Angle : 0.589 20.870 53599 Z= 0.379 Chirality : 0.043 0.217 6077 Planarity : 0.004 0.063 6189 Dihedral : 19.209 173.344 15803 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Rotamer: Outliers : 2.90 % Allowed : 24.74 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.13), residues: 4231 helix: 1.20 (0.13), residues: 1659 sheet: 0.43 (0.22), residues: 573 loop : -0.02 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 169 TYR 0.025 0.001 TYR B 233 PHE 0.031 0.001 PHE B 116 TRP 0.008 0.001 TRP B 342 HIS 0.012 0.001 HIS G 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.23 (39096) covalent geometry : angle 0.57471 / 0.38 (53587) SS BOND : bond 0.00573 / 0.28 ( 3) SS BOND : angle 9.91799 / 3.78 ( 6) hydrogen bonds : bond 0.12457 / 8.12 ( 1748) hydrogen bonds : angle 5.97645 / 4.08 ( 4826) metal coordination : bond 0.01042 / 0.53 ( 4) metal coordination : angle 6.84308 / 3.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 796 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7433 (t80) REVERT: A 53 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7675 (tm-30) REVERT: A 57 ASP cc_start: 0.6163 (OUTLIER) cc_final: 0.5825 (t0) REVERT: A 154 GLU cc_start: 0.7450 (tm-30) cc_final: 0.6945 (tm-30) REVERT: A 170 TYR cc_start: 0.8400 (t80) cc_final: 0.8172 (t80) REVERT: A 184 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7620 (mtm180) REVERT: A 226 GLU cc_start: 0.6418 (mt-10) cc_final: 0.6123 (mt-10) REVERT: A 236 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7691 (m) REVERT: A 238 LYS cc_start: 0.6286 (OUTLIER) cc_final: 0.5649 (mmpt) REVERT: A 241 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7855 (mmtt) REVERT: A 266 THR cc_start: 0.7498 (OUTLIER) cc_final: 0.7073 (p) REVERT: A 349 THR cc_start: 0.8321 (t) cc_final: 0.8017 (m) REVERT: A 361 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7407 (tt0) REVERT: B 46 VAL cc_start: 0.8074 (t) cc_final: 0.7854 (m) REVERT: B 54 MET cc_start: 0.6030 (mmt) cc_final: 0.5683 (mmm) REVERT: B 118 LYS cc_start: 0.8301 (mttt) cc_final: 0.7948 (mttt) REVERT: B 128 ARG cc_start: 0.7770 (ttt180) cc_final: 0.7314 (ttt180) REVERT: B 180 MET cc_start: 0.8154 (ttp) cc_final: 0.7892 (ttp) REVERT: B 222 GLU cc_start: 0.7646 (pp20) cc_final: 0.7226 (pp20) REVERT: B 226 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6785 (tp30) REVERT: B 322 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7659 (pp) REVERT: B 333 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7673 (mtpp) REVERT: B 348 MET cc_start: 0.6585 (tpp) cc_final: 0.6243 (tpp) REVERT: B 350 LYS cc_start: 0.7386 (mtmt) cc_final: 0.6838 (mtmt) REVERT: B 356 GLU cc_start: 0.7332 (pm20) cc_final: 0.6981 (pm20) REVERT: B 361 GLU cc_start: 0.7255 (tp30) cc_final: 0.6983 (tp30) REVERT: B 364 ILE cc_start: 0.6729 (tp) cc_final: 0.6386 (tp) REVERT: C 29 LEU cc_start: 0.8514 (tp) cc_final: 0.8305 (tp) REVERT: C 59 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7704 (ttmm) REVERT: C 91 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8223 (tptt) REVERT: C 147 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6910 (tm-30) REVERT: C 165 LYS cc_start: 0.6620 (OUTLIER) cc_final: 0.6219 (mmtm) REVERT: C 169 GLU cc_start: 0.7342 (tt0) cc_final: 0.6928 (tt0) REVERT: C 182 LYS cc_start: 0.8249 (mtpm) cc_final: 0.8043 (mtpp) REVERT: C 217 MET cc_start: 0.7405 (mtm) cc_final: 0.7145 (mmm) REVERT: C 250 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6960 (mtp) REVERT: D 10 ASP cc_start: 0.7365 (m-30) cc_final: 0.7164 (m-30) REVERT: D 17 SER cc_start: 0.8446 (t) cc_final: 0.8222 (m) REVERT: D 27 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7095 (ptm-80) REVERT: D 153 VAL cc_start: 0.8896 (t) cc_final: 0.8545 (p) REVERT: D 178 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8316 (tttp) REVERT: D 188 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7732 (ttp-170) REVERT: E 50 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7895 (mt-10) REVERT: E 74 GLU cc_start: 0.7730 (mp0) cc_final: 0.7127 (mp0) REVERT: E 107 LYS cc_start: 0.8259 (mtpm) cc_final: 0.7745 (ptmm) REVERT: E 226 MET cc_start: 0.8009 (tpp) cc_final: 0.7687 (mpp) REVERT: F 73 TYR cc_start: 0.8270 (p90) cc_final: 0.7775 (p90) REVERT: F 93 SER cc_start: 0.8051 (p) cc_final: 0.7759 (m) REVERT: F 152 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8619 (t) REVERT: F 161 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8681 (p0) REVERT: F 304 TYR cc_start: 0.6711 (m-80) cc_final: 0.6429 (m-80) REVERT: F 391 TYR cc_start: 0.8200 (t80) cc_final: 0.7759 (t80) REVERT: F 398 SER cc_start: 0.8728 (m) cc_final: 0.8201 (p) REVERT: F 430 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8208 (mtt90) REVERT: F 440 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.7354 (m-40) REVERT: F 553 LYS cc_start: 0.8538 (tttt) cc_final: 0.8316 (tttt) REVERT: F 567 LEU cc_start: 0.8812 (mt) cc_final: 0.8595 (mt) REVERT: F 741 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.8058 (m) REVERT: F 764 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7621 (mtp) REVERT: F 789 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7960 (mt-10) REVERT: F 842 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7778 (mmmt) REVERT: F 866 LEU cc_start: 0.8819 (mp) cc_final: 0.8547 (mt) REVERT: F 900 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6301 (mtp85) REVERT: F 928 GLN cc_start: 0.7794 (tp-100) cc_final: 0.7575 (tp-100) REVERT: F 1010 ASN cc_start: 0.7523 (t0) cc_final: 0.6724 (t0) REVERT: F 1014 ASP cc_start: 0.6924 (m-30) cc_final: 0.6281 (m-30) REVERT: F 1019 SER cc_start: 0.8570 (m) cc_final: 0.8145 (p) REVERT: F 1268 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7854 (mp0) REVERT: G 41 ASN cc_start: 0.8287 (t0) cc_final: 0.7923 (m-40) REVERT: G 114 ARG cc_start: 0.8166 (tpp-160) cc_final: 0.7899 (mmt90) REVERT: G 119 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7698 (mptp) REVERT: G 200 ASP cc_start: 0.8204 (t0) cc_final: 0.7927 (t0) REVERT: G 206 ASP cc_start: 0.7940 (t0) cc_final: 0.7614 (t0) REVERT: G 242 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7339 (mt-10) REVERT: G 306 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: G 318 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: G 377 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7922 (mt-10) REVERT: G 385 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8028 (mp) REVERT: G 643 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8513 (mtp) REVERT: G 672 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7399 (tm-30) REVERT: G 675 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7344 (tm-30) REVERT: G 768 ASN cc_start: 0.8007 (m-40) cc_final: 0.7753 (m-40) REVERT: G 792 LYS cc_start: 0.7741 (mttt) cc_final: 0.7248 (mttm) REVERT: G 1051 ILE cc_start: -0.0775 (OUTLIER) cc_final: -0.1050 (mt) REVERT: G 1146 GLU cc_start: 0.8385 (tt0) cc_final: 0.8091 (tt0) REVERT: G 1149 GLU cc_start: 0.7886 (mp0) cc_final: 0.7608 (mm-30) REVERT: G 1283 HIS cc_start: 0.7608 (t-90) cc_final: 0.7244 (t-90) REVERT: G 1356 SER cc_start: 0.8727 (m) cc_final: 0.8390 (p) REVERT: G 1358 GLN cc_start: 0.8303 (mt0) cc_final: 0.7989 (mt0) REVERT: G 1396 VAL cc_start: 0.8691 (t) cc_final: 0.8315 (m) REVERT: G 1408 ASP cc_start: 0.7912 (m-30) cc_final: 0.7610 (p0) REVERT: G 1424 MET cc_start: 0.3814 (mmt) cc_final: 0.3531 (mmt) REVERT: H 1 MET cc_start: -0.1153 (mtt) cc_final: -0.1425 (mtt) outliers start: 108 outliers final: 67 residues processed: 852 average time/residue: 0.7022 time to fit residues: 718.5067 Evaluate side-chains 882 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 789 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 158 ASN Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 174 LYS Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 382 LYS Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 440 ASN Chi-restraints excluded: chain F residue 456 LYS Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 685 VAL Chi-restraints excluded: chain F residue 696 LYS Chi-restraints excluded: chain F residue 741 VAL Chi-restraints excluded: chain F residue 764 MET Chi-restraints excluded: chain F residue 798 ASP Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 900 ARG Chi-restraints excluded: chain F residue 1055 LYS Chi-restraints excluded: chain F residue 1070 LEU Chi-restraints excluded: chain F residue 1259 LYS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 306 GLU Chi-restraints excluded: chain G residue 318 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 420 LYS Chi-restraints excluded: chain G residue 447 HIS Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain G residue 543 ILE Chi-restraints excluded: chain G residue 613 ASN Chi-restraints excluded: chain G residue 643 MET Chi-restraints excluded: chain G residue 661 ILE Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 717 ILE Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain G residue 903 GLN Chi-restraints excluded: chain G residue 1051 ILE Chi-restraints excluded: chain G residue 1163 ASP Chi-restraints excluded: chain G residue 1357 LEU Chi-restraints excluded: chain G residue 1414 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 40.0000 chunk 424 optimal weight: 9.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN F 10 ASN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 773 ASN G 857 HIS ** G1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.182728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.142160 restraints weight = 55632.391| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.22 r_work: 0.3481 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.0507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 39103 Z= 0.219 Angle : 0.549 12.325 53599 Z= 0.302 Chirality : 0.045 0.250 6077 Planarity : 0.004 0.076 6189 Dihedral : 17.698 175.150 7386 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 4.00 % Allowed : 22.35 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.13), residues: 4231 helix: 1.23 (0.13), residues: 1670 sheet: 0.42 (0.22), residues: 574 loop : -0.02 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 56 TYR 0.016 0.002 TYR G 71 PHE 0.020 0.002 PHE G1362 TRP 0.010 0.001 TRP A 342 HIS 0.006 0.001 HIS G 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (39096) covalent geometry : angle 0.54097 / 0.30 (53587) SS BOND : bond 0.00694 / 0.34 ( 3) SS BOND : angle 7.08981 / 3.00 ( 6) hydrogen bonds : bond 0.04935 / 3.29 ( 1748) hydrogen bonds : angle 4.90683 / 3.35 ( 4826) metal coordination : bond 0.01386 / 0.70 ( 4) metal coordination : angle 5.10302 / 2.