Starting phenix.real_space_refine on Wed Oct 28 19:27:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pij_20351/10_2026/6pij_20351.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pij_20351/10_2026/6pij_20351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pij_20351/10_2026/6pij_20351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pij_20351/10_2026/6pij_20351.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pij_20351/10_2026/6pij_20351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pij_20351/10_2026/6pij_20351.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6pij_20351/10_2026/6pij_20351.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pij_20351/10_2026/6pij_20351.cif" } resolution = 2.9 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= 0.005 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 95 5.49 5 S 142 5.16 5 C 18531 2.51 5 N 5143 2.21 5 O 5760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29671 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2782 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 330} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2714 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2715 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2710 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2509 Classifications: {'peptide': 310} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 292} Chain breaks: 2 Chain: "G" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4009 Classifications: {'peptide': 511} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 486} Chain breaks: 2 Chain: "H" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1606 Classifications: {'peptide': 197} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 187} Chain: "I" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2928 Classifications: {'peptide': 358} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 336} Chain breaks: 3 Chain: "J" Number of atoms: 2983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2983 Classifications: {'peptide': 369} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 348} Chain breaks: 2 Chain: "1" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNAv2': 60} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 15, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 24, 'rna3p': 35} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 561 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "3" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 178 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Time building chain proxies: 6.38, per 1000 atoms: 0.22 Number of scatterers: 29671 At special positions: 0 Unit cell: (130.442, 156.954, 185.588, 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 142 16.00 P 95 15.00 O 5760 8.00 N 5143 7.00 C 18531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 905.7 milliseconds 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6578 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 42 sheets defined 30.9% alpha, 15.4% beta 25 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.856A pdb=" N GLN A 67 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.844A pdb=" N ASN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.502A pdb=" N LEU A 142 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 183 removed outlier: 3.567A pdb=" N PHE A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.789A pdb=" N GLU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 344 removed outlier: 4.227A pdb=" N ASN A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.830A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 removed outlier: 3.743A pdb=" N GLN B 67 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 123 removed outlier: 3.524A pdb=" N GLN B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.856A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 305 through 311 removed outlier: 3.525A pdb=" N GLN B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 322 removed outlier: 3.514A pdb=" N SER B 321 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.548A pdb=" N LYS B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 63 through 67 removed outlier: 3.765A pdb=" N GLN C 67 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 99 removed outlier: 4.104A pdb=" N GLN C 99 " --> pdb=" O GLU C 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 96 through 99' Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.923A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 261 through 269 removed outlier: 3.565A pdb=" N GLY C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'C' and resid 312 through 320 Processing helix chain 'C' and resid 330 through 342 Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.643A pdb=" N ALA D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 123 Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.628A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 186 through 192 removed outlier: 3.764A pdb=" N ILE D 190 " --> pdb=" O ASN D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 200 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 330 through 344 removed outlier: 3.558A pdb=" N PHE D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.651A pdb=" N ALA E 49 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 66 Processing helix chain 'E' and resid 107 through 123 Processing helix chain 'E' and resid 125 through 138 removed outlier: 3.633A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.725A pdb=" N LEU E 142 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 183 removed outlier: 3.601A pdb=" N PHE E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 192 removed outlier: 4.668A pdb=" N TRP E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER E 188 " --> pdb=" O ASN E 184 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ALA E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 200 Processing helix chain 'E' and resid 260 through 269 removed outlier: 3.811A pdb=" N THR E 264 " --> pdb=" O GLY E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 312 through 320 removed outlier: 3.868A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 342 removed outlier: 3.506A pdb=" N PHE E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 123 removed outlier: 3.542A pdb=" N THR F 111 " --> pdb=" O LYS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 138 removed outlier: 3.748A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 177 through 182 removed outlier: 3.742A pdb=" N PHE F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 192 Processing helix chain 'F' and resid 194 through 200 Processing helix chain 'F' and resid 262 through 269 removed outlier: 3.697A pdb=" N ILE F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 311 Processing helix chain 'F' and resid 312 through 320 removed outlier: 4.216A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL F 319 " --> pdb=" O HIS F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 343 removed outlier: 3.509A pdb=" N PHE F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 20 through 27 removed outlier: 3.608A pdb=" N PHE G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 47 removed outlier: 4.423A pdb=" N ILE G 45 " --> pdb=" O ASP G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 82 removed outlier: 3.888A pdb=" N ASN G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS G 81 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL G 82 " --> pdb=" O CYS G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 119 Processing helix chain 'G' and resid 151 through 156 removed outlier: 3.779A pdb=" N LEU G 155 " --> pdb=" O CYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 170 Processing helix chain 'G' and resid 176 through 185 Processing helix chain 'G' and resid 221 through 232 removed outlier: 3.767A pdb=" N HIS G 227 " --> pdb=" O SER G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 251 removed outlier: 3.662A pdb=" N MET G 250 " --> pdb=" O ARG G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.778A pdb=" N CYS G 257 " --> pdb=" O THR G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 431 removed outlier: 3.778A pdb=" N PHE G 418 " --> pdb=" O SER G 414 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG G 431 " --> pdb=" O ARG G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 502 Processing helix chain 'G' and resid 527 through 534 removed outlier: 3.521A pdb=" N ALA G 531 " --> pdb=" O THR G 527 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU G 533 " --> pdb=" O GLU G 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 552 through 561 removed outlier: 3.548A pdb=" N LEU G 556 " --> pdb=" O ASN G 552 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 31 removed outlier: 3.603A pdb=" N LEU H 20 " --> pdb=" O ASN H 16 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 70 removed outlier: 3.817A pdb=" N LEU H 70 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 81 removed outlier: 3.739A pdb=" N GLN H 80 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU H 81 " --> pdb=" O GLN H 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 76 through 81' Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.547A pdb=" N SER H 137 " --> pdb=" O ASP H 134 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE H 138 " --> pdb=" O PRO H 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 134 through 138' Processing helix chain 'I' and resid 18 through 23 removed outlier: 3.970A