Starting phenix.real_space_refine on Sun Feb 8 01:05:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n9q_49176/02_2026/9n9q_49176.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n9q_49176/02_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_49176/02_2026/9n9q_49176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n9q_49176/02_2026/9n9q_49176.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n9q_49176/02_2026/9n9q_49176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n9q_49176/02_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 7.77, per 1000 atoms: 0.20 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: 2.91 Conformation dependent library (CDL) restraints added in 1.5 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: 5.29 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: 12.81 Time building geometry restraints manager: 3.88 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=" CG1 ILE C 20 " pdb=" CD1 ILE C 20 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.96e+00 bond pdb=" CG1 ILE A 45 " pdb=" CD1 ILE A 45 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.40e+00 bond pdb=" C TYR B 233 " pdb=" N PRO B 234 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.14e+00 bond pdb=" C3' DG b -34 " pdb=" O3' DG b -34 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" CD GLU B 26 " pdb=" OE1 GLU B 26 " ideal model delta sigma weight residual 1.249 1.224 0.025 1.90e-02 2.77e+03 1.77e+00 ... (remaining 39091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 53242 2.66 - 5.31: 309 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=" 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=" N ILE B 331 " pdb=" CA ILE B 331 " pdb=" C ILE B 331 " ideal model delta sigma weight residual 111.81 108.15 3.66 8.60e-01 1.35e+00 1.81e+01 angle pdb=" N ILE A 79 " pdb=" CA ILE A 79 " pdb=" C ILE A 79 " ideal model delta sigma weight residual 112.96 108.83 4.13 1.00e+00 1.00e+00 1.70e+01 angle pdb=" CA GLU B 250 " pdb=" CB GLU B 250 " pdb=" CG GLU B 250 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+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: 4585 0.043 - 0.087: 1084 0.087 - 0.130: 387 0.130 - 0.174: 16 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: 3.780 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: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 45.770 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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= 0.139 Angle : 0.564 20.870 53599 Z= 0.303 Chirality : 0.042 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 covalent geometry : bond 0.00310 (39096) covalent geometry : angle 0.54943 (53587) SS BOND : bond 0.00573 ( 3) SS BOND : angle 9.91799 ( 6) hydrogen bonds : bond 0.12457 ( 1748) hydrogen bonds : angle 5.97645 ( 4826) metal coordination : bond 0.01042 ( 4) metal coordination : angle 6.84308 ( 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 : 1.355 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: 0.7808 time to fit residues: 792.9857 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 : 1.273 ------------------------------------------------------------------------------- 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: 3.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 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: 4.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN F 10 ASN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 482 GLN G 773 ASN G 857 HIS ** G1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.182304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141761 restraints weight = 55597.521| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.19 r_work: 0.3466 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 39103 Z= 0.243 Angle : 0.565 13.081 53599 Z= 0.301 Chirality : 0.044 0.204 6077 Planarity : 0.005 0.085 6189 Dihedral : 17.569 173.751 7386 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.17 % Favored : 96.76 % Rotamer: Outliers : 4.16 % Allowed : 22.11 % Favored : 73.72 % 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: 0.69 (0.13), residues: 4231 helix: 1.18 (0.13), residues: 1664 sheet: 0.38 (0.22), residues: 564 loop : -0.03 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 56 TYR 0.018 0.002 TYR G 71 PHE 0.021 0.002 PHE G1362 TRP 0.010 0.001 TRP A 342 HIS 0.008 0.001 HIS G 788 Details of bonding type rmsd covalent geometry : bond 0.00566 (39096) covalent geometry : angle 0.55653 (53587) SS BOND : bond 0.00780 ( 3) SS BOND : angle 7.35605 ( 6) hydrogen bonds : bond 0.04948 ( 1748) hydrogen bonds : angle 4.85457 ( 4826) metal coordination : bond 0.01417 ( 4) metal coordination : angle 5.31998 ( 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 987 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 832 time to evaluate : 1.506 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: symmetry clash REVERT: A 52 GLN cc_start: 0.8917 (pm20) cc_final: 0.8702 (pm20) REVERT: A 90 ARG cc_start: 0.7460 (tpp-160) cc_final: 0.7252 (tpp80) REVERT: A 100 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.5745 (pp-130) REVERT: A 127 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5884 (pt0) REVERT: A 154 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6772 (tm-30) REVERT: A 226 GLU cc_start: 0.6363 (mt-10) cc_final: 0.6023 (mt-10) REVERT: A 236 VAL cc_start: 0.7845 (OUTLIER) cc_final: 0.7578 (m) REVERT: A 241 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7741 (mmtt) REVERT: A 266 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7149 (p) REVERT: A 349 THR cc_start: 0.8162 (t) cc_final: 0.7886 (m) REVERT: B 118 LYS cc_start: 0.8300 (mttt) cc_final: 0.7929 (mttt) REVERT: B 128 ARG cc_start: 0.7623 (ttt180) cc_final: 0.7131 (ttt180) REVERT: B 156 LYS cc_start: 0.7164 (tppp) cc_final: 0.6941 (tppp) REVERT: B 180 MET cc_start: 0.8126 (ttp) cc_final: 0.7855 (ttp) REVERT: B 222 GLU cc_start: 0.7577 (pp20) cc_final: 0.7154 (pp20) REVERT: B 243 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.6034 (tmm-80) REVERT: B 322 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7547 (pp) REVERT: B 333 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7548 (mtpp) REVERT: B 346 GLU cc_start: 0.7889 (mp0) cc_final: 0.7436 (mp0) REVERT: B 348 MET cc_start: 0.6212 (tpp) cc_final: 0.5794 (tpp) REVERT: B 350 LYS cc_start: 0.7090 (mtmt) cc_final: 0.6527 (mtmt) REVERT: B 361 GLU cc_start: 0.7331 (tp30) cc_final: 0.7053 (tp30) REVERT: C 91 LYS cc_start: 0.8227 (tptt) cc_final: 0.8018 (tptt) REVERT: C 147 GLU cc_start: 0.6914 (tm-30) cc_final: 0.6459 (tm-30) REVERT: C 165 LYS cc_start: 0.6410 (OUTLIER) cc_final: 0.6045 (mmtm) REVERT: C 169 GLU cc_start: 0.7231 (tt0) cc_final: 0.6859 (tt0) REVERT: C 182 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7949 (mtpm) REVERT: C 187 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7509 (tppp) REVERT: C 217 MET cc_start: 0.7376 (mtm) cc_final: 0.7080 (mmm) REVERT: C 249 LEU cc_start: 0.5380 (OUTLIER) cc_final: 0.5172 (pt) REVERT: C 250 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6885 (mtt) REVERT: D 11 LYS cc_start: 0.7595 (ptpt) cc_final: 0.7297 (ptpt) REVERT: D 17 SER cc_start: 0.8387 (t) cc_final: 0.8151 (m) REVERT: D 27 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7171 (ptm-80) REVERT: D 148 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8358 (ttmm) REVERT: D 153 VAL cc_start: 0.8779 (t) cc_final: 0.8447 (p) REVERT: D 178 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8254 (tttp) REVERT: D 190 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7324 (mm-30) REVERT: D 197 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8363 (tttm) REVERT: E 50 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7658 (mt-10) REVERT: E 74 GLU cc_start: 0.7487 (mp0) cc_final: 0.6915 (mp0) REVERT: E 194 ASP cc_start: 0.6452 (p0) cc_final: 0.6008 (p0) REVERT: E 196 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7016 (mt-10) REVERT: F 54 MET cc_start: 0.8011 (mmm) cc_final: 0.7209 (mtm) REVERT: F 93 SER cc_start: 0.7803 (OUTLIER) cc_final: 0.7529 (m) REVERT: F 152 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8521 (t) REVERT: F 173 PHE cc_start: 0.8322 (t80) cc_final: 0.8093 (t80) REVERT: F 384 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6965 (t70) REVERT: F 391 TYR cc_start: 0.7997 (t80) cc_final: 0.7523 (t80) REVERT: F 398 SER cc_start: 0.8604 (m) cc_final: 0.8106 (p) REVERT: F 430 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8044 (mtt90) REVERT: F 553 LYS cc_start: 0.8288 (tttt) cc_final: 0.8069 (tttt) REVERT: F 567 LEU cc_start: 0.8716 (mt) cc_final: 0.8452 (mt) REVERT: F 741 VAL cc_start: 0.8026 (t) cc_final: 0.7779 (m) REVERT: F 764 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7470 (mtp) REVERT: F 842 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7728 (mtmm) REVERT: F 866 LEU cc_start: 0.8723 (mp) cc_final: 0.8403 (mt) REVERT: F 900 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6197 (mtp85) REVERT: F 928 GLN cc_start: 0.7794 (tp-100) cc_final: 0.7568 (tp-100) REVERT: F 1010 ASN cc_start: 0.7492 (t0) cc_final: 0.6839 (t160) REVERT: F 1014 ASP cc_start: 0.6718 (m-30) cc_final: 0.6124 (m-30) REVERT: F 1019 SER cc_start: 0.8544 (m) cc_final: 0.8086 (p) REVERT: G 114 ARG cc_start: 0.8145 (tpp-160) cc_final: 0.7797 (mmt90) REVERT: G 144 GLN cc_start: 0.6648 (tp-100) cc_final: 0.6408 (tp-100) REVERT: G 206 ASP cc_start: 0.7733 (t0) cc_final: 0.7431 (t0) REVERT: G 208 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7520 (mt-10) REVERT: G 209 GLN cc_start: 0.7791 (mp10) cc_final: 0.7398 (mp-120) REVERT: G 210 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8201 (tt) REVERT: G 224 LYS cc_start: 0.7279 (mptt) cc_final: 0.6961 (mppt) REVERT: G 242 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6960 (mt-10) REVERT: G 306 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: G 318 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: G 377 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7562 (mt-10) REVERT: G 385 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8080 (mp) REVERT: G 672 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: G 700 ASP cc_start: 0.7589 (t0) cc_final: 0.7192 (m-30) REVERT: G 768 ASN cc_start: 0.7844 (m-40) cc_final: 0.7598 (m-40) REVERT: G 792 LYS cc_start: 0.7589 (mttt) cc_final: 0.7042 (mttm) REVERT: G 1146 GLU cc_start: 0.8178 (tt0) cc_final: 0.7887 (tt0) REVERT: G 1283 HIS cc_start: 0.7271 (t-90) cc_final: 0.6867 (t-90) REVERT: G 1356 SER cc_start: 0.8584 (m) cc_final: 0.8241 (p) REVERT: G 1358 GLN cc_start: 0.8097 (mt0) cc_final: 0.7757 (mt0) REVERT: G 1396 VAL cc_start: 0.8630 (t) cc_final: 0.8282 (m) REVERT: G 1424 MET cc_start: 0.3786 (mmt) cc_final: 0.3516 (mmt) REVERT: H 1 MET cc_start: -0.1135 (mtt) cc_final: -0.1364 (mtt) outliers start: 155 outliers final: 66 residues processed: 904 average time/residue: 0.7857 time to fit residues: 847.0411 Evaluate side-chains 900 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 808 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 29 ASP 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 C residue 61 GLU Chi-restraints excluded: chain C residue 76 ARG 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 187 LYS Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 249 LEU 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 