Starting phenix.real_space_refine on Fri Aug 7 20:10:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fuk_29459/08_2026/8fuk_29459.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fuk_29459/08_2026/8fuk_29459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8fuk_29459/08_2026/8fuk_29459.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fuk_29459/08_2026/8fuk_29459.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fuk_29459/08_2026/8fuk_29459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fuk_29459/08_2026/8fuk_29459.map" model { file = "/net/cci-nas-00/data/ceres_data/8fuk_29459/08_2026/8fuk_29459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fuk_29459/08_2026/8fuk_29459.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 108 5.16 5 C 14806 2.51 5 N 4091 2.21 5 O 4544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23608 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1280 Classifications: {'RNAv2': 60} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p_pur': 20, 'rna3p_pyr': 14} Link IDs: {'rna2p': 26, 'rna3p': 33} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2635 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 16, 'TRANS': 312} Chain breaks: 2 Chain: "B" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2696 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Chain: "C" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2630 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 311} Chain breaks: 2 Chain: "D" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2687 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 318} Chain breaks: 1 Chain: "E" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2662 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 315} Chain breaks: 2 Chain: "F" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2377 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 280} Chain breaks: 3 Chain: "G" Number of atoms: 2653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2653 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 17, 'TRANS': 321} Chain breaks: 4 Chain: "H" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1611 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "I" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1507 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain breaks: 2 Chain: "J" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 870 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain breaks: 3 Time building chain proxies: 4.99, per 1000 atoms: 0.21 Number of scatterers: 23608 At special positions: 0 Unit cell: (118.44, 168.26, 174.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 59 15.00 O 4544 8.00 N 4091 7.00 C 14806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5300 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 43 sheets defined 37.9% alpha, 18.4% beta 6 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.583A pdb=" N ASN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 146 removed outlier: 6.857A pdb=" N LYS A 144 " --> pdb=" O TRP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 260 through 268 removed outlier: 3.665A pdb=" N THR A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.714A pdb=" N GLU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 344 removed outlier: 3.528A pdb=" N LYS A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.826A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 Processing helix chain 'B' and resid 105 through 123 Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.922A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 136 " --> pdb=" O TYR B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 removed outlier: 6.627A pdb=" N LYS B 144 " --> pdb=" O TRP B 141 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 146 " --> pdb=" O TRP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 Processing helix chain 'B' and resid 186 through 199 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 291 through 294 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 312 through 323 removed outlier: 3.894A pdb=" N ASN B 323 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 344 Processing helix chain 'C' and resid 45 through 50 Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.655A pdb=" N GLN C 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 66 Processing helix chain 'C' and resid 105 through 123 removed outlier: 3.532A pdb=" N LYS C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 Processing helix chain 'C' and resid 139 through 147 removed outlier: 6.710A pdb=" N LYS C 144 " --> pdb=" O TRP C 141 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 146 " --> pdb=" O TRP C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 186 through 200 removed outlier: 3.783A pdb=" N GLU C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 291 through 294 Processing helix chain 'C' and resid 299 through 303 Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 328 through 344 Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 61 through 66 Processing helix chain 'D' and resid 105 through 123 removed outlier: 3.581A pdb=" N LYS D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.603A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 removed outlier: 6.576A pdb=" N LYS D 144 " --> pdb=" O TRP D 141 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR D 146 " --> pdb=" O TRP D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 186 through 199 removed outlier: 3.632A pdb=" N ILE D 194 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 312 through 321 Processing helix chain 'D' and resid 327 through 344 Processing helix chain 'E' and resid 45 through 51 removed outlier: 3.715A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 67 Processing helix chain 'E' and resid 105 through 123 removed outlier: 3.577A pdb=" N LYS E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 138 removed outlier: 3.611A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 146 removed outlier: 6.630A pdb=" N LYS E 144 " --> pdb=" O TRP E 141 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR E 146 " --> pdb=" O TRP E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 175 removed outlier: 3.677A pdb=" N TYR E 175 