pdb=" N ARG I 23 " --> pdb=" O SER I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 48 removed outlier: 3.714A pdb=" N ILE I 47 " --> pdb=" O PHE I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 82 removed outlier: 3.650A pdb=" N THR I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 148 removed outlier: 4.130A pdb=" N PHE I 147 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLN I 148 " --> pdb=" O TRP I 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 144 through 148' Processing helix chain 'I' and resid 199 through 204 removed outlier: 3.736A pdb=" N VAL I 203 " --> pdb=" O ALA I 199 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER I 204 " --> pdb=" O ALA I 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 199 through 204' Processing helix chain 'I' and resid 219 through 230 removed outlier: 3.766A pdb=" N GLY I 225 " --> pdb=" O SER I 221 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP I 230 " --> pdb=" O LEU I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 268 removed outlier: 3.663A pdb=" N PHE I 254 " --> pdb=" O TRP I 250 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N HIS I 255 " --> pdb=" O PRO I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 288 Processing helix chain 'I' and resid 300 through 313 Processing helix chain 'I' and resid 327 through 336 removed outlier: 4.087A pdb=" N THR I 332 " --> pdb=" O ALA I 328 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL I 333 " --> pdb=" O LEU I 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 348 removed outlier: 4.164A pdb=" N ALA I 343 " --> pdb=" O LEU I 339 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 383 Processing helix chain 'I' and resid 389 through 393 removed outlier: 3.757A pdb=" N PHE I 392 " --> pdb=" O ASN I 389 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.638A pdb=" N LYS J 27 " --> pdb=" O ARG J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 46 Processing helix chain 'J' and resid 70 through 84 Processing helix chain 'J' and resid 199 through 209 Processing helix chain 'J' and resid 219 through 234 removed outlier: 4.100A pdb=" N GLY J 225 " --> pdb=" O SER J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 245 Processing helix chain 'J' and resid 249 through 263 removed outlier: 4.051A pdb=" N PHE J 254 " --> pdb=" O TRP J 250 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N HIS J 255 " --> pdb=" O PRO J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 313 removed outlier: 3.531A pdb=" N GLY J 304 " --> pdb=" O ASN J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 331 through 336 Processing helix chain 'J' and resid 341 through 347 Processing helix chain 'J' and resid 372 through 383 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.567A pdb=" N CYS A 151 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 251 Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 290 removed outlier: 3.787A pdb=" N THR A 295 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 14 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 14 removed outlier: 3.583A pdb=" N CYS B 151 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 41 Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 15 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 15 Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 41 Processing sheet with id=AB3, first strand: chain 'C' and resid 248 through 251 Processing sheet with id=AB4, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AB5, first strand: chain 'D' and resid 13 through 15 Processing sheet with id=AB6, first strand: chain 'D' and resid 13 through 15 Processing sheet with id=AB7, first strand: chain 'D' and resid 35 through 42 Processing sheet with id=AB8, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AB9, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AC1, first strand: chain 'E' and resid 13 through 15 Processing sheet with id=AC2, first strand: chain 'E' and resid 13 through 15 removed outlier: 3.511A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 35 through 42 Processing sheet with id=AC4, first strand: chain 'E' and resid 248 through 251 Processing sheet with id=AC5, first strand: chain 'E' and resid 270 through 272 Processing sheet with id=AC6, first strand: chain 'F' and resid 13 through 15 Processing sheet with id=AC7, first strand: chain 'F' and resid 13 through 15 removed outlier: 3.631A pdb=" N CYS F 151 " --> pdb=" O HIS F 214 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 72 through 75 removed outlier: 6.800A pdb=" N SER F 36 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE H 146 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR F 38 " --> pdb=" O ILE H 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AD1, first strand: chain 'F' and resid 270 through 272 Processing sheet with id=AD2, first strand: chain 'G' and resid 204 through 207 removed outlier: 9.272A pdb=" N ALA G 592 " --> pdb=" O TYR G 213 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER G 215 " --> pdb=" O ALA G 592 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ALA G 594 " --> pdb=" O SER G 215 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER G 217 " --> pdb=" O ALA G 594 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N CYS G 596 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 204 through 207 removed outlier: 9.272A pdb=" N ALA G 592 " --> pdb=" O TYR G 213 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER G 215 " --> pdb=" O ALA G 592 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ALA G 594 " --> pdb=" O SER G 215 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER G 217 " --> pdb=" O ALA G 594 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N CYS G 596 " --> pdb=" O SER G 217 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE G 593 " --> pdb=" O LEU G 575 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LEU G 575 " --> pdb=" O ILE G 593 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU G 595 " --> pdb=" O TYR G 573 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR G 573 " --> pdb=" O GLU G 595 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE G 597 " --> pdb=" O VAL G 571 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 441 through 447 removed outlier: 6.545A pdb=" N PHE G 441 " --> pdb=" O ASN G 487 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN G 487 " --> pdb=" O PHE G 441 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE G 443 " --> pdb=" O ILE G 485 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE G 485 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL G 445 " --> pdb=" O SER G 483 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER G 483 " --> pdb=" O VAL G 445 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU G 484 " --> pdb=" O PRO G 394 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU G 486 " --> pdb=" O VAL G 392 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL G 392 " --> pdb=" O LEU G 486 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER G 511 " --> pdb=" O CYS G 399 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 441 through 447 removed outlier: 6.545A pdb=" N PHE G 441 " --> pdb=" O ASN G 487 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN G 487 " --> pdb=" O PHE G 441 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE G 443 " --> pdb=" O ILE G 485 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE G 485 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL G 445 " --> pdb=" O SER G 483 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER G 483 " --> pdb=" O VAL G 445 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU G 484 " --> pdb=" O PRO G 394 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU G 486 " --> pdb=" O VAL G 392 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL G 392 " --> pdb=" O LEU G 486 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 401 through 402 Processing sheet with id=AD7, first strand: chain 'G' and resid 460 through 461 Processing sheet with id=AD8, first strand: chain 'G' and resid 618 through 619 Processing sheet with id=AD9, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AE1, first strand: chain 'H' and resid 55 through 56 Processing sheet with id=AE2, first strand: chain 'H' and resid 100 through 103 Processing sheet with id=AE3, first strand: chain 'I' and resid 98 through 99 Processing sheet with id=AE4, first strand: chain 'I' and resid 325 through 326 Processing sheet with id=AE5, first strand: chain 'J' and resid 98 through 99 Processing sheet with id=AE6, first strand: chain 'J' and resid 325 through 326 890 hydrogen bonds defined for protein. 