Starting phenix.real_space_refine on Fri Aug 7 11:34:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdy_60017/08_2026/8zdy_60017_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdy_60017/08_2026/8zdy_60017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zdy_60017/08_2026/8zdy_60017_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdy_60017/08_2026/8zdy_60017_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zdy_60017/08_2026/8zdy_60017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdy_60017/08_2026/8zdy_60017.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 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 58 5.49 5 S 91 5.16 5 C 13569 2.51 5 N 3669 2.21 5 O 4177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21564 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2556 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 15, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2490 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 15, 'TRANS': 305} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 7, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2507 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'GLU:plan': 9, 'HIS:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "D" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2520 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 15, 'TRANS': 307} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 5, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "E" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2413 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 12, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 9, 'ASP:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "F" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2249 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 11, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "G" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2436 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASN:plan1': 3, 'GLN:plan1': 4, 'TYR:plan': 3, 'GLU:plan': 14, 'ASP:plan': 5, 'ARG:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 152 Chain: "H" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1856 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1288 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain breaks: 1 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 8, 'ARG:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "L" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1249 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 10, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna2p': 30, 'rna3p': 27} Chain breaks: 1 Time building chain proxies: 4.29, per 1000 atoms: 0.20 Number of scatterers: 21564 At special positions: 0 Unit cell: (119.84, 144.664, 144.664, 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 91 16.00 P 58 15.00 O 4177 8.00 N 3669 7.00 C 13569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 996.8 milliseconds 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5008 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 32 sheets defined 31.6% alpha, 9.3% beta 6 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 101 through 104 Processing helix chain 'A' and resid 111 through 127 Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.615A pdb=" N ILE A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 312 through 326 removed outlier: 3.618A pdb=" N ILE A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 66 through 73 removed outlier: 3.560A pdb=" N ASP B 73 " --> pdb=" O LYS B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 112 through 128 Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.734A pdb=" N GLY B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 296 through 305 removed outlier: 5.392A pdb=" N ASP B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.597A pdb=" N MET B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.746A pdb=" N ILE B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 63 through 72 removed outlier: 3.840A pdb=" N GLU C 68 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 186 through 202 Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 267 through 272 removed outlier: 3.539A pdb=" N TYR C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 305 removed outlier: 4.292A pdb=" N ASP C 302 " --> pdb=" O TYR C 298 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.540A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 145 removed outlier: 3.578A pdb=" N ALA D 145 " --> pdb=" O ASN D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 152 Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.603A pdb=" N THR D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.977A pdb=" N TYR D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 305 removed outlier: 4.572A pdb=" N ASP D 302 " --> pdb=" O TYR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.646A pdb=" N ALA E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 153 removed outlier: 3.638A pdb=" N LEU E 148 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 202 Processing helix chain 'E' and resid 250 through 260 Processing helix chain 'E' and resid 297 through 306 removed outlier: 3.518A pdb=" N ASP E 302 " --> pdb=" O TYR E 298 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ARG E 303 " --> pdb=" O LYS E 299 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 326 