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 821 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7198 (t80) REVERT: A 53 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7574 (tm-30) REVERT: A 90 ARG cc_start: 0.7410 (tpp-160) cc_final: 0.7122 (tpp80) REVERT: A 100 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.5788 (pp-130) REVERT: A 127 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.5851 (pt0) REVERT: A 154 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6748 (tm-30) REVERT: A 226 GLU cc_start: 0.6361 (mt-10) cc_final: 0.6080 (mt-10) REVERT: A 236 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7579 (m) REVERT: A 241 LYS cc_start: 0.8106 (mmtt) cc_final: 0.7752 (mmtt) REVERT: A 266 THR cc_start: 0.7571 (OUTLIER) cc_final: 0.7072 (p) REVERT: A 349 THR cc_start: 0.8157 (t) cc_final: 0.7873 (m) REVERT: B 118 LYS cc_start: 0.8264 (mttt) cc_final: 0.7884 (mttt) REVERT: B 128 ARG cc_start: 0.7617 (ttt180) cc_final: 0.7134 (ttt180) REVERT: B 180 MET cc_start: 0.8105 (ttp) cc_final: 0.7837 (ttp) REVERT: B 222 GLU cc_start: 0.7559 (pp20) cc_final: 0.7148 (pp20) REVERT: B 243 ARG cc_start: 0.6371 (OUTLIER) cc_final: 0.5996 (tmm-80) REVERT: B 251 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6924 (tm-30) REVERT: B 322 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7472 (pp) REVERT: B 333 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7564 (mtpp) REVERT: B 346 GLU cc_start: 0.7865 (mp0) cc_final: 0.7591 (mp0) REVERT: B 348 MET cc_start: 0.6145 (tpp) cc_final: 0.5743 (tpp) REVERT: B 350 LYS cc_start: 0.7168 (mtmt) cc_final: 0.6561 (mtmt) REVERT: B 361 GLU cc_start: 0.7271 (tp30) cc_final: 0.6982 (tp30) REVERT: B 364 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.6136 (tp) REVERT: C 91 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.8017 (tptt) REVERT: C 147 GLU cc_start: 0.6874 (tm-30) cc_final: 0.6423 (tm-30) REVERT: C 165 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.6030 (mmtm) REVERT: C 169 GLU cc_start: 0.7180 (tt0) cc_final: 0.6732 (tt0) REVERT: C 182 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7769 (mtpp) REVERT: C 217 MET cc_start: 0.7356 (mtm) cc_final: 0.7078 (mmm) REVERT: C 250 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6915 (mtt) REVERT: D 11 LYS cc_start: 0.7582 (ptpt) cc_final: 0.7287 (ptpt) REVERT: D 17 SER cc_start: 0.8375 (t) cc_final: 0.8133 (m) REVERT: D 27 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7104 (ptm-80) REVERT: D 148 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8343 (ttmm) REVERT: D 153 VAL cc_start: 0.8766 (t) cc_final: 0.8419 (p) REVERT: D 190 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7353 (mm-30) REVERT: D 197 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8378 (tttm) REVERT: E 50 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7633 (mt-10) REVERT: E 74 GLU cc_start: 0.7478 (mp0) cc_final: 0.6915 (mp0) REVERT: E 107 LYS cc_start: 0.8156 (mtpm) cc_final: 0.7622 (ptmm) REVERT: E 196 GLU cc_start: 0.7687 (mt-10) cc_final: 0.6965 (mt-10) REVERT: F 93 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7506 (m) REVERT: F 152 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8526 (t) REVERT: F 384 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6884 (t70) REVERT: F 391 TYR cc_start: 0.7981 (t80) cc_final: 0.7567 (t80) REVERT: F 398 SER cc_start: 0.8600 (m) cc_final: 0.8088 (p) REVERT: F 430 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8067 (mtt90) REVERT: F 553 LYS cc_start: 0.8248 (tttt) cc_final: 0.8012 (tttt) REVERT: F 567 LEU cc_start: 0.8708 (mt) cc_final: 0.8489 (mt) REVERT: F 741 VAL cc_start: 0.8023 (t) cc_final: 0.7784 (m) REVERT: F 764 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7439 (mtp) REVERT: F 842 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7755 (mtmm) REVERT: F 866 LEU cc_start: 0.8729 (mp) cc_final: 0.8423 (mt) REVERT: F 900 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6273 (mtp85) REVERT: F 1010 ASN cc_start: 0.7431 (t0) cc_final: 0.6605 (t0) REVERT: F 1014 ASP cc_start: 0.6697 (m-30) cc_final: 0.6066 (m-30) REVERT: F 1019 SER cc_start: 0.8530 (m) cc_final: 0.8078 (p) REVERT: F 1268 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7477 (mt-10) REVERT: G 144 GLN cc_start: 0.6624 (tp-100) cc_final: 0.6409 (tp-100) REVERT: G 200 ASP cc_start: 0.7930 (t0) cc_final: 0.7648 (t0) REVERT: G 206 ASP cc_start: 0.7702 (t0) cc_final: 0.7416 (t0) REVERT: G 208 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7491 (mt-10) REVERT: G 224 LYS cc_start: 0.7280 (mptt) cc_final: 0.6967 (mppt) REVERT: G 242 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6961 (mt-10) REVERT: G 256 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8117 (mtm) REVERT: G 302 ILE cc_start: 0.8040 (pp) cc_final: 0.7831 (pt) REVERT: G 306 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: G 318 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: G 385 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8052 (mp) REVERT: G 643 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8420 (mtp) REVERT: G 672 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: G 768 ASN cc_start: 0.7819 (m-40) cc_final: 0.7576 (m-40) REVERT: G 792 LYS cc_start: 0.7571 (mttt) cc_final: 0.7031 (mttm) REVERT: G 1146 GLU cc_start: 0.8182 (tt0) cc_final: 0.7895 (tt0) REVERT: G 1283 HIS cc_start: 0.7245 (t-90) cc_final: 0.6847 (t-90) REVERT: G 1356 SER cc_start: 0.8586 (m) cc_final: 0.8235 (p) REVERT: G 1358 GLN cc_start: 0.8099 (mt0) cc_final: 0.7745 (mt0) REVERT: G 1396 VAL cc_start: 0.8624 (t) cc_final: 0.8273 (m) REVERT: G 1408 ASP cc_start: 0.7700 (m-30) cc_final: 0.7493 (p0) REVERT: G 1424 MET cc_start: 0.3806 (mmt) cc_final: 0.3534 (mmt) REVERT: H 1 MET cc_start: -0.1129 (mtt) cc_final: -0.1368 (mtt) outliers start: 149 outliers final: 65 residues processed: 888 average time/residue: 0.7652 time to fit residues: 815.1211 Evaluate side-chains 899 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 806 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 354 ARG Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 685 VAL Chi-restraints excluded: chain F residue 764 MET Chi-restraints excluded: chain F residue 882 LEU Chi-restraints excluded: chain F residue 900 ARG Chi-restraints excluded: chain F residue 1007 ILE Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain G residue 306 GLU Chi-restraints excluded: chain G residue 318 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 556 GLU Chi-restraints excluded: chain G residue 613 ASN Chi-restraints excluded: chain G residue 643 MET Chi-restraints excluded: chain G residue 672 GLU Chi-restraints excluded: chain G residue 675 GLU Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 742 ILE Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 1111 MET Chi-restraints excluded: chain G residue 1210 MET Chi-restraints excluded: chain G residue 1357 LEU Chi-restraints excluded: chain G residue 1414 VAL Chi-restraints excluded: chain H residue 25 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 418 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 332 optimal weight: 0.5980 chunk 316 optimal weight: 0.7980 chunk 363 optimal weight: 0.6980 chunk 391 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 302 optimal weight: 0.5980 chunk 421 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN D 158 ASN F 10 ASN G 41 ASN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 741 GLN G 773 ASN ** G1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.183567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.142246 restraints weight = 55564.462| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.22 r_work: 0.3500 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39103 Z= 0.147 Angle : 0.514 12.648 53599 Z= 0.281 Chirality : 0.043 0.248 6077 Planarity : 0.004 0.076 6189 Dihedral : 17.406 174.496 7264 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.07 % Rotamer: Outliers : 4.30 % Allowed : 22.35 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.13), residues: 4231 helix: 1.41 (0.13), residues: 1659 sheet: 0.43 (0.22), residues: 562 loop : 0.02 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 56 TYR 0.018 0.001 TYR A 163 PHE 0.022 0.001 PHE B 116 TRP 0.007 0.001 TRP F 248 HIS 0.008 0.001 HIS G 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (39096) covalent geometry : angle 0.50624 / 0.28 (53587) SS BOND : bond 0.00575 / 0.27 ( 3) SS BOND : angle 6.75808 / 2.86 ( 6) hydrogen bonds : bond 0.04387 / 2.92 ( 1748) hydrogen bonds : angle 4.63772 / 3.18 ( 4826) metal coordination : bond 0.00762 / 0.38 ( 4) metal coordination : angle 4.68931 / 2.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 818 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.7489 (tpp-160) cc_final: 0.7146 (tpp-160) REVERT: A 100 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.5922 (pp-130) REVERT: A 127 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6017 (pt0) REVERT: A 154 GLU cc_start: 0.7453 (tm-30) cc_final: 0.6961 (tm-30) REVERT: A 226 GLU cc_start: 0.6556 (mt-10) cc_final: 0.6188 (mt-10) REVERT: A 236 VAL cc_start: 0.7903 (OUTLIER) cc_final: 0.7636 (m) REVERT: A 241 LYS cc_start: 0.8253 (mmtt) cc_final: 0.7902 (mmtt) REVERT: A 266 THR cc_start: 0.7624 (OUTLIER) cc_final: 0.7133 (p) REVERT: A 349 THR cc_start: 0.8268 (t) cc_final: 0.7990 (m) REVERT: B 40 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7715 (mtm-85) REVERT: B 54 MET cc_start: 0.6026 (mmt) cc_final: 0.5760 (mmm) REVERT: B 118 LYS cc_start: 0.8290 (mttt) cc_final: 0.7921 (mttt) REVERT: B 128 ARG cc_start: 0.7760 (ttt180) cc_final: 0.7282 (ttt180) REVERT: B 137 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7582 (pp-130) REVERT: B 180 MET cc_start: 0.8181 (ttp) cc_final: 0.7908 (ttp) REVERT: B 222 GLU cc_start: 0.7714 (pp20) cc_final: 0.7310 (pp20) REVERT: B 243 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.6223 (tmm-80) REVERT: B 322 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7422 (pp) REVERT: B 333 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7667 (mtpp) REVERT: B 346 GLU cc_start: 0.7930 (mp0) cc_final: 0.7327 (mp0) REVERT: B 348 MET cc_start: 0.6465 (tpp) cc_final: 0.6178 (tpp) REVERT: B 350 LYS cc_start: 0.7108 (mtmt) cc_final: 0.6568 (mtmt) REVERT: B 353 TYR cc_start: 0.6912 (t80) cc_final: 0.6607 (t80) REVERT: B 354 LYS cc_start: 0.7281 (ttmt) cc_final: 0.5710 (ttmt) REVERT: B 361 GLU cc_start: 0.7358 (tp30) cc_final: 0.7092 (tp30) REVERT: B 364 ILE cc_start: 0.6562 (OUTLIER) cc_final: 0.6175 (tp) REVERT: C 29 LEU cc_start: 0.8522 (tp) cc_final: 0.8300 (tp) REVERT: C 84 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8000 (mmtm) REVERT: C 91 LYS cc_start: 0.8439 (tptt) cc_final: 0.8171 (tptt) REVERT: C 147 GLU cc_start: 0.7384 (tm-30) cc_final: 0.6950 (tm-30) REVERT: C 165 LYS cc_start: 0.6554 (OUTLIER) cc_final: 0.6247 (mmtm) REVERT: C 169 GLU cc_start: 0.7390 (tt0) cc_final: 0.6994 (tt0) REVERT: C 217 MET cc_start: 0.7425 (mtm) cc_final: 0.7126 (mmm) REVERT: C 250 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6890 (mtt) REVERT: D 11 LYS cc_start: 0.7759 (ptpt) cc_final: 0.7439 (ptpt) REVERT: D 17 SER cc_start: 0.8456 (t) cc_final: 0.8238 (m) REVERT: D 153 VAL cc_start: 0.8824 (t) cc_final: 0.8485 (p) REVERT: D 178 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8277 (tttp) REVERT: D 188 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7742 (ttp-110) REVERT: D 190 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7483 (mm-30) REVERT: E 50 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7886 (mt-10) REVERT: E 63 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7575 (tt0) REVERT: E 74 GLU cc_start: 0.7687 (mp0) cc_final: 0.7092 (mp0) REVERT: E 148 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8570 (tttm) REVERT: E 194 ASP cc_start: 0.6634 (p0) cc_final: 0.6187 (p0) REVERT: F 73 TYR cc_start: 0.8291 (p90) cc_final: 0.8088 (p90) REVERT: F 93 SER cc_start: 0.8009 (p) cc_final: 0.7720 (m) REVERT: F 152 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8612 (t) REVERT: F 373 ILE cc_start: 0.8379 (mp) cc_final: 0.8106 (mp) REVERT: F 384 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.7110 (t70) REVERT: F 391 TYR cc_start: 0.8170 (t80) cc_final: 0.7737 (t80) REVERT: F 398 SER cc_start: 0.8670 (m) cc_final: 0.8177 (p) REVERT: F 430 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8237 (mtt90) REVERT: F 553 LYS cc_start: 0.8564 (tttt) cc_final: 0.8347 (tttt) REVERT: F 567 LEU cc_start: 0.8813 (mt) cc_final: 0.8554 (mt) REVERT: F 741 VAL cc_start: 0.8116 (t) cc_final: 0.7903 (m) REVERT: F 764 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7655 (mtp) REVERT: F 789 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7993 (mt-10) REVERT: F 842 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7852 (mtmm) REVERT: F 866 LEU cc_start: 0.8773 (mp) cc_final: 0.8448 (mt) REVERT: F 1010 ASN cc_start: 0.7560 (t0) cc_final: 0.6729 (t0) REVERT: F 1014 ASP cc_start: 0.6924 (m-30) cc_final: 0.6251 (m-30) REVERT: F 1019 SER cc_start: 0.8566 (m) cc_final: 0.8137 (p) REVERT: F 1166 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8213 (mtt) REVERT: F 1268 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7703 (mt-10) REVERT: G 144 GLN cc_start: 0.6777 (tp-100) cc_final: 0.6560 (tp-100) REVERT: G 200 ASP cc_start: 0.8169 (t0) cc_final: 0.7899 (t0) REVERT: G 206 ASP cc_start: 0.7932 (t0) cc_final: 0.7591 (t0) REVERT: G 209 GLN cc_start: 0.7962 (mp10) cc_final: 0.7585 (mp-120) REVERT: G 210 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8217 (tt) REVERT: G 242 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7299 (mt-10) REVERT: G 256 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8196 (mtm) REVERT: G 306 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: G 318 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: G 385 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8054 (mp) REVERT: G 643 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8504 (mtp) REVERT: G 672 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: G 700 ASP cc_start: 0.7846 (t0) cc_final: 0.7434 (m-30) REVERT: G 768 ASN cc_start: 0.8004 (m-40) cc_final: 0.7754 (m-40) REVERT: G 788 HIS cc_start: 0.7700 (m170) cc_final: 0.7467 (m170) REVERT: G 792 LYS cc_start: 0.7739 (mttt) cc_final: 0.7192 (mttm) REVERT: G 1146 GLU cc_start: 0.8346 (tt0) cc_final: 0.8056 (tt0) REVERT: G 1283 HIS cc_start: 0.7570 (t-90) cc_final: 0.7200 (t-90) REVERT: G 1356 SER cc_start: 0.8688 (m) cc_final: 0.8358 (p) REVERT: G 1358 GLN cc_start: 0.8315 (mt0) cc_final: 0.7972 (mt0) REVERT: G 1396 VAL cc_start: 0.8682 (t) cc_final: 0.8325 (m) REVERT: G 1424 MET cc_start: 0.3797 (mmt) cc_final: 0.3541 (mmt) REVERT: H 1 MET cc_start: -0.1156 (mtt) cc_final: -0.1431 (mtt) outliers start: 160 outliers final: 83 residues processed: 895 average time/residue: 0.7908 time to fit residues: 847.0579 Evaluate side-chains 912 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 804 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 354 ARG Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 382 LYS Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 685 VAL Chi-restraints excluded: chain F residue 764 MET Chi-restraints excluded: chain F residue 797 ILE Chi-restraints excluded: chain F residue 862 GLU Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 882 LEU Chi-restraints excluded: chain F residue 889 ARG Chi-restraints excluded: chain F residue 1007 ILE Chi-restraints excluded: chain F residue 1166 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain G residue 306 GLU Chi-restraints excluded: chain G residue 318 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 420 LYS Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 447 HIS Chi-restraints excluded: chain G residue 543 ILE Chi-restraints excluded: chain G residue 613 ASN Chi-restraints excluded: chain G residue 643 MET Chi-restraints excluded: chain G residue 672 GLU Chi-restraints excluded: chain G residue 717 ILE Chi-restraints excluded: chain G residue 742 ILE Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain G residue 903 GLN Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 1111 MET Chi-restraints excluded: chain G residue 1163 ASP Chi-restraints excluded: chain G residue 1353 THR Chi-restraints excluded: chain G residue 1357 LEU Chi-restraints excluded: chain G residue 1414 VAL Chi-restraints excluded: chain H residue 25 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 294 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 260 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 42 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 183 optimal weight: 0.7980 chunk 245 optimal weight: 0.9980 chunk 253 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN F 10 ASN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 741 GLN G 773 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.183962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143482 restraints weight = 55570.787| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.17 r_work: 0.3518 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 39103 Z= 0.117 Angle : 0.496 12.082 53599 Z= 0.270 Chirality : 0.042 0.247 6077 Planarity : 0.004 0.073 6189 Dihedral : 17.352 174.741 7249 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.62 % Favored : 97.31 % Rotamer: Outliers : 4.27 % Allowed : 22.49 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.13), residues: 4231 helix: 1.59 (0.13), residues: 1654 sheet: 0.49 (0.22), residues: 556 loop : 0.08 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 241 TYR 0.022 0.001 TYR A 163 PHE 0.019 0.001 PHE B 116 TRP 0.006 0.001 TRP F 248 HIS 0.005 0.001 HIS F1137 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (39096) covalent geometry : angle 0.48933 / 0.27 (53587) SS BOND : bond 0.00525 / 0.25 ( 3) SS BOND : angle 6.34068 / 2.69 ( 6) hydrogen bonds : bond 0.03999 / 2.65 ( 1748) hydrogen bonds : angle 4.43201 / 3.04 ( 4826) metal coordination : bond 0.00462 / 0.23 ( 4) metal coordination : angle 4.03546 / 1.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 826 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8501 (mtmt) cc_final: 0.8282 (mtmt) REVERT: A 39 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7414 (t80) REVERT: A 53 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7699 (tm-30) REVERT: A 90 ARG cc_start: 0.7419 (tpp-160) cc_final: 0.7063 (tpp-160) REVERT: A 100 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.5904 (pp-130) REVERT: A 127 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.5966 (pt0) REVERT: A 154 GLU cc_start: 0.7446 (tm-30) cc_final: 0.6963 (tm-30) REVERT: A 184 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7467 (mtm180) REVERT: A 226 GLU cc_start: 0.6526 (mt-10) cc_final: 0.6189 (mt-10) REVERT: A 236 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7632 (m) REVERT: A 241 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7948 (mmtt) REVERT: A 266 THR cc_start: 0.7510 (OUTLIER) cc_final: 0.7047 (p) REVERT: A 349 THR cc_start: 0.8226 (t) cc_final: 0.7961 (m) REVERT: B 40 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7729 (mtm-85) REVERT: B 118 LYS cc_start: 0.8253 (mttt) cc_final: 0.7899 (mttp) REVERT: B 128 ARG cc_start: 0.7712 (ttt180) cc_final: 0.7237 (ttt180) REVERT: B 180 MET cc_start: 0.8132 (ttp) cc_final: 0.7880 (ttp) REVERT: B 222 GLU cc_start: 0.7701 (pp20) cc_final: 0.7300 (pp20) REVERT: B 226 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6300 (tp30) REVERT: B 243 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6229 (tmm-80) REVERT: B 322 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7574 (pp) REVERT: B 333 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7649 (mtpp) REVERT: B 346 GLU cc_start: 0.7885 (mp0) cc_final: 0.6921 (mm-30) REVERT: B 350 LYS cc_start: 0.7042 (mtmt) cc_final: 0.6502 (mtmt) REVERT: B 353 TYR cc_start: 0.6979 (t80) cc_final: 0.6627 (t80) REVERT: B 356 GLU cc_start: 0.7295 (pm20) cc_final: 0.6746 (pm20) REVERT: C 29 LEU cc_start: 0.8522 (tp) cc_final: 0.8304 (tp) REVERT: C 84 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7991 (mmtm) REVERT: C 91 LYS cc_start: 0.8428 (tptt) cc_final: 0.8146 (tptt) REVERT: C 147 GLU cc_start: 0.7379 (tm-30) cc_final: 0.6951 (tm-30) REVERT: C 151 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7974 (ttpt) REVERT: C 165 LYS cc_start: 0.6591 (OUTLIER) cc_final: 0.6337 (mmtm) REVERT: C 169 GLU cc_start: 0.7364 (tt0) cc_final: 0.7055 (tt0) REVERT: C 250 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6904 (mtt) REVERT: D 11 LYS cc_start: 0.7703 (ptpt) cc_final: 0.7387 (ptpt) REVERT: D 17 SER cc_start: 0.8454 (t) cc_final: 0.8231 (m) REVERT: D 153 VAL cc_start: 0.8796 (t) cc_final: 0.8447 (p) REVERT: D 178 LYS cc_start: 0.8669 (ttmm) cc_final: 0.8252 (tttp) REVERT: D 188 ARG cc_start: 0.8125 (ttp-110) cc_final: 0.7680 (ttp-110) REVERT: D 190 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7420 (mm-30) REVERT: E 50 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7877 (mt-10) REVERT: E 63 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7550 (tt0) REVERT: E 74 GLU cc_start: 0.7672 (mp0) cc_final: 0.7087 (mp0) REVERT: E 194 ASP cc_start: 0.6626 (p0) cc_final: 0.6187 (p0) REVERT: F 73 TYR cc_start: 0.8284 (p90) cc_final: 0.8068 (p90) REVERT: F 93 SER cc_start: 0.8025 (p) cc_final: 0.7741 (m) REVERT: F 373 ILE cc_start: 0.8372 (mp) cc_final: 0.8105 (mp) REVERT: F 384 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.7053 (t70) REVERT: F 391 TYR cc_start: 0.8155 (t80) cc_final: 0.7715 (t80) REVERT: F 398 SER cc_start: 0.8659 (m) cc_final: 0.8232 (t) REVERT: F 430 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8228 (mtt90) REVERT: F 553 LYS cc_start: 0.8537 (tttt) cc_final: 0.8325 (tttt) REVERT: F 567 LEU cc_start: 0.8806 (mt) cc_final: 0.8561 (mt) REVERT: F 764 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7620 (mtp) REVERT: F 842 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7838 (mtmm) REVERT: F 866 LEU cc_start: 0.8765 (mp) cc_final: 0.8441 (mt) REVERT: F 900 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6323 (mtp85) REVERT: F 1010 ASN cc_start: 0.7525 (t0) cc_final: 0.6688 (t0) REVERT: F 1014 ASP cc_start: 0.6891 (m-30) cc_final: 0.6218 (m-30) REVERT: F 1019 SER cc_start: 0.8573 (m) cc_final: 0.8130 (p) REVERT: F 1221 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8199 (t) REVERT: G 41 ASN cc_start: 0.8237 (t0) cc_final: 0.7761 (m-40) REVERT: G 77 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7778 (mmm-85) REVERT: G 90 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7703 (mp0) REVERT: G 200 ASP cc_start: 0.8114 (t0) cc_final: 0.7833 (t0) REVERT: G 206 ASP cc_start: 0.7925 (t0) cc_final: 0.7608 (t0) REVERT: G 208 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7528 (mm-30) REVERT: G 209 GLN cc_start: 0.7956 (mp10) cc_final: 0.7591 (mp-120) REVERT: G 210 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8219 (tt) REVERT: G 241 ARG cc_start: 0.8638 (mtm110) cc_final: 0.8415 (mtm180) REVERT: G 242 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7314 (mt-10) REVERT: G 306 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: G 318 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: G 385 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8028 (mp) REVERT: G 501 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7904 (mtt) REVERT: G 672 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: G 700 ASP cc_start: 0.7824 (t0) cc_final: 0.7395 (m-30) REVERT: G 711 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7671 (mm-30) REVERT: G 768 ASN cc_start: 0.7986 (m-40) cc_final: 0.7729 (m-40) REVERT: G 792 LYS cc_start: 0.7747 (mttt) cc_final: 0.7196 (mttm) REVERT: G 1051 ILE cc_start: -0.0899 (OUTLIER) cc_final: -0.1176 (mt) REVERT: G 1146 GLU cc_start: 0.8361 (tt0) cc_final: 0.8082 (tt0) REVERT: G 1283 HIS cc_start: 0.7569 (t-90) cc_final: 0.7227 (t-90) REVERT: G 1356 SER cc_start: 0.8696 (m) cc_final: 0.8363 (p) REVERT: G 1396 VAL cc_start: 0.8669 (t) cc_final: 0.8311 (m) REVERT: G 1408 ASP cc_start: 0.7900 (m-30) cc_final: 0.7606 (p0) REVERT: G 1424 MET cc_start: 0.3760 (mmt) cc_final: 0.3524 (mmt) REVERT: H 1 MET cc_start: -0.1127 (mtt) cc_final: -0.1406 (mtt) outliers start: 159 outliers final: 86 residues processed: 903 average time/residue: 0.7995 time to fit residues: 863.2157 Evaluate side-chains 912 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 802 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 6 PHE Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 354 ARG Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 382 LYS Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 572 GLU Chi-restraints excluded: chain F residue 764 MET Chi-restraints excluded: chain F residue 797 ILE Chi-restraints excluded: chain F residue 798 ASP Chi-restraints excluded: chain F residue 862 GLU Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 894 ASP Chi-restraints excluded: chain F residue 900 ARG Chi-restraints excluded: chain F residue 920 MET Chi-restraints excluded: chain F residue 1007 ILE Chi-restraints excluded: chain F residue 1221 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 306 GLU Chi-restraints excluded: chain G residue 318 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 420 LYS Chi-restraints excluded: chain G residue 447 HIS Chi-restraints excluded: chain G residue 501 MET Chi-restraints excluded: chain G residue 543 ILE Chi-restraints