2418 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 5.24 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5545 1.33 - 1.46: 8410 1.46 - 1.58: 16274 1.58 - 1.70: 188 1.70 - 1.82: 205 Bond restraints: 30622 Sorted by residual: bond pdb=" N ILE B 258 " pdb=" CA ILE B 258 " ideal model delta sigma weight residual 1.460 1.500 -0.040 8.60e-03 1.35e+04 2.16e+01 bond pdb=" N ILE C 258 " pdb=" CA ILE C 258 " ideal model delta sigma weight residual 1.460 1.500 -0.039 8.60e-03 1.35e+04 2.11e+01 bond pdb=" N ILE E 190 " pdb=" CA ILE E 190 " ideal model delta sigma weight residual 1.459 1.500 -0.041 9.10e-03 1.21e+04 2.03e+01 bond pdb=" N ILE F 258 " pdb=" CA ILE F 258 " ideal model delta sigma weight residual 1.456 1.499 -0.043 9.50e-03 1.11e+04 2.02e+01 bond pdb=" N GLU E 280 " pdb=" CA GLU E 280 " ideal model delta sigma weight residual 1.453 1.494 -0.041 9.20e-03 1.18e+04 1.99e+01 ... (remaining 30617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 35002 2.47 - 4.94: 6608 4.94 - 7.41: 374 7.41 - 9.88: 8 9.88 - 12.35: 2 Bond angle restraints: 41994 Sorted by residual: angle pdb=" CA GLY G 107 " pdb=" C GLY G 107 " pdb=" O GLY G 107 " ideal model delta sigma weight residual 122.45 118.45 4.00 7.20e-01 1.93e+00 3.08e+01 angle pdb=" N ASP G 234 " pdb=" CA ASP G 234 " pdb=" C ASP G 234 " ideal model delta sigma weight residual 112.26 105.03 7.23 1.32e+00 5.74e-01 3.00e+01 angle pdb=" O GLY D 54 " pdb=" C GLY D 54 " pdb=" N GLN D 55 " ideal model delta sigma weight residual 121.85 124.82 -2.97 5.60e-01 3.19e+00 2.82e+01 angle pdb=" CA ASP F 293 " pdb=" CB ASP F 293 " pdb=" CG ASP F 293 " ideal model delta sigma weight residual 112.60 117.80 -5.20 1.00e+00 1.00e+00 2.70e+01 angle pdb=" CA LYS G 520 " pdb=" C LYS G 520 " pdb=" O LYS G 520 " ideal model delta sigma weight residual 119.55 116.39 3.16 6.10e-01 2.69e+00 2.69e+01 ... (remaining 41989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.35: 16683 26.35 - 52.69: 1070 52.69 - 79.04: 207 79.04 - 105.38: 9 105.38 - 131.72: 2 Dihedral angle restraints: 17971 sinusoidal: 7846 harmonic: 10125 Sorted by residual: dihedral pdb=" C4' U 1 27 " pdb=" C3' U 1 27 " pdb=" C2' U 1 27 " pdb=" C1' U 1 27 " ideal model delta sinusoidal sigma weight residual 36.35 -39.46 75.80 1 3.10e+00 1.04e-01 7.54e+02 dihedral pdb=" C4' G 1 3 " pdb=" C3' G 1 3 " pdb=" C2' G 1 3 " pdb=" C1' G 1 3 " ideal model delta sinusoidal sigma weight residual 36.34 -39.40 75.75 1 3.10e+00 1.04e-01 7.53e+02 dihedral pdb=" C4' A 1 39 " pdb=" C3' A 1 39 " pdb=" C2' A 1 39 " pdb=" C1' A 1 39 " ideal model delta sinusoidal sigma weight residual 36.35 -38.92 75.26 1 3.10e+00 1.04e-01 7.45e+02 ... (remaining 17968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 3504 0.102 - 0.205: 1022 0.205 - 0.307: 117 0.307 - 0.409: 1 0.409 - 0.512: 2 Chirality restraints: 4646 Sorted by residual: chirality pdb=" C3' DG 2 36 " pdb=" C4' DG 2 36 " pdb=" O3' DG 2 36 " pdb=" C2' DG 2 36 " both_signs ideal model delta sigma weight residual False -2.73 -2.22 -0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" C3' DA 2 40 " pdb=" C4' DA 2 40 " pdb=" O3' DA 2 40 " pdb=" C2' DA 2 40 " both_signs ideal model delta sigma weight residual False -2.73 -2.25 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C2' U 1 27 " pdb=" C3' U 1 27 " pdb=" O2' U 1 27 " pdb=" C1' U 1 27 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 4643 not shown) Planarity restraints: 5036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG 2 49 " -0.044 2.00e-02 2.50e+03 1.89e-02 1.08e+01 pdb=" N9 DG 2 49 " 0.046 2.00e-02 2.50e+03 pdb=" C8 DG 2 49 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DG 2 49 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG 2 49 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG 2 49 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG 2 49 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG 2 49 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG 2 49 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DG 2 49 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG 2 49 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG 2 49 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA 2 51 " -0.037 2.00e-02 2.50e+03 1.64e-02 7.41e+00 pdb=" N9 DA 2 51 " 0.037 2.00e-02 2.50e+03 pdb=" C8 DA 2 51 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DA 2 51 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DA 2 51 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA 2 51 " -0.007 2.00e-02 2.50e+03 pdb=" N6 DA 2 51 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA 2 51 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA 2 51 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA 2 51 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DA 2 51 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG 2 44 " 0.034 2.00e-02 2.50e+03 1.53e-02 7.04e+00 pdb=" N9 DG 2 44 " -0.039 2.00e-02 2.50e+03 pdb=" C8 DG 2 44 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG 2 44 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG 2 44 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG 2 44 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG 2 44 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG 2 44 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG 2 44 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG 2 44 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG 2 44 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG 2 44 " -0.002 2.00e-02 2.50e+03 ... (remaining 5033 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4371 2.80 - 3.33: 28694 3.33 - 3.85: 46154 3.85 - 4.38: 62145 4.38 - 4.90: 98755 Nonbonded interactions: 240119 Sorted by model distance: nonbonded pdb=" O LYS G 520 " pdb=" N ILE G 522 " model vdw 2.277 3.120 nonbonded pdb=" O LEU I 218 " pdb=" NE ARG I 223 " model vdw 2.319 3.120 nonbonded pdb=" NZ LYS C 230 " pdb=" O4 U 1 21 " model vdw 2.330 3.120 nonbonded pdb=" O VAL J 33 " pdb=" N ARG J 35 " model vdw 2.346 3.120 nonbonded pdb=" O TYR F 9 " pdb=" O2' U 1 35 " model vdw 2.348 3.040 ... (remaining 240114 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 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'B' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'C' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'D' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'E' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 3 through 196 or resid 198 through 235 or resid 239 throug \ h 354 or resid 364 through 381 or resid 383 through 396)) selection = (chain 'J' and (resid 3 through 165 or resid 167 or resid 169 or resid 199 throu \ gh 354 or resid 364 through 381 or resid 383 through 396)) } 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: 4.330 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 27.600 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 0.013 0.046 30622 Z= 1.020 Angle : 1.757 12.346 41994 Z= 1.238 Chirality : 0.090 0.512 4646 Planarity : 0.004 0.061 5036 Dihedral : 17.142 131.725 11393 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 3.44 % Allowed : 14.21 % Favored : 82.35 % Rotamer: Outliers : 0.66 % Allowed : 6.56 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 3.03 % Twisted General : 0.95 % 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: -4.59 (0.12), residues: 3406 helix: -2.69 (0.13), residues: 977 sheet: -1.95 (0.19), residues: 515 loop : -3.72 (0.12), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 117 TYR 0.026 0.002 TYR H 74 PHE 0.022 0.002 PHE E 227 TRP 0.028 0.002 TRP J 379 HIS 0.009 0.002 HIS I 228 Details of bonding type rmsd/Z covalent geometry : bond 0.01340 / 1.02 (30622) covalent geometry : angle 1.75704 / 1.24 (41994) hydrogen bonds : bond 0.20447 / 13.70 ( 937) hydrogen bonds : angle 8.38047 / 6.00 ( 2540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 453 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.7966 (t0) cc_final: 0.7687 (t0) REVERT: A 286 ARG cc_start: 0.7799 (ttm170) cc_final: 0.7432 (mtp180) REVERT: B 55 GLN cc_start: 0.7753 (pm20) cc_final: 0.7455 (mp10) REVERT: B 99 GLN cc_start: 0.7986 (pm20) cc_final: 0.7713 (pt0) REVERT: B 110 GLN cc_start: 0.7858 (pt0) cc_final: 0.7596 (pp30) REVERT: B 210 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.8210 (ttm170) REVERT: B 280 GLU cc_start: 0.8332 (pm20) cc_final: 0.8058 (pm20) REVERT: C 148 LYS cc_start: 0.8656 (mttt) cc_final: 0.8443 (mttp) REVERT: C 210 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7856 (ttp-110) REVERT: C 291 ARG cc_start: 0.7692 (ttp80) cc_final: 0.7198 (mmt90) REVERT: C 314 GLU cc_start: 0.8295 (mp0) cc_final: 0.8083 (mp0) REVERT: C 338 MET cc_start: 0.8823 (mmt) cc_final: 0.8597 (mmp) REVERT: D 63 GLU cc_start: 0.8073 (tt0) cc_final: 0.7558 (mp0) REVERT: D 99 GLN cc_start: 0.8387 (mt0) cc_final: 0.8169 (mt0) REVERT: D 170 ASP cc_start: 0.8129 (t0) cc_final: 0.7870 (t70) REVERT: D 220 MET cc_start: 0.7858 (ttp) cc_final: 0.7653 (ttp) REVERT: D 268 ILE cc_start: 0.8356 (pt) cc_final: 0.8050 (mt) REVERT: D 292 GLU cc_start: 0.7864 (tt0) cc_final: 0.7664 (tt0) REVERT: E 44 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7587 (mt-10) REVERT: E 99 GLN cc_start: 0.8235 (tt0) cc_final: 0.8006 (tt0) REVERT: E 162 ASN cc_start: 0.8258 (p0) cc_final: 0.7981 (p0) REVERT: E 210 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7318 (ttp80) REVERT: E 252 ASP cc_start: 0.7731 (t70) cc_final: 0.7143 (t0) REVERT: F 37 ARG cc_start: 0.7617 (mtm180) cc_final: 0.7258 (mtt90) REVERT: F 323 ASN cc_start: 0.7189 (t0) cc_final: 0.6916 (p0) REVERT: F 334 MET cc_start: 0.8607 (mmm) cc_final: 0.8237 (mmm) REVERT: G 237 ARG cc_start: 0.8207 (mtp180) cc_final: 0.7878 (mtp85) REVERT: G 564 HIS cc_start: 0.7164 (p-80) cc_final: 0.6191 (m170) REVERT: G 582 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7837 (mmtm) REVERT: G 613 ASN cc_start: 0.7395 (t0) cc_final: 0.7114 (t0) REVERT: H 77 GLN cc_start: 0.7717 (tp-100) cc_final: 0.7460 (tp-100) REVERT: H 85 HIS cc_start: 0.6624 (t-90) cc_final: 0.6219 (t-170) REVERT: H 102 ARG cc_start: 0.6833 (ttp-110) cc_final: 0.6588 (ttm170) REVERT: I 55 PHE cc_start: 0.4448 (t80) cc_final: 0.4018 (t80) REVERT: I 61 ARG cc_start: 0.6060 (ttm170) cc_final: 0.5395 (mtt90) REVERT: I 250 TRP cc_start: 0.7736 (t-100) cc_final: 0.7515 (t-100) REVERT: I 