removed outlier: 3.644A pdb=" N ALA E 321 " --> pdb=" O HIS E 317 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE E 324 " --> pdb=" O MET E 320 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 186 through 202 Processing helix chain 'F' and resid 250 through 259 Processing helix chain 'F' and resid 267 through 272 removed outlier: 3.747A pdb=" N TYR F 271 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 302 Processing helix chain 'F' and resid 312 through 324 removed outlier: 3.768A pdb=" N TYR F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 10 removed outlier: 3.787A pdb=" N ILE G 10 " --> pdb=" O ILE G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 31 removed outlier: 3.671A pdb=" N GLU G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE G 31 " --> pdb=" O LEU G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 44 No H-bonds generated for 'chain 'G' and resid 42 through 44' Processing helix chain 'G' and resid 103 through 109 Processing helix chain 'G' and resid 112 through 122 Processing helix chain 'G' and resid 124 through 134 removed outlier: 3.750A pdb=" N ILE G 128 " --> pdb=" O LYS G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 181 removed outlier: 3.538A pdb=" N ASN G 170 " --> pdb=" O SER G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 206 removed outlier: 3.592A pdb=" N SER G 204 " --> pdb=" O SER G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 231 Processing helix chain 'G' and resid 255 through 266 removed outlier: 3.523A pdb=" N ILE G 259 " --> pdb=" O LEU G 255 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY G 263 " --> pdb=" O ILE G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 277 Processing helix chain 'G' and resid 281 through 290 removed outlier: 4.220A pdb=" N VAL G 285 " --> pdb=" O LYS G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 340 removed outlier: 3.629A pdb=" N PHE G 339 " --> pdb=" O HIS G 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 46 removed outlier: 3.677A pdb=" N PHE H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA H 36 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 130 removed outlier: 4.083A pdb=" N GLU H 130 " --> pdb=" O LYS H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 154 Processing helix chain 'H' and resid 163 through 169 removed outlier: 3.744A pdb=" N LEU H 167 " --> pdb=" O ARG H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 184 Processing helix chain 'H' and resid 236 through 240 Processing helix chain 'I' and resid 15 through 23 removed outlier: 3.838A pdb=" N ILE I 19 " --> pdb=" O SER I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 35 removed outlier: 4.124A pdb=" N VAL I 27 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER I 30 " --> pdb=" O PRO I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 71 Processing helix chain 'I' and resid 72 through 77 removed outlier: 3.786A pdb=" N LEU I 77 " --> pdb=" O LEU I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 removed outlier: 3.680A pdb=" N ARG I 118 " --> pdb=" O ARG I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 140 removed outlier: 3.946A pdb=" N GLU I 128 " --> pdb=" O GLY I 124 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS I 132 " --> pdb=" O GLU I 128 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN I 137 " --> pdb=" O LYS I 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 27 current: chain 'A' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 45 through 46 current: chain 'A' and resid 167 through 168 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 262 removed outlier: 3.540A pdb=" N ILE A 275 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 21 Processing sheet with id=AA7, first strand: chain 'B' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 27 current: chain 'B' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 45 through 46 current: chain 'B' and resid 172 through 173 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 50 through 55 Processing sheet with id=AA9, first strand: chain 'B' and resid 227 through 228 removed outlier: 4.409A pdb=" N LYS B 239 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 21 Processing sheet with id=AB2, first strand: chain 'C' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 45 through 46 current: chain 'C' and resid 167 through 173 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 167 through 173 current: chain 'C' and resid 239 through 243 removed outlier: 4.450A pdb=" N PHE C 241 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 50 through 55 Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 21 removed outlier: 6.224A pdb=" N SER D 20 " --> pdb=" O TYR D 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 27 current: chain 'D' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 46 current: chain 'D' and resid 172 through 173 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 172 through 173 current: chain 'D' and resid 246 through 249 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 50 through 55 removed outlier: 4.336A pdb=" N CYS D 82 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 260 through 262 removed outlier: 3.544A pdb=" N ILE D 275 " --> pdb=" O ASP D 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 19 through 21 removed outlier: 6.682A pdb=" N SER E 20 " --> pdb=" O TYR E 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 27 current: chain 