excluded: chain G residue 613 ASN Chi-restraints excluded: chain G residue 672 GLU Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 717 ILE Chi-restraints excluded: chain G residue 814 VAL Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain G residue 903 GLN Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 1051 ILE Chi-restraints excluded: chain G residue 1111 MET Chi-restraints excluded: chain G residue 1163 ASP Chi-restraints excluded: chain G residue 1357 LEU Chi-restraints excluded: chain G residue 1361 SER Chi-restraints excluded: chain G residue 1414 VAL Chi-restraints excluded: chain H residue 25 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 55 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 236 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 347 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 417 optimal weight: 20.0000 chunk 308 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 200 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN F 10 ASN F1008 GLN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 HIS G 741 GLN G 773 ASN G 857 HIS ** G1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.182876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141916 restraints weight = 55392.905| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.23 r_work: 0.3474 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 39103 Z= 0.244 Angle : 0.566 13.640 53599 Z= 0.304 Chirality : 0.045 0.235 6077 Planarity : 0.004 0.053 6189 Dihedral : 17.324 175.088 7238 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.24 % Favored : 96.69 % Rotamer: Outliers : 4.67 % Allowed : 22.41 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.13), residues: 4231 helix: 1.35 (0.13), residues: 1661 sheet: 0.43 (0.22), residues: 562 loop : 0.00 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 255 TYR 0.020 0.002 TYR B 123 PHE 0.024 0.002 PHE A 252 TRP 0.011 0.001 TRP A 342 HIS 0.007 0.001 HIS G 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.24 (39096) covalent geometry : angle 0.55930 / 0.30 (53587) SS BOND : bond 0.00492 / 0.24 ( 3) SS BOND : angle 6.74748 / 2.80 ( 6) hydrogen bonds : bond 0.04687 / 3.11 ( 1748) hydrogen bonds : angle 4.55255 / 3.13 ( 4826) metal coordination : bond 0.01161 / 0.58 ( 4) metal coordination : angle 4.92341 / 2.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 812 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 90 ARG cc_start: 0.7354 (tpp-160) cc_final: 0.7141 (tpp-160) REVERT: A 100 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.5712 (pp-130) REVERT: A 127 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5835 (pt0) REVERT: A 154 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6782 (tm-30) REVERT: A 226 GLU cc_start: 0.6399 (mt-10) cc_final: 0.6079 (mt-10) REVERT: A 236 VAL cc_start: 0.7830 (OUTLIER) cc_final: 0.7569 (m) REVERT: A 241 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7767 (mmtt) REVERT: A 266 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7129 (p) REVERT: A 349 THR cc_start: 0.8145 (t) cc_final: 0.7876 (m) REVERT: B 118 LYS cc_start: 0.8265 (mttt) cc_final: 0.7887 (mttp) REVERT: B 128 ARG cc_start: 0.7575 (ttt180) cc_final: 0.7076 (ttt180) REVERT: B 180 MET cc_start: 0.8245 (ttp) cc_final: 0.7981 (ttp) REVERT: B 222 GLU cc_start: 0.7601 (pp20) cc_final: 0.7177 (pp20) REVERT: B 243 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.6144 (tmm-80) REVERT: B 322 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7496 (pp) REVERT: B 333 LYS cc_start: 0.7809 (mtpp) cc_final: 0.7572 (mtpp) REVERT: B 346 GLU cc_start: 0.7851 (mp0) cc_final: 0.6792 (mm-30) REVERT: B 350 LYS cc_start: 0.6972 (mtmt) cc_final: 0.6377 (mtmt) REVERT: B 353 TYR cc_start: 0.6922 (t80) cc_final: 0.6687 (t80) REVERT: C 29 LEU cc_start: 0.8407 (tp) cc_final: 0.8190 (tp) REVERT: C 43 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: C 91 LYS cc_start: 0.8223 (tptt) cc_final: 0.7961 (tptt) REVERT: C 147 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6460 (tm-30) REVERT: C 165 LYS cc_start: 0.6441 (OUTLIER) cc_final: 0.6110 (mmtm) REVERT: C 169 GLU cc_start: 0.7234 (tt0) cc_final: 0.6892 (tt0) REVERT: C 182 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7847 (mtpp) REVERT: C 217 MET cc_start: 0.7435 (mtm) cc_final: 0.7155 (mmm) REVERT: C 250 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6890 (mtt) REVERT: D 11 LYS cc_start: 0.7606 (ptpt) cc_final: 0.7309 (ptpt) REVERT: D 17 SER cc_start: 0.8379 (t) cc_final: 0.8128 (m) REVERT: D 27 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7132 (ptm-80) REVERT: D 30 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6916 (mm-30) REVERT: D 64 HIS cc_start: 0.7384 (p90) cc_final: 0.7177 (p90) REVERT: D 153 VAL cc_start: 0.8785 (t) cc_final: 0.8441 (p) REVERT: D 178 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8152 (tttp) REVERT: D 188 ARG cc_start: 0.8025 (ttp-110) cc_final: 0.7599 (ttp-110) REVERT: D 190 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7217 (mm-30) REVERT: D 197 LYS cc_start: 0.8651 (tptm) cc_final: 0.8369 (tttm) REVERT: E 50 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7670 (mt-10) REVERT: E 63 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7185 (tt0) REVERT: E 74 GLU cc_start: 0.7476 (mp0) cc_final: 0.6936 (mp0) REVERT: E 148 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8441 (tttm) REVERT: E 194 ASP cc_start: 0.6458 (p0) cc_final: 0.5989 (p0) REVERT: F 76 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: F 93 SER cc_start: 0.7808 (OUTLIER) cc_final: 0.7531 (m) REVERT: F 152 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8506 (t) REVERT: F 173 PHE cc_start: 0.8336 (t80) cc_final: 0.8118 (t80) REVERT: F 391 TYR cc_start: 0.7951 (t80) cc_final: 0.7490 (t80) REVERT: F 398 SER cc_start: 0.8543 (m) cc_final: 0.8141 (t) REVERT: F 430 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8050 (mtt90) REVERT: F 553 LYS cc_start: 0.8276 (tttt) cc_final: 0.8061 (tttt) REVERT: F 567 LEU cc_start: 0.8714 (mt) cc_final: 0.8446 (mt) REVERT: F 764 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7449 (mtp) REVERT: F 842 LYS cc_start: 0.8007 (mtpt) cc_final: 0.7730 (mtmm) REVERT: F 866 LEU cc_start: 0.8699 (mp) cc_final: 0.8340 (mt) REVERT: F 900 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6248 (mtp85) REVERT: F 1010 ASN cc_start: 0.7474 (t0) cc_final: 0.6605 (t0) REVERT: F 1014 ASP cc_start: 0.6710 (m-30) cc_final: 0.6031 (m-30) REVERT: F 1166 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8183 (mtt) REVERT: F 1221 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8164 (t) REVERT: G 41 ASN cc_start: 0.8026 (t0) cc_final: 0.7766 (m-40) REVERT: G 49 ARG cc_start: 0.8395 (ttt-90) cc_final: 0.7596 (ttt-90) REVERT: G 56 ARG cc_start: 0.7974 (mtt90) cc_final: 0.7490 (mtt90) REVERT: G 144 GLN cc_start: 0.6637 (tp-100) cc_final: 0.6399 (tp-100) REVERT: G 200 ASP cc_start: 0.7949 (t0) cc_final: 0.7676 (t0) REVERT: G 206 ASP cc_start: 0.7682 (t0) cc_final: 0.7424 (t0) REVERT: G 208 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7294 (mm-30) REVERT: G 242 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6983 (mt-10) REVERT: G 256 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8109 (mtm) REVERT: G 306 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: G 318 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: G 385 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8097 (mp) REVERT: G 501 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7839 (mtt) REVERT: G 672 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: G 700 ASP cc_start: 0.7517 (t0) cc_final: 0.7126 (m-30) REVERT: G 768 ASN cc_start: 0.7813 (m-40) cc_final: 0.7570 (m-40) REVERT: G 792 LYS cc_start: 0.7552 (mttt) cc_final: 0.6927 (mttm) REVERT: G 1051 ILE cc_start: -0.0841 (OUTLIER) cc_final: -0.1116 (mt) REVERT: G 1146 GLU cc_start: 0.8178 (tt0) cc_final: 0.7885 (tt0) REVERT: G 1283 HIS cc_start: 0.7243 (t-90) cc_final: 0.6829 (t-90) REVERT: G 1356 SER cc_start: 0.8573 (m) cc_final: 0.8234 (p) REVERT: G 1358 GLN cc_start: 0.8098 (mt0) cc_final: 0.7753 (mt0) REVERT: G 1396 VAL cc_start: 0.8622 (t) cc_final: 0.8284 (m) REVERT: G 1424 MET cc_start: 0.3756 (mmt) cc_final: 0.3550 (mmt) REVERT: H 1 MET cc_start: -0.1155 (mtt) cc_final: -0.1362 (mtt) outliers start: 174 outliers final: 101 residues processed: 890 average time/residue: 0.7682 time to fit residues: 820.9968 Evaluate side-chains 926 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 799 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 354 ARG Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 382 LYS Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 685 VAL Chi-restraints excluded: chain F residue 740 LYS Chi-restraints excluded: chain F residue 741 VAL Chi-restraints excluded: chain F residue 764 MET Chi-restraints excluded: chain F residue 797 ILE Chi-restraints excluded: chain F residue 798 ASP Chi-restraints excluded: chain F residue 862 GLU Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 882 LEU Chi-restraints excluded: chain F residue 900 ARG Chi-restraints excluded: chain F residue 1007 ILE Chi-restraints excluded: chain F residue 1166 MET Chi-restraints excluded: chain F residue 1221 VAL Chi-restraints excluded: chain F residue 1235 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain G residue 306 GLU Chi-restraints excluded: chain G residue 318 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 420 LYS Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 447 HIS Chi-restraints excluded: chain G residue 501 MET Chi-restraints excluded: chain G residue 543 ILE Chi-restraints excluded: chain G residue 613 ASN Chi-restraints excluded: chain G residue 672 GLU Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 717 ILE Chi-restraints excluded: chain G residue 742 ILE Chi-restraints excluded: chain G residue 797 THR Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain G residue 903 GLN Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 1051 ILE Chi-restraints excluded: chain G residue 1163 ASP Chi-restraints excluded: chain G residue 1353 THR Chi-restraints excluded: chain G residue 1357 LEU Chi-restraints excluded: chain G residue 1361 SER Chi-restraints excluded: chain G residue 1414 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 175 optimal weight: 0.0570 chunk 436 optimal weight: 7.9990 chunk 325 optimal weight: 1.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 ASN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 HIS G 741 GLN G 773 ASN ** G1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.183761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.142535 restraints weight = 55411.030| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.21 r_work: 0.3498 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 39103 Z= 0.157 Angle : 0.527 12.565 53599 Z= 0.284 Chirality : 0.043 0.239 6077 Planarity : 0.004 0.054 6189 Dihedral : 17.309 175.006 7238 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.81 % Favored : 97.12 % Rotamer: Outliers : 4.16 % Allowed : 23.40 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.13), residues: 4231 helix: 1.47 (0.13), residues: 1662 sheet: 0.44 (0.22), residues: 560 loop : 0.03 (0.14), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 169 TYR 0.022 0.001 TYR A 163 PHE 0.025 0.001 PHE B 116 TRP 0.007 0.001 TRP G 702 HIS 0.009 0.001 HIS G 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (39096) covalent geometry : angle 0.52024 / 0.28 (53587) SS BOND : bond 0.00492 / 0.24 ( 3) SS BOND : angle 6.41810 / 2.69 ( 6) hydrogen bonds : bond 0.04229 / 2.81 ( 1748) hydrogen bonds : angle 4.44763 / 3.05 ( 4826) metal coordination : bond 0.00614 / 0.31 ( 4) metal coordination : angle 4.68490 / 2.