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 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 167 SER Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 197 LYS 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 889 ARG 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 190 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 432 VAL Chi-restraints excluded: chain G residue 556 GLU Chi-restraints excluded: chain G residue 613 ASN 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 822 THR 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 1210 MET Chi-restraints excluded: chain G residue 1357 LEU Chi-restraints excluded: chain G residue 1414 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 418 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 332 optimal weight: 0.9980 chunk 316 optimal weight: 0.8980 chunk 363 optimal weight: 7.9990 chunk 391 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 302 optimal weight: 0.6980 chunk 421 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN F 10 ASN F1008 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.182821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141867 restraints weight = 55545.408| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.28 r_work: 0.3491 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 39103 Z= 0.166 Angle : 0.520 12.777 53599 Z= 0.278 Chirality : 0.042 0.200 6077 Planarity : 0.004 0.073 6189 Dihedral : 17.241 173.653 7260 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.07 % Rotamer: Outliers : 4.49 % Allowed : 22.17 % 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: 0.83 (0.13), residues: 4231 helix: 1.38 (0.13), residues: 1653 sheet: 0.40 (0.22), residues: 562 loop : -0.01 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 255 TYR 0.016 0.001 TYR A 163 PHE 0.021 0.001 PHE A 158 TRP 0.009 0.001 TRP B 342 HIS 0.009 0.001 HIS G 788 Details of bonding type rmsd covalent geometry : bond 0.00383 (39096) covalent geometry : angle 0.51320 (53587) SS BOND : bond 0.00507 ( 3) SS BOND : angle 6.66291 ( 6) hydrogen bonds : bond 0.04276 ( 1748) hydrogen bonds : angle 4.58333 ( 4826) metal coordination : bond 0.00827 ( 4) metal coordination : angle 4.51437 ( 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 979 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 812 time to evaluate : 1.449 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 52 GLN cc_start: 0.8839 (pm20) cc_final: 0.8625 (pm20) REVERT: A 53 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7538 (tm-30) REVERT: A 56 LYS cc_start: 0.8276 (mmtp) cc_final: 0.8075 (mmmm) REVERT: A 90 ARG cc_start: 0.7420 (tpp-160) cc_final: 0.7154 (tpm170) REVERT: A 100 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.5792 (pp-130) REVERT: A 127 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5722 (pt0) REVERT: A 154 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6813 (tm-30) REVERT: A 226 GLU cc_start: 0.6313 (mt-10) cc_final: 0.6010 (mt-10) REVERT: A 236 VAL cc_start: 0.7824 (OUTLIER) cc_final: 0.7563 (m) REVERT: A 241 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7752 (mmtt) REVERT: A 266 THR cc_start: 0.7579 (OUTLIER) cc_final: 0.7082 (p) REVERT: A 349 THR cc_start: 0.8124 (t) cc_final: 0.7850 (m) REVERT: B 40 ARG cc_start: 0.7916 (mtm-85) cc_final: 0.7542 (mtm-85) REVERT: B 118 LYS cc_start: 0.8261 (mttt) cc_final: 0.7892 (mttp) REVERT: B 128 ARG cc_start: 0.7534 (ttt180) cc_final: 0.7034 (ttt180) REVERT: B 180 MET cc_start: 0.8132 (ttp) cc_final: 0.7868 (ttp) REVERT: B 222 GLU cc_start: 0.7597 (pp20) cc_final: 0.7182 (pp20) REVERT: B 243 ARG cc_start: 0.6395 (OUTLIER) cc_final: 0.6007 (tmm-80) REVERT: B 251 GLU cc_start: 0.7279 (tm-30) cc_final: 0.7030 (tm-30) REVERT: B 322 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7338 (pp) REVERT: B 333 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7506 (mtpp) REVERT: B 346 GLU cc_start: 0.7808 (mp0) cc_final: 0.7154 (mp0) REVERT: B 350 LYS cc_start: 0.7040 (mtmt) cc_final: 0.6471 (mtmt) REVERT: B 353 TYR cc_start: 0.6791 (t80) cc_final: 0.6525 (t80) REVERT: B 354 LYS cc_start: 0.7179 (ttmm) cc_final: 0.6663 (ttmt) REVERT: B 363 ILE cc_start: 0.5605 (OUTLIER) cc_final: 0.5349 (mt) REVERT: C 29 LEU cc_start: 0.8403 (tp) cc_final: 0.8184 (tp) REVERT: C 84 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7786 (mmtm) REVERT: C 91 LYS cc_start: 0.8219 (tptt) cc_final: 0.7985 (tptt) REVERT: C 147 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6455 (tm-30) REVERT: C 165 LYS cc_start: 0.6490 (OUTLIER) cc_final: 0.6074 (mmtm) REVERT: C 169 GLU cc_start: 0.7162 (tt0) cc_final: 0.6706 (tt0) REVERT: C 182 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7883 (mtpm) REVERT: C 187 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7477 (tppp) REVERT: C 250 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6892 (mtt) REVERT: D 11 LYS cc_start: 0.7574 (ptpt) cc_final: 0.7271 (ptpt) REVERT: D 17 SER cc_start: 0.8369 (t) cc_final: 0.8160 (m) REVERT: D 27 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7140 (ptm-80) REVERT: D 153 VAL cc_start: 0.8749 (t) cc_final: 0.8405 (p) REVERT: D 178 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8051 (tttp) REVERT: D 190 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7314 (mm-30) REVERT: E 50 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7653 (mt-10) REVERT: E 63 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7195 (tt0) REVERT: E 74 GLU cc_start: 0.7463 (mp0) cc_final: 0.6895 (mp0) REVERT: E 148 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8474 (tttm) REVERT: E 194 ASP cc_start: 0.6447 (p0) cc_final: 0.5974 (p0) REVERT: F 93 SER cc_start: 0.7795 (OUTLIER) cc_final: 0.7510 (m) REVERT: F 152 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8510 (t) REVERT: F 173 PHE cc_start: 0.8322 (t80) cc_final: 0.8114 (t80) REVERT: F 384 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6859 (t70) REVERT: F 391 TYR cc_start: 0.7961 (t80) cc_final: 0.7509 (t80) REVERT: F 398 SER cc_start: 0.8609 (m) cc_final: 0.8192 (t) REVERT: F 430 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8077 (mtt90) REVERT: F 509 ASP cc_start: 0.7570 (m-30) cc_final: 0.7357 (m-30) REVERT: F 553 LYS cc_start: 0.8284 (tttt) cc_final: 0.8071 (tttt) REVERT: F 567 LEU cc_start: 0.8691 (mt) cc_final: 0.8435 (mt) REVERT: F 741 VAL cc_start: 0.7999 (t) cc_final: 0.7796 (m) REVERT: F 764 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7453 (mtp) REVERT: F 789 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7748 (mt-10) REVERT: F 842 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7732 (mtmm) REVERT: F 866 LEU cc_start: 0.8705 (mp) cc_final: 0.8341 (mt) REVERT: F 928 GLN cc_start: 0.7748 (tp-100) cc_final: 0.7521 (tp-100) REVERT: F 1010 ASN cc_start: 0.7473 (t0) cc_final: 0.6625 (t0) REVERT: F 1014 ASP cc_start: 0.6698 (m-30) cc_final: 0.6048 (m-30) REVERT: F 1166 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8154 (mtt) REVERT: G 144 GLN cc_start: 0.6600 (tp-100) cc_final: 0.6354 (tp-100) REVERT: G 200 ASP cc_start: 0.7950 (t0) cc_final: 0.7681 (t0) REVERT: G 206 ASP cc_start: 0.7693 (t0) cc_final: 0.7410 (t0) REVERT: G 209 GLN cc_start: 0.7764 (mp10) cc_final: 0.7390 (mp-120) REVERT: G 210 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8174 (tt) REVERT: G 224 LYS cc_start: 0.7221 (mptt) cc_final: 0.6743 (mptt) REVERT: G 242 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6931 (mt-10) REVERT: G 306 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: G 318 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: G 377 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7535 (mt-10) REVERT: G 385 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8064 (mp) REVERT: G 501 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7737 (mtt) REVERT: G 672 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: G 700 ASP cc_start: 0.7553 (t0) cc_final: 0.7181 (m-30) REVERT: G 714 MET cc_start: 0.7978 (tpp) cc_final: 0.7776 (mmt) REVERT: G 768 ASN cc_start: 0.7812 (m-40) cc_final: 0.7574 (m-40) REVERT: G 788 HIS cc_start: 0.7413 (m170) cc_final: 0.7210 (m170) REVERT: G 792 LYS cc_start: 0.7527 (mttt) cc_final: 0.6897 (mttm) REVERT: G 1146 GLU cc_start: 0.8167 (tt0) cc_final: 0.7871 (tt0) REVERT: G 1283 HIS cc_start: 0.7254 (t-90) cc_final: 0.6868 (t-90) REVERT: G 1356 SER cc_start: 0.8579 (m) cc_final: 0.8232 (p) REVERT: G 1358 GLN cc_start: 0.8076 (mt0) cc_final: 0.7708 (mt0) REVERT: G 1396 VAL cc_start: 0.8615 (t) cc_final: 0.8277 (m) REVERT: G 1408 ASP cc_start: 0.7672 (m-30) cc_final: 0.7434 (p0) REVERT: G 1424 MET cc_start: 0.3783 (mmt) cc_final: 0.3526 (mmt) REVERT: H 1 MET cc_start: -0.1157 (mtt) cc_final: -0.1375 (mtt) outliers start: 167 outliers final: 82 residues processed: 894 average time/residue: 0.7867 time to fit residues: 836.9737 Evaluate side-chains 907 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 798 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 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 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 233 TYR Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 363 ILE 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 149 CYS Chi-restraints excluded: chain C residue 165 LYS Chi-restraints excluded: chain C residue 182 LYS 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 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 78 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 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 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 764 MET Chi-restraints excluded: chain F residue 797 ILE Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 882 LEU Chi-restraints excluded: chain F residue 1007 ILE Chi-restraints excluded: chain F residue 1166 MET Chi-restraints excluded: chain F residue 1218 ILE 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 210 LEU 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 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 675 GLU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 294 optimal weight: 0.0040 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 260 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 245 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4244 r_free = 0.4244 target = 0.182949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.141886 restraints weight = 55172.196| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.15 r_work: 0.3505 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 39103 Z= 0.158 Angle : 0.524 13.208 53599 Z= 0.277 Chirality : 0.042 0.199 6077 Planarity : 0.004 0.084 6189 Dihedral : 17.147 174.303 7249 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 4.22 % Allowed : 22.68 % Favored : 73.11 % 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: 0.89 (0.13), residues: 4231 helix: 1.45 (0.13), residues: 1655 sheet: 0.42 (0.22), residues: 562 loop : 0.01 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 169 TYR 0.019 0.001 TYR A 163 PHE 0.018 0.001 PHE B 116 TRP 0.007 0.001 TRP G 702 HIS 0.009 0.001 HIS B 290 Details of bonding type rmsd covalent geometry : bond 0.00364 (39096) covalent geometry : angle 0.51811 (53587) SS BOND : bond 0.00513 ( 3) SS BOND : angle 6.46473 ( 6) hydrogen bonds : bond 0.04149 ( 1748) hydrogen bonds : angle 4.46322 ( 4826) metal coordination : bond 0.00824 ( 4) metal coordination : angle 4.26857 ( 