'E' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 46 current: chain 'E' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 167 through 168 current: chain 'E' and resid 246 through 249 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AC2, first strand: chain 'F' and resid 19 through 21 removed outlier: 6.350A pdb=" N SER F 20 " --> pdb=" O TYR F 107 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 27 current: chain 'F' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 45 through 46 current: chain 'F' and resid 172 through 173 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 30 through 31 Processing sheet with id=AC5, first strand: chain 'F' and resid 260 through 262 Processing sheet with id=AC6, first strand: chain 'G' and resid 35 through 37 removed outlier: 3.596A pdb=" N ASP G 78 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 39 through 40 Processing sheet with id=AC8, first strand: chain 'G' and resid 148 through 154 removed outlier: 4.325A pdb=" N LYS G 148 " --> pdb=" O ILE G 163 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 157 through 163 current: chain 'H' and resid 215 through 229 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 215 through 229 current: chain 'H' and resid 249 through 253 Processing sheet with id=AC9, first strand: chain 'G' and resid 187 through 188 Processing sheet with id=AD1, first strand: chain 'G' and resid 301 through 305 Processing sheet with id=AD2, first strand: chain 'H' and resid 2 through 17 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 2 through 17 current: chain 'H' and resid 101 through 114 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'H' and resid 66 through 68 Processing sheet with id=AD4, first strand: chain 'I' and resid 40 through 42 Processing sheet with id=AD5, first strand: chain 'I' and resid 99 through 101 removed outlier: 4.006A pdb=" N ALA I 142 " --> pdb=" O LEU I 159 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 2.45 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: 5122 1.33 - 1.46: 5281 1.46 - 1.58: 11497 1.58 - 1.70: 118 1.70 - 1.82: 137 Bond restraints: 22155 Sorted by residual: bond pdb=" C PRO G 308 " pdb=" N LEU G 309 " ideal model delta sigma weight residual 1.335 1.434 -0.100 1.25e-02 6.40e+03 6.37e+01 bond pdb=" C SER B 110 " pdb=" N ASP B 111 " ideal model delta sigma weight residual 1.330 1.434 -0.104 1.31e-02 5.83e+03 6.26e+01 bond pdb=" C LEU G 323 " pdb=" N SER G 324 " ideal model delta sigma weight residual 1.330 1.426 -0.096 1.31e-02 5.83e+03 5.34e+01 bond pdb=" C ASP B 198 " pdb=" N THR B 199 " ideal model delta sigma weight residual 1.335 1.431 -0.096 1.38e-02 5.25e+03 4.84e+01 bond pdb=" C GLU F 124 " pdb=" N TYR F 125 " ideal model delta sigma weight residual 1.334 1.238 0.096 1.41e-02 5.03e+03 4.61e+01 ... (remaining 22150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 28239 2.57 - 5.14: 1785 5.14 - 7.71: 261 7.71 - 10.28: 59 10.28 - 12.85: 5 Bond angle restraints: 30349 Sorted by residual: angle pdb=" O ASP B 198 " pdb=" C ASP B 198 " pdb=" N THR B 199 " ideal model delta sigma weight residual 122.15 129.40 -7.25 1.14e+00 7.69e-01 4.04e+01 angle pdb=" N THR E 263 " pdb=" CA THR E 263 " pdb=" C THR E 263 " ideal model delta sigma weight residual 114.31 106.46 7.85 1.29e+00 6.01e-01 3.70e+01 angle pdb=" O LEU G 169 " pdb=" C LEU G 169 " pdb=" N ASN G 170 " ideal model delta sigma weight residual 122.12 128.54 -6.42 1.06e+00 8.90e-01 3.67e+01 angle pdb=" O LYS C 167 " pdb=" C LYS C 167 " pdb=" N GLU C 168 " ideal model delta sigma weight residual 123.27 116.21 7.06 1.17e+00 7.31e-01 3.64e+01 angle pdb=" N THR C 199 " pdb=" CA THR C 199 " pdb=" C THR C 199 " ideal model delta sigma weight residual 113.28 106.10 7.18 1.22e+00 6.72e-01 3.47e+01 ... (remaining 30344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 12791 34.43 - 68.87: 536 68.87 - 103.30: 32 103.30 - 137.73: 0 137.73 - 172.17: 5 Dihedral angle restraints: 13364 sinusoidal: 5619 harmonic: 7745 Sorted by residual: dihedral pdb=" O4' C L 38 " pdb=" C1' C L 38 " pdb=" N1 C L 38 " pdb=" C2 C L 38 " ideal model delta sinusoidal sigma weight residual 200.00 35.34 164.66 1 1.50e+01 4.44e-03 8.38e+01 dihedral pdb=" O4' U L 37 " pdb=" C1' U L 37 " pdb=" N1 U L 37 " pdb=" C2 U L 37 " ideal model delta sinusoidal sigma weight residual 200.00 41.16 158.84 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' C L 52 " pdb=" C1' C L 52 " pdb=" N1 C L 52 " pdb=" C2 C L 52 " ideal model delta sinusoidal sigma weight residual -128.00 39.83 -167.83 1 1.70e+01 3.46e-03 6.57e+01 ... (remaining 13361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2899 0.104 - 0.208: 527 0.208 - 0.313: 29 0.313 - 0.417: 2 0.417 - 0.521: 19 Chirality restraints: 3476 Sorted by residual: chirality pdb=" P C L 52 " pdb=" OP1 C L 52 " pdb=" OP2 C L 52 " pdb=" O5' C L 52 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" P G L 25 " pdb=" OP1 G L 25 " pdb=" OP2 G L 25 " pdb=" O5' G L 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" P C L 35 " pdb=" OP1 C L 35 " pdb=" OP2 C L 35 " pdb=" O5' C L 35 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.48e+00 ... (remaining 3473 not shown) Planarity restraints: 3676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 280 " -0.566 9.50e-02 1.11e+02 2.54e-01 3.94e+01 pdb=" NE ARG G 280 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG G 280 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG G 280 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG G 280 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 272 " 0.475 9.50e-02 1.11e+02 2.13e-01 2.79e+01 pdb=" NE ARG G 272 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG G 272 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG G 272 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 272 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 288 " 0.087 5.00e-02 4.00e+02 1.30e-01 2.72e+01 pdb=" N PRO D 289 " -0.225 5.00e-02 4.00e+02 pdb=" CA PRO D 289 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO D 289 " 0.068 5.00e-02 4.00e+02 ... (remaining 3673 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4598 2.79 - 3.31: 20074 3.31 - 3.84: 36453 3.84 - 4.37: 43481 4.37 - 4.90: 70470 Nonbonded interactions: 175076 Sorted by model distance: nonbonded pdb=" O GLU B 278 " pdb=" OH TYR B 318 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR D 35 " pdb=" OG1 THR D 90 " model vdw 2.264 3.040 nonbonded pdb=" O LEU D 55 " pdb=" O2' G L 51 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR B 50 " pdb=" O SER B 81 " model vdw 2.296 3.040 nonbonded pdb=" O GLU E 61 " pdb=" OH TYR F 280 " model vdw 2.305 3.040 ... (remaining 175071 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 11 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name N or nam \ e CA or name C or name O or name CB )) or resid 18 through 28 or (resid 29 throu \ gh 30 and (name N or name CA or name C or name O or name CB )) or resid 31 throu \ gh 33 or (resid 34 and (name N or name CA or name C or name O or name CB )) or r \ esid 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) or \ resid 37 or (resid 38 through 39 and (name N or name CA or name C or name O or \ name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB )) or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 or (resid 81 and (name N or name CA or na \ me C or name O or name CB )) or resid 82 through 86 or (resid 87 through 88 and \ (name N or name CA or name C or name O or name CB )) or resid 89 through 105 or \ (resid 106 and (name N or name CA or name C or name O or name CB )) or resid 107 \ or (resid 108 and (name N or name CA or name C or name O or name CB )) or resid \ 109 through 110 or (resid 111 and (name N or name CA or name C or name O or nam \ e CB )) or resid 112 through 120 or (resid 121 and (name N or name CA or name C \ or name O or name CB )) or resid 122 or (resid 123 through 124 and (name N or na \ me CA or name C or name O or name CB )) or resid 125 through 127 or (resid 128 t \ hrough 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ through 139 or (resid 140 and (name N or name CA or name C or name O or name CB \ )) or resid 141 through 165 or (resid 166 and (name N or name CA or name C or n \ ame O or name CB )) or resid 167 through 178 or (resid 179 through 180 and (name \ N or name CA or name C or name O or name CB )) or resid 181 through 183 or (res \ id 184 through 185 and (name N or name CA or name C or name O or name CB )) or r \ esid 186 through 190 or (resid 191 and (name N or name CA or name C or name O or \ name CB )) or resid 192 through 197 or (resid 198 through 199 and (name N or na \ me CA or name C or name O or name CB )) or resid 200 through 204 or (resid 205 a \ nd (name N or name CA or name C or name O or name CB )) or resid 206 through 220 \ or (resid 221 through 222 and (name N or name CA or name C or name O or name CB \ )) or resid 223 through 228 or (resid 229 and (name N or name CA or name C or n \ ame O or name CB )) or resid 237 through 238 or (resid 239 and (name N or name C \ A or name C or name O or name CB )) or resid 240 through 241 or (resid 242 and ( \ name N or name CA or name C or name O or name CB )) or resid 243 through 271 or \ (resid 272 and (name N or name CA or name C or name O or name CB )) or resid 273 \ through 277 or (resid 278 and (name N or name CA or name C or name O or name CB \ )) or resid 279 through 283 or (resid 284 and (name N or name CA or name C or n \ ame O or name CB )) or resid 285 or (resid 286 and (name N or name CA or name C \ or name O or name CB )) or resid 287 through 303 or (resid 304 through 305 and ( \ name N or name CA or name C or name O or name CB )) or resid 306 or (resid 307 a \ nd (name N or name CA or name C or name O or name CB )) or resid 308 through 309 \ or (resid 310 and (name N or name CA or name C or name O or name CB )) or resid \ 311 through 314 or (resid 315 and (name N or name CA or name C or name O or nam \ e CB )) or resid 316 through 327 or (resid 328 through 329 and (name N or name C \ A or name C or name O or name CB )) or resid 330)) selection = (chain 'B' and (resid 11 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name N or nam \ e CA or name C or name O or name CB )) or resid 18 through 28 or (resid 29 throu \ gh 30 and (name N or name CA or name C or name O or name CB )) or resid 31 throu \ gh 33 or (resid 34 and (name N or name CA or name C or name O or name CB )) or r \ esid 35 through 37 or (resid 38 through 39 and (name N or name CA or name C or n \ ame O or name CB )) or resid 40 through 50 or (resid 51 and (name N or name CA o \ r name C or name O or name CB )) or (resid 79 and (name N or name CA or name C o \ r name O or name CB )) or resid 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 87 or (resid 88 and (name N or name \ CA or name C or