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'E' and resid 186 through 200 removed outlier: 3.874A pdb=" N ILE E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 194 " --> pdb=" O ILE E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 269 Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 312 through 322 Processing helix chain 'E' and resid 327 through 343 Processing helix chain 'F' and resid 105 through 123 removed outlier: 3.686A pdb=" N LYS F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 138 removed outlier: 3.825A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 147 removed outlier: 6.520A pdb=" N LYS F 144 " --> pdb=" O TRP F 141 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR F 146 " --> pdb=" O TRP F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 183 Processing helix chain 'F' and resid 186 through 200 removed outlier: 3.649A pdb=" N ILE F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 269 Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 305 through 311 Processing helix chain 'F' and resid 312 through 323 removed outlier: 3.812A pdb=" N ASN F 323 " --> pdb=" O VAL F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 344 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 218 through 230 removed outlier: 3.771A pdb=" N ARG G 228 " --> pdb=" O HIS G 224 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN G 230 " --> pdb=" O HIS G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 411 through 428 removed outlier: 3.753A pdb=" N ARG G 428 " --> pdb=" O ARG G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 492 through 499 Processing helix chain 'G' and resid 513 through 519 removed outlier: 4.337A pdb=" N LYS G 517 " --> pdb=" O ASP G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 530 removed outlier: 3.874A pdb=" N GLU G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 561 removed outlier: 3.835A pdb=" N GLU G 559 " --> pdb=" O ALA G 555 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP G 560 " --> pdb=" O ALA G 556 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 612 Processing helix chain 'H' and resid 16 through 35 Processing helix chain 'H' and resid 62 through 70 Processing helix chain 'H' and resid 72 through 80 removed outlier: 3.748A pdb=" N GLN H 80 " --> pdb=" O VAL H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 111 removed outlier: 3.800A pdb=" N LYS H 109 " --> pdb=" O GLN H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 Processing helix chain 'I' and resid 198 through 206 removed outlier: 3.968A pdb=" N ASN I 202 " --> pdb=" O CYS I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 230 removed outlier: 4.269A pdb=" N GLY I 229 " --> pdb=" O HIS I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 245 removed outlier: 4.408A pdb=" N GLN I 242 " --> pdb=" O PHE I 238 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE I 243 " --> pdb=" O SER I 239 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE I 244 " --> pdb=" O PHE I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 265 Processing helix chain 'I' and resid 274 through 279 Processing helix chain 'I' and resid 279 through 288 removed outlier: 4.282A pdb=" N ARG I 288 " --> pdb=" O PHE I 284 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 Processing helix chain 'I' and resid 317 through 320 removed outlier: 3.710A pdb=" N ASN I 320 " --> pdb=" O LEU I 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 317 through 320' Processing helix chain 'I' and resid 324 through 333 Processing helix chain 'I' and resid 335 through 345 Processing helix chain 'I' and resid 369 through 380 Processing helix chain 'I' and resid 386 through 390 Processing helix chain 'J' and resid 13 through 26 removed outlier: 3.947A pdb=" N GLY J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 45 Processing helix chain 'J' and resid 60 through 64 removed outlier: 3.735A pdb=" N ALA J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 81 removed outlier: 3.775A pdb=" N ARG J 71 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 139 removed outlier: 3.887A pdb=" N ALA J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER J 139 " --> pdb=" O ASN J 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 134 through 139' Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 15 removed outlier: 3.613A pdb=" N HIS A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 13 through 15 Processing sheet with id=AA4, first strand: chain 'A' and resid 35 through 42 removed outlier: 7.942A pdb=" N SER A 243 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLN A 72 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 251 Processing sheet with id=AA6, first strand: chain 'A' and resid 288 through 290 removed outlier: 3.631A pdb=" N HIS A 290 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 295 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 9 Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.516A pdb=" N SER B 88 " --> pdb=" O CYS B 19 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS B 84 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AB1, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AB2, first strand: chain 'B' and resid 289 through 290 Processing sheet with id=AB3, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AB4, first strand: chain 'C' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 23 current: chain 'C' and resid 151 through 159 Processing sheet with id=AB5, first strand: chain 'C' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 94 current: chain 'C' and resid 248 through 251 Processing sheet with id=AB6, first strand: chain 'C' and resid 35 through 42 removed outlier: 8.624A pdb=" N SER C 243 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N GLN C 72 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AB8, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.519A pdb=" N THR C 295 " --> pdb=" O HIS C 290 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 102 through 103 Processing sheet with id=AC1, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.510A pdb=" N SER D 88 " --> pdb=" O CYS D 19 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AC3, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AC4, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AC5, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AC6, first