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 975 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 818 time to evaluate : 1.406 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: 0.7923 (OUTLIER) cc_final: 0.7428 (t80) REVERT: A 52 GLN cc_start: 0.8846 (pm20) cc_final: 0.7885 (pm20) REVERT: A 90 ARG cc_start: 0.7551 (tpp-160) cc_final: 0.7339 (tpp-160) REVERT: A 100 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.5853 (pp-130) REVERT: A 127 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6017 (pt0) REVERT: A 184 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7496 (mtm180) REVERT: A 226 GLU cc_start: 0.6629 (mt-10) cc_final: 0.6322 (mt-10) REVERT: A 236 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7640 (m) REVERT: A 241 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7930 (mmtt) REVERT: A 266 THR cc_start: 0.7625 (OUTLIER) cc_final: 0.7096 (p) REVERT: A 349 THR cc_start: 0.8242 (t) cc_final: 0.7979 (m) REVERT: B 40 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7749 (mtm-85) REVERT: B 54 MET cc_start: 0.5916 (mmt) cc_final: 0.5661 (mmm) REVERT: B 118 LYS cc_start: 0.8312 (mttt) cc_final: 0.7957 (mttp) REVERT: B 128 ARG cc_start: 0.7696 (ttt180) cc_final: 0.7235 (ttt180) REVERT: B 180 MET cc_start: 0.8242 (ttp) cc_final: 0.7978 (ttp) REVERT: B 222 GLU cc_start: 0.7736 (pp20) cc_final: 0.7308 (pp20) REVERT: B 226 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6421 (tp30) REVERT: B 241 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7795 (mtmm) REVERT: B 243 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.6275 (tmm-80) REVERT: B 322 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7578 (pp) REVERT: B 333 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7633 (mtpp) REVERT: B 346 GLU cc_start: 0.7931 (mp0) cc_final: 0.7025 (mm-30) REVERT: B 350 LYS cc_start: 0.7187 (mtmt) cc_final: 0.6606 (mtmt) REVERT: B 353 TYR cc_start: 0.6995 (t80) cc_final: 0.6713 (t80) REVERT: C 29 LEU cc_start: 0.8512 (tp) cc_final: 0.8297 (tp) REVERT: C 52 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7927 (ttmt) REVERT: C 91 LYS cc_start: 0.8432 (tptt) cc_final: 0.8191 (tptt) REVERT: C 147 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6951 (tm-30) REVERT: C 165 LYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6362 (mmtm) REVERT: C 169 GLU cc_start: 0.7430 (tt0) cc_final: 0.7021 (tt0) REVERT: C 182 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8048 (mtpm) REVERT: C 187 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7275 (tppp) REVERT: C 217 MET cc_start: 0.7471 (mtm) cc_final: 0.7198 (mmm) REVERT: C 250 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6903 (mtt) REVERT: D 11 LYS cc_start: 0.7764 (ptpt) cc_final: 0.7434 (ptpt) REVERT: D 17 SER cc_start: 0.8496 (t) cc_final: 0.8258 (m) REVERT: D 27 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7280 (ptm-80) REVERT: D 153 VAL cc_start: 0.8876 (t) cc_final: 0.8521 (p) REVERT: D 178 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8253 (tttp) REVERT: D 188 ARG cc_start: 0.8092 (ttp-110) cc_final: 0.7661 (ttp-110) REVERT: D 190 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7393 (mm-30) REVERT: E 50 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7923 (mt-10) REVERT: E 63 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7526 (tt0) REVERT: E 74 GLU cc_start: 0.7667 (mp0) cc_final: 0.7067 (mp0) REVERT: E 138 VAL cc_start: 0.8453 (t) cc_final: 0.8166 (p) REVERT: E 194 ASP cc_start: 0.6632 (p0) cc_final: 0.6188 (p0) REVERT: F 54 MET cc_start: 0.8171 (mmm) cc_final: 0.7559 (mtm) REVERT: F 76 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7557 (m-30) REVERT: F 93 SER cc_start: 0.8039 (p) cc_final: 0.7751 (m) REVERT: F 173 PHE cc_start: 0.8434 (t80) cc_final: 0.8193 (t80) REVERT: F 384 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7135 (t70) REVERT: F 391 TYR cc_start: 0.8186 (t80) cc_final: 0.7738 (t80) REVERT: F 398 SER cc_start: 0.8636 (m) cc_final: 0.8214 (t) REVERT: F 430 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8221 (mtt90) REVERT: F 509 ASP cc_start: 0.7777 (m-30) cc_final: 0.7463 (m-30) REVERT: F 553 LYS cc_start: 0.8539 (tttt) cc_final: 0.8327 (tttt) REVERT: F 567 LEU cc_start: 0.8798 (mt) cc_final: 0.8555 (mt) REVERT: F 695 ILE cc_start: 0.7558 (tt) cc_final: 0.7355 (pt) REVERT: F 741 VAL cc_start: 0.8130 (t) cc_final: 0.7900 (m) REVERT: F 764 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7608 (mtp) REVERT: F 789 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7913 (mt-10) REVERT: F 842 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7828 (mtmm) REVERT: F 866 LEU cc_start: 0.8764 (mp) cc_final: 0.8412 (mt) REVERT: F 900 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6281 (mtp85) REVERT: F 928 GLN cc_start: 0.7795 (tp-100) cc_final: 0.7568 (tp-100) REVERT: F 1010 ASN cc_start: 0.7491 (t0) cc_final: 0.6659 (t0) REVERT: F 1014 ASP cc_start: 0.6863 (m-30) cc_final: 0.6207 (m-30) REVERT: F 1019 SER cc_start: 0.8585 (m) cc_final: 0.8123 (p) REVERT: F 1221 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8255 (t) REVERT: G 41 ASN cc_start: 0.8266 (t0) cc_final: 0.7873 (m-40) REVERT: G 77 ARG cc_start: 0.8144 (mmm160) cc_final: 0.7842 (mmm-85) REVERT: G 90 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7679 (mp0) REVERT: G 144 GLN cc_start: 0.6775 (tp-100) cc_final: 0.6499 (tp-100) REVERT: G 200 ASP cc_start: 0.8193 (t0) cc_final: 0.7919 (t0) REVERT: G 206 ASP cc_start: 0.7964 (t0) cc_final: 0.7623 (t0) REVERT: G 208 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7568 (mm-30) REVERT: G 209 GLN cc_start: 0.7959 (mp10) cc_final: 0.7580 (mp-120) REVERT: G 210 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8187 (tt) REVERT: G 224 LYS cc_start: 0.7390 (mptt) cc_final: 0.7059 (mppt) REVERT: G 242 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7307 (mt-10) REVERT: G 306 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: G 318 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: G 377 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7863 (mt-10) REVERT: G 385 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8093 (mp) REVERT: G 501 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7924 (mtt) REVERT: G 672 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: G 700 ASP cc_start: 0.7818 (t0) cc_final: 0.7365 (m-30) REVERT: G 768 ASN cc_start: 0.8019 (m-40) cc_final: 0.7770 (m-40) REVERT: G 792 LYS cc_start: 0.7721 (mttt) cc_final: 0.7152 (mttm) REVERT: G 1146 GLU cc_start: 0.8299 (tt0) cc_final: 0.8000 (tt0) REVERT: G 1283 HIS cc_start: 0.7480 (t-90) cc_final: 0.7099 (t-90) REVERT: G 1356 SER cc_start: 0.8709 (m) cc_final: 0.8378 (p) REVERT: G 1358 GLN cc_start: 0.8274 (mt0) cc_final: 0.7932 (mt0) REVERT: G 1396 VAL cc_start: 0.8676 (t) cc_final: 0.8332 (m) REVERT: G 1424 MET cc_start: 0.3777 (mmt) cc_final: 0.3575 (mmt) REVERT: H 1 MET cc_start: -0.1146 (mtt) cc_final: -0.1397 (mtt) outliers start: 157 outliers final: 85 residues processed: 890 average time/residue: 0.8299 time to fit residues: 876.1814 Evaluate side-chains 920 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 806 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 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 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 226 GLU Chi-restraints excluded: chain B residue 241 LYS 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 B residue 333 LYS Chi-restraints excluded: chain C residue 52 LYS 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 182 LYS Chi-restraints excluded: chain C residue 187 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 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 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 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 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 141 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 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 740 LYS 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 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 81 CYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 210 LEU 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 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 583 LEU Chi-restraints excluded: chain G residue 613 ASN 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 698 VAL Chi-restraints excluded: chain G residue 717 ILE Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain G residue 909 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 55 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 134 optimal weight: 0.0970 chunk 236 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 347 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 417 optimal weight: 40.0000 chunk 308 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** 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 745 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.182278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141170 restraints weight = 55125.925| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.24 r_work: 0.3492 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39103 Z= 0.188 Angle : 0.541 12.784 53599 Z= 0.285 Chirality : 0.043 0.209 6077 Planarity : 0.004 0.070 6189 Dihedral : 17.117 174.495 7246 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Rotamer: Outliers : 4.41 % Allowed : 22.84 % Favored : 72.76 % 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: 0.87 (0.13), residues: 4231 helix: 1.40 (0.13), residues: 1661 sheet: 0.40 (0.22), residues: 567 loop : 0.02 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 169 TYR 0.020 0.001 TYR A 163 PHE 0.021 0.001 PHE B 116 TRP 0.009 0.001 TRP A 342 HIS 0.007 0.001 HIS G 788 Details of bonding type rmsd covalent geometry : bond 0.00440 (39096) covalent geometry : angle 0.53491 (53587) SS BOND : bond 0.00470 ( 3) SS BOND : angle 6.46012 ( 6) hydrogen bonds : bond 0.04267 ( 1748) hydrogen bonds : angle 4.45636 ( 4826) metal coordination : bond 0.00877 ( 4) metal coordination : angle 4.42684 ( 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 984 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 820 time to evaluate : 1.354 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: 0.7937 (OUTLIER) cc_final: 0.7404 (t80) REVERT: A 90 ARG cc_start: 0.7530 (tpp-160) cc_final: 0.7315 (tpp-160) REVERT: A 100 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.5823 (pp-130) REVERT: A 127 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6076 (pt0) REVERT: A 184 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7503 (mtm180) REVERT: A 226 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6348 (mt-10) REVERT: A 236 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7638 (m) REVERT: A 241 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7934 (mmtt) REVERT: A 266 THR cc_start: 0.7693 (OUTLIER) cc_final: 0.7151 (p) REVERT: A 349 THR cc_start: 0.8258 (t) cc_final: 0.7991 (m) REVERT: B 40 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7748 (mtm-85) REVERT: B 54 MET cc_start: 0.6025 (mmt) cc_final: 0.5758 (mmm) REVERT: B 118 LYS cc_start: 0.8326 (mttt) cc_final: 0.7964 (mttp) REVERT: B 128 ARG cc_start: 0.7716 (ttt180) cc_final: 0.7237 (ttt180) REVERT: B 180 MET cc_start: 0.8278 (ttp) cc_final: 0.8018 (ttp) REVERT: B 222 GLU cc_start: 0.7774 (pp20) cc_final: 0.7343 (pp20) REVERT: B 226 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6023 (mp0) REVERT: B 241 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7693 (mtmm) REVERT: B 243 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6453 (tmm-80) REVERT: B 322 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7607 (pp) REVERT: B 333 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7692 (mtpp) REVERT: B 346 GLU cc_start: 0.7947 (mp0) cc_final: 0.6715 (mm-30) REVERT: B 347 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.5827 (tp) REVERT: B 350 LYS cc_start: 0.7273 (mtmt) cc_final: 0.6597 (mtmt) REVERT: B 353 TYR cc_start: 0.7055 (t80) cc_final: 0.6790 (t80) REVERT: B 361 GLU cc_start: 0.7439 (tp30) cc_final: 0.7235 (tp30) REVERT: B 363 ILE cc_start: 0.5616 (OUTLIER) cc_final: 0.5404 (mt) REVERT: C 29 LEU cc_start: 0.8521 (tp) cc_final: 0.8321 (tp) REVERT: C 52 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7884 (ttmt) REVERT: C 91 LYS cc_start: 0.8452 (tptt) cc_final: 0.8204 (tptt) REVERT: C 147 GLU cc_start: 0.7463 (tm-30) cc_final: 0.6986 (tm-30) REVERT: C 165 LYS cc_start: 0.6692 (mmtm) cc_final: 0.6280 (mmtm) REVERT: C 169 GLU cc_start: 0.7404 (tt0) cc_final: 0.7062 (tt0) REVERT: C 182 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8106 (mtpm) REVERT: C 187 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7631 (tppp) REVERT: C 217 MET cc_start: 0.7450 (mtm) cc_final: 0.7177 (mmm) REVERT: C 250 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6917 (mtt) REVERT: D 11 LYS cc_start: 0.7802 (ptpt) cc_final: 0.7472 (ptpt) REVERT: D 17 SER cc_start: 0.8499 (t) cc_final: 0.8225 (m) REVERT: D 27 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7323 (ptm-80) REVERT: D 153 VAL cc_start: 0.8896 (t) cc_final: 0.8537 (p) REVERT: D 178 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8266 (tttp) REVERT: D 188 ARG cc_start: 0.8108 (ttp-110) cc_final: 0.7645 (ttp-110) REVERT: D 190 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7403 (mm-30) REVERT: D 197 LYS cc_start: 0.8689 (tptm) cc_final: 0.8386 (tttm) REVERT: E 50 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7996 (mt-10) REVERT: E 63 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7574 (tt0) REVERT: E 74 GLU cc_start: 0.7698 (mp0) cc_final: 0.7095 (mp0) REVERT: E 148 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8514 (tttm) REVERT: E 194 ASP cc_start: 0.6669 (p0) cc_final: 0.6225 (p0) REVERT: F 76 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: F 79 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.6934 (mmm160) REVERT: F 93 SER cc_start: 0.8047 (OUTLIER) cc_final: 0.7761 (m) REVERT: F 152 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8640 (t) REVERT: F 173 PHE cc_start: 0.8462 (t80) cc_final: 0.8238 (t80) REVERT: F 384 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7117 (t70) REVERT: F 391 TYR cc_start: 0.8182 (t80) cc_final: 0.7716 (t80) REVERT: F 398 SER cc_start: 0.8616 (m) cc_final: 0.8213 (t) REVERT: F 430 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8200 (mtt90) REVERT: F 553 LYS cc_start: 0.8543 (tttt) cc_final: 0.8337 (tttt) REVERT: F 567 LEU cc_start: 0.8807 (mt) cc_final: 0.8568 (mt) REVERT: F 695 ILE cc_start: 0.7615 (tt) cc_final: 0.7326 (pt) REVERT: F 764 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7634 (mtp) REVERT: F 842 LYS cc_start: 0.8157 (mtpt) cc_final: 0.7822 (mtmm) REVERT: F 866 LEU cc_start: 0.8759 (mp) cc_final: 0.8406 (mt) REVERT: F 900 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6272 (mtp85) REVERT: F 928 GLN cc_start: 0.7808 (tp-100) cc_final: 0.7583 (tp-100) REVERT: F 1010 ASN cc_start: 0.7513 (t0) cc_final: 0.6651 (t0) REVERT: F 1014 ASP cc_start: 0.6869 (m-30) cc_final: 0.6197 (m-30) REVERT: F 1221 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8262 (t) REVERT: G 41 ASN cc_start: 0.8292 (t0) cc_final: 0.7760 (m-40) REVERT: G 90 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7805 (mt-10) REVERT: G 119 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7542 (mppt) REVERT: G 144 GLN cc_start: 0.6826 (tp-100) cc_final: 0.6474 (tp-100) REVERT: G 200 ASP cc_start: 0.8223 (t0) cc_final: 0.7933 (t0) REVERT: G 206 ASP cc_start: 0.7982 (t0) cc_final: 0.7650 (t0) REVERT: G 208 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7629 (mm-30) REVERT: G 209 GLN cc_start: 0.7958 (mp10) cc_final: 0.7570 (mp-120) REVERT: G 224 LYS cc_start: 0.7404 (mptt) cc_final: 0.7071 (mppt) REVERT: G 242 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7360 (mt-10) REVERT: G 306 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: G 318 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: G 385 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8095 (mp) REVERT: G 501 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7967 (mtt) REVERT: G 672 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: G 788 HIS cc_start: 0.7644 (m170) cc_final: 0.7418 (m170) REVERT: G 792 LYS cc_start: 0.7738 (mttt) cc_final: 0.7171 (mttm) REVERT: G 1146 GLU cc_start: 0.8318 (tt0) cc_final: 0.8020 (tt0) REVERT: G 1283 HIS cc_start: 0.7514 (t-90) cc_final: 0.7119 (t-90) REVERT: G 1356 SER cc_start: 0.8696 (m) cc_final: 0.8364 (p) REVERT: G 1358 GLN cc_start: 0.8310 (mt0) cc_final: 0.7983 (mt0) REVERT: G 1396 VAL cc_start: 0.8689 (t) cc_final: 0.8356 (m) REVERT: G 1408 ASP cc_start: 0.7879 (m-30) cc_final: 0.7483 (p0) REVERT: H 1 MET cc_start: -0.1169 (mtt) cc_final: -0.1414 (mtt) outliers start: 164 outliers final: 92 residues processed: 902 average time/residue: 0.8270 time to fit residues: 892.6013 Evaluate side-chains 931 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 806 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 113 ILE 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 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 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 226 GLU Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 242 ASN 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 B residue 363 ILE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 52 LYS 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 182 LYS 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 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 60 ASP 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 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 93 SER Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 152 VAL 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 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 685 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 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 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 119 LYS 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 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 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 583 LEU Chi-restraints excluded: chain G residue 613 ASN 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 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 909 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 0.0060 chunk 318 optimal weight: 0.0870 chunk 203 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 216 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 175 optimal weight: 0.0470 chunk 436 optimal weight: 4.9990 chunk 325 optimal weight: 4.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 200 ASN A 299 HIS ** 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 482 GLN G 741 GLN G 773 ASN G 873 GLN ** 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 = 0.4262 r_free = 0.4262 target = 0.184415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143382 restraints weight = 55294.376| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.19 r_work: 0.3541 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 39103 Z= 0.108 Angle : 0.507 12.753 53599 Z= 0.267 Chirality : 0.041 0.195 6077 Planarity : 0.004 0.090 6189 Dihedral : 17.018 174.841 7234 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.62 % Favored : 97.31 % Rotamer: Outliers : 3.82 % Allowed : 23.62 % Favored : 72.57 % 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: 1.07 (0.13), residues: 4231 helix: 1.62 (0.13), residues: 1664 sheet: 0.46 (0.22), residues: 552 loop : 0.10 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 56 TYR 0.018 0.001 TYR F 73 PHE 0.015 0.001 PHE A 139 TRP 0.013 0.001 TRP B 342 HIS 0.004 0.001 HIS G 788 Details of bonding type rmsd covalent geometry : bond 0.00236 (39096) covalent geometry : angle 0.50161 (53587) SS BOND : bond 0.00520 ( 3) SS BOND : angle 5.71651 ( 6) hydrogen bonds : bond 0.03613 ( 1748) hydrogen bonds : angle 4.24964 ( 4826) metal coordination : bond 0.00453 ( 4) metal coordination : angle 4.26138 ( 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 966 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 824 time to evaluate : 1.420 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: 0.7876 (OUTLIER) cc_final: 0.7491 (t80) REVERT: A 40 ARG cc_start: 0.7541 (mtt180) cc_final: 0.7083 (mtt180) REVERT: A 100 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.5878 (pp-130) REVERT: A 183 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: A 184 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7477 (mtm180) REVERT: A 226 GLU cc_start: 0.6619 (mt-10) cc_final: 0.6310 (mt-10) REVERT: A 236 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7646 (m) REVERT: A 241 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7885 (mmtt) REVERT: A 266 THR cc_start: 0.7476 (OUTLIER) cc_final: 0.7044 (p) REVERT: A 296 TYR cc_start: 0.8377 (t80) cc_final: 0.8176 (t80) REVERT: A 349 THR cc_start: 0.8190 (t) cc_final: 0.7923 (m) REVERT: B 118 LYS cc_start: 0.8254 (mttt) cc_final: 0.7918 (mttp) REVERT: B 128 ARG cc_start: 0.7639 (ttt180) cc_final: 0.7155 (ttt180) REVERT: B 170 TYR cc_start: 0.7104 (t80) cc_final: 0.6769 (t80) REVERT: B 180 MET cc_start: 0.8269 (ttp) cc_final: 0.8027 (ttp) REVERT: B 222 GLU cc_start: 0.7738 (pp20) cc_final: 0.7301 (pp20) REVERT: B 226 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5721 (mp0) REVERT: B 243 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6266 (tmm-80) REVERT: B 250 GLU cc_start: 0.7156 (pm20) cc_final: 0.6939 (pm20) REVERT: B 251 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7284 (tm-30) REVERT: B 322 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7430 (pp) REVERT: B 333 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7646 (mtpp) REVERT: B 346 GLU cc_start: 0.7872 (mp0) cc_final: 0.6919 (mm-30) REVERT: B 347 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.5912 (tt) REVERT: B 349 THR cc_start: 0.7003 (m) cc_final: 0.6767 (t) REVERT: B 350 LYS cc_start: 0.7250 (mtmt) cc_final: 0.6502 (mtmt) REVERT: B 353 TYR cc_start: 0.6973 (t80) cc_final: 0.6736 (t80) REVERT: B 354 LYS cc_start: 0.7648 (mttm) cc_final: 0.7398 (mtpt) REVERT: B 363 ILE cc_start: 0.5423 (OUTLIER) cc_final: 0.5162 (mt) REVERT: C 29 LEU cc_start: 0.8474 (tp) cc_final: 0.8268 (tp) REVERT: C 91 LYS cc_start: 0.8423 (tptt) cc_final: 0.8167 (tptt) REVERT: C 137 LEU cc_start: 0.8549 (tt) cc_final: 0.8326 (tp) REVERT: C 147 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7004 (tm-30) REVERT: C 151 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7883 (tmmt) REVERT: C 165 LYS cc_start: 0.6657 (mmtm) cc_final: 0.6338 (mmtm) REVERT: C 169 GLU cc_start: 0.7388 (tt0) cc_final: 