name O or name CB )) or resid 89 through 105 or (resid 106 and \ (name N or name CA or name C or name O or name CB )) or resid 107 or (resid 108 \ and (name N or name CA or name C or name O or name CB )) or resid 109 through 12 \ 0 or (resid 121 and (name N or name CA or name C or name O or name CB )) or resi \ d 122 or (resid 123 through 124 and (name N or name CA or name C or name O or na \ me CB )) or resid 125 through 149 or (resid 150 and (name N or name CA or name C \ or name O or name CB )) or resid 151 through 155 or (resid 156 and (name N or n \ ame CA or name C or name O or name CB )) or resid 157 through 178 or (resid 179 \ through 180 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 1 through 183 or (resid 184 through 185 and (name N or name CA or name C or name \ O or name CB )) or resid 186 through 190 or (resid 191 and (name N or name CA o \ r name C or name O or name CB )) or resid 192 through 197 or (resid 198 through \ 199 and (name N or name CA or name C or name O or name CB )) or resid 200 throug \ h 204 or (resid 205 and (name N or name CA or name C or name O or name CB )) or \ resid 206 through 220 or (resid 221 through 222 and (name N or name CA or name C \ or name O or name CB )) or resid 223 through 229 or resid 237 through 241 or (r \ esid 242 and (name N or name CA or name C or name O or name CB )) or resid 243 t \ hrough 271 or (resid 272 and (name N or name CA or name C or name O or name CB ) \ ) or resid 273 through 277 or (resid 278 and (name N or name CA or name C or nam \ e O or name CB )) or resid 279 through 283 or (resid 284 and (name N or name CA \ or name C or name O or name CB )) or resid 285 or (resid 286 and (name N or name \ CA or name C or name O or name CB )) or resid 287 through 303 or (resid 304 thr \ ough 305 and (name N or name CA or name C or name O or name CB )) or resid 306 o \ r (resid 307 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 08 through 309 or (resid 310 and (name N or name CA or name C or name O or name \ CB )) or resid 311 through 327 or (resid 328 through 329 and (name N or name CA \ or name C or name O or name CB )) or resid 330)) selection = (chain 'C' and (resid 11 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 33 or (resid 34 and (name N or nam \ e CA or name C or name O or name CB )) or resid 35 or (resid 36 and (name N or n \ ame CA or name C or name O or name CB )) or resid 37 or (resid 38 through 39 and \ (name N or name CA or name C or name O or name CB )) or resid 40 through 43 or \ (resid 44 and (name N or name CA or name C or name O or name CB )) or resid 45 t \ hrough 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) \ or (resid 79 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 0 or (resid 81 and (name N or name CA or name C or name O or name CB )) or resid \ 82 through 86 or (resid 87 through 88 and (name N or name CA or name C or name \ O or name CB )) or resid 89 through 105 or (resid 106 and (name N or name CA or \ name C or name O or name CB )) or resid 107 or (resid 108 and (name N or name CA \ or name C or name O or name CB )) or resid 109 through 110 or (resid 111 and (n \ ame N or name CA or name C or name O or name CB )) or resid 112 through 120 or ( \ resid 121 and (name N or name CA or name C or name O or name CB )) or resid 122 \ or (resid 123 through 124 and (name N or name CA or name C or name O or name CB \ )) or resid 125 through 127 or (resid 128 through 129 and (name N or name CA or \ name C or name O or name CB )) or resid 130 through 139 or (resid 140 and (name \ N or name CA or name C or name O or name CB )) or resid 141 through 149 or (resi \ d 150 and (name N or name CA or name C or name O or name CB )) or resid 151 thro \ ugh 155 or (resid 156 and (name N or name CA or name C or name O or name CB )) o \ r resid 157 through 165 or (resid 166 and (name N or name CA or name C or name O \ or name CB )) or resid 167 or (resid 168 and (name N or name CA or name C or na \ me O or name CB )) or resid 169 through 178 or (resid 179 through 180 and (name \ N or name CA or name C or name O or name CB )) or resid 181 through 183 or (resi \ d 184 through 185 and (name N or name CA or name C or name O or name CB )) or re \ sid 186 through 197 or (resid 198 through 199 and (name N or name CA or name C o \ r name O or name CB )) or resid 200 through 204 or (resid 205 and (name N or nam \ e CA or name C or name O or name CB )) or resid 206 through 220 or (resid 221 th \ rough 222 and (name N or name CA or name C or name O or name CB )) or resid 223 \ through 228 or (resid 229 and (name N or name CA or name C or name O or name CB \ )) or resid 237 through 238 or (resid 239 and (name N or name CA or name C or na \ me O or name CB )) or resid 240 through 241 or (resid 242 and (name N or name CA \ or name C or name O or name CB )) or resid 243 through 283 or (resid 284 and (n \ ame N or name CA or name C or name O or name CB )) or resid 285 or (resid 286 an \ d (name N or name CA or name C or name O or name CB )) or resid 287 through 292 \ or (resid 293 and (name N or name CA or name C or name O or name CB )) or resid \ 294 through 303 or (resid 304 through 305 and (name N or name CA or name C or na \ me O or name CB )) or resid 306 or (resid 307 and (name N or name CA or name C o \ r name O or name CB )) or resid 308 through 314 or (resid 315 and (name N or nam \ e CA or name C or name O or name CB )) or resid 