strand: chain 'D' and resid 289 through 290 Processing sheet with id=AC7, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AC8, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.551A pdb=" N SER E 92 " --> pdb=" O ASP E 14 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER E 88 " --> pdb=" O CYS E 19 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 23 current: chain 'E' and resid 152 through 159 Processing sheet with id=AC9, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.524A pdb=" N SER E 88 " --> pdb=" O CYS E 19 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 84 through 94 current: chain 'E' and resid 248 through 251 Processing sheet with id=AD1, first strand: chain 'E' and resid 35 through 42 Processing sheet with id=AD2, first strand: chain 'F' and resid 102 through 103 Processing sheet with id=AD3, first strand: chain 'F' and resid 29 through 31 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 31 removed outlier: 4.260A pdb=" N PHE F 20 " --> pdb=" O PRO F 257 " (cutoff:3.500A) removed outlier: 10.465A pdb=" N VAL F 22 " --> pdb=" O ARG F 255 " (cutoff:3.500A) removed outlier: 14.001A pdb=" N ARG F 255 " --> pdb=" O VAL F 22 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 72 through 75 removed outlier: 6.415A pdb=" N SER F 36 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE H 146 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR F 38 " --> pdb=" O ILE H 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 288 through 289 Processing sheet with id=AD7, first strand: chain 'G' and resid 201 through 203 removed outlier: 3.909A pdb=" N GLY G 569 " --> pdb=" O ILE G 594 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL G 568 " --> pdb=" O VAL G 625 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 236 through 240 Processing sheet with id=AD9, first strand: chain 'G' and resid 508 through 511 Processing sheet with id=AE1, first strand: chain 'G' and resid 508 through 511 removed outlier: 5.787A pdb=" N PHE G 387 " --> pdb=" O THR G 485 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR G 485 " --> pdb=" O PHE G 387 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL G 389 " --> pdb=" O LEU G 483 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU G 483 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU G 481 " --> pdb=" O PRO G 391 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL G 478 " --> pdb=" O HIS G 443 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER G 437 " --> pdb=" O ASN G 484 " (cutoff:3.500A) removed outlier: 15.508A pdb=" N PHE G 438 " --> pdb=" O LEU G 542 " (cutoff:3.500A) removed outlier: 10.628A pdb=" N LEU G 542 " --> pdb=" O PHE G 438 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE G 440 " --> pdb=" O LEU G 540 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 398 through 399 removed outlier: 4.037A pdb=" N ASP G 472 " --> pdb=" O ARG G 450 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG G 450 " --> pdb=" O ASP G 472 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 41 through 43 Processing sheet with id=AE4, first strand: chain 'H' and resid 41 through 43 removed outlier: 3.600A pdb=" N TYR H 5 " --> pdb=" O VAL H 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 167 through 171 Processing sheet with id=AE6, first strand: chain 'I' and resid 322 through 323 Processing sheet with id=AE7, first strand: chain 'J' and resid 95 through 96 921 hydrogen bonds defined for protein. 2445 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 2.33 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: 7250 1.34 - 1.46: 4634 1.46 - 1.58: 12162 1.58 - 1.70: 119 1.70 - 1.82: 160 Bond restraints: 24325 Sorted by residual: bond pdb=" CB PRO J 87 " pdb=" CG PRO J 87 " ideal model delta sigma weight residual 1.492 1.651 -0.159 5.00e-02 4.00e+02 1.01e+01 bond pdb=" CG PRO J 86 " pdb=" CD PRO J 86 " ideal model delta sigma weight residual 1.503 1.549 -0.046 3.40e-02 8.65e+02 1.81e+00 bond pdb=" SD MET I 228 " pdb=" CE MET I 228 " ideal model delta sigma weight residual 1.791 1.764 0.027 2.50e-02 1.60e+03 1.20e+00 bond pdb=" CB PRO J 86 " pdb=" CG PRO J 86 " ideal model delta sigma weight residual 1.492 1.546 -0.054 5.00e-02 4.00e+02 1.17e+00 bond pdb=" CA ASN H 188 " pdb=" CB ASN H 188 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.84e-02 2.95e+03 1.02e+00 ... (remaining 24320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 32609 2.09 - 4.19: 601 4.19 - 6.28: 72 6.28 - 8.38: 11 8.38 - 10.47: 2 Bond angle restraints: 33295 Sorted by residual: angle pdb=" CA PRO J 87 " pdb=" N PRO J 87 " pdb=" CD PRO J 87 " ideal model delta sigma weight residual 112.00 101.53 10.47 1.40e+00 5.10e-01 5.60e+01 angle pdb=" N HIS J 31 " pdb=" CA HIS J 31 " pdb=" C HIS J 31 " ideal model delta sigma weight residual 113.29 105.80 7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" N MET I 228 " pdb=" CA MET I 228 " pdb=" CB MET I 228 " ideal model delta sigma weight residual 110.01 115.10 -5.09 1.45e+00 4.76e-01 1.23e+01 angle pdb=" CA LYS G 577 " pdb=" CB LYS G 577 " pdb=" CG LYS G 577 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N PRO J 87 " pdb=" CD PRO J 87 " pdb=" CG PRO J 87 " ideal model delta sigma weight residual 103.20 98.24 4.96 1.50e+00 4.44e-01 1.10e+01 ... (remaining 33290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 12373 17.75 - 35.50: 1468 35.50 - 53.25: 396 53.25 - 70.99: 195 70.99 - 88.74: 54 Dihedral angle restraints: 14486 sinusoidal: 6336 harmonic: 8150 Sorted by residual: dihedral pdb=" C4' G 1 20 " pdb=" C3' G 1 20 " pdb=" C2' G 1 20 " pdb=" C1' G 1 20 " ideal model delta sinusoidal sigma weight residual 36.34 -42.07 78.42 1 3.10e+00 1.04e-01 7.98e+02 dihedral pdb=" C4' C 1 21 " pdb=" C3' C 1 21 " pdb=" C2' C 1 21 " pdb=" C1' C 1 21 " ideal model delta sinusoidal sigma weight residual 36.34 -40.85 77.19 1 3.10e+00 1.04e-01 7.78e+02 dihedral pdb=" C4' U 1 33 " pdb=" C3' U 1 33 " pdb=" C2' U 1 33 " pdb=" C1' U 1 33 " ideal model delta sinusoidal sigma weight residual 36.34 -40.25 76.59 1 3.10e+00 1.04e-01 7.67e+02 ... (remaining 14483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3169 0.062 - 0.124: 404 0.124 - 0.186: 36 0.186 - 