264 PHE cc_start: 0.8138 (t80) cc_final: 0.7884 (t80) REVERT: I 291 ARG cc_start: 0.7784 (mtp180) cc_final: 0.7031 (ttt180) REVERT: I 302 ILE cc_start: 0.8922 (mm) cc_final: 0.8689 (mt) REVERT: I 305 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7199 (mp0) REVERT: I 347 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7651 (tm-30) REVERT: I 348 GLN cc_start: 0.8531 (mt0) cc_final: 0.8192 (mt0) REVERT: J 122 LEU cc_start: 0.7364 (mp) cc_final: 0.7117 (mt) REVERT: J 136 ARG cc_start: 0.6239 (mmt-90) cc_final: 0.4823 (ttm170) REVERT: J 138 ASN cc_start: 0.6282 (OUTLIER) cc_final: 0.5940 (t0) REVERT: J 231 MET cc_start: 0.5804 (tpt) cc_final: 0.5558 (tpp) REVERT: J 257 ILE cc_start: 0.6408 (tp) cc_final: 0.6153 (mp) REVERT: J 312 ASN cc_start: 0.5148 (t0) cc_final: 0.4548 (p0) REVERT: J 368 TYR cc_start: 0.2569 (m-80) cc_final: 0.2335 (m-80) outliers start: 20 outliers final: 11 residues processed: 470 average time/residue: 0.6743 time to fit residues: 369.9839 Evaluate side-chains 296 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 284 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 276 PRO Chi-restraints excluded: chain B residue 276 PRO Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 276 PRO Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 276 PRO Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 276 PRO Chi-restraints excluded: chain F residue 276 PRO Chi-restraints excluded: chain J residue 138 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN A 114 GLN A 174 ASN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN B 183 ASN C 104 ASN C 174 ASN C 311 GLN D 110 GLN D 135 ASN D 174 ASN D 183 ASN D 311 GLN D 312 GLN E 104 ASN E 153 ASN E 290 HIS E 311 GLN E 335 HIS F 183 ASN F 311 GLN F 312 GLN F 349 HIS ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 HIS G 225 GLN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 423 HIS G 621 ASN H 17 ASN ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 GLN I 49 HIS I 205 ASN I 255 HIS I 341 GLN ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN J 87 ASN J 146 HIS J 156 HIS ** J 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 268 HIS J 384 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.148215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112532 restraints weight = 47315.403| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.84 r_work: 0.3217 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30622 Z= 0.217 Angle : 1.142 29.491 41994 Z= 0.528 Chirality : 0.086 1.145 4646 Planarity : 0.006 0.087 5036 Dihedral : 15.910 142.366 4852 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.76 % Allowed : 14.36 % Favored : 84.88 % Rotamer: Outliers : 3.23 % Allowed : 12.09 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 3.64 % Twisted General : 1.26 % 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: -3.56 (0.13), residues: 3406 helix: -1.35 (0.15), residues: 1004 sheet: -1.21 (0.22), residues: 527 loop : -3.45 (0.12), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 74 TYR 0.030 0.002 TYR I 140 PHE 0.025 0.002 PHE I 147 TRP 0.020 0.002 TRP D 152 HIS 0.007 0.001 HIS F 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.22 (30622) covalent geometry : angle 1.14217 / 0.53 (41994) hydrogen bonds : bond 0.05228 / 3.53 ( 937) hydrogen bonds : angle 5.79088 / 4.11 ( 2540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 300 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7504 (p0) REVERT: A 286 ARG cc_start: 0.8138 (ttm170) cc_final: 0.7903 (mtp180) REVERT: B 210 ARG cc_start: 0.8913 (ttm-80) cc_final: 0.8701 (ttm170) REVERT: D 63 GLU cc_start: 0.8544 (tt0) cc_final: 0.8098 (mp0) REVERT: D 347 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8098 (p90) REVERT: E 44 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7598 (mt-10) REVERT: E 210 ARG cc_start: 0.8540 (ttm170) cc_final: 0.8246 (ttp80) REVERT: E 252 ASP cc_start: 0.8268 (t70) cc_final: 0.7906 (t0) REVERT: F 222 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7702 (mtm180) REVERT: F 294 VAL cc_start: 0.9054 (m) cc_final: 0.8851 (t) REVERT: F 323 ASN cc_start: 0.6993 (t0) cc_final: 0.6786 (p0) REVERT: F 348 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7779 (pp30) REVERT: G 8 LYS cc_start: 0.6717 (mptt) cc_final: 0.6318 (tttt) REVERT: G 46 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7869 (mp) REVERT: G 439 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: G 538 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: G 613 ASN cc_start: 0.7472 (t0) cc_final: 0.7253 (t0) REVERT: H 4 TYR cc_start: 0.6273 (m-80) cc_final: 0.5874 (m-80) REVERT: H 77 GLN cc_start: 0.7745 (tp-100) cc_final: 0.7329 (tp-100) REVERT: I 61 ARG cc_start: 0.5610 (ttm170) cc_final: 0.5114 (mtt90) REVERT: I 230 TRP cc_start: 0.7689 (t-100) cc_final: 0.7405 (t-100) REVERT: I 291 ARG cc_start: 0.7864 (mtp180) cc_final: 0.6970 (ttt180) REVERT: I 305 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7313 (mm-30) REVERT: I 334 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7695 (ttm) REVERT: I 348 GLN cc_start: 0.8666 (mt0) cc_final: 0.8412 (mt0) REVERT: I 387 GLU cc_start: 0.7892 (pt0) cc_final: 0.7651 (mm-30) REVERT: J 34 HIS cc_start: 0.7545 (m170) cc_final: 0.7158 (t70) REVERT: J 136 ARG cc_start: 0.6129 (mmt-90) cc_final: 0.4807 (ttm170) REVERT: J 231 MET cc_start: 0.5670 (tpt) cc_final: 0.5428 (tpp) REVERT: J 246 PHE cc_start: 0.6538 (t80) cc_final: 0.6334 (t80) REVERT: J 264 PHE cc_start: 0.3658 (OUTLIER) cc_final: 0.2977 (t80) REVERT: J 312 ASN cc_start: 0.4689 (t0) cc_final: 0.4255 (p0) REVERT: J 368 TYR cc_start: 0.2110 (m-80) cc_final: 0.1790 (m-80) outliers start: 98 outliers final: 35 residues processed: 364 average time/residue: 0.6181 time to fit residues: 266.9831 Evaluate side-chains 292 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 276 PRO Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 439 GLU Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 538 GLU Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 334 MET Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 264 PHE Chi-restraints excluded: chain J residue 279 LYS Chi-restraints excluded: chain J residue 334 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [188, 132, 31, 237, 334, 82, 119, 225, 94, 166, 33] chunk 188 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 237 optimal weight: 0.6980 chunk 334 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN A 218 ASN A 299 HIS ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN C 104 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 290 HIS ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN F 186 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 230 GLN G 238 HIS ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 521 HIS G 565 GLN ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 HIS H 158 GLN ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 GLN I 341 GLN ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN J 83 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.147421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.111482 restraints weight = 47312.086| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.89 r_work: 0.3199 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30622 Z= 0.234 Angle : 0.981 28.560 41994 Z= 0.475 Chirality : 0.067 0.719 4646 Planarity : 0.006 0.091 5036 Dihedral : 16.504 159.828 4834 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.73 % Allowed : 15.83 % Favored : 83.44 % Rotamer: Outliers : 4.32 % Allowed : 13.54 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 3.03 % Twisted General : 1.23 % 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: -3.29 (0.13), residues: 3406 helix: -1.03 (0.16), residues: 1016 sheet: -0.91 (0.23), residues: 516 loop : -3.40 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 291 TYR 0.039 0.002 TYR I 140 PHE 0.027 0.002 PHE I 241 TRP 0.021 0.002 TRP C 152 HIS 0.007 0.001 HIS I 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (30622) covalent geometry : angle 0.98061 / 0.48 (41994) hydrogen bonds : bond 0.04860 / 3.26 ( 937) hydrogen bonds : angle 5.57205 / 3.95 ( 2540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 266 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7453 (p0) REVERT: A 286 ARG cc_start: 0.8231 (ttm170) cc_final: 0.7991 (mtp180) REVERT: B 96 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: B 170 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8067 (p0) REVERT: B 210 ARG cc_start: 0.8944 (ttm-80) cc_final: 0.8700 (ttm170) REVERT: B 280 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8416 (pm20) REVERT: D 63 GLU cc_start: 0.8581 (tt0) cc_final: 0.8119 (mp0) REVERT: D 347 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8556 (p90) REVERT: E 210 ARG cc_start: 0.8537 (ttm170) cc_final: 0.8248 (ttp80) REVERT: E 252 ASP cc_start: 0.8296 (t70) cc_final: 0.7953 (t0) REVERT: F 147 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7873 (mtp85) REVERT: F 222 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7704 (mtm180) REVERT: F 280 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7850 (pt0) REVERT: F 294 VAL cc_start: 0.9038 (m) cc_final: 0.8788 (t) REVERT: F 323 ASN cc_start: 0.6855 (t0) cc_final: 0.6624 (p0) REVERT: F 348 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7617 (pp30) REVERT: G 8 LYS cc_start: 0.6495 (mptt) cc_final: 0.6176 (tttt) REVERT: G 46 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7857 (mp) REVERT: G 66 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6108 (mtmt) REVERT: G 439 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6584 (tm-30) REVERT: G 440 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.7348 (m) REVERT: G 538 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: G 613 ASN cc_start: 0.7377 (t0) cc_final: 0.7154 (t0) REVERT: H 4 TYR cc_start: 0.6316 (m-80) cc_final: 0.6016 (m-80) REVERT: H 77 GLN cc_start: 0.7766 (tp-100) cc_final: 0.7489 (tp-100) REVERT: H 142 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.5713 (pp20) REVERT: I 55 PHE cc_start: 0.4497 (t80) cc_final: 0.4114 (t80) REVERT: I 61 ARG cc_start: 0.5566 (ttm170) cc_final: 0.5130 (mtt90) REVERT: I 157 ASN cc_start: 0.4899 (OUTLIER) cc_final: 0.4609 (m-40) REVERT: I 230 TRP cc_start: 0.7605 (t-100) cc_final: 0.7266 (t-100) REVERT: I 291 ARG cc_start: 0.7856 (mtp180) cc_final: 0.6920 (ttt180) REVERT: I 334 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7475 (tpp) REVERT: I 352 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8983 (mttt) REVERT: I 387 GLU cc_start: 0.8004 (pt0) cc_final: 0.7697 (mm-30) REVERT: J 136 ARG cc_start: 0.6221 (mmt-90) cc_final: 0.4690 (ttm170) REVERT: J 143 TYR cc_start: 0.5378 (t80) cc_final: 0.4853 (t80) REVERT: J 231 MET cc_start: 0.5657 (tpt) cc_final: 0.5409 (tpp) REVERT: J 261 GLU cc_start: 0.6832 (mm-30) cc_final: 0.6507 (mp0) REVERT: J 264 PHE cc_start: 0.3975 (OUTLIER) cc_final: 0.3316 (t80) REVERT: J 312 ASN cc_start: 0.4841 (t0) cc_final: 0.4382 (p0) outliers start: 131 outliers final: 55 residues processed: 358 average time/residue: 0.5899 time to fit residues: 252.0178 Evaluate side-chains 314 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 240 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 276 PRO Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 276 PRO Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 439 GLU Chi-restraints excluded: chain G residue 440 SER Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 538 GLU Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 157 ASN Chi-restraints excluded: chain I residue 334 MET Chi-restraints excluded: chain I residue 352 LYS Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 264 PHE Chi-restraints excluded: chain J residue 279 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [120, 105, 272, 82, 124, 274, 163, 294, 300, 158, 328] chunk 120 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 274 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 chunk 294 optimal weight: 0.0570 chunk 300 optimal weight: 0.6980 chunk 158 optimal weight: 6.9990 chunk 328 optimal weight: 0.0000 overall best weight: 0.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN F 299 HIS ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 HIS H 158 GLN I 34 HIS I 341 GLN J 45 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.151159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.115425 restraints weight = 47227.754| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.02 r_work: 0.3259 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30622 Z= 0.146 Angle : 0.862 16.907 41994 Z= 0.422 Chirality : 0.057 0.542 4646 Planarity : 0.006 0.090 5036 Dihedral : 16.518 169.523 4834 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.56 % Allowed : 14.47 % Favored : 84.97 % Rotamer: Outliers : 3.62 % Allowed : 15.32 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 3.64 % Twisted General : 1.19 % 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: -2.92 (0.14), residues: 3406 helix: -0.58 (0.16), residues: 1002 sheet: -0.76 (0.23), residues: 520 loop : -3.22 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 286 TYR 0.036 0.001 TYR H 149 PHE 0.023 0.001 PHE I 241 TRP 0.016 0.001 TRP F 152 HIS 0.028 0.001 HIS H 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (30622) covalent geometry : angle 0.86176 / 0.42 (41994) hydrogen bonds : bond 0.03918 / 2.65 ( 937) hydrogen bonds : angle 5.36614 / 3.81 ( 2540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 293 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.8566 (ttm) cc_final: 0.8283 (mpp) REVERT: A 286 ARG cc_start: 0.8221 (ttm170) cc_final: 0.7969 (mtp180) REVERT: B 210 ARG cc_start: 0.8915 (ttm-80) cc_final: 0.8674 (ttm170) REVERT: D 63 GLU cc_start: 0.8568 (tt0) cc_final: 0.8063 (mp0) REVERT: D 96 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: D 347 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.7916 (p90) REVERT: E 210 ARG cc_start: 0.8511 (ttm170) cc_final: 0.8227 (ttp80) REVERT: E 252 ASP cc_start: 0.8156 (t70) cc_final: 0.7806 (t0) REVERT: F 222 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7820 (mtm180) REVERT: G 8 LYS cc_start: 0.6274 (mptt) cc_final: 0.5518 (tmmt) REVERT: G 66 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.6173 (ttpt) REVERT: G 439 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: G 538 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: G 613 ASN cc_start: 0.7136 (t0) cc_final: 0.6912 (t0) REVERT: H 4 TYR cc_start: 0.6308 (m-80) cc_final: 0.5925 (m-80) REVERT: H 77 GLN cc_start: 0.7727 (tp-100) cc_final: 0.7461 (tp-100) REVERT: H 143 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7284 (m90) REVERT: I 34 HIS cc_start: 0.3281 (OUTLIER) cc_final: 0.3077 (m-70) REVERT: I 55 PHE cc_start: 0.4550 (t80) cc_final: 0.4105 (t80) REVERT: I 61 ARG cc_start: 0.5662 (ttm170) cc_final: 0.5216 (mtt90) REVERT: I 157 ASN cc_start: 0.4851 (OUTLIER) cc_final: 0.4566 (m-40) REVERT: I 230 TRP cc_start: 0.7619 (t-100) cc_final: 0.7276 (t-100) REVERT: I 291 ARG cc_start: 0.7813 (mtp180) cc_final: 0.6994 (ttt90) REVERT: I 387 GLU cc_start: 0.7992 (pt0) cc_final: 0.7676 (mm-30) REVERT: J 136 ARG cc_start: 0.5980 (mmt-90) cc_final: 0.4562 (ttm170) REVERT: J 143 TYR cc_start: 0.5423 (t80) cc_final: 0.4902 (t80) REVERT: J 231 MET cc_start: 0.5730 (tpt) cc_final: 0.5523 (tpp) REVERT: J 252 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7386 (tpt170) REVERT: J 261 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6580 (mp0) REVERT: J 264 PHE cc_start: 0.3896 (OUTLIER) cc_final: 0.3247 (t80) REVERT: J 278 LEU cc_start: 0.4957 (tp) cc_final: 0.3766 (pp) REVERT: J 312 ASN cc_start: 0.4687 (t0) cc_final: 0.4324 (p0) REVERT: J 330 GLU cc_start: 0.3359 (mp0) cc_final: 0.3118 (mp0) outliers start: 110 outliers final: 44 residues processed: 367 average time/residue: 0.6085 time to fit residues: 266.0017 Evaluate side-chains 303 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 248 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 439 GLU Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 538 GLU Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 157 ASN Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 34 HIS Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 264 PHE Chi-restraints excluded: chain J residue 279 LYS Chi-restraints excluded: chain J residue 308 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [238, 155, 151, 90, 308, 316, 59, 105, 279, 337, 274] chunk 238 optimal weight: 0.0370 chunk 155 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 308 optimal weight: 0.0000 chunk 316 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 chunk 337 optimal weight: 8.9990 chunk 274 optimal weight: 6.9990 overall best weight: 1.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 ASN A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 HIS H 158 GLN I 34 HIS I 205 ASN I 341 GLN J 45 GLN ** J 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.150945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.115293 restraints weight = 47315.455| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.10 r_work: 0.3250 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30622 Z= 0.158 Angle : 0.853 16.087 41994 Z= 0.420 Chirality : 0.056 0.516 4646 Planarity : 0.006 0.089 5036 Dihedral : 16.380 167.516 4831 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.62 % Allowed : 14.71 % Favored : 84.67 % Rotamer: Outliers : 4.22 % Allowed : 16.11 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 3.03 % Twisted General : 1.04 % 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: -2.77 (0.14), residues: 3406 helix: -0.44 (0.17), residues: 1000 sheet: -0.62 (0.23), residues: 492 loop : -3.14 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 291 TYR 0.035 0.001 TYR H 149 PHE 0.025 0.001 PHE I 241 TRP 0.018 0.001 TRP F 152 HIS 0.006 0.001 HIS H 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (30622) covalent geometry : angle 0.85330 / 0.42 (41994) hydrogen bonds : bond 0.03840 / 2.59 ( 937) hydrogen bonds : angle 5.30097 / 3.77 ( 2540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 258 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ARG cc_start: 0.8259 (ttm170) cc_final: 0.8015 (mtp180) REVERT: B 39 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9083 (pp) REVERT: B 96 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: B 210 ARG cc_start: 0.8921 (ttm-80) cc_final: 0.8667 (ttm170) REVERT: D 63 GLU cc_start: 0.8582 (tt0) cc_final: 0.8084 (mp0) REVERT: D 96 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: D 347 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8437 (p90) REVERT: E 210 ARG cc_start: 0.8549 (ttm170) cc_final: 0.8241 (ttp80) REVERT: E 252 ASP cc_start: 0.8163 (t70) cc_final: 0.7817 (t0) REVERT: F 222 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7747 (mtm180) REVERT: G 8 LYS cc_start: 0.6258 (mptt) cc_final: 