316 through 327 or (resid 328 th \ rough 329 and (name N or name CA or name C or name O or name CB )) or resid 330) \ ) selection = (chain 'D' and (resid 11 through 28 or (resid 29 through 30 and (name N or name \ CA or name C or name O or name CB )) or resid 31 through 33 or (resid 34 and (na \ me N or name CA or name C or name O or name CB )) or resid 35 or (resid 36 and ( \ name N or name CA or name C or name O or name CB )) or resid 37 or (resid 38 thr \ ough 39 and (name N or name CA or name C or name O or name CB )) or resid 40 thr \ ough 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or \ resid 45 through 51 or resid 79 through 86 or (resid 87 through 88 and (name N \ or name CA or name C or name O or name CB )) or resid 89 through 105 or (resid 1 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 107 or (res \ id 108 and (name N or name CA or name C or name O or name CB )) or resid 109 thr \ ough 110 or (resid 111 and (name N or name CA or name C or name O or name CB )) \ or resid 112 through 120 or (resid 121 and (name N or name CA or name C or name \ O or name CB )) or resid 122 through 139 or (resid 140 and (name N or name CA or \ name C or name O or name CB )) or resid 141 through 149 or (resid 150 and (name \ N or name CA or name C or name O or name CB )) or resid 151 through 155 or (res \ id 156 and (name N or name CA or name C or name O or name CB )) or resid 157 thr \ ough 164 or (resid 165 through 166 and (name N or name CA or name C or name O or \ name CB )) or resid 167 or (resid 168 and (name N or name CA or name C or name \ O or name CB )) or resid 169 through 178 or (resid 179 through 180 and (name N o \ r name CA or name C or name O or name CB )) or resid 181 through 183 or (resid 1 \ 84 through 185 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or nam \ e CB )) or resid 192 through 204 or (resid 205 and (name N or name CA or name C \ or name O or name CB )) or resid 206 through 220 or (resid 221 through 222 and ( \ name N or name CA or name C or name O or name CB )) or resid 223 through 229 or \ resid 237 through 238 or (resid 239 and (name N or name CA or name C or name O o \ r name CB )) or resid 240 through 271 or (resid 272 and (name N or name CA or na \ me C or name O or name CB )) or resid 273 through 277 or (resid 278 and (name N \ or name CA or name C or name O or name CB )) or resid 279 through 285 or (resid \ 286 and (name N or name CA or name C or name O or name CB )) or resid 287 throug \ h 292 or (resid 293 and (name N or name CA or name C or name O or name CB )) or \ resid 294 through 303 or (resid 304 through 305 and (name N or name CA or name C \ or name O or name CB )) or resid 306 or (resid 307 and (name N or name CA or na \ me C or name O or name CB )) or resid 308 through 309 or (resid 310 and (name N \ or name CA or name C or name O or name CB )) or resid 311 through 314 or (resid \ 315 and (name N or name CA or name C or name O or name CB )) or resid 316 throug \ h 330)) selection = (chain 'E' and (resid 11 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name N or nam \ e CA or name C or name O or name CB )) or resid 18 through 28 or (resid 29 throu \ gh 30 and (name N or name CA or name C or name O or name CB )) or resid 31 throu \ gh 33 or (resid 34 and (name N or name CA or name C or name O or name CB )) or r \ esid 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) or \ resid 37 or (resid 38 through 39 and (name N or name CA or name C or name O or \ name CB )) or resid 40 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB )) or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 or (resid 81 and (name N or name CA or na \ me C or name O or name CB )) or resid 82 through 87 or (resid 88 and (name N or \ name CA or name C or name O or name CB )) or resid 89 through 107 or (resid 108 \ and (name N or name CA or name C or name O or name CB )) or resid 109 through 11 \ 0 or (resid 111 and (name N or name CA or name C or name O or name CB )) or resi \ d 112 through 120 or (resid 121 and (name N or name CA or name C or name O or na \ me CB )) or resid 122 through 127 or (resid 128 through 129 and (name N or name \ CA or name C or name O or name CB )) or resid 130 through 139 or (resid 140 and \ (name N or name CA or name C or name O or name CB )) or resid 141 through 149 or \ (resid 150 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 1 through 155 or (resid 156 and (name N or name CA or name C or name O or name C \ B )) or resid 157 through 165 or (resid 166 and (name N or name CA or name C or \ name O or name CB )) or resid 167 through 178 or (resid 179 through 180 and (nam \ e N or name CA or name C or name O or name CB )) or resid 181 through 198 or (re \ sid 199 and (name N or name CA or name C or name O or name CB )) or resid 200 th \ rough 220 or (resid 221 through 222 and (name N or name CA or name C or name O o \ r name CB )) or resid 223 through 229 or resid 237 through 238 or (resid 239 and \ (name N or name CA or name C or name O or name CB )) or resid 240 through 241 o \ r (resid 242 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 43 through 283 or (resid 284 and (name N or name CA or name C or name O or name \ CB )) or resid 285 through 303 or (resid 304 through 305 and (name N or name CA \ or name C or name O or name CB )) or resid 306 or (resid 307 and (name N or name \ CA or name C or name O or name CB )) or resid 308 through 