0.248: 65 0.248 - 0.310: 31 Chirality restraints: 3705 Sorted by residual: chirality pdb=" C2' C 1 44 " pdb=" C3' C 1 44 " pdb=" O2' C 1 44 " pdb=" C1' C 1 44 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" P A 1 55 " pdb=" OP1 A 1 55 " pdb=" OP2 A 1 55 " pdb=" O5' A 1 55 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C2' A 1 53 " pdb=" C3' A 1 53 " pdb=" O2' A 1 53 " pdb=" C1' A 1 53 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 3702 not shown) Planarity restraints: 4033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 281 " 0.411 9.50e-02 1.11e+02 1.85e-01 2.67e+01 pdb=" NE ARG I 281 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG I 281 " 0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG I 281 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG I 281 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO J 86 " -0.061 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO J 87 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO J 87 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO J 87 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 274 " -0.258 9.50e-02 1.11e+02 1.17e-01 1.07e+01 pdb=" NE ARG I 274 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG I 274 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG I 274 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG I 274 " -0.000 2.00e-02 2.50e+03 ... (remaining 4030 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 286 2.63 - 3.20: 21234 3.20 - 3.77: 36377 3.77 - 4.33: 49444 4.33 - 4.90: 83092 Nonbonded interactions: 190433 Sorted by model distance: nonbonded pdb=" OG SER A 94 " pdb=" OE1 GLU A 96 " model vdw 2.068 3.040 nonbonded pdb=" O HIS F 299 " pdb=" OG1 THR F 302 " model vdw 2.217 3.040 nonbonded pdb=" OE1 GLU I 256 " pdb=" OH TYR I 306 " model vdw 2.217 3.040 nonbonded pdb=" OG SER A 95 " pdb=" O ALA A 197 " model vdw 2.227 3.040 nonbonded pdb=" OE2 GLU D 44 " pdb=" NZ LYS E 343 " model vdw 2.240 3.120 ... (remaining 190428 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 2 through 25 or resid 28 through 40 or resid 71 through 22 \ 8 or resid 243 through 272 or resid 283 through 317 or resid 327 through 348)) selection = (chain 'B' and (resid 2 through 25 or resid 28 through 40 or resid 71 through 22 \ 8 or resid 243 through 272 or resid 283 through 317 or resid 327 through 348)) selection = (chain 'C' and (resid 2 through 25 or resid 28 through 40 or resid 71 through 22 \ 8 or resid 243 through 272 or resid 283 through 348)) selection = (chain 'D' and (resid 2 through 25 or resid 28 through 40 or resid 71 through 22 \ 8 or resid 243 through 272 or resid 283 through 317 or resid 327 through 348)) selection = (chain 'E' and (resid 2 through 40 or resid 71 through 228 or resid 243 through \ 272 or resid 283 through 317 or resid 327 through 348)) selection = (chain 'F' and (resid 2 through 25 or resid 28 through 317 or resid 327 through \ 348)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.890 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.340 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 0.159 24325 Z= 0.133 Angle : 0.625 10.475 33295 Z= 0.309 Chirality : 0.057 0.310 3705 Planarity : 0.006 0.185 4033 Dihedral : 18.265 88.743 9186 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.24 % Allowed : 20.04 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.29 (0.16), residues: 2724 helix: 0.59 (0.18), residues: 883 sheet: 0.76 (0.24), residues: 497 loop : -0.20 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG I 281 TYR 0.020 0.001 TYR E 275 PHE 0.028 0.001 PHE A 306 TRP 0.010 0.001 TRP G 539 HIS 0.014 0.001 HIS J 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (24325) covalent geometry : angle 0.62479 / 0.31 (33295) hydrogen bonds : bond 0.21344 / 11.00 ( 907) hydrogen bonds : angle 7.59582 / 3.48 ( 2473) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 234 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 132 GLN cc_start: 0.7603 (pm20) cc_final: 0.7053 (mm-40) REVERT: H 173 GLN cc_start: 0.7109 (tm-30) cc_final: 0.5909 (pm20) REVERT: I 388 SER cc_start: 0.7526 (t) cc_final: 0.7315 (p) outliers start: 6 outliers final: 2 residues processed: 236 average time/residue: 0.1542 time to fit residues: 57.6240 Evaluate side-chains 233 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 231 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain G residue 263 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0370 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN E 218 ASN F 179 GLN ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.098824 restraints weight = 35786.318| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.12 r_work: 0.3146 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24325 Z= 0.187 Angle : 0.773 14.112 33295 Z= 0.356 Chirality : 0.065 1.009 3705 Planarity : 0.004 0.045 4033 Dihedral : 14.943 154.888 3904 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.54 % Allowed : 17.52 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.24 (0.16), residues: 2724 helix: 0.59 (0.17), residues: 915 sheet: 0.65 (0.24), residues: 501 loop : -0.24 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 291 TYR 0.016 0.001 TYR B 275 PHE 0.021 0.001 PHE A 306 TRP 0.012 0.001 TRP H 47 HIS 0.008 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (24325) covalent geometry : angle 0.77267 / 0.36 (33295) hydrogen bonds : bond 0.04354 / 2.26 ( 907) hydrogen bonds : angle 5.36581 / 2.42 ( 2473) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 243 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8968 (pp) REVERT: A 306 PHE cc_start: 0.7476 (t80) cc_final: 0.7157 (t80) REVERT: B 97 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8833 (pt) REVERT: H 18 GLU cc_start: 0.8906 (mp0) cc_final: 0.8656 (mp0) REVERT: H 94 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6720 (tm-30) REVERT: H 173 GLN cc_start: 0.7296 (tm-30) cc_final: 0.5507 (pm20) REVERT: H 190 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7017 (pm20) REVERT: I 287 ILE cc_start: 0.8048 (mm) cc_final: 0.7768 (mm) REVERT: J 39 ARG cc_start: 0.7713 (mtp-110) cc_final: 0.7483 (mtm110) outliers start: 87 outliers final: 50 residues processed: 303 average time/residue: 0.1552 time to fit residues: 