0.7036 (tt0) REVERT: C 217 MET cc_start: 0.7446 (mtm) cc_final: 0.7173 (mmm) REVERT: C 250 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6914 (mtt) REVERT: D 11 LYS cc_start: 0.7708 (ptpt) cc_final: 0.7447 (ptpt) REVERT: D 17 SER cc_start: 0.8491 (t) cc_final: 0.8209 (m) REVERT: D 30 GLU cc_start: 0.7245 (mm-30) cc_final: 0.7031 (mm-30) REVERT: D 64 HIS cc_start: 0.7373 (p-80) cc_final: 0.7093 (p-80) REVERT: D 153 VAL cc_start: 0.8864 (t) cc_final: 0.8488 (p) REVERT: D 178 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8278 (tttp) REVERT: D 188 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7607 (ttp-110) REVERT: D 190 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7394 (mm-30) REVERT: E 50 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7947 (mt-10) REVERT: E 63 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7600 (tt0) REVERT: E 74 GLU cc_start: 0.7652 (mp0) cc_final: 0.7067 (mp0) REVERT: E 98 GLU cc_start: 0.7986 (tt0) cc_final: 0.7347 (tt0) REVERT: F 73 TYR cc_start: 0.8283 (p90) cc_final: 0.8081 (p90) REVERT: F 79 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.6921 (mmm160) REVERT: F 93 SER cc_start: 0.8037 (p) cc_final: 0.7752 (m) REVERT: F 97 LYS cc_start: 0.8129 (pttm) cc_final: 0.7895 (ptpp) REVERT: F 391 TYR cc_start: 0.8182 (t80) cc_final: 0.7772 (t80) REVERT: F 398 SER cc_start: 0.8588 (m) cc_final: 0.8159 (t) REVERT: F 430 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8178 (mtt90) REVERT: F 509 ASP cc_start: 0.7818 (m-30) cc_final: 0.7427 (m-30) REVERT: F 553 LYS cc_start: 0.8516 (tttt) cc_final: 0.8313 (tttt) REVERT: F 567 LEU cc_start: 0.8781 (mt) cc_final: 0.8547 (mt) REVERT: F 741 VAL cc_start: 0.8058 (t) cc_final: 0.7836 (m) REVERT: F 764 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7596 (mtp) REVERT: F 789 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7877 (mt-10) REVERT: F 803 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6821 (mm-30) REVERT: F 842 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7829 (mtmm) REVERT: F 866 LEU cc_start: 0.8717 (mp) cc_final: 0.8368 (mt) REVERT: F 900 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6343 (mtp85) REVERT: F 928 GLN cc_start: 0.7746 (tp-100) cc_final: 0.7538 (tp-100) REVERT: F 1010 ASN cc_start: 0.7407 (t0) cc_final: 0.6583 (t0) REVERT: F 1014 ASP cc_start: 0.6797 (m-30) cc_final: 0.6113 (m-30) REVERT: F 1019 SER cc_start: 0.8551 (m) cc_final: 0.8075 (p) REVERT: G 41 ASN cc_start: 0.8215 (t0) cc_final: 0.7949 (m-40) REVERT: G 77 ARG cc_start: 0.8054 (mmm160) cc_final: 0.7830 (mmm-85) REVERT: G 90 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7656 (mp0) REVERT: G 144 GLN cc_start: 0.6762 (tp-100) cc_final: 0.6493 (tp-100) REVERT: G 174 LEU cc_start: 0.8022 (tp) cc_final: 0.7802 (tm) REVERT: G 200 ASP cc_start: 0.8162 (t0) cc_final: 0.7877 (t0) REVERT: G 206 ASP cc_start: 0.7954 (t0) cc_final: 0.7637 (t0) REVERT: G 242 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7271 (mt-10) REVERT: G 276 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7496 (mmm160) REVERT: G 302 ILE cc_start: 0.7982 (pp) cc_final: 0.7763 (pt) REVERT: G 306 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: G 318 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: G 672 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: G 714 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7607 (mmm) REVERT: G 768 ASN cc_start: 0.8019 (m-40) cc_final: 0.7761 (m-40) REVERT: G 792 LYS cc_start: 0.7740 (mttt) cc_final: 0.7129 (mttm) REVERT: G 1051 ILE cc_start: -0.0853 (OUTLIER) cc_final: -0.1126 (mt) REVERT: G 1146 GLU cc_start: 0.8286 (tt0) cc_final: 0.8010 (tt0) REVERT: G 1283 HIS cc_start: 0.7467 (t-90) cc_final: 0.7055 (t-90) REVERT: G 1356 SER cc_start: 0.8698 (m) cc_final: 0.8372 (p) REVERT: G 1396 VAL cc_start: 0.8665 (t) cc_final: 0.8307 (m) REVERT: G 1408 ASP cc_start: 0.7898 (m-30) cc_final: 0.7547 (p0) REVERT: H 1 MET cc_start: -0.1152 (mtt) cc_final: -0.1420 (mtt) outliers start: 142 outliers final: 76 residues processed: 895 average time/residue: 0.8169 time to fit residues: 869.0916 Evaluate side-chains 906 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 808 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 113 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 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 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 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 233 TYR Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain C residue 31 ILE 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 86 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 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 99 THR Chi-restraints excluded: chain D residue 137 LYS 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 78 GLU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 128 ASP 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 79 ARG Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 119 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 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 740 LYS Chi-restraints excluded: chain F residue 764 MET Chi-restraints excluded: chain F residue 797 ILE Chi-restraints excluded: chain F residue 803 GLU Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain F residue 900 ARG Chi-restraints excluded: chain F residue 1218 ILE Chi-restraints excluded: chain G residue 1 MET 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 520 SER 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 690 THR Chi-restraints excluded: chain G residue 714 MET 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 1223 LEU 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: 20.0000 chunk 111 optimal weight: 0.6980 chunk 252 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 430 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 116 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 395 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 ASN F 56 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 = 0.183498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.142199 restraints weight = 55163.099| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.24 r_work: 0.3521 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 39103 Z= 0.154 Angle : 0.539 14.964 53599 Z= 0.281 Chirality : 0.042 0.203 6077 Planarity : 0.004 0.094 6189 Dihedral : 16.975 175.188 7223 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 3.82 % Allowed : 23.99 % Favored : 72.19 % 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: 1656 sheet: 0.47 (0.22), residues: 559 loop : 0.10 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 169 TYR 0.014 0.001 TYR B 254 PHE 0.021 0.001 PHE B 116 TRP 0.027 0.001 TRP B 342 HIS 0.007 0.001 HIS G 788 Details of bonding type rmsd covalent geometry : bond 0.00356 (39096) covalent geometry : angle 0.53334 (53587) SS BOND : bond 0.00491 ( 3) SS BOND : angle 5.92716 ( 6) hydrogen bonds : bond 0.03897 ( 1748) hydrogen bonds : angle 4.29353 ( 4826) metal coordination : bond 0.00938 ( 4) metal coordination : angle 4.35584 ( 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 956 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 814 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: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7512 (t80) REVERT: A 40 ARG cc_start: 0.7545 (mtt180) cc_final: 0.7241 (mtt180) REVERT: A 100 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.5902 (pp-130) REVERT: A 127 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5997 (pt0) REVERT: A 163 TYR cc_start: 0.6609 (m-10) cc_final: 0.6144 (m-10) REVERT: A 184 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7459 (mtm180) REVERT: A 226 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6332 (mt-10) REVERT: A 236 VAL cc_start: 0.7943 (OUTLIER) cc_final: 0.7658 (m) REVERT: A 241 LYS cc_start: 0.8241 (mmtt) cc_final: 0.7887 (mmtt) REVERT: A 296 TYR cc_start: 0.8403 (t80) cc_final: 0.8202 (t80) REVERT: A 349 THR cc_start: 0.8195 (t) cc_final: 0.7934 (m) REVERT: B 29 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7309 (t0) REVERT: B 118 LYS cc_start: 0.8277 (mttt) cc_final: 0.7934 (mttp) REVERT: B 128 ARG cc_start: 0.7656 (ttt180) cc_final: 0.7180 (ttt180) REVERT: B 170 TYR cc_start: 0.7175 (t80) cc_final: 0.6824 (t80) REVERT: B 180 MET cc_start: 0.8291 (ttp) cc_final: 0.8046 (ttp) REVERT: B 222 GLU cc_start: 0.7736 (pp20) cc_final: 0.7297 (pp20) REVERT: B 226 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.5712 (mp0) REVERT: B 243 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6238 (tmm-80) REVERT: B 322 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7445 (pp) REVERT: B 333 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7651 (mtpp) REVERT: B 346 GLU cc_start: 0.7904 (mp0) cc_final: 0.7012 (mm-30) REVERT: B 349 THR cc_start: 0.7006 (m) cc_final: 0.6741 (t) REVERT: B 350 LYS cc_start: 0.7235 (mtmt) cc_final: 0.6482 (mtmt) REVERT: B 361 GLU cc_start: 0.7385 (tp30) cc_final: 0.7181 (tp30) REVERT: B 363 ILE cc_start: 0.5431 (OUTLIER) cc_final: 0.4939 (mt) REVERT: B 364 ILE cc_start: 0.5948 (OUTLIER) cc_final: 0.5232 (mm) REVERT: C 29 LEU cc_start: 0.8488 (tp) cc_final: 0.8275 (tp) REVERT: C 91 LYS cc_start: 0.8425 (tptt) cc_final: 0.8175 (tptt) REVERT: C 137 LEU cc_start: 0.8577 (tt) cc_final: 0.8367 (tp) REVERT: C 147 GLU cc_start: 0.7460 (tm-30) cc_final: 0.6991 (tm-30) REVERT: C 165 LYS cc_start: 0.6676 (mmtm) cc_final: 0.6338 (mmtm) REVERT: C 169 GLU cc_start: 0.7392 (tt0) cc_final: 0.7030 (tt0) REVERT: C 182 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8027 (mtpm) REVERT: C 187 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7388 (tppp) REVERT: C 217 MET cc_start: 0.7452 (mtm) cc_final: 0.7175 (mmm) REVERT: C 250 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6955 (mtt) REVERT: D 11 LYS cc_start: 0.7764 (ptpt) cc_final: 0.7500 (ptpt) REVERT: D 17 SER cc_start: 0.8488 (t) cc_final: 0.8216 (m) REVERT: D 30 GLU cc_start: 0.7286 (mm-30) cc_final: 0.7078 (mm-30) REVERT: D 64 HIS cc_start: 0.7443 (p-80) cc_final: 0.7146 (p-80) REVERT: D 153 VAL cc_start: 0.8895 (t) cc_final: 0.8523 (p) REVERT: D 178 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8321 (tttp) REVERT: D 188 ARG cc_start: 0.8088 (ttp-110) cc_final: 0.7603 (ttp-110) REVERT: D 190 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7373 (mm-30) REVERT: E 50 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7992 (mt-10) REVERT: E 63 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7631 (tt0) REVERT: E 74 GLU cc_start: 0.7650 (mp0) cc_final: 0.7071 (mp0) REVERT: E 148 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8516 (tttm) REVERT: E 184 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8532 (mm) REVERT: E 194 ASP cc_start: 0.6669 (p0) cc_final: 0.6244 (p0) REVERT: F 79 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.6923 (mmm160) REVERT: F 93 SER cc_start: 0.8056 (p) cc_final: 0.7760 (m) REVERT: F 391 TYR cc_start: 0.8214 (t80) cc_final: 0.7800 (t80) REVERT: F 398 SER cc_start: 0.8608 (m) cc_final: 0.8190 (t) REVERT: F 430 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8224 (mtt90) REVERT: F 553 LYS cc_start: 0.8528 (tttt) cc_final: 0.8324 (tttt) REVERT: F 567 LEU cc_start: 0.8791 (mt) cc_final: 0.8541 (mt) REVERT: F 741 VAL cc_start: 0.7994 (t) cc_final: 0.7749 (m) REVERT: F 764 