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 812 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7762 (tm-30) REVERT: A 100 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.5878 (pp-130) REVERT: A 127 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.6040 (pt0) REVERT: A 154 GLU cc_start: 0.7448 (tm-30) cc_final: 0.6957 (tm-30) REVERT: A 184 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7432 (mtm180) REVERT: A 226 GLU cc_start: 0.6545 (mt-10) cc_final: 0.6199 (mt-10) REVERT: A 236 VAL cc_start: 0.7909 (OUTLIER) cc_final: 0.7638 (m) REVERT: A 241 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7926 (mmtt) REVERT: A 266 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7153 (p) REVERT: A 296 TYR cc_start: 0.8420 (t80) cc_final: 0.8219 (t80) REVERT: A 349 THR cc_start: 0.8258 (t) cc_final: 0.7998 (m) REVERT: B 118 LYS cc_start: 0.8278 (mttt) cc_final: 0.7964 (mttp) REVERT: B 128 ARG cc_start: 0.7713 (ttt180) cc_final: 0.7241 (ttt180) REVERT: B 180 MET cc_start: 0.8260 (ttp) cc_final: 0.7996 (ttp) REVERT: B 222 GLU cc_start: 0.7750 (pp20) cc_final: 0.7327 (pp20) REVERT: B 226 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.5910 (mp0) REVERT: B 243 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6292 (tmm-80) REVERT: B 322 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7642 (pp) REVERT: B 333 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7664 (mtpp) REVERT: B 346 GLU cc_start: 0.7941 (mp0) cc_final: 0.6619 (mm-30) REVERT: B 350 LYS cc_start: 0.7053 (mtmt) cc_final: 0.6488 (mtmt) REVERT: B 353 TYR cc_start: 0.7034 (t80) cc_final: 0.6778 (t80) REVERT: C 29 LEU cc_start: 0.8535 (tp) cc_final: 0.8329 (tp) REVERT: C 91 LYS cc_start: 0.8435 (tptt) cc_final: 0.8212 (tptt) REVERT: C 147 GLU cc_start: 0.7439 (tm-30) cc_final: 0.6984 (tm-30) REVERT: C 165 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.6149 (mmtm) REVERT: C 169 GLU cc_start: 0.7321 (tt0) cc_final: 0.6900 (tt0) REVERT: C 217 MET cc_start: 0.7451 (mtm) cc_final: 0.7184 (mmm) REVERT: C 250 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6923 (mtt) REVERT: D 11 LYS cc_start: 0.7781 (ptpt) cc_final: 0.7456 (ptpt) REVERT: D 17 SER cc_start: 0.8469 (t) cc_final: 0.8205 (m) REVERT: D 27 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7217 (ptm-80) REVERT: D 30 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7125 (mm-30) REVERT: D 153 VAL cc_start: 0.8851 (t) cc_final: 0.8503 (p) REVERT: D 178 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8269 (tttp) REVERT: D 188 ARG cc_start: 0.8128 (ttp-110) cc_final: 0.7655 (ttp-110) REVERT: D 190 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7446 (mm-30) REVERT: D 197 LYS cc_start: 0.8696 (tptm) cc_final: 0.8419 (tttm) REVERT: E 50 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7976 (mt-10) REVERT: E 63 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7651 (tt0) REVERT: E 74 GLU cc_start: 0.7690 (mp0) cc_final: 0.7116 (mp0) REVERT: E 148 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8536 (tttm) REVERT: E 194 ASP cc_start: 0.6645 (p0) cc_final: 0.6216 (p0) REVERT: F 76 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: F 79 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6945 (mmm160) REVERT: F 93 SER cc_start: 0.8015 (p) cc_final: 0.7733 (m) REVERT: F 152 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8611 (t) REVERT: F 173 PHE cc_start: 0.8460 (t80) cc_final: 0.8232 (t80) REVERT: F 384 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.7082 (t70) REVERT: F 391 TYR cc_start: 0.8176 (t80) cc_final: 0.7718 (t80) REVERT: F 398 SER cc_start: 0.8608 (m) cc_final: 0.8199 (t) REVERT: F 430 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8237 (mtt90) REVERT: F 553 LYS cc_start: 0.8544 (tttt) cc_final: 0.8337 (tttt) REVERT: F 567 LEU cc_start: 0.8805 (mt) cc_final: 0.8584 (mt) REVERT: F 764 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7652 (mtp) REVERT: F 842 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7827 (mtmm) REVERT: F 866 LEU cc_start: 0.8756 (mp) cc_final: 0.8401 (mt) REVERT: F 900 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6323 (mtp85) REVERT: F 1010 ASN cc_start: 0.7603 (t0) cc_final: 0.6763 (t0) REVERT: F 1014 ASP cc_start: 0.6904 (m-30) cc_final: 0.6237 (m-30) REVERT: F 1019 SER cc_start: 0.8585 (m) cc_final: 0.8119 (p) REVERT: F 1221 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8227 (t) REVERT: G 41 ASN cc_start: 0.8236 (t0) cc_final: 0.7947 (m-40) REVERT: G 49 ARG cc_start: 0.8515 (ttt-90) cc_final: 0.7779 (ttt-90) REVERT: G 56 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7698 (mtt90) REVERT: G 77 ARG cc_start: 0.8104 (mmm160) cc_final: 0.7822 (mmm-85) REVERT: G 90 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7712 (mp0) REVERT: G 119 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7534 (mppt) REVERT: G 144 GLN cc_start: 0.6790 (tp-100) cc_final: 0.6504 (tp-100) REVERT: G 200 ASP cc_start: 0.8182 (t0) cc_final: 0.7951 (t0) REVERT: G 206 ASP cc_start: 0.7950 (t0) cc_final: 0.7653 (t0) REVERT: G 208 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7628 (mm-30) REVERT: G 242 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7357 (mt-10) REVERT: G 302 ILE cc_start: 0.8073 (pp) cc_final: 0.7860 (pt) REVERT: G 306 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: G 318 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: G 385 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8086 (mp) REVERT: G 501 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7908 (mtt) REVERT: G 672 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: G 700 ASP cc_start: 0.7844 (t0) cc_final: 0.7367 (m-30) REVERT: G 788 HIS cc_start: 0.7701 (m170) cc_final: 0.7480 (m170) REVERT: G 792 LYS cc_start: 0.7740 (mttt) cc_final: 0.7128 (mttm) REVERT: G 1051 ILE cc_start: -0.0811 (OUTLIER) cc_final: -0.1087 (mt) REVERT: G 1146 GLU cc_start: 0.8374 (tt0) cc_final: 0.8093 (tt0) REVERT: G 1283 HIS cc_start: 0.7521 (t-90) cc_final: 0.7111 (t-90) REVERT: G 1356 SER cc_start: 0.8678 (m) cc_final: 0.8342 (p) REVERT: G 1396 VAL cc_start: 0.8671 (t) cc_final: 0.8332 (m) REVERT: G 1408 ASP cc_start: 0.7876 (m-30) cc_final: 0.7526 (p0) REVERT: G 1424 MET cc_start: 0.3781 (mmt) cc_final: 0.3575 (mmt) REVERT: H 1 MET cc_start: -0.1152 (mtt) cc_final: -0.1402 (mtt) outliers start: 155 outliers final: 86 residues processed: 881 average time/residue: 0.7934 time to fit residues: 839.5119 Evaluate side-chains 914 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 800 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 354 ARG Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 382 LYS Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 685 VAL Chi-restraints excluded: chain F residue 741 VAL Chi-restraints excluded: chain F residue 764 MET Chi-restraints excluded: chain F residue 797 ILE Chi-restraints excluded: chain F residue 862 GLU Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 882 LEU Chi-restraints excluded: chain F residue 900 ARG Chi-restraints excluded: chain F residue 920 MET Chi-restraints excluded: chain F residue 1007 ILE Chi-restraints excluded: chain F residue 1218 ILE Chi-restraints excluded: chain F residue 1221 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 306 GLU Chi-restraints excluded: chain G residue 318 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 420 LYS Chi-restraints excluded: chain G residue 447 HIS Chi-restraints excluded: chain G residue 501 MET Chi-restraints excluded: chain G residue 543 ILE Chi-restraints excluded: chain G residue 613 ASN Chi-restraints excluded: chain G residue 672 GLU Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 717 ILE Chi-restraints excluded: chain G residue 797 THR Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain G residue 903 GLN Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 1051 ILE Chi-restraints excluded: chain G residue 1163 ASP Chi-restraints excluded: chain G residue 1353 THR Chi-restraints excluded: chain G residue 1357 LEU Chi-restraints excluded: chain G residue 1414 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 376 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 252 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 430 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 395 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 ASN F1008 GLN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 HIS G 741 GLN G 773 ASN G 873 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.183161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141859 restraints weight = 55293.978| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.22 r_work: 0.3507 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 39103 Z= 0.136 Angle : 0.523 12.492 53599 Z= 0.281 Chirality : 0.043 0.240 6077 Planarity : 0.004 0.057 6189 Dihedral : 17.271 175.414 7233 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Rotamer: Outliers : 4.14 % Allowed : 23.83 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.13), residues: 4231 helix: 1.56 (0.13), residues: 1651 sheet: 0.45 (0.22), residues: 565 loop : 0.06 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 169 TYR 0.019 0.001 TYR B 254 PHE 0.022 0.001 PHE B 116 TRP 0.016 0.001 TRP B 342 HIS 0.005 0.001 HIS G 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (39096) covalent geometry : angle 0.51708 / 0.28 (53587) SS BOND : bond 0.00505 / 0.24 ( 3) SS BOND : angle 6.19429 / 2.60 ( 6) hydrogen bonds : bond 0.04038 / 2.68 ( 1748) hydrogen bonds : angle 4.37532 / 3.00 ( 4826) metal coordination : bond 0.00551 / 0.28 ( 4) metal coordination : angle 4.54051 / 2.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 808 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.7256 (t80) REVERT: A 40 ARG cc_start: 0.7280 (mtt180) cc_final: 0.6968 (mtt180) REVERT: A 90 ARG cc_start: 0.7339 (tpm170) cc_final: 0.7127 (tpp80) REVERT: A 127 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5693 (pt0) REVERT: A 154 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6788 (tm-30) REVERT: A 158 PHE cc_start: 0.7543 (m-80) cc_final: 0.7063 (m-80) REVERT: A 184 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7364 (mtm180) REVERT: A 226 GLU cc_start: 0.6480 (mt-10) cc_final: 0.6112 (mt-10) REVERT: A 236 VAL cc_start: 0.7852 (OUTLIER) cc_final: 0.7586 (m) REVERT: A 241 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7787 (mmtt) REVERT: A 266 THR cc_start: 0.7531 (OUTLIER) cc_final: 0.7036 (p) REVERT: A 349 THR cc_start: 0.8066 (t) cc_final: 0.7811 (m) REVERT: B 22 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6925 (t0) REVERT: B 40 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7541 (mtm-85) REVERT: B 58 PHE cc_start: 0.7235 (m-80) cc_final: 0.7015 (t80) REVERT: B 118 LYS cc_start: 0.8230 (mttt) cc_final: 0.7893 (mttp) REVERT: B 128 ARG cc_start: 0.7491 (ttt180) cc_final: 0.7009 (ttt180) REVERT: B 180 MET cc_start: 0.8188 (ttp) cc_final: 0.7923 (ttp) REVERT: B 222 GLU cc_start: 0.7603 (pp20) cc_final: 0.7176 (pp20) REVERT: B 226 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.5443 (mp0) REVERT: B 243 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.6076 (tmm-80) REVERT: B 322 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7354 (pp) REVERT: B 333 LYS cc_start: 0.7811 (mtpp) cc_final: 0.7534 (mtpp) REVERT: B 346 GLU cc_start: 0.7775 (mp0) cc_final: 0.6725 (mm-30) REVERT: B 350 LYS cc_start: 0.6866 (mtmt) cc_final: 0.6313 (mtmt) REVERT: B 353 TYR cc_start: 0.6865 (t80) cc_final: 0.6647 (t80) REVERT: C 29 LEU cc_start: 0.8387 (tp) cc_final: 0.8174 (tp) REVERT: C 91 LYS cc_start: 0.8208 (tptt) cc_final: 0.7982 (tptt) REVERT: C 147 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6477 (tm-30) REVERT: C 151 LYS cc_start: 0.8149 (ttpt) cc_final: 0.7779 (tmmt) REVERT: C 165 LYS cc_start: 0.6336 (mmtm) cc_final: 0.5962 (mmtm) REVERT: C 169 GLU cc_start: 0.7264 (tt0) cc_final: 0.6863 (tt0) REVERT: C 217 MET cc_start: 0.7368 (mtm) cc_final: 0.7079 (mmm) REVERT: C 250 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6895 (mtt) REVERT: D 11 LYS cc_start: 0.7571 (ptpt) cc_final: 0.7328 (ptpt) REVERT: D 17 SER cc_start: 0.8403 (t) cc_final: 0.8136 (m) REVERT: D 27 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7101 (ptm-80) REVERT: D 64 HIS cc_start: 0.7394 (p90) cc_final: 