76.7345 Evaluate side-chains 276 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 455 GLU Chi-restraints excluded: chain G residue 482 ILE Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 220 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 250 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 235 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 348 GLN E 104 ASN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 626 GLN ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.142410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.101012 restraints weight = 35613.286| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.12 r_work: 0.3182 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24325 Z= 0.133 Angle : 0.636 13.091 33295 Z= 0.302 Chirality : 0.053 0.544 3705 Planarity : 0.004 0.042 4033 Dihedral : 15.121 154.023 3901 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.99 % Allowed : 18.00 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.25 (0.16), residues: 2724 helix: 0.70 (0.18), residues: 911 sheet: 0.53 (0.24), residues: 511 loop : -0.27 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 291 TYR 0.015 0.001 TYR E 275 PHE 0.023 0.001 PHE I 238 TRP 0.010 0.001 TRP A 152 HIS 0.007 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (24325) covalent geometry : angle 0.63560 / 0.30 (33295) hydrogen bonds : bond 0.03592 / 1.87 ( 907) hydrogen bonds : angle 4.92418 / 2.21 ( 2473) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 235 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8498 (mmp) cc_final: 0.8245 (mmt) REVERT: B 97 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8803 (pt) REVERT: B 348 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8120 (pp30) REVERT: E 57 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8463 (tp) REVERT: E 324 LYS cc_start: 0.8613 (mtmm) cc_final: 0.8225 (ptmm) REVERT: H 33 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.7221 (m-80) REVERT: H 94 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6642 (tm-30) REVERT: H 154 GLU cc_start: 0.7505 (tp30) cc_final: 0.7099 (tp30) REVERT: H 173 GLN cc_start: 0.7135 (tm-30) cc_final: 0.5366 (pm20) REVERT: H 190 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: I 287 ILE cc_start: 0.8120 (mm) cc_final: 0.7758 (mm) REVERT: J 15 GLU cc_start: 0.8555 (mp0) cc_final: 0.8296 (mp0) outliers start: 98 outliers final: 56 residues processed: 308 average time/residue: 0.1443 time to fit residues: 71.8613 Evaluate side-chains 283 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 222 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 153 ASN Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 525 LEU Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 62 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 260 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 240 optimal weight: 0.9980 chunk 234 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 54 optimal weight: 0.0980 chunk 50 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 348 GLN E 290 HIS F 299 HIS ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 105 GLN ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 ASN I 265 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.143802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102215 restraints weight = 35670.039| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.19 r_work: 0.3200 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24325 Z= 0.112 Angle : 0.590 11.722 33295 Z= 0.282 Chirality : 0.049 0.407 3705 Planarity : 0.004 0.043 4033 Dihedral : 14.990 160.159 3901 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.67 % Allowed : 19.35 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.36 (0.16), residues: 2724 helix: 0.84 (0.18), residues: 906 sheet: 0.54 (0.24), residues: 510 loop : -0.22 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 20 TYR 0.017 0.001 TYR E 275 PHE 0.015 0.001 PHE I 238 TRP 0.010 0.001 TRP H 47 HIS 0.006 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (24325) covalent geometry : angle 0.59018 / 0.28 (33295) hydrogen bonds : bond 0.03226 / 1.68 ( 907) hydrogen bonds : angle 4.72039 / 2.12 ( 2473) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 247 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8569 (mmp) cc_final: 0.8369 (mmt) REVERT: B 97 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8742 (pt) REVERT: B 283 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7361 (ttt90) REVERT: C 183 ASN cc_start: 0.8200 (m-40) cc_final: 0.7941 (m-40) REVERT: D 55 GLN cc_start: 0.8987 (tt0) cc_final: 0.8726 (tp40) REVERT: E 57 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8466 (tp) REVERT: E 324 LYS cc_start: 0.8620 (mtmm) cc_final: 0.8280 (ptmm) REVERT: F 292 GLU cc_start: 0.7705 (mp0) cc_final: 0.7478 (mp0) REVERT: G 455 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: H 33 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.7072 (m-80) REVERT: H 94 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6654 (tm-30) REVERT: H 173 GLN cc_start: 0.7039 (tm-30) cc_final: 0.5351 (pm20) REVERT: H 190 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7256 (pm20) REVERT: I 372 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7631 (mt) REVERT: J 88 GLU cc_start: 0.7847 (tp30) cc_final: 0.7555 (tp30) outliers start: 90 outliers final: 55 residues processed: 312 average time/residue: 0.1568 time to fit residues: 79.1075 Evaluate side-chains 279 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 455 GLU Chi-restraints excluded: chain G residue 525 LEU Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 89 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 277 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 GLN C 67 GLN E 6 ASN ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 520 ASN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.140621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.098802 restraints weight = 35864.085| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.20 r_work: 0.3147 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24325 Z= 0.165 Angle : 0.627 10.928 33295 Z= 0.303 Chirality : 0.051 0.430 3705 Planarity : 0.004 0.046 4033 Dihedral : 15.002 161.004 3901 