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7637 (mtp) REVERT: F 789 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7904 (mt-10) REVERT: F 803 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6706 (mm-30) REVERT: F 842 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7824 (mtmm) REVERT: F 866 LEU cc_start: 0.8763 (mp) cc_final: 0.8403 (mt) REVERT: F 900 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6354 (mtp85) REVERT: F 928 GLN cc_start: 0.7777 (tp-100) cc_final: 0.7571 (tp-100) REVERT: F 1010 ASN cc_start: 0.7449 (t0) cc_final: 0.6644 (t0) REVERT: F 1014 ASP cc_start: 0.6836 (m-30) cc_final: 0.6190 (m-30) REVERT: F 1019 SER cc_start: 0.8572 (m) cc_final: 0.8096 (p) REVERT: F 1221 VAL cc_start: 0.8401 (p) cc_final: 0.8160 (t) REVERT: G 41 ASN cc_start: 0.8243 (t0) cc_final: 0.7943 (m-40) REVERT: G 77 ARG cc_start: 0.8110 (mmm160) cc_final: 0.7820 (mmm-85) REVERT: G 90 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7655 (mp0) REVERT: G 144 GLN cc_start: 0.6796 (tp-100) cc_final: 0.6541 (tp-100) REVERT: G 200 ASP cc_start: 0.8194 (t0) cc_final: 0.7904 (t0) REVERT: G 206 ASP cc_start: 0.7966 (t0) cc_final: 0.7637 (t0) REVERT: G 208 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7575 (mm-30) REVERT: G 242 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7303 (mt-10) REVERT: G 306 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: G 318 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: G 501 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7807 (mtt) REVERT: G 672 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: G 700 ASP cc_start: 0.7742 (t0) cc_final: 0.7315 (m-30) REVERT: G 768 ASN cc_start: 0.8035 (m-40) cc_final: 0.7787 (m-40) REVERT: G 792 LYS cc_start: 0.7770 (mttt) cc_final: 0.7204 (mttm) REVERT: G 1051 ILE cc_start: -0.0806 (OUTLIER) cc_final: -0.1068 (mt) REVERT: G 1146 GLU cc_start: 0.8305 (tt0) cc_final: 0.8029 (tt0) REVERT: G 1283 HIS cc_start: 0.7458 (t-90) cc_final: 0.7073 (t-90) REVERT: G 1356 SER cc_start: 0.8717 (m) cc_final: 0.8374 (p) REVERT: G 1396 VAL cc_start: 0.8676 (t) cc_final: 0.8334 (m) REVERT: G 1408 ASP cc_start: 0.7875 (m-30) cc_final: 0.7515 (p0) REVERT: H 1 MET cc_start: -0.1162 (mtt) cc_final: -0.1415 (mtt) outliers start: 142 outliers final: 79 residues processed: 887 average time/residue: 0.8275 time to fit residues: 873.1984 Evaluate side-chains 905 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 800 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 100 MET Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 184 ARG 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 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 294 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain C residue 31 ILE 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 86 LYS 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 182 LYS 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 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 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 78 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 184 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 79 ARG Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 119 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 695 ILE 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 876 ASP Chi-restraints excluded: chain F residue 900 ARG Chi-restraints excluded: chain F residue 1218 ILE Chi-restraints excluded: chain F residue 1235 SER Chi-restraints excluded: chain G residue 1 MET 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 501 MET Chi-restraints excluded: chain G residue 520 SER 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 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: 3.9990 chunk 114 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 326 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 389 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 299 HIS ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN C 94 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.183267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141902 restraints weight = 54904.474| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.33 r_work: 0.3506 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 39103 Z= 0.172 Angle : 0.553 13.445 53599 Z= 0.289 Chirality : 0.043 0.214 6077 Planarity : 0.004 0.099 6189 Dihedral : 16.968 175.008 7223 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.05 % Rotamer: Outliers : 3.65 % Allowed : 24.34 % Favored : 72.00 % 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: 0.97 (0.13), residues: 4231 helix: 1.50 (0.13), residues: 1657 sheet: 0.45 (0.22), residues: 564 loop : 0.08 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 169 TYR 0.025 0.001 TYR B 254 PHE 0.029 0.001 PHE B 116 TRP 0.040 0.001 TRP B 342 HIS 0.010 0.001 HIS G 788 Details of bonding type rmsd covalent geometry : bond 0.00401 (39096) covalent geometry : angle 0.54749 (53587) SS BOND : bond 0.00503 ( 3) SS BOND : angle 6.03334 ( 6) hydrogen bonds : bond 0.04069 ( 1748) hydrogen bonds : angle 4.34100 ( 4826) metal coordination : bond 0.00977 ( 4) metal coordination : angle 4.62774 ( 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 943 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 807 time to evaluate : 1.521 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: A 25 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8162 (mtmt) REVERT: A 39 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7306 (t80) REVERT: A 40 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6964 (mtt180) REVERT: A 90 ARG cc_start: 0.7313 (tpp-160) cc_final: 0.7110 (ttm-80) REVERT: A 100 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.5785 (pp-130) REVERT: A 163 TYR cc_start: 0.6515 (m-10) cc_final: 0.6181 (m-10) REVERT: A 226 GLU cc_start: 0.6463 (mt-10) cc_final: 0.6177 (mt-10) REVERT: A 236 VAL cc_start: 0.7866 (OUTLIER) cc_final: 0.7596 (m) REVERT: A 241 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7823 (mmtt) REVERT: A 341 ASN cc_start: 0.8109 (m-40) cc_final: 0.7907 (m-40) REVERT: A 349 THR cc_start: 0.8083 (t) cc_final: 0.7832 (m) REVERT: B 26 GLU cc_start: 0.7059 (mp0) cc_final: 0.6762 (mp0) REVERT: B 29 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7253 (t0) REVERT: B 118 LYS cc_start: 0.8247 (mttt) cc_final: 0.7900 (mttp) REVERT: B 128 ARG cc_start: 0.7500 (ttt180) cc_final: 0.7009 (ttt180) REVERT: B 170 TYR cc_start: 0.7075 (t80) cc_final: 0.6727 (t80) REVERT: B 180 MET cc_start: 0.8199 (ttp) cc_final: 0.7944 (ttp) REVERT: B 222 GLU cc_start: 0.7598 (pp20) cc_final: 0.7159 (pp20) REVERT: B 226 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5403 (mp0) REVERT: B 243 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.6077 (tmm-80) REVERT: B 293 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6815 (tt0) REVERT: B 322 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7267 (pp) REVERT: B 333 LYS cc_start: 0.7825 (mtpp) cc_final: 0.7539 (mtpp) REVERT: B 346 GLU cc_start: 0.7770 (mp0) cc_final: 0.7374 (mp0) REVERT: B 349 THR cc_start: 0.7036 (m) cc_final: 0.6821 (t) REVERT: B 350 LYS cc_start: 0.7127 (mtmt) cc_final: 0.6422 (mtmt) REVERT: B 354 LYS cc_start: 0.7569 (mtpt) cc_final: 0.7295 (mtpt) REVERT: B 363 ILE cc_start: 0.5175 (OUTLIER) cc_final: 0.4753 (mt) REVERT: B 364 ILE cc_start: 0.5771 (OUTLIER) cc_final: 0.5118 (mm) REVERT: C 29 LEU cc_start: 0.8363 (tp) cc_final: 0.8150 (tp) REVERT: C 91 LYS cc_start: 0.8225 (tptt) cc_final: 0.7985 (tptt) REVERT: C 94 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7964 (m110) REVERT: C 147 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6478 (tm-30) REVERT: C 165 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.5976 (mmtm) REVERT: C 169 GLU cc_start: 0.7260 (tt0) cc_final: 0.6894 (tt0) REVERT: C 182 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7927 (mtpm) REVERT: C 187 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7261 (tppp) REVERT: C 217 MET cc_start: 0.7444 (mtm) cc_final: 0.7137 (mmm) REVERT: C 250 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6925 (mtt) REVERT: D 11 LYS cc_start: 0.7602 (ptpt) cc_final: 0.7364 (ptpt) REVERT: D 17 SER cc_start: 0.8384 (t) cc_final: 0.8116 (m) REVERT: D 27 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7162 (ptm-80) REVERT: D 64 HIS cc_start: 0.7379 (p-80) cc_final: 0.7142 (p-80) REVERT: D 153 VAL cc_start: 0.8819 (t) cc_final: 0.8447 (p) REVERT: D 178 LYS cc_start: 0.8584 (ttmm) cc_final: 0.8208 (tttp) REVERT: D 188 ARG cc_start: 0.7985 (ttp-110) cc_final: 0.7514 (ttp-110) REVERT: D 190 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7131 (mm-30) REVERT: E 50 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7706 (mt-10) REVERT: E 63 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7214 (tt0) REVERT: E 74 GLU cc_start: 0.7421 (mp0) cc_final: 0.6878 (mp0) REVERT: E 148 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8407 (tttm) REVERT: E 184 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8462 (mm) REVERT: E 194 ASP cc_start: 0.6472 (p0) cc_final: 0.6022 (p0) REVERT: F 54 MET cc_start: 0.7909 (mmm) cc_final: 0.7212 (mtm) REVERT: F 79 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6790 (mmm160) REVERT: F 93 SER cc_start: 0.7839 (p) cc_final: 0.7546 (m) REVERT: F 97 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7618 (pttm) REVERT: F 384 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6939 (t0) REVERT: F 391 TYR cc_start: 0.7994 (t80) cc_final: 0.7551 (t80) REVERT: F 398 SER cc_start: 0.8515 (m) cc_final: 0.8111 (t) REVERT: F 430 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8085 (mtt90) REVERT: F 553 LYS cc_start: 0.8288 (tttt) cc_final: 0.8068 (tttt) REVERT: F 567 LEU cc_start: 0.8689 (mt) cc_final: 0.8472 (mt) REVERT: F 741 VAL cc_start: 0.7830 (t) cc_final: 0.7572 (m) REVERT: F 764 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7420 (mtp) REVERT: F 842 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7699 (mtmm) REVERT: F 866 LEU cc_start: 0.8700 (mp) cc_final: 0.8321 (mt) REVERT: F 900 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6145 (mtp85) REVERT: F 928 GLN cc_start: 0.7796 (tp-100) cc_final: 0.7574 (tp-100) REVERT: F 1010 ASN cc_start: 0.7345 (t0) cc_final: 0.6498 (t0) REVERT: F 1014 ASP cc_start: 0.6672 (m-30) cc_final: 0.6002 (m-30) REVERT: F 1061 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8567 (mp) REVERT: G 41 ASN cc_start: 0.8052 (t0) cc_final: 0.7767 (m-40) REVERT: G 77 ARG cc_start: 0.7902 (mmm160) cc_final: 0.7585 (mmm-85) REVERT: G 90 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7424 (mp0) REVERT: G 144 GLN cc_start: 0.6628 (tp-100) cc_final: 0.6392 (tp-100) REVERT: G 206 ASP cc_start: 0.7702 (t0) cc_final: 0.7434 (t0) REVERT: G 306 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: G 318 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: G 385 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8068 (mp) REVERT: G 501 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7698 (mtt) REVERT: G 672 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: G 768 ASN cc_start: 0.7832 (m-40) cc_final: 0.7597 (m-40) REVERT: G 792 LYS cc_start: 0.7541 (mttt) cc_final: 0.6957 (mttm) REVERT: G 1051 ILE cc_start: -0.0791 (OUTLIER) cc_final: -0.1055 (mt) REVERT: G 1146 GLU cc_start: 0.8149 (tt0) cc_final: 0.7866 (tt0) REVERT: G 1283 HIS