0.7162 (p-80) REVERT: D 153 VAL cc_start: 0.8788 (t) cc_final: 0.8416 (p) REVERT: D 178 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8165 (tttp) REVERT: D 188 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7533 (ttp-110) REVERT: D 190 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7151 (mm-30) REVERT: D 197 LYS cc_start: 0.8603 (tptm) cc_final: 0.8329 (tttm) REVERT: E 50 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7608 (mt-10) REVERT: E 74 GLU cc_start: 0.7437 (mp0) cc_final: 0.6886 (mp0) REVERT: F 54 MET cc_start: 0.7903 (mmm) cc_final: 0.7257 (mtm) REVERT: F 76 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7374 (m-30) REVERT: F 79 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.6770 (mmm160) REVERT: F 93 SER cc_start: 0.7796 (p) cc_final: 0.7521 (m) REVERT: F 152 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8526 (t) REVERT: F 173 PHE cc_start: 0.8312 (t80) cc_final: 0.8103 (t80) REVERT: F 384 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6829 (t70) REVERT: F 391 TYR cc_start: 0.7953 (t80) cc_final: 0.7488 (t80) REVERT: F 398 SER cc_start: 0.8517 (m) cc_final: 0.8103 (t) REVERT: F 430 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8080 (mtt90) REVERT: F 553 LYS cc_start: 0.8284 (tttt) cc_final: 0.8062 (tttt) REVERT: F 567 LEU cc_start: 0.8684 (mt) cc_final: 0.8477 (mt) REVERT: F 572 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: F 764 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7406 (mtp) REVERT: F 842 LYS cc_start: 0.8005 (mtpt) cc_final: 0.7697 (mtmm) REVERT: F 866 LEU cc_start: 0.8660 (mp) cc_final: 0.8306 (mt) REVERT: F 900 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6246 (mtp85) REVERT: F 1010 ASN cc_start: 0.7297 (t0) cc_final: 0.6460 (t0) REVERT: F 1014 ASP cc_start: 0.6644 (m-30) cc_final: 0.5961 (m-30) REVERT: F 1019 SER cc_start: 0.8499 (m) cc_final: 0.8027 (p) REVERT: F 1031 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7072 (tp) REVERT: F 1221 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8149 (t) REVERT: G 41 ASN cc_start: 0.8036 (t0) cc_final: 0.7768 (m-40) REVERT: G 49 ARG cc_start: 0.8399 (ttt-90) cc_final: 0.7551 (ttt-90) REVERT: G 56 ARG cc_start: 0.7935 (mtt90) cc_final: 0.7384 (mtt90) REVERT: G 77 ARG cc_start: 0.7876 (mmm160) cc_final: 0.7566 (mmm-85) REVERT: G 90 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7443 (mp0) REVERT: G 119 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7361 (mppt) REVERT: G 144 GLN cc_start: 0.6593 (tp-100) cc_final: 0.6329 (tp-100) REVERT: G 174 LEU cc_start: 0.7968 (tp) cc_final: 0.7758 (tm) REVERT: G 200 ASP cc_start: 0.7942 (t0) cc_final: 0.7698 (t0) REVERT: G 206 ASP cc_start: 0.7685 (t0) cc_final: 0.7401 (t0) REVERT: G 242 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6915 (mt-10) REVERT: G 306 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: G 318 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: G 385 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8003 (mp) REVERT: G 672 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: G 768 ASN cc_start: 0.7819 (m-40) cc_final: 0.7577 (m-40) REVERT: G 792 LYS cc_start: 0.7554 (mttt) cc_final: 0.6936 (mttm) REVERT: G 1051 ILE cc_start: -0.0801 (OUTLIER) cc_final: -0.1084 (mt) REVERT: G 1146 GLU cc_start: 0.8151 (tt0) cc_final: 0.7866 (tt0) REVERT: G 1283 HIS cc_start: 0.7155 (t-90) cc_final: 0.6789 (t-90) REVERT: G 1356 SER cc_start: 0.8596 (m) cc_final: 0.8240 (p) REVERT: G 1396 VAL cc_start: 0.8607 (t) cc_final: 0.8261 (m) REVERT: G 1408 ASP cc_start: 0.7650 (m-30) cc_final: 0.7394 (p0) REVERT: H 1 MET cc_start: -0.1181 (mtt) cc_final: -0.1389 (mtt) outliers start: 154 outliers final: 87 residues processed: 881 average time/residue: 0.7657 time to fit residues: 806.7656 Evaluate side-chains 910 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 796 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 354 ARG Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 382 LYS Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 456 LYS Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 572 GLU Chi-restraints excluded: chain F residue 685 VAL Chi-restraints excluded: chain F residue 740 LYS Chi-restraints excluded: chain F residue 741 VAL Chi-restraints excluded: chain F residue 764 MET Chi-restraints excluded: chain F residue 797 ILE Chi-restraints excluded: chain F residue 798 ASP Chi-restraints excluded: chain F residue 803 GLU Chi-restraints excluded: chain F residue 862 GLU Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 882 LEU Chi-restraints excluded: chain F residue 900 ARG Chi-restraints excluded: chain F residue 1007 ILE Chi-restraints excluded: chain F residue 1031 LEU Chi-restraints excluded: chain F residue 1218 ILE Chi-restraints excluded: chain F residue 1221 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 306 GLU Chi-restraints excluded: chain G residue 318 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 420 LYS Chi-restraints excluded: chain G residue 543 ILE Chi-restraints excluded: chain G residue 583 LEU Chi-restraints excluded: chain G residue 613 ASN Chi-restraints excluded: chain G residue 672 GLU Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 717 ILE Chi-restraints excluded: chain G residue 797 THR Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain G residue 903 GLN Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 1051 ILE Chi-restraints excluded: chain G residue 1163 ASP Chi-restraints excluded: chain G residue 1223 LEU Chi-restraints excluded: chain G residue 1353 THR Chi-restraints excluded: chain G residue 1357 LEU Chi-restraints excluded: chain G residue 1414 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 165 optimal weight: 50.0000 chunk 284 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 187 optimal weight: 0.0170 chunk 190 optimal weight: 0.9990 chunk 326 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 389 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN B 33 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 ASN F 56 ASN F 397 ASN F 422 GLN F1008 GLN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 HIS G 741 GLN G 773 ASN ** G1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.182584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141665 restraints weight = 55064.984| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.19 r_work: 0.3500 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 39103 Z= 0.172 Angle : 0.544 12.529 53599 Z= 0.291 Chirality : 0.044 0.236 6077 Planarity : 0.004 0.064 6189 Dihedral : 17.249 175.713 7227 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 3.90 % Allowed : 24.37 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.13), residues: 4231 helix: 1.49 (0.13), residues: 1656 sheet: 0.45 (0.22), residues: 565 loop : 0.05 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 169 TYR 0.020 0.001 TYR B 254 PHE 0.030 0.002 PHE B 116 TRP 0.029 0.001 TRP B 342 HIS 0.009 0.001 HIS G 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (39096) covalent geometry : angle 0.53758 / 0.29 (53587) SS BOND : bond 0.00474 / 0.23 ( 3) SS BOND : angle 6.28788 / 2.61 ( 6) hydrogen bonds : bond 0.04219 / 2.80 ( 1748) hydrogen bonds : angle 4.41353 / 3.03 ( 4826) metal coordination : bond 0.00780 / 0.39 ( 4) metal coordination : angle 4.59348 / 2.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 803 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7439 (t80) REVERT: A 40 ARG cc_start: 0.7522 (mtt180) cc_final: 0.7144 (mtt180) REVERT: A 53 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7854 (tm-30) REVERT: A 127 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.6053 (pt0) REVERT: A 154 GLU cc_start: 0.7441 (tm-30) cc_final: 0.6950 (tm-30) REVERT: A 226 GLU cc_start: 0.6635 (mt-10) cc_final: 0.6280 (mt-10) REVERT: A 236 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7655 (m) REVERT: A 241 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7890 (mmtt) REVERT: A 266 THR cc_start: 0.7633 (OUTLIER) cc_final: 0.7120 (p) REVERT: A 349 THR cc_start: 0.8252 (t) cc_final: 0.7995 (m) REVERT: B 26 GLU cc_start: 0.7109 (mp0) cc_final: 0.6861 (mp0) REVERT: B 58 PHE cc_start: 0.7517 (m-80) cc_final: 0.7264 (t80) REVERT: B 118 LYS cc_start: 0.8277 (mttt) cc_final: 0.7944 (mttp) REVERT: B 128 ARG cc_start: 0.7689 (ttt180) cc_final: 0.7215 (ttt180) REVERT: B 170 TYR cc_start: 0.7125 (t80) cc_final: 0.6795 (t80) REVERT: B 180 MET cc_start: 0.8254 (ttp) cc_final: 0.7999 (ttp) REVERT: B 222 GLU cc_start: 0.7750 (pp20) cc_final: 0.7307 (pp20) REVERT: B 226 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.5897 (mp0) REVERT: B 243 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6386 (tmm-80) REVERT: B 251 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7279 (tm-30) REVERT: B 322 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7558 (pp) REVERT: B 333 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7673 (mtpp) REVERT: B 346 GLU cc_start: 0.7940 (mp0) cc_final: 0.6590 (mm-30) REVERT: B 350 LYS cc_start: 0.6976 (mtmt) cc_final: 0.6403 (mtmt) REVERT: C 91 LYS cc_start: 0.8419 (tptt) cc_final: 0.8198 (tptt) REVERT: C 147 GLU cc_start: 0.7447 (tm-30) cc_final: 0.6973 (tm-30) REVERT: C 151 LYS cc_start: 0.8360 (ttpt) cc_final: 0.8074 (ttpt) REVERT: C 165 LYS cc_start: 0.6679 (mmtm) cc_final: 0.6221 (mmtm) REVERT: C 169 GLU cc_start: 0.7442 (tt0) cc_final: 0.7101 (tt0) REVERT: C 217 MET cc_start: 0.7460 (mtm) cc_final: 0.7183 (mmm) REVERT: C 250 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6921 (mtt) REVERT: D 11 LYS cc_start: 0.7783 (ptpt) cc_final: 0.7516 (ptpt) REVERT: D 17 SER cc_start: 0.8498 (t) cc_final: 0.8231 (m) REVERT: D 27 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7251 (ptm-80) REVERT: D 64 HIS cc_start: 0.7530 (p90) cc_final: 0.7204 (p-80) REVERT: D 153 VAL cc_start: 0.8896 (t) cc_final: 0.8529 (p) REVERT: D 178 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8292 (tttp) REVERT: D 188 ARG cc_start: 0.8094 (ttp-110) cc_final: 0.7613 (ttp-110) REVERT: D 190 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7353 (mm-30) REVERT: D 197 LYS cc_start: 0.8684 (tptm) cc_final: 0.8447 (tttm) REVERT: E 50 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7983 (mt-10) REVERT: E 74 GLU cc_start: 0.7674 (mp0) cc_final: 0.7095 (mp0) REVERT: E 148 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8492 (tttm) REVERT: E 194 ASP cc_start: 0.6673 (p0) cc_final: 0.6244 (p0) REVERT: F 76 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7655 (m-30) REVERT: F 79 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6971 (mmm160) REVERT: F 93 SER cc_start: 0.7994 (p) cc_final: 0.7740 (m) REVERT: F 152 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8636 (t) REVERT: F 384 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7083 (t70) REVERT: F 391 TYR cc_start: 0.8204 (t80) cc_final: 0.7735 (t80) REVERT: F 398 SER cc_start: 0.8584 (m) cc_final: 0.8178 (t) REVERT: F 430 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8226 (mtt90) REVERT: F 567 LEU cc_start: 0.8803 (mt) cc_final: 0.8564 (mt) REVERT: F 572 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: F 764 MET cc_start: 0.8011 (mmp) cc_final: 0.7631 (mtp) REVERT: F 789 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7912 (mt-10) REVERT: F 803 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6659 (mm-30) REVERT: F 842 LYS cc_start: 0.8120 (mtpt) cc_final: 0.7815 (mtmm) REVERT: F 866 LEU cc_start: 0.8759 (mp) cc_final: 0.8395 (mt) REVERT: F 900 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6330 (mtp85) REVERT: F 1010 ASN cc_start: 0.7489 (t0) cc_final: 0.6663 (t0) REVERT: F 1014 ASP cc_start: 0.6838 (m-30) cc_final: 0.6180 (m-30) REVERT: F 1019 SER cc_start: 0.8577 (m) cc_final: 0.8113 (p) REVERT: F 1221 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8241 (t) REVERT: G 41 ASN cc_start: 0.8239 (t0) cc_final: 0.7899 (m-40) REVERT: G 49 ARG cc_start: 0.8523 (ttt-90) cc_final: 0.7658 (ttt-90) REVERT: G 56 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7486 (mtt90) REVERT: G 77 ARG cc_start: 0.8125 (mmm160) cc_final: 0.7877 (mmm-85) REVERT: G 90 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7687 (mp0) REVERT: G 119 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7570 (mppt) REVERT: G 144 GLN cc_start: 0.6807 (tp-100) cc_final: 0.6514 (tp-100) REVERT: G 200 ASP cc_start: 0.8211 (t0) cc_final: 0.7972 (t0) REVERT: G 206 ASP cc_start: 0.7961 (t0) cc_final: 0.7647 (t0) REVERT: G 208 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7442 (mm-30) REVERT: G 242 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7341 (mt-10) REVERT: G 306 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: G 318 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: G 385 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8045 (mp) REVERT: G 672 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: G 768 ASN cc_start: 0.8038 (m-40) cc_final: 0.7791 (m-40) REVERT: G 792 LYS cc_start: 0.7745 (mttt) cc_final: 0.7138 (mttm) REVERT: G 1051 ILE cc_start: -0.0824 (OUTLIER) cc_final: -0.1094 (mt) REVERT: G 1146 GLU cc_start: 0.8329 (tt0) cc_final: 0.8045 (tt0) REVERT: G 1283 HIS cc_start: 0.7484 (t-90) cc_final: 0.7101 (t-90) REVERT: G 1356 SER cc_start: 0.8691 (m) cc_final: 0.8353 (p) REVERT: G 1396 VAL cc_start: 0.8679 (t) cc_final: 0.8340 (m) REVERT: G 1408 ASP cc_start: 0.7871 (m-30) cc_final: 0.7508 (p0) REVERT: G 1424 MET cc_start: 0.3786 (mmt) cc_final: 0.3562 (mmt) REVERT: H 1 MET cc_start: -0.1181 (mtt) cc_final: -0.1430 (mtt) outliers start: 145 outliers final: 88 residues processed: 877 average time/residue: 0.7884 time to fit residues: 828.0326 Evaluate side-chains 904 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 791 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 354 ARG Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 382 LYS Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 456 LYS Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 572 GLU Chi-restraints excluded: chain F residue 685 VAL Chi-restraints excluded: chain F residue 740 LYS Chi-restraints excluded: chain F residue 741 VAL Chi-restraints excluded: chain F residue 797 ILE Chi-restraints excluded: chain F residue 798 ASP Chi-restraints excluded: chain F residue 803 GLU Chi-restraints excluded: chain F residue 862 GLU Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 882 LEU Chi-restraints excluded: chain F residue 900 ARG Chi-restraints excluded: chain F residue 1007 ILE Chi-restraints excluded: chain F residue 1218 ILE Chi-restraints excluded: chain F residue 1221 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 306 GLU Chi-restraints excluded: chain G residue 318 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 420 LYS Chi-restraints excluded: chain G residue 447 HIS Chi-restraints excluded: chain G residue 543 ILE Chi-restraints excluded: chain G residue 613 ASN Chi-restraints excluded: chain G residue 643 MET Chi-restraints excluded: chain G residue 661 ILE Chi-restraints excluded: chain G residue 672 GLU Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 717 ILE Chi-restraints excluded: chain G residue 797 THR Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain G residue 903 GLN Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 1051 ILE Chi-restraints excluded: chain G residue 1163 ASP Chi-restraints excluded: chain G residue 1353 THR Chi-restraints excluded: chain G residue 1357 LEU Chi-restraints excluded: chain G residue 1414 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 18 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 321 optimal weight: 0.0970 chunk 222 optimal weight: 0.0030 chunk 83 optimal weight: 0.6980 chunk 315 optimal weight: 0.9980 chunk 274 optimal weight: 2.9990 chunk 436 optimal weight: 8.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN B 33 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 ASN F 397 ASN F 422 GLN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 HIS G 741 GLN G 773 ASN ** G1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.183975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.142935 restraints weight = 55474.342| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.16 r_work: 0.3521 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39103 Z= 0.121 Angle : 0.532 12.760 53599 Z= 0.285 Chirality : 0.043 0.239 6077 Planarity : 0.004 0.063 6189 Dihedral : 17.221 175.746 7220 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.19 % Rotamer: Outliers : 3.12 % Allowed : 25.31 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.13), residues: 4231 helix: 1.59 (0.13), residues: 1660 sheet: 0.47 (0.22), residues: 565 loop : 0.10 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 169 TYR 0.022 0.001 TYR B 296 PHE 0.033 0.001 PHE B 116 TRP 0.043 0.001 TRP B 342 HIS 0.011 0.001 HIS G 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (39096) covalent geometry : angle 0.52646 / 0.28 (53587) SS BOND : bond 0.00479 / 0.23 ( 3) SS BOND : angle 5.99593 / 2.52 ( 6) hydrogen bonds : bond 0.03886 / 2.57 ( 1748) hydrogen bonds : angle 4.33528 / 2.98 ( 4826) metal coordination : bond 0.00492 / 0.25 ( 4) metal coordination : angle 4.29412 / 2.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 792 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.7470 (mtt180) cc_final: 0.7136 (mtt180) REVERT: A 53 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7794 (tm-30) REVERT: A 127 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5959 (pt0) REVERT: A 154 GLU cc_start: 0.7460 (tm-30) cc_final: 0.6974 (tm-30) REVERT: A 226 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6289 (mt-10) REVERT: A 236 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7652 (m) REVERT: A 241 LYS cc_start: 0.8264 (mmtt) cc_final: 0.7912 (mmtt) REVERT: A 266 THR cc_start: 0.7544 (OUTLIER) cc_final: 0.7073 (p) REVERT: A 349 THR cc_start: 0.8200 (t) cc_final: 0.7942 (m) REVERT: B 26 GLU cc_start: 0.7097 (mp0) cc_final: 0.6867 (mp0) REVERT: B 58 PHE cc_start: 0.7432 (m-80) cc_final: 0.7186 (t80) REVERT: B 118 LYS cc_start: 0.8237 (mttt) cc_final: 0.7892 (mttp) REVERT: B 128 ARG cc_start: 0.7637 (ttt180) cc_final: 0.7154 (ttt180) REVERT: B 170 TYR cc_start: 0.7154 (t80) cc_final: 0.6839 (t80) REVERT: B 180 MET cc_start: 0.8267 (ttp) cc_final: 0.8013 (ttp) REVERT: B 222 GLU cc_start: 0.7738 (pp20) cc_final: 0.7298 (pp20) REVERT: B 226 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5769 (mp0) REVERT: B 243 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.6302 (tmm-80) REVERT: B 250 GLU cc_start: 0.7080 (pm20) cc_final: 0.6854 (pm20) REVERT: B 322 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7425 (pp) REVERT: B 333 LYS cc_start: 0.7952 (mtpp) cc_final: 0.7648 (mtpp) REVERT: B 346 GLU cc_start: 0.7874 (mp0) cc_final: 0.6881 (mm-30) REVERT: B 348 MET cc_start: 0.6427 (tpp) cc_final: 0.5882 (tpp) REVERT: B 350 LYS cc_start: 0.6923 (mtmt) cc_final: 0.6317 (mtmt) REVERT: B 354 LYS cc_start: 0.7759 (mttm) cc_final: 0.7467 (mtpt) REVERT: C 91 LYS cc_start: 0.8411 (tptt) cc_final: 0.8178 (tptt) REVERT: C 147 GLU cc_start: 0.7453 (tm-30) cc_final: 0.6997 (tm-30) REVERT: C 165 LYS cc_start: 0.6563 (mmtm) cc_final: 0.6243 (mmtm) REVERT: C 169 GLU cc_start: 0.7378 (tt0) cc_final: 0.7038 (tt0) REVERT: C 217 MET cc_start: 0.7459 (mtm) cc_final: 0.7181 (mmm) REVERT: C 250 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6917 (mtt) REVERT: D 11 LYS cc_start: 0.7757 (ptpt) cc_final: 0.7502 (ptpt) REVERT: D 17 SER cc_start: 0.8515 (t) cc_final: 0.8237 (m) REVERT: D 27 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7233 (ptm-80) REVERT: D 64 HIS cc_start: 0.7510 (p90) cc_final: 0.7181 (p-80) REVERT: D 153 VAL cc_start: 0.8884 (t) cc_final: 0.8509 (p) REVERT: D 178 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8316 (tttp) REVERT: D 188 ARG cc_start: 0.8100 (ttp-110) cc_final: 0.7614 (ttp-110) REVERT: D 190 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7390 (mm-30) REVERT: D 197 LYS cc_start: 0.8673 (tptm) cc_final: 0.8424 (tttm) REVERT: E 50 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7946 (mt-10) REVERT: E 74 GLU cc_start: 0.7668 (mp0) cc_final: 0.7090 (mp0) REVERT: E 148 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8495 (tttm) REVERT: F 29 LYS cc_start: 0.8380 (ttmm) cc_final: 0.8119 (mtpp) REVERT: F 76 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: F 79 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6926 (mmm160) REVERT: F 93 SER cc_start: 0.7981 (p) cc_final: 0.7738 (m) REVERT: F 152 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8619 (t) REVERT: F 384 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7097 (t0) REVERT: F 391 TYR cc_start: 0.8185 (t80) cc_final: 0.7754 (t80) REVERT: F 398 SER cc_start: 0.8584 (m) cc_final: 0.8175 (t) REVERT: F 430 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8170 (mtt90) REVERT: F 567 LEU cc_start: 0.8789 (mt) cc_final: 0.8589 (mt) REVERT: F 764 MET cc_start: 0.7963 (mmp) cc_final: 0.7621 (mtp) REVERT: F 789 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7881 (mt-10) REVERT: F 842 LYS cc_start: 0.8132 (mtpt) cc_final: 0.7814 (mtmm) REVERT: F 866 LEU cc_start: 0.8728 (mp) cc_final: 0.8370 (mt) REVERT: F 900 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6318 (mtp85) REVERT: F 1010 ASN cc_start: 0.7430 (t0) cc_final: 0.6635 (t0) REVERT: F 1014 ASP cc_start: 0.6841 (m-30) cc_final: 0.6188 (m-30) REVERT: F 1019 SER cc_start: 0.8562 (m) cc_final: 0.8105 (p) REVERT: F 1221 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8203 (t) REVERT: G 41 ASN cc_start: 0.8222 (t0) cc_final: 0.7926 (m-40) REVERT: G 49 ARG cc_start: 0.8525 (ttt-90) cc_final: 0.7699 (ttt-90) REVERT: G 56 ARG cc_start: 0.8134 (mtt90) cc_final: 0.7524 (mtt90) REVERT: G 77 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7801 (mmm-85) REVERT: G 90 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7637 (mp0) REVERT: G 144 GLN cc_start: 0.6764 (tp-100) cc_final: 0.6494 (tp-100) REVERT: G 174 LEU cc_start: 0.8007 (tp) cc_final: 0.7779 (tm) REVERT: G 200 ASP cc_start: 0.8191 (t0) cc_final: 0.7908 (t0) REVERT: G 206 ASP cc_start: 0.7956 (t0) cc_final: 0.7626 (t0) REVERT: G 208 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7389 (mm-30) REVERT: G 242 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7316 (mt-10) REVERT: G 306 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: G 318 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: G 553 GLU cc_start: 0.8089 (tt0) cc_final: 0.7862 (tt0) REVERT: G 672 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: G 768 ASN cc_start: 0.8036 (m-40) cc_final: 0.7786 (m-40) REVERT: G 792 LYS cc_start: 0.7723 (mttt) cc_final: 0.7103 (mttm) REVERT: G 1051 ILE cc_start: -0.0822 (OUTLIER) cc_final: -0.1097 (mt) REVERT: G 1146 GLU cc_start: 0.8308 (tt0) cc_final: 0.8034 (tt0) REVERT: G 1283 HIS cc_start: 0.7471 (t-90) cc_final: 0.7113 (t-90) REVERT: G 1356 SER cc_start: 0.8706 (m) cc_final: 0.8368 (p) REVERT: G 1396 VAL cc_start: 0.8672 (t) cc_final: 0.8314 (m) REVERT: G 1408 ASP cc_start: 0.7864 (m-30) cc_final: 0.7506 (p0) REVERT: G 1424 MET cc_start: 0.3866 (mmt) cc_final: 0.3585 (mmt) REVERT: H 1 MET cc_start: -0.1176 (mtt) cc_final: -0.1423 (mtt) outliers start: 116 outliers final: 73 residues processed: 850 average time/residue: 0.7929 time to fit residues: 804.6137 Evaluate side-chains 881 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 788 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 354 ARG Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 382 LYS Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 456 LYS Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 558 LYS Chi-restraints excluded: chain F residue 685 VAL Chi-restraints excluded: chain F residue 741 VAL Chi-restraints excluded: chain F residue 797 ILE Chi-restraints excluded: chain F residue 900 ARG Chi-restraints excluded: chain F residue 1218 ILE Chi-restraints excluded: chain F residue 1221 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 306 GLU Chi-restraints excluded: chain G residue 