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.11 % Allowed : 19.43 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.20 (0.16), residues: 2724 helix: 0.70 (0.17), residues: 909 sheet: 0.44 (0.23), residues: 508 loop : -0.31 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 20 TYR 0.017 0.001 TYR B 275 PHE 0.016 0.001 PHE J 17 TRP 0.012 0.001 TRP H 47 HIS 0.006 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (24325) covalent geometry : angle 0.62678 / 0.30 (33295) hydrogen bonds : bond 0.03554 / 1.85 ( 907) hydrogen bonds : angle 4.77439 / 2.13 ( 2473) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 220 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8959 (pp) REVERT: B 97 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8834 (pt) REVERT: D 55 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8667 (tp40) REVERT: E 57 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8506 (tp) REVERT: E 324 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8186 (ptmm) REVERT: F 156 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7773 (pp) REVERT: G 455 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: H 33 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.7108 (m-80) REVERT: H 94 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6647 (tm-30) REVERT: H 105 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7707 (mt0) REVERT: I 372 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7689 (mt) REVERT: I 386 ASN cc_start: 0.7895 (t0) cc_final: 0.7452 (t0) REVERT: J 15 GLU cc_start: 0.8564 (mp0) cc_final: 0.8319 (mp0) REVERT: J 137 TYR cc_start: 0.7018 (m-80) cc_final: 0.6688 (m-80) outliers start: 101 outliers final: 68 residues processed: 295 average time/residue: 0.1561 time to fit residues: 74.6417 Evaluate side-chains 291 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 214 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 453 THR Chi-restraints excluded: chain G residue 455 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 131 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 171 optimal weight: 0.4980 chunk 193 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.099629 restraints weight = 35903.398| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.17 r_work: 0.3161 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24325 Z= 0.144 Angle : 0.606 10.235 33295 Z= 0.292 Chirality : 0.050 0.403 3705 Planarity : 0.004 0.044 4033 Dihedral : 15.036 162.154 3901 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.44 % Allowed : 19.63 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.22 (0.16), residues: 2724 helix: 0.73 (0.17), residues: 909 sheet: 0.44 (0.23), residues: 511 loop : -0.31 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 20 TYR 0.017 0.001 TYR E 275 PHE 0.019 0.001 PHE J 17 TRP 0.012 0.001 TRP H 47 HIS 0.005 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (24325) covalent geometry : angle 0.60610 / 0.29 (33295) hydrogen bonds : bond 0.03395 / 1.76 ( 907) hydrogen bonds : angle 4.68956 / 2.09 ( 2473) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 225 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7408 (mpp) REVERT: B 97 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8798 (pt) REVERT: D 55 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8602 (tp40) REVERT: E 57 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8504 (tp) REVERT: E 180 ASP cc_start: 0.8439 (t0) cc_final: 0.8131 (t0) REVERT: E 324 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8175 (ptmm) REVERT: F 27 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8615 (t70) REVERT: F 156 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7753 (pp) REVERT: G 455 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: H 33 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.7073 (m-80) REVERT: H 94 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6656 (tm-30) REVERT: I 372 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7668 (mt) REVERT: I 386 ASN cc_start: 0.7912 (t0) cc_final: 0.7643 (t0) REVERT: J 88 GLU cc_start: 0.7974 (tp30) cc_final: 0.7642 (tp30) REVERT: J 137 TYR cc_start: 0.7067 (m-80) cc_final: 0.6867 (m-80) outliers start: 109 outliers final: 75 residues processed: 305 average time/residue: 0.1596 time to fit residues: 78.8042 Evaluate side-chains 295 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 211 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 455 GLU Chi-restraints excluded: chain G residue 593 CYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 34 optimal weight: 0.3980 chunk 277 optimal weight: 7.9990 chunk 135 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 205 optimal weight: 8.9990 chunk 150 optimal weight: 0.5980 chunk 223 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 182 optimal weight: 0.0370 chunk 238 optimal weight: 3.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN I 265 HIS J 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.144201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.102616 restraints weight = 35639.422| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.15 r_work: 0.3208 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24325 Z= 0.105 Angle : 0.581 9.874 33295 Z= 0.278 Chirality : 0.047 0.288 3705 Planarity : 0.004 0.047 4033 Dihedral : 14.982 159.708 3901 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.42 % Allowed : 20.69 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.38 (0.16), residues: 2724 helix: 0.92 (0.18), residues: 909 sheet: 0.46 (0.23), residues: 520 loop : -0.22 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 20 TYR 0.014 0.001 TYR E 275 PHE 0.021 0.001 PHE J 17 TRP 0.011 0.001 TRP G 539 HIS 0.007 0.001 HIS J 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (24325) covalent geometry : angle 0.58132 / 0.28 (33295) hydrogen bonds : bond 0.03056 / 1.58 ( 907) hydrogen bonds : angle 4.53000 / 2.04 ( 2473) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 231 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8087 (t80) cc_final: 0.7786 (t80) REVERT: A 96 GLU cc_start: 0.8107 (mp0) cc_final: 0.7553 (mp0) REVERT: A 346 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7641 (mpp) REVERT: B 97 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8717 (pt) REVERT: B 283 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7394 (ttt90) REVERT: C 183 ASN cc_start: 0.8188 (m-40) cc_final: 0.7901 (m-40) REVERT: D 55 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8646 (tp40) REVERT: E 57 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8487 (tp) REVERT: E 180 ASP cc_start: 0.8391 (t0) cc_final: 0.8086 (t0) REVERT: E 324 LYS cc_start: 0.8614 (mtmm) cc_final: 0.8251 (ptmm) REVERT: F 291 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7024 (ttp80) REVERT: H 33 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.7039 (m-80) REVERT: H 94 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6651 (tm-30) REVERT: I 333 ASN cc_start: 0.8642 (t0) cc_final: 0.8349 (t0) REVERT: I 372 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7666 (mt) REVERT: J 15 GLU cc_start: 0.8514 (mp0) cc_final: 0.8245 (mp0) REVERT: J 39 ARG cc_start: 0.7916 (mmm160) cc_final: 0.7364 (mtp-110) outliers start: 84 outliers final: 61 residues processed: 293 average time/residue: 0.1661 time to fit residues: 77.6411 Evaluate side-chains 285 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 217 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 455 GLU Chi-restraints excluded: chain G residue 593 CYS Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 191 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 273 optimal weight: 0.9990 chunk 201 optimal weight: 0.0870 chunk 171 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.143931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102376 restraints weight = 35374.204| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.16 r_work: 0.3203 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24325 Z= 0.111 Angle : 0.582 9.637 33295 Z= 0.278 Chirality : 0.047 0.291 3705 Planarity : 0.004 0.049 4033 Dihedral : 14.917 162.044 3901 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.87 % Allowed : 20.77 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.41 (0.16), residues: 2724 helix: 0.90 (0.17), residues: 922 sheet: 0.55 (0.23), residues: 512 loop : -0.21 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 20 TYR 0.017 0.001 TYR E 275 PHE 0.020 0.001 PHE J 17 TRP 0.010 0.001 TRP A 152 HIS 0.005 0.001 HIS H 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (24325) covalent geometry : angle 0.58199 / 0.28 (33295) hydrogen bonds : bond 0.03095 / 1.60 ( 907) hydrogen bonds : angle 4.49260 / 2.01 ( 2473) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 229 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8167 (t80) cc_final: 0.7920 (t80) REVERT: A 96 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: A 220 MET cc_start: 0.8559 (mmp) cc_final: 0.8340 (mmt) REVERT: A 346 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7544 (mpp) REVERT: B 97 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8709 (pt) REVERT: B 283 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7413 (ttt90) REVERT: D 55 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8661 (tp40) REVERT: E 57 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8483 (tp) REVERT: E 180 ASP cc_start: 0.8394 (t0) cc_final: 0.8081 (t0) REVERT: E 324 LYS cc_start: 0.8592 (mtmm) cc_final: 0.8243 (ptmm) REVERT: F 291 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7012 (ttp80) REVERT: F 316 TYR cc_start: 0.8384 (m-10) cc_final: 0.8115 (m-10) REVERT: G 590 ILE cc_start: 0.5079 (OUTLIER) cc_final: 0.4818 (mp) REVERT: H 33 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.7082 (m-80) REVERT: H 94 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6643 (tm-30) REVERT: H 102 ARG cc_start: 0.5212 (mtt180) cc_final: 0.4505 (mtt-85) REVERT: H 154 GLU cc_start: 0.7494 (tp30) cc_final: 0.6689 (tp30) REVERT: I 333 ASN cc_start: 0.8668 (t0) cc_final: 0.8388 (t0) REVERT: I 372 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7652 (mt) REVERT: J 15 GLU cc_start: 0.8502 (mp0) cc_final: 0.8218 (mp0) REVERT: J 39 ARG cc_start: 0.7954 (mmm160) cc_final: 0.7382 (mtp-110) outliers start: 95 outliers final: 73 residues processed: 299 average time/residue: 0.1663 time to fit residues: 79.5486 Evaluate side-chains 297 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 215 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 455 GLU Chi-restraints excluded: chain G residue 590 ILE Chi-restraints excluded: chain G residue 593 CYS Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 247 TRP Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 207 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 202 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 273 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS J 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.142963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102361 restraints weight = 35732.112| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.30 r_work: 0.3180 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24325 Z= 0.128 Angle : 0.597 9.636 33295 Z= 0.286 Chirality : 0.048 0.306 3705 Planarity : 0.004 0.052 4033 Dihedral : 14.887 168.367 3901 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.03 % Allowed : 20.61 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.37 (0.16), residues: 2724 helix: 0.88 (0.17), residues: 921 sheet: 0.52 (0.23), residues: 514 loop : -0.24 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 20 TYR 0.016 0.001 TYR E 275 PHE 0.021 0.001 PHE J 17 TRP 0.010 0.001 TRP H 47 HIS 0.009 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (24325) covalent geometry : angle 0.59697 / 0.29 (33295) hydrogen bonds : bond 0.03209 / 1.66 ( 907) hydrogen bonds : angle 4.52017 / 2.02 ( 2473) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 220 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8017 (t80) REVERT: A 96 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: A 220 MET cc_start: 0.8557 (mmp) cc_final: 0.8250 (mmt) REVERT: A 346 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7574 (mpp) REVERT: D 55 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8675 (tp40) REVERT: E 57 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8502 (tp) REVERT: E 180 ASP cc_start: 0.8413 (t0) cc_final: 0.8128 (t0) REVERT: E 324 LYS cc_start: 0.8607 (mtmm) cc_final: 0.8257 (ptmm) REVERT: F 156 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7758 (pp) REVERT: F 291 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7108 (ttp80) REVERT: F 316 TYR cc_start: 0.8444 (m-10) cc_final: 0.8128 (m-10) REVERT: G 455 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: G 590 ILE cc_start: 0.5104 (OUTLIER) cc_final: 0.4839 (mp) REVERT: H 33 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.7089 (m-80) REVERT: H 94 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6629 (tm-30) REVERT: H 154 GLU cc_start: 0.7577 (tp30) cc_final: 0.6782 (tp30) REVERT: H 190 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: I 333 ASN cc_start: 0.8653 (t0) cc_final: 0.8401 (t0) REVERT: I 372 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7756 (mt) REVERT: J 15 GLU cc_start: 0.8542 (mp0) cc_final: 0.8258 (mp0) REVERT: J 39 ARG cc_start: 0.8009 (mmm160) cc_final: 0.7423 (mtp-110) outliers start: 99 outliers final: 79 residues processed: 294 average time/residue: 0.1604 time to fit residues: 75.8850 Evaluate side-chains 306 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 216 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 455 GLU Chi-restraints excluded: chain G residue 590 ILE Chi-restraints excluded: chain G residue 593 CYS Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 236 optimal weight: 8.9990 chunk 153 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 178 optimal weight: 0.0980 chunk 105 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 198 optimal weight: 8.9990 chunk 216 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS I 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.099401 restraints weight = 35752.353| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.14 r_work: 0.3159 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24325 Z= 0.156 Angle : 0.624 10.800 33295 Z= 0.300 Chirality : 0.049 0.339 3705 Planarity : 0.004 0.051 4033 Dihedral : 14.973 169.103 3901 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.95 % Allowed : 20.77 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.27 (0.16), residues: 2724 helix: 0.80 (0.17), residues: 920 sheet: 0.47 (0.23), residues: 512 loop : -0.30 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 102 TYR 0.018 0.001 TYR A 316 PHE 0.020 0.001 PHE J 17 TRP 0.015 0.001 TRP H 47 HIS 0.009 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (24325) covalent geometry : angle 0.62440 / 0.30 (33295) hydrogen bonds : bond 0.03396 / 1.76 ( 907) hydrogen bonds : angle 4.60937 / 2.06 ( 2473) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 219 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8965 (mtp-110) cc_final: 0.8731 (ttp-110) REVERT: A 75 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8056 (t80) REVERT: A 96 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: A 346 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7500 (mpp) REVERT: B 97 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8793 (pt) REVERT: D 55 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8597 (tp40) REVERT: E 57 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8493 (tp) REVERT: E 180 ASP cc_start: 0.8426 (t0) cc_final: 0.8110 (t0) REVERT: E 277 GLU cc_start: 0.7275 (pt0) cc_final: 0.6939 (pm20) REVERT: E 324 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8188 (ptmm) REVERT: F 156 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7738 (pp) REVERT: F 291 ARG cc_start: 0.7927 (ttp80) cc_final: 0.6903 (ttp80) REVERT: F 316 TYR cc_start: 0.8461 (m-10) cc_final: 0.8145 (m-10) REVERT: G 455 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: H 33 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.7073 (m-80) REVERT: H 94 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6558 (tm-30) REVERT: H 154 GLU cc_start: 0.7572 (tp30) cc_final: 0.6924 (tp30) REVERT: H 190 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7332 (pm20) REVERT: I 255 ILE cc_start: 0.7315 (mt) cc_final: 0.7115 (mt) REVERT: I 333 ASN cc_start: 0.8694 (t0) cc_final: 0.8456 (t0) REVERT: I 372 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7739 (mt) REVERT: J 39 ARG cc_start: 0.7987 (mmm160) cc_final: 0.7385 (mtp-110) outliers start: 97 outliers final: 78 residues processed: 294 average time/residue: 0.1659 time to fit residues: 78.3428 Evaluate side-chains 299 residues out of total 2455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 210 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 103 CYS Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 204 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 453 THR Chi-restraints excluded: chain G residue 455 GLU Chi-restraints excluded: chain G residue 593 CYS Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 148 HIS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 247 TRP Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 47 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 36 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 164 optimal weight: 0.3980 chunk 165 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 271 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.144036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.102367 restraints weight = 35537.625| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.15 r_work: 0.3204 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24325 Z= 0.108 Angle : 0.588 10.220 33295 Z= 0.281 Chirality : 0.047 0.273 3705 Planarity : 0.004 0.059 4033 Dihedral : 14.945 168.106 3901 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.50 % Allowed : 21.43 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.82 % 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: 0.41 (0.16), residues: 2724 helix: 0.94 (0.17), residues: 922 sheet: 0.52 (0.23), residues: 513 loop : -0.22 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 20 TYR 0.023 0.001 TYR A 316 PHE 0.022 0.001 PHE J 17 TRP 0.012 0.001 TRP H 47 HIS 0.006 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (24325) covalent geometry : angle 0.58778 / 0.28 (33295) hydrogen bonds : bond 0.03059 / 1.58 ( 907) hydrogen bonds : angle 4.47217 / 2.01 ( 2473) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6681.83 seconds wall clock time: 115 minutes 19.47 seconds (6919.47 seconds total)