cc_start: 0.7158 (t-90) cc_final: 0.6771 (t-90) REVERT: G 1356 SER cc_start: 0.8604 (m) cc_final: 0.8250 (p) REVERT: G 1396 VAL cc_start: 0.8611 (t) cc_final: 0.8275 (m) REVERT: G 1408 ASP cc_start: 0.7633 (m-30) cc_final: 0.7374 (p0) REVERT: H 1 MET cc_start: -0.1189 (mtt) cc_final: -0.1392 (mtt) outliers start: 136 outliers final: 83 residues processed: 874 average time/residue: 0.7822 time to fit residues: 812.6982 Evaluate side-chains 907 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 794 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 165 VAL Chi-restraints excluded: chain A residue 197 ILE 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 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 242 ASN 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 363 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain C residue 31 ILE 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 86 LYS Chi-restraints excluded: chain C residue 94 ASN 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 182 LYS 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 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 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 78 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 184 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 79 ARG Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 119 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 695 ILE 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 876 ASP Chi-restraints excluded: chain F residue 900 ARG Chi-restraints excluded: chain F residue 1061 ILE Chi-restraints excluded: chain F residue 1218 ILE Chi-restraints excluded: chain F residue 1235 SER Chi-restraints excluded: chain G residue 1 MET 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 501 MET Chi-restraints excluded: chain G residue 520 SER 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 675 GLU Chi-restraints excluded: chain G residue 690 THR 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 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 Chi-restraints excluded: chain H residue 25 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 18 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 321 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 83 optimal weight: 0.0980 chunk 315 optimal weight: 0.9990 chunk 274 optimal weight: 2.9990 chunk 436 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 299 HIS ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN F 10 ASN F 56 ASN F 397 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.183562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142263 restraints weight = 55258.035| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.29 r_work: 0.3512 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 39103 Z= 0.163 Angle : 0.559 13.171 53599 Z= 0.293 Chirality : 0.043 0.252 6077 Planarity : 0.004 0.104 6189 Dihedral : 16.956 175.280 7223 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.07 % Rotamer: Outliers : 3.30 % Allowed : 24.93 % Favored : 71.76 % 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: 0.97 (0.13), residues: 4231 helix: 1.49 (0.13), residues: 1657 sheet: 0.49 (0.22), residues: 566 loop : 0.06 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 169 TYR 0.024 0.001 TYR B 254 PHE 0.033 0.001 PHE B 116 TRP 0.057 0.002 TRP B 342 HIS 0.013 0.001 HIS G 788 Details of bonding type rmsd covalent geometry : bond 0.00379 (39096) covalent geometry : angle 0.55347 (53587) SS BOND : bond 0.00503 ( 3) SS BOND : angle 5.91597 ( 6) hydrogen bonds : bond 0.04021 ( 1748) hydrogen bonds : angle 4.33719 ( 4826) metal coordination : bond 0.00905 ( 4) metal coordination : angle 4.36053 ( 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 924 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 801 time to evaluate : 1.416 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: A 25 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8262 (mtmt) REVERT: A 39 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7530 (t80) REVERT: A 40 ARG cc_start: 0.7514 (mtt180) cc_final: 0.7214 (mtt180) REVERT: A 100 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.5916 (pp-130) REVERT: A 127 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6033 (pt0) REVERT: A 226 GLU cc_start: 0.6616 (mt-10) cc_final: 0.6331 (mt-10) REVERT: A 236 VAL cc_start: 0.7940 (OUTLIER) cc_final: 0.7652 (m) REVERT: A 241 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7932 (mmtt) REVERT: A 349 THR cc_start: 0.8201 (t) cc_final: 0.7958 (m) REVERT: B 29 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7343 (t0) REVERT: B 49 LEU cc_start: 0.8203 (tt) cc_final: 0.7957 (tt) REVERT: B 118 LYS cc_start: 0.8282 (mttt) cc_final: 0.7932 (mttp) REVERT: B 128 ARG cc_start: 0.7697 (ttt180) cc_final: 0.7210 (ttt180) REVERT: B 180 MET cc_start: 0.8258 (ttp) cc_final: 0.8002 (ttp) REVERT: B 222 GLU cc_start: 0.7753 (pp20) cc_final: 0.7300 (pp20) REVERT: B 226 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.6048 (tp30) REVERT: B 293 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6992 (tt0) REVERT: B 307 LYS cc_start: 0.8479 (tptm) cc_final: 0.8119 (mmmm) REVERT: B 322 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7453 (pp) REVERT: B 333 LYS cc_start: 0.7954 (mtpp) cc_final: 0.7647 (mtpp) REVERT: B 349 THR cc_start: 0.7024 (m) cc_final: 0.6805 (t) REVERT: B 354 LYS cc_start: 0.7662 (mtpt) cc_final: 0.7405 (mtpt) REVERT: B 363 ILE cc_start: 0.5345 (OUTLIER) cc_final: 0.5078 (mt) REVERT: B 364 ILE cc_start: 0.6014 (OUTLIER) cc_final: 0.5339 (mm) REVERT: C 91 LYS cc_start: 0.8433 (tptt) cc_final: 0.8176 (tptt) REVERT: C 142 LYS cc_start: 0.7867 (mmmm) cc_final: 0.7653 (mmtm) REVERT: C 147 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7006 (tm-30) REVERT: C 151 LYS cc_start: 0.8231 (ttpt) cc_final: 0.8013 (ttpt) REVERT: C 165 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6284 (mmtm) REVERT: C 169 GLU cc_start: 0.7407 (tt0) cc_final: 0.7052 (tt0) REVERT: C 182 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8088 (mtpm) REVERT: C 187 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7383 (tppp) REVERT: C 217 MET cc_start: 0.7530 (mtm) cc_final: 0.7241 (mmm) REVERT: C 250 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6945 (mtt) REVERT: D 11 LYS cc_start: 0.7779 (ptpt) cc_final: 0.7521 (ptpt) REVERT: D 17 SER cc_start: 0.8486 (t) cc_final: 0.8223 (m) REVERT: D 27 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7294 (ptm-80) REVERT: D 64 HIS cc_start: 0.7523 (p-80) cc_final: 0.7211 (p-80) REVERT: D 153 VAL cc_start: 0.8910 (t) cc_final: 0.8530 (p) REVERT: D 178 LYS cc_start: 0.8672 (ttmm) cc_final: 0.8317 (tttp) REVERT: D 188 ARG cc_start: 0.8102 (ttp-110) cc_final: 0.7601 (ttp-110) REVERT: D 190 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7363 (mm-30) REVERT: E 50 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7895 (mt-10) REVERT: E 63 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7623 (tt0) REVERT: E 74 GLU cc_start: 0.7667 (mp0) cc_final: 0.7092 (mp0) REVERT: E 148 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8493 (tttm) REVERT: E 184 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8544 (mm) REVERT: E 194 ASP cc_start: 0.6660 (p0) cc_final: 0.6227 (p0) REVERT: F 79 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.6952 (mmm160) REVERT: F 93 SER cc_start: 0.8055 (p) cc_final: 0.7778 (m) REVERT: F 97 LYS cc_start: 0.8289 (ptpp) cc_final: 0.7871 (pttm) REVERT: F 384 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7155 (t0) REVERT: F 391 TYR cc_start: 0.8223 (t80) cc_final: 0.7780 (t80) REVERT: F 398 SER cc_start: 0.8584 (m) cc_final: 0.8180 (t) REVERT: F 430 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8170 (mtt90) REVERT: F 567 LEU cc_start: 0.8802 (mt) cc_final: 0.8552 (mt) REVERT: F 741 VAL cc_start: 0.7977 (t) cc_final: 0.7719 (m) REVERT: F 764 MET cc_start: 0.7969 (mmp) cc_final: 0.7622 (mtp) REVERT: F 842 LYS cc_start: 0.8120 (mtpt) cc_final: 0.7825 (mtmm) REVERT: F 866 LEU cc_start: 0.8763 (mp) cc_final: 0.8391 (mt) REVERT: F 900 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6354 (mtp85) REVERT: F 928 GLN cc_start: 0.7799 (tp-100) cc_final: 0.7517 (tp-100) REVERT: F 1010 ASN cc_start: 0.7462 (t0) cc_final: 0.6649 (t0) REVERT: F 1014 ASP cc_start: 0.6845 (m-30) cc_final: 0.6201 (m-30) REVERT: G 41 ASN cc_start: 0.8249 (t0) cc_final: 0.7933 (m-40) REVERT: G 77 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7809 (mmm-85) REVERT: G 90 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7657 (mp0) REVERT: G 119 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7791 (mptm) REVERT: G 144 GLN cc_start: 0.6798 (tp-100) cc_final: 0.6543 (tp-100) REVERT: G 200 ASP cc_start: 0.8218 (t0) cc_final: 0.7936 (t0) REVERT: G 206 ASP cc_start: 0.8000 (t0) cc_final: 0.7657 (t0) REVERT: G 209 GLN cc_start: 0.7927 (mp10) cc_final: 0.7574 (mp-120) REVERT: G 306 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: G 318 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: G 351 LYS cc_start: 0.8384 (ttpp) cc_final: 0.8127 (mtpp) REVERT: G 385 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8084 (mp) REVERT: G 672 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: G 768 ASN cc_start: 0.8047 (m-40) cc_final: 0.7810 (m-40) REVERT: G 792 LYS cc_start: 0.7691 (mttt) cc_final: 0.7108 (mttm) REVERT: G 1051 ILE cc_start: -0.0812 (OUTLIER) cc_final: -0.1071 (mt) REVERT: G 1146 GLU cc_start: 0.8335 (tt0) cc_final: 0.8061 (tt0) REVERT: G 1283 HIS cc_start: 0.7483 (t-90) cc_final: 0.7120 (t-90) REVERT: G 1356 SER cc_start: 0.8707 (m) cc_final: 0.8364 (p) REVERT: G 1396 VAL cc_start: 0.8682 (t) cc_final: 0.8346 (m) REVERT: G 1424 MET cc_start: 0.3776 (mmt) cc_final: 0.3520 (mmt) REVERT: H 1 MET cc_start: -0.1192 (mtt) cc_final: -0.1414 (mtt) outliers start: 123 outliers final: 83 residues processed: 862 average time/residue: 0.8085 time to fit residues: 829.5170 Evaluate side-chains 900 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 791 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 165 VAL Chi-restraints excluded: chain A residue 197 ILE 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 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 219 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 364 ILE 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 86 LYS 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 182 LYS 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 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 78 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 184 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 79 ARG Chi-restraints excluded: chain F residue 86 ILE 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 695 ILE Chi-restraints excluded: chain F residue 797 ILE Chi-restraints excluded: chain F residue 876 ASP 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 1235 SER 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 389 MET Chi-restraints excluded: chain G residue 420 LYS Chi-restraints excluded: chain G residue 447 HIS Chi-restraints excluded: chain G residue 520 SER 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 675 GLU Chi-restraints excluded: chain G residue 690 THR 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 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 Chi-restraints