0.5700 (ttpp) REVERT: G 66 LYS cc_start: 0.6642 (OUTLIER) cc_final: 0.6145 (ttpt) REVERT: G 86 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8293 (mp10) REVERT: G 439 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6840 (tm-30) REVERT: G 440 SER cc_start: 0.7452 (OUTLIER) cc_final: 0.7223 (m) REVERT: G 538 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: G 613 ASN cc_start: 0.7084 (t0) cc_final: 0.6850 (t0) REVERT: H 4 TYR cc_start: 0.6368 (m-80) cc_final: 0.5952 (m-80) REVERT: H 77 GLN cc_start: 0.7692 (tp-100) cc_final: 0.7405 (tp-100) REVERT: H 142 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6169 (pp20) REVERT: I 34 HIS cc_start: 0.3856 (OUTLIER) cc_final: 0.3651 (m-70) REVERT: I 61 ARG cc_start: 0.5672 (ttm170) cc_final: 0.5173 (mtt90) REVERT: I 146 HIS cc_start: 0.4245 (m170) cc_final: 0.2998 (p90) REVERT: I 147 PHE cc_start: 0.4622 (OUTLIER) cc_final: 0.3389 (t80) REVERT: I 157 ASN cc_start: 0.4895 (OUTLIER) cc_final: 0.4614 (m-40) REVERT: I 230 TRP cc_start: 0.7634 (t-100) cc_final: 0.7281 (t-100) REVERT: I 282 LEU cc_start: 0.8997 (tt) cc_final: 0.8796 (tm) REVERT: I 291 ARG cc_start: 0.7840 (mtp180) cc_final: 0.6997 (ttt90) REVERT: I 387 GLU cc_start: 0.8072 (pt0) cc_final: 0.7735 (mm-30) REVERT: J 120 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.5281 (mmt180) REVERT: J 136 ARG cc_start: 0.5939 (mmt-90) cc_final: 0.4513 (ttm170) REVERT: J 143 TYR cc_start: 0.5492 (t80) cc_final: 0.5018 (t80) REVERT: J 160 LEU cc_start: 0.5269 (OUTLIER) cc_final: 0.5049 (tm) REVERT: J 211 GLU cc_start: 0.4620 (OUTLIER) cc_final: 0.4159 (tp30) REVERT: J 252 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7437 (tpt170) REVERT: J 256 SER cc_start: 0.5508 (m) cc_final: 0.5217 (p) REVERT: J 261 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6574 (mp0) REVERT: J 264 PHE cc_start: 0.3784 (OUTLIER) cc_final: 0.3139 (t80) REVERT: J 278 LEU cc_start: 0.4926 (tp) cc_final: 0.3582 (pp) REVERT: J 312 ASN cc_start: 0.4581 (t0) cc_final: 0.4252 (p0) outliers start: 128 outliers final: 62 residues processed: 349 average time/residue: 0.5771 time to fit residues: 241.1045 Evaluate side-chains 319 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 238 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 439 GLU Chi-restraints excluded: chain G residue 440 SER Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 538 GLU Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 157 ASN Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 34 HIS Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 118 PHE Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 211 GLU Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 264 PHE Chi-restraints excluded: chain J residue 279 LYS Chi-restraints excluded: chain J residue 308 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [118, 22, 89, 131, 18, 108, 52, 290, 91, 16, 107] chunk 118 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 89 optimal weight: 0.0670 chunk 131 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 290 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 HIS ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 HIS H 158 GLN I 34 HIS I 205 ASN I 341 GLN I 348 GLN J 87 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.152099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116484 restraints weight = 47253.220| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.88 r_work: 0.3288 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30622 Z= 0.140 Angle : 0.826 14.328 41994 Z= 0.408 Chirality : 0.054 0.470 4646 Planarity : 0.005 0.091 5036 Dihedral : 16.258 167.792 4831 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.56 % Allowed : 14.68 % Favored : 84.76 % Rotamer: Outliers : 4.09 % Allowed : 16.64 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 3.03 % Twisted General : 1.01 % 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: -2.62 (0.14), residues: 3406 helix: -0.25 (0.17), residues: 993 sheet: -0.54 (0.24), residues: 492 loop : -3.06 (0.13), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 262 TYR 0.039 0.001 TYR H 149 PHE 0.025 0.001 PHE I 43 TRP 0.018 0.001 TRP F 152 HIS 0.015 0.001 HIS I 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (30622) covalent geometry : angle 0.82630 / 0.41 (41994) hydrogen bonds : bond 0.03624 / 2.45 ( 937) hydrogen bonds : angle 5.21718 / 3.71 ( 2540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 261 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8005 (t0) cc_final: 0.7776 (t0) REVERT: A 286 ARG cc_start: 0.8233 (ttm170) cc_final: 0.8005 (mtp180) REVERT: B 39 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9030 (pp) REVERT: B 96 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: B 210 ARG cc_start: 0.8896 (ttm-80) cc_final: 0.8625 (ttm170) REVERT: B 280 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8359 (pm20) REVERT: C 222 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7687 (mtm-85) REVERT: C 228 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7746 (m) REVERT: D 63 GLU cc_start: 0.8554 (tt0) cc_final: 0.7996 (mp0) REVERT: D 96 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: D 347 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8383 (p90) REVERT: E 44 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7613 (mt-10) REVERT: E 210 ARG cc_start: 0.8431 (ttm170) cc_final: 0.8212 (ttp80) REVERT: E 252 ASP cc_start: 0.8107 (t70) cc_final: 0.7758 (t0) REVERT: F 147 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7831 (ttp80) REVERT: F 222 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7612 (mtm180) REVERT: G 8 LYS cc_start: 0.6271 (mptt) cc_final: 0.5493 (tmmt) REVERT: G 66 LYS cc_start: 0.6558 (OUTLIER) cc_final: 0.6097 (ttpt) REVERT: G 86 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: G 538 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: G 625 TYR cc_start: 0.8373 (p90) cc_final: 0.7795 (p90) REVERT: H 2 LYS cc_start: 0.5604 (OUTLIER) cc_final: 0.4975 (pmtt) REVERT: H 4 TYR cc_start: 0.6331 (m-80) cc_final: 0.5896 (m-80) REVERT: H 77 GLN cc_start: 0.7652 (tp-100) cc_final: 0.7376 (tp-100) REVERT: I 61 ARG cc_start: 0.5604 (ttm170) cc_final: 0.4876 (mtt90) REVERT: I 146 HIS cc_start: 0.4465 (m170) cc_final: 0.3063 (p90) REVERT: I 147 PHE cc_start: 0.4482 (OUTLIER) cc_final: 0.3176 (t80) REVERT: I 157 ASN cc_start: 0.4896 (OUTLIER) cc_final: 0.4666 (m-40) REVERT: I 230 TRP cc_start: 0.7611 (t-100) cc_final: 0.7247 (t-100) REVERT: I 291 ARG cc_start: 0.7752 (mtp180) cc_final: 0.6878 (ttt90) REVERT: I 348 GLN cc_start: 0.8637 (mt0) cc_final: 0.8391 (mt0) REVERT: I 387 GLU cc_start: 0.8069 (pt0) cc_final: 0.7698 (mm-30) REVERT: J 18 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: J 120 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.5250 (mmt180) REVERT: J 136 ARG cc_start: 0.5827 (mmt-90) cc_final: 0.4415 (ttm170) REVERT: J 143 TYR cc_start: 0.5450 (t80) cc_final: 0.5178 (t80) REVERT: J 252 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7427 (tpt170) REVERT: J 264 PHE cc_start: 0.3788 (OUTLIER) cc_final: 0.3118 (t80) REVERT: J 278 LEU cc_start: 0.4944 (tp) cc_final: 0.3490 (pp) REVERT: J 312 ASN cc_start: 0.4554 (t0) cc_final: 0.4317 (p0) REVERT: J 326 MET cc_start: 0.1330 (mmt) cc_final: 0.0440 (mmt) outliers start: 124 outliers final: 53 residues processed: 348 average time/residue: 0.5567 time to fit residues: 233.1613 Evaluate side-chains 307 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 235 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 538 GLU Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 157 ASN Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 34 HIS Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 118 PHE Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 264 PHE Chi-restraints excluded: chain J residue 308 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [174, 245, 226, 202, 89, 21, 195, 343, 302, 200, 337] chunk 174 optimal weight: 0.5980 chunk 245 optimal weight: 8.9990 chunk 226 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 195 optimal weight: 10.0000 chunk 343 optimal weight: 5.9990 chunk 302 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 337 optimal weight: 0.0020 overall best weight: 0.7368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 ASN A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN D 110 GLN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 GLN I 341 GLN J 83 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.152758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117327 restraints weight = 47504.840| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.96 r_work: 0.3296 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30622 Z= 0.142 Angle : 0.828 14.904 41994 Z= 0.409 Chirality : 0.054 0.459 4646 Planarity : 0.005 0.090 5036 Dihedral : 16.149 167.253 4831 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.56 % Allowed : 14.47 % Favored : 84.97 % Rotamer: Outliers : 3.69 % Allowed : 17.50 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 3.64 % Twisted General : 0.92 % 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: -2.53 (0.14), residues: 3406 helix: -0.14 (0.17), residues: 984 sheet: -0.44 (0.24), residues: 481 loop : -3.02 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 291 TYR 0.041 0.001 TYR H 149 PHE 0.027 0.001 PHE I 43 TRP 0.017 0.001 TRP F 152 HIS 0.007 0.001 HIS H 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (30622) covalent geometry : angle 0.82768 / 0.41 (41994) hydrogen bonds : bond 0.03521 / 2.38 ( 937) hydrogen bonds : angle 5.14974 / 3.67 ( 2540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 248 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.7975 (t0) cc_final: 0.7769 (t0) REVERT: A 286 ARG cc_start: 0.8281 (ttm170) cc_final: 0.8040 (mtp180) REVERT: B 39 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9024 (pp) REVERT: B 210 ARG cc_start: 0.8908 (ttm-80) cc_final: 0.8636 (ttm170) REVERT: B 280 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8342 (pm20) REVERT: B 346 MET cc_start: 0.8003 (mtp) cc_final: 0.7769 (mpp) REVERT: C 228 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7720 (m) REVERT: D 63 GLU cc_start: 0.8538 (tt0) cc_final: 0.8014 (mp0) REVERT: D 96 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: D 347 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8530 (p90) REVERT: E 44 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7618 (mt-10) REVERT: E 183 ASN cc_start: 0.5409 (m-40) cc_final: 0.5202 (p0) REVERT: E 210 ARG cc_start: 0.8433 (ttm170) cc_final: 0.8229 (ttp80) REVERT: E 252 ASP cc_start: 0.8121 (t70) cc_final: 0.7788 (t0) REVERT: F 147 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7828 (ttp80) REVERT: F 222 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7641 (mtm180) REVERT: G 8 LYS cc_start: 0.6247 (mptt) cc_final: 0.5628 (ttpt) REVERT: G 66 LYS cc_start: 0.6399 (OUTLIER) cc_final: 0.6043 (ttpt) REVERT: G 437 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7124 (tpp-160) REVERT: G 625 TYR cc_start: 0.8308 (p90) cc_final: 0.7934 (p90) REVERT: H 4 TYR cc_start: 0.6358 (m-80) cc_final: 0.6001 (m-80) REVERT: H 77 GLN cc_start: 0.7588 (tp-100) cc_final: 0.7310 (tp-100) REVERT: I 61 ARG cc_start: 0.5277 (ttm170) cc_final: 0.4809 (mtt90) REVERT: I 146 HIS cc_start: 0.4540 (m170) cc_final: 0.3175 (p90) REVERT: I 147 PHE cc_start: 0.4537 (OUTLIER) cc_final: 0.3223 (t80) REVERT: I 157 ASN cc_start: 0.4847 (OUTLIER) cc_final: 0.4605 (m-40) REVERT: I 230 TRP cc_start: 0.7651 (t-100) cc_final: 0.7307 (t-100) REVERT: I 282 LEU cc_start: 0.9018 (tt) cc_final: 0.8817 (tm) REVERT: I 291 ARG cc_start: 0.7705 (mtp180) cc_final: 0.6845 (ttt90) REVERT: I 387 GLU cc_start: 0.8066 (pt0) cc_final: 0.7699 (mm-30) REVERT: J 18 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: J 120 ARG cc_start: 0.6407 (OUTLIER) cc_final: 0.5226 (mmt180) REVERT: J 136 ARG cc_start: 0.5876 (mmt-90) cc_final: 0.4435 (ttm170) REVERT: J 252 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7494 (tpt170) REVERT: J 278 LEU cc_start: 0.4792 (tp) cc_final: 0.3490 (pp) REVERT: J 297 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5209 (mm) outliers start: 112 outliers final: 55 residues processed: 335 average time/residue: 0.5519 time to fit residues: 223.0637 Evaluate side-chains 298 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 228 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 437 ARG Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain G residue 615 ILE Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 157 ASN Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 34 HIS Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 118 PHE Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 297 LEU Chi-restraints excluded: chain J residue 308 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [17, 61, 217, 36, 1, 311, 70, 315, 233, 276, 174] chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 311 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 233 optimal weight: 0.0970 chunk 276 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 GLN I 34 HIS I 341 GLN I 348 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.152729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.117076 restraints weight = 47593.587| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.09 r_work: 0.3276 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30622 Z= 0.152 Angle : 0.835 13.831 41994 Z= 0.412 Chirality : 0.054 0.480 4646 Planarity : 0.005 0.091 5036 Dihedral : 16.094 165.220 4831 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.56 % Allowed : 14.39 % Favored : 85.06 % Rotamer: Outliers : 3.20 % Allowed : 18.39 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 3.64 % Twisted General : 0.89 % 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: -2.47 (0.14), residues: 3406 helix: -0.06 (0.17), residues: 981 sheet: -0.37 (0.24), residues: 481 loop : -3.00 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 252 TYR 0.043 0.001 TYR H 149 PHE 0.036 0.001 PHE J 246 TRP 0.016 0.001 TRP C 152 HIS 0.007 0.001 HIS I 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (30622) covalent geometry : angle 0.83467 / 0.41 (41994) hydrogen bonds : bond 0.03597 / 2.43 ( 937) hydrogen bonds : angle 5.11646 / 3.65 ( 2540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 238 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 ARG cc_start: 0.8330 (ttm170) cc_final: 0.8049 (mtp180) REVERT: B 39 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9060 (pp) REVERT: B 210 ARG cc_start: 0.8921 (ttm-80) cc_final: 0.8641 (ttm170) REVERT: B 346 MET cc_start: 0.8122 (mtp) cc_final: 0.7861 (mpp) REVERT: C 228 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7733 (m) REVERT: D 63 GLU cc_start: 0.8531 (tt0) cc_final: 0.8011 (mp0) REVERT: D 96 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: D 347 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8671 (p90) REVERT: E 183 ASN cc_start: 0.5409 (m-40) cc_final: 0.5195 (p0) REVERT: E 210 ARG cc_start: 0.8529 (ttm170) cc_final: 0.8205 (ttp80) REVERT: E 252 ASP cc_start: 0.8160 (t70) cc_final: 0.7801 (t0) REVERT: F 43 MET cc_start: 0.4890 (mpp) cc_final: 0.1868 (tpt) REVERT: F 147 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7827 (ttp80) REVERT: F 222 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7722 (mtm180) REVERT: G 8 LYS cc_start: 0.6222 (mptt) cc_final: 0.5352 (pptt) REVERT: G 66 LYS cc_start: 0.6323 (OUTLIER) cc_final: 0.5946 (ttpt) REVERT: G 625 TYR cc_start: 0.8166 (p90) cc_final: 0.7865 (p90) REVERT: H 2 LYS cc_start: 0.5592 (OUTLIER) cc_final: 0.4875 (pmtt) REVERT: H 4 TYR cc_start: 0.6435 (m-80) cc_final: 0.6046 (m-80) REVERT: H 77 GLN cc_start: 0.7581 (tp-100) cc_final: 0.7341 (tp-100) REVERT: I 61 ARG cc_start: 0.5273 (ttm170) cc_final: 0.4838 (mtt90) REVERT: I 112 VAL cc_start: 0.0908 (OUTLIER) cc_final: -0.0596 (t) REVERT: I 146 HIS cc_start: 0.4522 (m170) cc_final: 0.3099 (p90) REVERT: I 147 PHE cc_start: 0.4535 (OUTLIER) cc_final: 0.3276 (t80) REVERT: I 157 ASN cc_start: 0.4817 (OUTLIER) cc_final: 0.4590 (m-40) REVERT: I 222 TYR cc_start: 0.7798 (m-80) cc_final: 0.7420 (m-80) REVERT: I 230 TRP cc_start: 0.7719 (t-100) cc_final: 0.7360 (t-100) REVERT: I 291 ARG cc_start: 0.7808 (mtp180) cc_final: 0.6890 (ttt90) REVERT: I 387 GLU cc_start: 0.8030 (pt0) cc_final: 0.7679 (mm-30) REVERT: J 18 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: J 120 ARG cc_start: 0.6575 (OUTLIER) cc_final: 0.5403 (mmt180) REVERT: J 136 ARG cc_start: 0.5942 (mmt-90) cc_final: 0.4402 (ttm170) REVERT: J 252 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7483 (tpt170) REVERT: J 264 PHE cc_start: 0.3825 (OUTLIER) cc_final: 0.3296 (t80) REVERT: J 278 LEU cc_start: 0.4852 (tp) cc_final: 0.3470 (pp) REVERT: J 330 GLU cc_start: 0.3537 (mp0) cc_final: 0.3306 (mp0) REVERT: J 386 ASP cc_start: 0.6133 (p0) cc_final: 0.5929 (t70) outliers start: 97 outliers final: 60 residues processed: 314 average time/residue: 0.5507 time to fit residues: 208.8507 Evaluate side-chains 302 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 227 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain G residue 615 ILE Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 157 ASN Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 34 HIS Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 118 PHE Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 264 PHE Chi-restraints excluded: chain J residue 308 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [325, 293, 70, 65, 117, 6, 32, 218, 344, 156, 163] chunk 325 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 70 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 344 optimal weight: 9.9990 chunk 156 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 ASN A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 GLN I 341 GLN I 348 GLN ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.151961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116105 restraints weight = 47552.018| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.14 r_work: 0.3257 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30622 Z= 0.168 Angle : 0.846 17.045 41994 Z= 0.417 Chirality : 0.055 0.498 4646 Planarity : 0.006 0.091 5036 Dihedral : 16.070 163.045 4831 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.53 % Allowed : 14.65 % Favored : 84.82 % Rotamer: Outliers : 3.36 % Allowed : 18.35 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 3.64 % Twisted General : 0.86 % 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: -2.43 (0.14), residues: 3406 helix: -0.04 (0.17), residues: 989 sheet: -0.36 (0.24), residues: 488 loop : -2.99 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 35 TYR 0.041 0.002 TYR H 74 PHE 0.031 0.002 PHE J 246 TRP 0.016 0.001 TRP C 152 HIS 0.033 0.001 HIS I 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (30622) covalent geometry : angle 0.84634 / 0.42 (41994) hydrogen bonds : bond 0.03710 / 2.50 ( 937) hydrogen bonds : angle 5.14251 / 3.66 ( 2540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 231 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ARG cc_start: 0.8353 (ttm170) cc_final: 0.8060 (mtp180) REVERT: B 39 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9096 (pp) REVERT: B 210 ARG cc_start: 0.8939 (ttm-80) cc_final: 0.8651 (ttm170) REVERT: B 346 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7913 (mpp) REVERT: C 228 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7754 (m) REVERT: D 63 GLU cc_start: 0.8529 (tt0) cc_final: 0.7998 (mp0) REVERT: D 96 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: D 347 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8759 (p90) REVERT: E 183 ASN cc_start: 0.5458 (m-40) cc_final: 0.5212 (p0) REVERT: E 210 ARG cc_start: 0.8546 (ttm170) cc_final: 0.8207 (ttp80) REVERT: E 252 ASP cc_start: 0.8181 (t70) cc_final: 0.7832 (t0) REVERT: F 43 MET cc_start: 0.4846 (mpp) cc_final: 0.1786 (tpt) REVERT: F 147 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7844 (mtp85) REVERT: F 222 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7987 (mtm180) REVERT: G 8 LYS cc_start: 0.6197 (mptt) cc_final: 0.5236 (pptt) REVERT: G 66 LYS cc_start: 0.6432 (OUTLIER) cc_final: 0.5935 (ttpt) REVERT: G 625 TYR cc_start: 0.8208 (p90) cc_final: 0.7974 (p90) REVERT: H 2 LYS cc_start: 0.5515 (OUTLIER) cc_final: 0.4812 (pmtt) REVERT: H 4 TYR cc_start: 0.6457 (m-80) cc_final: 0.5982 (m-80) REVERT: I 61 ARG cc_start: 0.5292 (ttm170) cc_final: 0.4844 (mtt90) REVERT: I 112 VAL cc_start: 0.0901 (OUTLIER) cc_final: -0.0493 (t) REVERT: I 146 HIS cc_start: 0.4464 (m170) cc_final: 0.3088 (p90) REVERT: I 147 PHE cc_start: 0.4523 (OUTLIER) cc_final: 0.3439 (t80) REVERT: I 157 ASN cc_start: 0.4917 (OUTLIER) cc_final: 0.4703 (m-40) REVERT: I 230 TRP cc_start: 0.7752 (t-100) cc_final: 0.7390 (t-100) REVERT: I 291 ARG cc_start: 0.7828 (mtp180) cc_final: 0.6889 (ttt180) REVERT: I 348 GLN cc_start: 0.8583 (mt0) cc_final: 0.8342 (mt0) REVERT: I 387 GLU cc_start: 0.8029 (pt0) cc_final: 0.7687 (mm-30) REVERT: J 18 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: J 120 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5471 (mmt180) REVERT: J 136 ARG cc_start: 0.5890 (mmt-90) cc_final: 0.4488 (ptp90) REVERT: J 264 PHE cc_start: 0.3463 (OUTLIER) cc_final: 0.3001 (t80) REVERT: J 278 LEU cc_start: 0.4830 (tp) cc_final: 0.3446 (pp) REVERT: J 297 LEU cc_start: 0.5394 (OUTLIER) cc_final: 0.5002 (mm) outliers start: 102 outliers final: 60 residues processed: 309 average time/residue: 0.5602 time to fit residues: 209.5565 Evaluate side-chains 303 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 227 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain G residue 615 ILE Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 157 ASN Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 34 HIS Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 264 PHE Chi-restraints excluded: chain J residue 297 LEU Chi-restraints excluded: chain J residue 308 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [209, 26, 258, 274, 36, 284, 331, 320, 231, 151, 322] chunk 209 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 chunk 274 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 284 optimal weight: 1.9990 chunk 331 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 322 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 ASN A 110 GLN A 315 HIS ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 299 HIS E 104 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN F 153 ASN F 186 ASN G 233 GLN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 621 ASN H 77 GLN H 158 GLN I 34 HIS I 249 ASN I 341 GLN ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.146988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110705 restraints weight = 47329.012| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.05 r_work: 0.3173 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 30622 Z= 0.314 Angle : 0.986 18.480 41994 Z= 0.485 Chirality : 0.065 0.611 4646 Planarity : 0.007 0.094 5036 Dihedral : 16.333 163.551 4831 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.53 % Allowed : 15.56 % Favored : 83.91 % Rotamer: Outliers : 3.10 % Allowed : 19.11 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 3.03 % Twisted General : 1.01 % 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: -2.69 (0.14), residues: 3406 helix: -0.34 (0.16), residues: 995 sheet: -0.49 (0.23), residues: 511 loop : -3.14 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 252 TYR 0.050 0.003 TYR H 74 PHE 0.031 0.002 PHE A 89 TRP 0.019 0.002 TRP C 152 HIS 0.011 0.002 HIS I 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.31 (30622) covalent geometry : angle 0.98607 / 0.48 (41994) hydrogen bonds : bond 0.04807 / 3.23 ( 937) hydrogen bonds : angle 5.34625 / 3.82 ( 2540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 219 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 286 ARG cc_start: 0.8380 (ttm170) cc_final: 0.8030 (mtm-85) REVERT: B 39 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9183 (pp) REVERT: B 210 ARG cc_start: 0.8988 (ttm-80) cc_final: 0.8691 (ttm170) REVERT: B 346 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8068 (mtp) REVERT: D 63 GLU cc_start: 0.8530 (tt0) cc_final: 0.8077 (mp0) REVERT: D 96 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: D 347 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8872 (p90) REVERT: E 210 ARG cc_start: 0.8617 (ttm170) cc_final: 0.8244 (ttp80) REVERT: E 252 ASP cc_start: 0.8345 (t70) cc_final: 0.8003 (t0) REVERT: F 43 MET cc_start: 0.4845 (mpp) cc_final: 0.1832 (tpt) REVERT: F 147 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7865 (mtp85) REVERT: F 222 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8077 (mtm180) REVERT: F 342 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.8952 (mp) REVERT: G 8 LYS cc_start: 0.6326 (mptt) cc_final: 0.5266 (pptt) REVERT: G 66 LYS cc_start: 0.6661 (OUTLIER) cc_final: 0.6135 (ttpt) REVERT: G 625 TYR cc_start: 0.8297 (p90) cc_final: 0.8021 (p90) REVERT: H 2 LYS cc_start: 0.5558 (OUTLIER) cc_final: 0.4840 (pmtt) REVERT: H 4 TYR cc_start: 0.6396 (m-80) cc_final: 0.6079 (m-80) REVERT: I 61 ARG cc_start: 0.5344 (ttm170) cc_final: 0.5003 (mtt90) REVERT: I 146 HIS cc_start: 0.4382 (m170) cc_final: 0.2951 (p90) REVERT: I 147 PHE cc_start: 0.4457 (OUTLIER) cc_final: 0.3256 (t80) REVERT: I 230 TRP cc_start: 0.7612 (t-100) cc_final: 0.7295 (t-100) REVERT: I 291 ARG cc_start: 0.7846 (mtp180) cc_final: 0.6951 (ttt180) REVERT: I 387 GLU cc_start: 0.8082 (pt0) cc_final: 0.7690 (mm-30) REVERT: J 18 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: J 120 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.5484 (mmt180) REVERT: J 136 ARG cc_start: 0.6041 (mmt-90) cc_final: 0.4416 (ttm170) REVERT: J 252 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7474 (ppt170) REVERT: J 264 PHE cc_start: 0.3718 (OUTLIER) cc_final: 0.3308 (t80) REVERT: J 278 LEU cc_start: 0.4737 (tp) cc_final: 0.3475 (pp) REVERT: J 297 LEU cc_start: 0.5519 (OUTLIER) cc_final: 0.5066 (mm) REVERT: J 372 PHE cc_start: 0.6760 (t80) cc_final: 0.6255 (t80) REVERT: J 386 ASP cc_start: 0.6106 (OUTLIER) cc_final: 0.5518 (m-30) outliers start: 94 outliers final: 56 residues processed: 294 average time/residue: 0.5640 time to fit residues: 200.0971 Evaluate side-chains 287 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 215 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 264 PHE Chi-restraints excluded: chain J residue 297 LEU Chi-restraints excluded: chain J residue 386 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: [109, 119, 317, 228, 254, 301, 44, 29, 194, 147, 117] chunk 109 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 317 optimal weight: 0.2980 chunk 228 optimal weight: 0.9990 chunk 254 optimal weight: 0.0770 chunk 301 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 ASN A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 ASN F 186 ASN G 233 GLN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN H 158 GLN I 34 HIS I 249 ASN I 341 GLN I 348 GLN ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.147325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111025 restraints weight = 47464.825| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.04 r_work: 0.3177 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.189 30622 Z= 0.268 Angle : 1.043 59.131 41994 Z= 0.529 Chirality : 0.070 2.135 4646 Planarity : 0.007 0.094 5036 Dihedral : 16.333 163.360 4831 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.53 % Allowed : 15.59 % Favored : 83.88 % Rotamer: Outliers : 2.97 % Allowed : 19.47 % Favored : 77.56 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 3.03 % Twisted General : 1.01 % 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: -2.67 (0.14), residues: 3406 helix: -0.31 (0.16), residues: 988 sheet: -0.47 (0.23), residues: 510 loop : -3.14 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 252 TYR 0.046 0.002 TYR H 74 PHE 0.029 0.002 PHE A 89 TRP 0.021 0.002 TRP C 152 HIS 0.008 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.27 (30622) covalent geometry : angle 1.04260 / 0.53 (41994) hydrogen bonds : bond 0.04675 / 3.15 ( 937) hydrogen bonds : angle 5.34688 / 3.82 ( 2540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10571.71 seconds wall clock time: 180 minutes 36.06 seconds (10836.06 seconds total)