318 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 420 LYS Chi-restraints excluded: chain G residue 543 ILE Chi-restraints excluded: chain G residue 613 ASN Chi-restraints excluded: chain G residue 672 GLU Chi-restraints excluded: chain G residue 717 ILE Chi-restraints excluded: chain G residue 797 THR Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain G residue 903 GLN Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 1051 ILE Chi-restraints excluded: chain G residue 1163 ASP Chi-restraints excluded: chain G residue 1223 LEU Chi-restraints excluded: chain G residue 1357 LEU Chi-restraints excluded: chain G residue 1414 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 92 optimal weight: 20.0000 chunk 406 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 384 optimal weight: 40.0000 chunk 247 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 418 optimal weight: 4.9990 chunk 278 optimal weight: 0.9990 chunk 274 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN B 33 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN F 10 ASN F 422 GLN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 741 GLN G 773 ASN G 857 HIS ** G1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.182465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.141589 restraints weight = 54954.877| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.20 r_work: 0.3496 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 39103 Z= 0.209 Angle : 0.577 12.744 53599 Z= 0.307 Chirality : 0.045 0.258 6077 Planarity : 0.004 0.071 6189 Dihedral : 17.195 175.901 7218 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 3.20 % Allowed : 25.47 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.13), residues: 4231 helix: 1.46 (0.13), residues: 1656 sheet: 0.40 (0.22), residues: 576 loop : 0.06 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 255 TYR 0.024 0.002 TYR B 254 PHE 0.027 0.002 PHE B 39 TRP 0.068 0.002 TRP B 342 HIS 0.014 0.001 HIS G 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (39096) covalent geometry : angle 0.57091 / 0.30 (53587) SS BOND : bond 0.00488 / 0.24 ( 3) SS BOND : angle 6.32678 / 2.60 ( 6) hydrogen bonds : bond 0.04406 / 2.97 ( 1748) hydrogen bonds : angle 4.42557 / 3.04 ( 4826) metal coordination : bond 0.00982 / 0.49 ( 4) metal coordination : angle 4.83099 / 2.37 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8462 Ramachandran restraints generated. 4231 Oldfield, 0 Emsley, 4231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 795 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8259 (mtmt) REVERT: A 28 MET cc_start: 0.7733 (tpp) cc_final: 0.7374 (tpp) REVERT: A 40 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7067 (mtt180) REVERT: A 127 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6070 (pt0) REVERT: A 154 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7000 (tm-30) REVERT: A 226 GLU cc_start: 0.6630 (mt-10) cc_final: 0.6292 (mt-10) REVERT: A 236 VAL cc_start: 0.7942 (OUTLIER) cc_final: 0.7652 (m) REVERT: A 241 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7919 (mmtt) REVERT: A 266 THR cc_start: 0.7625 (OUTLIER) cc_final: 0.7115 (p) REVERT: A 349 THR cc_start: 0.8237 (t) cc_final: 0.7985 (m) REVERT: B 26 GLU cc_start: 0.7049 (mp0) cc_final: 0.6838 (mp0) REVERT: B 58 PHE cc_start: 0.7447 (m-80) cc_final: 0.7203 (t80) REVERT: B 118 LYS cc_start: 0.8289 (mttt) cc_final: 0.7960 (mttp) REVERT: B 128 ARG cc_start: 0.7690 (ttt180) cc_final: 0.7215 (ttt180) REVERT: B 170 TYR cc_start: 0.7217 (t80) cc_final: 0.6856 (t80) REVERT: B 180 MET cc_start: 0.8250 (ttp) cc_final: 0.7987 (ttp) REVERT: B 222 GLU cc_start: 0.7741 (pp20) cc_final: 0.7292 (pp20) REVERT: B 226 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5842 (mp0) REVERT: B 243 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6339 (tmm-80) REVERT: B 250 GLU cc_start: 0.7129 (pm20) cc_final: 0.6897 (pm20) REVERT: B 322 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7349 (pp) REVERT: B 333 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7691 (mtpp) REVERT: B 346 GLU cc_start: 0.7943 (mp0) cc_final: 0.7308 (mp0) REVERT: B 348 MET cc_start: 0.6485 (tpp) cc_final: 0.5949 (tpp) REVERT: B 350 LYS cc_start: 0.6966 (mtmt) cc_final: 0.6405 (mtmt) REVERT: C 29 LEU cc_start: 0.8492 (tp) cc_final: 0.8251 (tp) REVERT: C 91 LYS cc_start: 0.8423 (tptt) cc_final: 0.8202 (tptt) REVERT: C 147 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6947 (tm-30) REVERT: C 151 LYS cc_start: 0.8262 (ttpt) cc_final: 0.8040 (tmmt) REVERT: C 165 LYS cc_start: 0.6615 (mmtm) cc_final: 0.6277 (mmtm) REVERT: C 169 GLU cc_start: 0.7391 (tt0) cc_final: 0.7048 (tt0) REVERT: C 187 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7451 (tppp) REVERT: C 217 MET cc_start: 0.7477 (mtm) cc_final: 0.7195 (mmm) REVERT: C 250 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6926 (mtt) REVERT: D 11 LYS cc_start: 0.7810 (ptpt) cc_final: 0.7550 (ptpt) REVERT: D 17 SER cc_start: 0.8503 (t) cc_final: 0.8242 (m) REVERT: D 27 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7269 (ptm-80) REVERT: D 64 HIS cc_start: 0.7573 (p90) cc_final: 0.7224 (p-80) REVERT: D 178 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8333 (tttp) REVERT: D 188 ARG cc_start: 0.8099 (ttp-110) cc_final: 0.7613 (ttp-110) REVERT: D 190 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7386 (mm-30) REVERT: D 197 LYS cc_start: 0.8697 (tptm) cc_final: 0.8470 (tttm) REVERT: E 50 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7971 (mt-10) REVERT: E 74 GLU cc_start: 0.7686 (mp0) cc_final: 0.7105 (mp0) REVERT: E 148 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8482 (tttm) REVERT: E 194 ASP cc_start: 0.6646 (p0) cc_final: 0.6227 (p0) REVERT: F 79 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.6958 (mmm160) REVERT: F 93 SER cc_start: 0.7955 (p) cc_final: 0.7727 (m) REVERT: F 152 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8624 (t) REVERT: F 391 TYR cc_start: 0.8207 (t80) cc_final: 0.7768 (t80) REVERT: F 398 SER cc_start: 0.8617 (m) cc_final: 0.8224 (t) REVERT: F 430 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8188 (mtt90) REVERT: F 764 MET cc_start: 0.7993 (mmp) cc_final: 0.7651 (mtp) REVERT: F 789 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7928 (mt-10) REVERT: F 842 LYS cc_start: 0.8119 (mtpt) cc_final: 0.7818 (mtmm) REVERT: F 866 LEU cc_start: 0.8769 (mp) cc_final: 0.8415 (mt) REVERT: F 900 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6339 (mtp85) REVERT: F 1010 ASN cc_start: 0.7498 (t0) cc_final: 0.6694 (t0) REVERT: F 1014 ASP cc_start: 0.6872 (m-30) cc_final: 0.6246 (m-30) REVERT: F 1221 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8244 (t) REVERT: G 41 ASN cc_start: 0.8229 (t0) cc_final: 0.7916 (m-40) REVERT: G 49 ARG cc_start: 0.8528 (ttt-90) cc_final: 0.7689 (ttt-90) REVERT: G 56 ARG cc_start: 0.8184 (mtt90) cc_final: 0.7578 (mtt90) REVERT: G 77 ARG cc_start: 0.8128 (mmm160) cc_final: 0.7824 (mmm-85) REVERT: G 90 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7698 (mp0) REVERT: G 119 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7830 (mptp) REVERT: G 144 GLN cc_start: 0.6803 (tp-100) cc_final: 0.6455 (tp-100) REVERT: G 200 ASP cc_start: 0.8201 (t0) cc_final: 0.7960 (t0) REVERT: G 206 ASP cc_start: 0.7956 (t0) cc_final: 0.7632 (t0) REVERT: G 208 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7395 (mm-30) REVERT: G 306 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: G 318 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: G 385 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8109 (mp) REVERT: G 672 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: G 768 ASN cc_start: 0.8059 (m-40) cc_final: 0.7817 (m-40) REVERT: G 792 LYS cc_start: 0.7757 (mttt) cc_final: 0.7161 (mttm) REVERT: G 936 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7640 (tm-30) REVERT: G 1051 ILE cc_start: -0.0782 (OUTLIER) cc_final: -0.1052 (mt) REVERT: G 1146 GLU cc_start: 0.8287 (tt0) cc_final: 0.8008 (tt0) REVERT: G 1283 HIS cc_start: 0.7465 (t-90) cc_final: 0.7056 (t-90) REVERT: G 1356 SER cc_start: 0.8691 (m) cc_final: 0.8357 (p) REVERT: G 1396 VAL cc_start: 0.8679 (t) cc_final: 0.8342 (m) REVERT: G 1408 ASP cc_start: 0.7876 (m-30) cc_final: 0.7506 (p0) REVERT: G 1424 MET cc_start: 0.3859 (mmt) cc_final: 0.3597 (mmt) REVERT: H 1 MET cc_start: -0.1177 (mtt) cc_final: -0.1422 (mtt) outliers start: 119 outliers final: 76 residues processed: 855 average time/residue: 0.8005 time to fit residues: 816.8648 Evaluate side-chains 884 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 787 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 149 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 354 ARG Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 381 THR Chi-restraints excluded: chain F residue 382 LYS Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 430 ARG Chi-restraints excluded: chain F residue 456 LYS Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 556 ASP Chi-restraints excluded: chain F residue 685 VAL Chi-restraints excluded: chain F residue 741 VAL Chi-restraints excluded: chain F residue 797 ILE Chi-restraints excluded: chain F residue 803 GLU Chi-restraints excluded: chain F residue 900 ARG Chi-restraints excluded: chain F residue 1221 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 306 GLU Chi-restraints excluded: chain G residue 318 GLU Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 385 LEU Chi-restraints excluded: chain G residue 389 MET Chi-restraints excluded: chain G residue 420 LYS Chi-restraints excluded: chain G residue 543 ILE Chi-restraints excluded: chain G residue 613 ASN Chi-restraints excluded: chain G residue 672 GLU Chi-restraints excluded: chain G residue 690 THR Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 717 ILE Chi-restraints excluded: chain G residue 797 THR Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain G residue 903 GLN Chi-restraints excluded: chain G residue 909 CYS Chi-restraints excluded: chain G residue 1051 ILE Chi-restraints excluded: chain G residue 1163 ASP Chi-restraints excluded: chain G residue 1357 LEU Chi-restraints excluded: chain G residue 1414 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 81 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 339 optimal weight: 3.9990 chunk 285 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 312 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 404 optimal weight: 0.9980 chunk 172 optimal weight: 8.9990 chunk 216 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN B 33 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 ASN F 422 GLN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 HIS G 741 GLN G 773 ASN G 857 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.182671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.141253 restraints weight = 55180.812| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.23 r_work: 0.3506 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 39103 Z= 0.185 Angle : 0.579 16.857 53599 Z= 0.307 Chirality : 0.045 0.258 6077 Planarity : 0.004 0.069 6189 Dihedral : 17.199 175.980 7218 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.95 % Rotamer: Outliers : 3.12 % Allowed : 25.74 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.13), residues: 4231 helix: 1.41 (0.13), residues: 1656 sheet: 0.42 (0.22), residues: 571 loop : 0.04 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 169 TYR 0.020 0.001 TYR F 73 PHE 0.031 0.002 PHE B 116 TRP 0.079 0.002 TRP B 342 HIS 0.014 0.001 HIS G 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (39096) covalent geometry : angle 0.57162 / 0.30 (53587) SS BOND : bond 0.00467 / 0.23 ( 3) SS BOND : angle 6.25241 / 2.60 ( 6) hydrogen bonds : bond 0.04343 / 2.92 ( 1748) hydrogen bonds : angle 4.42374 / 3.03 ( 4826) metal coordination : bond 0.02050 / 1.02 ( 4) metal coordination : angle 5.77713 / 2.69 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20340.49 seconds wall clock time: 345 minutes 19.90 seconds (20719.90 seconds total)