excluded: chain H residue 25 THR 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: 6.9990 chunk 384 optimal weight: 50.0000 chunk 247 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 418 optimal weight: 0.5980 chunk 278 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 182 optimal weight: 0.3980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 299 HIS B 8 HIS ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN E 186 ASN F 10 ASN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 741 GLN G 773 ASN G 857 HIS G1254 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.181953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.140612 restraints weight = 54712.271| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.17 r_work: 0.3494 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 39103 Z= 0.246 Angle : 0.609 13.061 53599 Z= 0.319 Chirality : 0.046 0.263 6077 Planarity : 0.005 0.114 6189 Dihedral : 16.997 175.483 7218 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 3.25 % Allowed : 25.20 % Favored : 71.55 % 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: 0.79 (0.13), residues: 4231 helix: 1.32 (0.13), residues: 1647 sheet: 0.37 (0.22), residues: 583 loop : 0.00 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 169 TYR 0.030 0.002 TYR B 296 PHE 0.033 0.002 PHE B 116 TRP 0.083 0.002 TRP B 342 HIS 0.013 0.001 HIS G 788 Details of bonding type rmsd covalent geometry : bond 0.00579 (39096) covalent geometry : angle 0.60344 (53587) SS BOND : bond 0.00539 ( 3) SS BOND : angle 6.27077 ( 6) hydrogen bonds : bond 0.04595 ( 1748) hydrogen bonds : angle 4.50638 ( 4826) metal coordination : bond 0.01300 ( 4) metal coordination : angle 4.87103 ( 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 939 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 818 time to evaluate : 1.449 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 25 LYS cc_start: 0.8460 (mtmt) cc_final: 0.8238 (mtmt) REVERT: A 39 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7491 (t80) REVERT: A 40 ARG cc_start: 0.7556 (mtt180) cc_final: 0.7222 (mtt180) REVERT: A 100 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.5879 (pp-130) REVERT: A 127 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6154 (pt0) REVERT: A 163 TYR cc_start: 0.6819 (OUTLIER) cc_final: 0.6506 (m-10) REVERT: A 226 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6286 (mt-10) REVERT: A 236 VAL cc_start: 0.7939 (OUTLIER) cc_final: 0.7632 (m) REVERT: A 241 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7893 (mmtt) REVERT: A 349 THR cc_start: 0.8267 (t) cc_final: 0.8008 (m) REVERT: B 29 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7357 (t0) REVERT: B 49 LEU cc_start: 0.8202 (tt) cc_final: 0.7880 (tt) REVERT: B 118 LYS cc_start: 0.8319 (mttt) cc_final: 0.7967 (mttp) REVERT: B 128 ARG cc_start: 0.7783 (ttt180) cc_final: 0.7299 (ttt180) REVERT: B 180 MET cc_start: 0.8249 (ttp) cc_final: 0.7992 (ttp) REVERT: B 222 GLU cc_start: 0.7772 (pp20) cc_final: 0.7329 (pp20) REVERT: B 226 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.5907 (mp0) REVERT: B 243 ARG cc_start: 0.6830 (tmm-80) cc_final: 0.6389 (tmm-80) REVERT: B 322 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7474 (pp) REVERT: B 333 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7617 (mtpp) REVERT: B 354 LYS cc_start: 0.7691 (mtpt) cc_final: 0.7397 (mtpt) REVERT: C 91 LYS cc_start: 0.8438 (tptt) cc_final: 0.8198 (tptt) REVERT: C 142 LYS cc_start: 0.7894 (mmmm) cc_final: 0.7681 (mmtm) REVERT: C 147 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6928 (tm-30) REVERT: C 165 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6312 (mmtm) REVERT: C 169 GLU cc_start: 0.7457 (tt0) cc_final: 0.7093 (tt0) REVERT: C 182 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8130 (mtpm) REVERT: C 187 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7399 (tppp) REVERT: C 217 MET cc_start: 0.7531 (mtm) cc_final: 0.7235 (mmm) REVERT: C 250 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6946 (mtt) REVERT: D 11 LYS cc_start: 0.7793 (ptpt) cc_final: 0.7536 (ptpt) REVERT: D 17 SER cc_start: 0.8481 (t) cc_final: 0.8229 (m) REVERT: D 27 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7320 (ptm-80) REVERT: D 64 HIS cc_start: 0.7619 (p-80) cc_final: 0.7302 (p-80) REVERT: D 153 VAL cc_start: 0.8912 (t) cc_final: 0.8545 (p) REVERT: D 178 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8382 (tttp) REVERT: D 188 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7587 (ttp-110) REVERT: D 190 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7388 (mm-30) REVERT: E 50 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7998 (mt-10) REVERT: E 63 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7515 (tt0) REVERT: E 74 GLU cc_start: 0.7664 (mp0) cc_final: 0.7101 (mp0) REVERT: E 148 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8456 (tttm) REVERT: E 184 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8563 (mm) REVERT: E 194 ASP cc_start: 0.6627 (p0) cc_final: 0.6174 (p0) REVERT: E 196 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7140 (mt-10) REVERT: F 79 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.6852 (mmm160) REVERT: F 93 SER cc_start: 0.8039 (p) cc_final: 0.7772 (m) REVERT: F 97 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7870 (pttt) REVERT: F 384 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7211 (t0) REVERT: F 391 TYR cc_start: 0.8216 (t80) cc_final: 0.7758 (t80) REVERT: F 398 SER cc_start: 0.8581 (m) cc_final: 0.8195 (t) REVERT: F 430 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8152 (mtt90) REVERT: F 567 LEU cc_start: 0.8810 (mt) cc_final: 0.8562 (mt) REVERT: F 741 VAL cc_start: 0.8007 (t) cc_final: 0.7724 (m) REVERT: F 764 MET cc_start: 0.7994 (mmp) cc_final: 0.7628 (mtp) REVERT: F 842 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7831 (mtmm) REVERT: F 866 LEU cc_start: 0.8755 (mp) cc_final: 0.8397 (mt) REVERT: F 900 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6231 (mtp85) REVERT: F 928 GLN cc_start: 0.7831 (tp-100) cc_final: 0.7556 (tp-100) REVERT: F 1010 ASN cc_start: 0.7586 (t0) cc_final: 0.6899 (t160) REVERT: F 1014 ASP cc_start: 0.6901 (m-30) cc_final: 0.6275 (m-30) REVERT: G 41 ASN cc_start: 0.8263 (t0) cc_final: 0.7882 (m-40) REVERT: G 77 ARG cc_start: 0.8182 (mmm160) cc_final: 0.7839 (mmm-85) REVERT: G 90 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7670 (mp0) REVERT: G 119 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7895 (mptp) REVERT: G 144 GLN cc_start: 0.6859 (tp-100) cc_final: 0.6555 (tp-100) REVERT: G 161 PHE cc_start: 0.8462 (m-80) cc_final: 0.8229 (m-80) REVERT: G 200 ASP cc_start: 0.8227 (t0) cc_final: 0.7997 (t0) REVERT: G 206 ASP cc_start: 0.7985 (t0) cc_final: 0.7654 (t0) REVERT: G 306 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: G 318 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: G 385 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8167 (mp) REVERT: G 672 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: G 768 ASN cc_start: 0.8053 (m-40) cc_final: 0.7835 (m-40) REVERT: G 792 LYS cc_start: 0.7744 (mttt) cc_final: 0.7142 (mttm) REVERT: G 1051 ILE cc_start: -0.0820 (OUTLIER) cc_final: -0.1079 (mt) REVERT: G 1146 GLU cc_start: 0.8301 (tt0) cc_final: 0.8006 (tt0) REVERT: G 1283 HIS cc_start: 0.7431 (t-90) cc_final: 0.7020 (t-90) REVERT: G 1356 SER cc_start: 0.8677 (m) cc_final: 0.8340 (p) REVERT: G 1396 VAL cc_start: 0.8682 (t) cc_final: 0.8366 (m) REVERT: G 1408 ASP cc_start: 0.7876 (m-30) cc_final: 0.7484 (p0) REVERT: H 1 MET cc_start: -0.1180 (mtt) cc_final: -0.1403 (mtt) outliers start: 121 outliers final: 83 residues processed: 875 average time/residue: 0.8339 time to fit residues: 869.2688 Evaluate side-chains 915 residues out of total 3722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 806 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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 163 TYR Chi-restraints excluded: chain A residue 165 VAL 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 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 226 GLU Chi-restraints excluded: chain B residue 242 ASN 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 364 ILE Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 86 LYS 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 182 LYS 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 8 LYS 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 108 GLU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 184 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 79 ARG Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 97 LYS 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 433 ARG Chi-restraints excluded: chain F residue 456 LYS Chi-restraints excluded: chain F residue 474 PHE Chi-restraints excluded: chain F residue 695 ILE Chi-restraints excluded: chain F residue 797 ILE Chi-restraints excluded: chain F residue 876 ASP 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 1235 SER Chi-restraints excluded: chain F residue 1265 ILE 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 156 ILE 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 447 HIS 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 675 GLU Chi-restraints excluded: chain G residue 690 THR 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 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 Chi-restraints excluded: chain H residue 25 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 81 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 339 optimal weight: 3.9990 chunk 285 optimal weight: 0.7980 chunk 148 optimal weight: 0.5980 chunk 312 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 307 optimal weight: 2.9990 chunk 404 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 216 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 299 HIS ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 ASN F 56 ASN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 741 GLN G 773 ASN G 857 HIS 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 = 0.182885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141549 restraints weight = 54995.109| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.33 r_work: 0.3503 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1310 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= 0.169 Angle : 0.576 12.976 53599 Z= 0.302 Chirality : 0.043 0.277 6077 Planarity : 0.004 0.117 6189 Dihedral : 16.976 175.714 7217 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.07 % Rotamer: Outliers : 2.98 % Allowed : 25.69 % 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: 0.85 (0.13), residues: 4231 helix: 1.38 (0.13), residues: 1656 sheet: 0.41 (0.22), residues: 572 loop : 0.01 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 169 TYR 0.034 0.001 TYR B 296 PHE 0.031 0.001 PHE B 116 TRP 0.093 0.002 TRP B 342 HIS 0.014 0.001 HIS G 788 Details of bonding type rmsd covalent geometry : bond 0.00392 (39096) covalent geometry : angle 0.57063 (53587) SS BOND : bond 0.00493 ( 3) SS BOND : angle 5.94387 ( 6) hydrogen bonds : bond 0.04175 ( 1748) hydrogen bonds : angle 4.42724 ( 4826) metal coordination : bond 0.00983 ( 4) metal coordination : angle 4.44969 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20671.69 seconds wall clock time: 350 minutes 54.44 seconds (21054.44 seconds total)