309 or (resid 310 and \ (name N or name CA or name C or name O or name CB )) or resid 311 through 314 o \ r (resid 315 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 16 through 327 or (resid 328 through 329 and (name N or name CA or name C or nam \ e O or name CB )) or resid 330)) selection = (chain 'F' and (resid 11 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 16 or (resid 17 and (name N or nam \ e CA or name C or name O or name CB )) or resid 18 through 28 or (resid 29 throu \ gh 30 and (name N or name CA or name C or name O or name CB )) or resid 31 throu \ gh 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) or r \ esid 37 through 43 or (resid 44 and (name N or name CA or name C or name O or na \ me CB )) or resid 45 through 50 or (resid 51 through 79 and (name N or name CA o \ r name C or name O or name CB )) or resid 80 or (resid 81 and (name N or name CA \ or name C or name O or name CB )) or resid 82 through 87 or (resid 88 and (name \ N or name CA or name C or name O or name CB )) or resid 89 through 105 or (resi \ d 106 and (name N or name CA or name C or name O or name CB )) or resid 107 thro \ ugh 110 or (resid 111 and (name N or name CA or name C or name O or name CB )) o \ r resid 112 through 122 or (resid 123 through 124 and (name N or name CA or name \ C or name O or name CB )) or resid 125 through 127 or (resid 128 through 129 an \ d (name N or name CA or name C or name O or name CB )) or resid 130 through 139 \ or (resid 140 and (name N or name CA or name C or name O or name CB )) or resid \ 141 through 149 or (resid 150 and (name N or name CA or name C or name O or name \ CB )) or resid 151 through 165 or (resid 166 and (name N or name CA or name C o \ r name O or name CB )) or resid 167 through 184 or (resid 185 and (name N or nam \ e CA or name C or name O or name CB )) or resid 186 through 190 or (resid 191 an \ d (name N or name CA or name C or name O or name CB )) or resid 192 through 198 \ or (resid 199 and (name N or name CA or name C or name O or name CB )) or resid \ 200 through 221 or (resid 222 and (name N or name CA or name C or name O or name \ CB )) or resid 223 through 241 or (resid 242 and (name N or name CA or name C o \ r name O or name CB )) or resid 243 through 277 or (resid 278 and (name N or nam \ e CA or name C or name O or name CB )) or resid 279 through 283 or (resid 284 an \ d (name N or name CA or name C or name O or name CB )) or resid 285 or (resid 28 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 287 through \ 292 or (resid 293 and (name N or name CA or name C or name O or name CB )) or re \ sid 294 through 309 or (resid 310 and (name N or name CA or name C or name O or \ name CB )) or resid 311 through 314 or (resid 315 and (name N or name CA or name \ C or name O or name CB )) or resid 316 through 327 or (resid 328 through 329 an \ d (name N or name CA or name C or name O or name CB )) or resid 330)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.430 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.030 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.010 0.104 22155 Z= 0.639 Angle : 1.403 12.851 30349 Z= 0.915 Chirality : 0.083 0.521 3476 Planarity : 0.014 0.254 3676 Dihedral : 18.130 172.166 8356 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.97 % Favored : 92.87 % Rotamer: Outliers : 1.97 % Allowed : 28.51 % Favored : 69.52 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.14), residues: 2596 helix: -2.07 (0.16), residues: 736 sheet: -0.47 (0.25), residues: 438 loop : -2.56 (0.13), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG E 150 TYR 0.048 0.003 TYR A 114 PHE 0.056 0.004 PHE C 297 TRP 0.063 0.004 TRP C 149 HIS 0.021 0.002 HIS G 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00968 / 0.64 (22155) covalent geometry : angle 1.40326 / 0.91 (30349) hydrogen bonds : bond 0.19074 / 12.67 ( 595) hydrogen bonds : angle 8.04910 / 5.67 ( 1650) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 802 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 THR cc_start: 0.7904 (p) cc_final: 0.7634 (p) REVERT: A 44 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8018 (ttpp) REVERT: A 318 TYR cc_start: 0.7910 (t80) cc_final: 0.7269 (t80) REVERT: A 328 MET cc_start: 0.8089 (mtp) cc_final: 0.7876 (mtp) REVERT: B 39 LYS cc_start: 0.8080 (ptpt) cc_final: 0.7835 (ptpp) REVERT: B 144 ASN cc_start: 0.8308 (p0) cc_final: 0.8091 (p0) REVERT: B 184 GLU cc_start: 0.7776 (mp0) cc_final: 0.7492 (mp0) REVERT: B 215 VAL cc_start: 0.8343 (p) cc_final: 0.8125 (m) REVERT: B 216 LYS cc_start: 0.8698 (tttt) cc_final: 0.8407 (tttm) REVERT: B 217 ILE cc_start: 0.8471 (pp) cc_final: 0.8188 (pt) REVERT: B 253 LYS cc_start: 0.8105 (tttt) cc_final: 0.7777 (tttt) REVERT: B 262 ASP cc_start: 0.8095 (t0) cc_final: 0.7851 (t0) REVERT: B 265 TYR cc_start: 0.7566 (p90) cc_final: 0.7186 (p90) REVERT: B 273 PHE cc_start: 0.8380 (p90) cc_final: 0.7902 (p90) REVERT: C 18 ASN cc_start: 0.8081 (m110) cc_final: 0.7842 (m-40) REVERT: C 89 ASP cc_start: 0.7901 (p0) cc_final: 0.7512 (p0) REVERT: C 111 ASP cc_start: 0.8027 (t0) cc_final: 0.7819 (t0) REVERT: C 159 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7045 (tp30) REVERT: C 161 ILE cc_start: 0.8829 (tt) cc_final: 0.8475 (pt) REVERT: C 172 PHE cc_start: 0.7301 (m-10) cc_final: 0.6759 (m-10) REVERT: C 221 MET cc_start: 0.7250 (tpp) cc_final: 0.7045 (mpp) REVERT: C 229 MET cc_start: 0.7608 (ppp) cc_final: 0.7216 (ppp) REVERT: C 242 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8204 (mtpp) REVERT: C 297 PHE cc_start: 0.7248 (t80) cc_final: 0.7042 (t80) REVERT: C 304 MET cc_start: 0.7587 (ttt) cc_final: 0.7273 (ttm) REVERT: C 309 GLU cc_start: 0.7959 (tt0) cc_final: 0.7716 (tm-30) REVERT: D 45 LEU cc_start: 0.8266 (mp) cc_final: 0.8044 (mp) REVERT: D 271 TYR cc_start: 0.7595 (m-10) cc_final: 0.7152 (m-10) REVERT: E 99 VAL cc_start: 0.8553 (t) cc_final: 0.8337 (t) REVERT: E 178 ASN cc_start: 0.8370 (t0) cc_final: 0.8099 (t0) REVERT: E 244 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7471 (mt-10) REVERT: E 290 PHE cc_start: 0.8014 (m-10) cc_final: 0.7777 (m-80) REVERT: E 299 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7944 (mtmt) REVERT: E 318 TYR cc_start: 0.7344 (t80) cc_final: 0.6792 (t80) REVERT: E 322 ILE cc_start: 0.8394 (tp) cc_final: 0.8068 (tt) REVERT: F 36 ASP cc_start: 0.8007 (t0) cc_final: 0.7698 (t0) REVERT: F 48 LEU cc_start: 0.8824 (mm) cc_final: 0.8620 (mp) REVERT: F 111 ASP cc_start: 0.7733 (t0) cc_final: 0.7296 (t0) REVERT: F 206 TYR cc_start: 0.7927 (p90) cc_final: 0.7726 (p90) REVERT: G 51 ASN cc_start: 0.7757 (t0) cc_final: 0.7501 (t0) REVERT: G 129 ARG cc_start: 0.6710 (ttt90) cc_final: 0.6302 (ttt90) REVERT: G 172 GLU cc_start: 0.7426 (tp30) cc_final: 0.7191 (tp30) REVERT: G 176 ARG cc_start: 0.7780 (ttm170) cc_final: 0.7552 (ttm170) REVERT: G 190 LEU cc_start: 0.7237 (mp) cc_final: 0.6872 (tt) REVERT: G 224 LEU cc_start: 0.8882 (tp) cc_final: 0.8556 (tt) REVERT: G 229 ASP cc_start: 0.7740 (m-30) cc_final: 0.7413 (m-30) REVERT: G 262 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6803 (tm-30) REVERT: G 265 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7476 (ttp-110) REVERT: H 126 LYS cc_start: 0.8278 (ttmm) cc_final: 0.7998 (ttmm) REVERT: H 240 LEU cc_start: 0.8110 (tp) cc_final: 0.7711 (tp) REVERT: I 83 TYR cc_start: 0.7472 (m-80) cc_final: 0.6920 (m-80) REVERT: I 132 LYS cc_start: 0.8141 (tptm) cc_final: 0.7889 (tptm) outliers start: 41 outliers final: 15 residues processed: 820 average time/residue: 0.1605 time to fit residues: 201.4198 Evaluate side-chains 737 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 721 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain I residue 155 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.0030 chunk 111 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 26 ASN C 113 ASN C 186 ASN C 195 GLN C 208 ASN C 308 ASN D 140 ASN E 18 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 140 ASN G 270 ASN G 327 HIS H 12 ASN H 17 ASN I 29 HIS I 106 ASN I 137 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098311 restraints weight = 40050.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.101287 restraints weight = 17159.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.103147 restraints weight = 9308.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.104335 restraints weight = 6013.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.105085 restraints weight = 4411.020| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22155 Z= 0.167 Angle : 0.687 9.492 30349 Z= 0.370 Chirality : 0.045 0.323 3476 Planarity : 0.006 0.076 3676 Dihedral : 15.784 179.027 3798 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.14 % Allowed : 24.42 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.15), residues: 2596 helix: -0.95 (0.17), residues: 755 sheet: -0.21 (0.26), residues: 416 loop : -2.20 (0.14), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 284 TYR 0.028 0.002 TYR E 224 PHE 0.027 0.002 PHE B 243 TRP 0.026 0.002 TRP C 149 HIS 0.007 0.001 HIS G 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (22155) covalent geometry : angle 0.68656 / 0.37 (30349) hydrogen bonds : bond 0.05429 / 3.70 ( 595) hydrogen bonds : angle 5.76289 / 3.95 ( 1650) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 748 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7611 (tp) REVERT: A 160 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7342 (t) REVERT: A 178 ASN cc_start: 0.7958 (m-40) cc_final: 0.7347 (p0) REVERT: A 253 LYS cc_start: 0.7616 (tttp) cc_final: 0.6854 (ttmt) REVERT: A 318 TYR cc_start: 0.7937 (t80) cc_final: 0.7679 (t80) REVERT: B 39 LYS cc_start: 0.7997 (ptpt) cc_final: 0.7753 (ptpp) REVERT: B 43 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6828 (t80) REVERT: B 55 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7453 (tp) REVERT: B 142 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7556 (mt) REVERT: B 216 LYS cc_start: 0.8617 (tttt) cc_final: 0.8363 (tttm) REVERT: B 217 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8157 (pt) REVERT: B 241 PHE cc_start: 0.8777 (t80) cc_final: 0.8512 (t80) REVERT: B 242 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8268 (ttpp) REVERT: B 253 LYS cc_start: 0.8071 (tttt) cc_final: 0.7678 (ttmt) REVERT: B 265 TYR cc_start: 0.7502 (p90) cc_final: 0.7169 (p90) REVERT: B 270 THR cc_start: 0.8176 (p) cc_final: 0.7826 (p) REVERT: B 273 PHE cc_start: 0.8336 (p90) cc_final: 0.7980 (p90) REVERT: B 278 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6494 (mt-10) REVERT: B 319 VAL cc_start: 0.8345 (p) cc_final: 0.8141 (p) REVERT: C 48 LEU cc_start: 0.8850 (mt) cc_final: 0.8648 (mm) REVERT: C 89 ASP cc_start: 0.7796 (p0) cc_final: 0.7385 (p0) REVERT: C 106 MET cc_start: 0.7806 (tpp) cc_final: 0.7589 (tpt) REVERT: C 111 ASP cc_start: 0.7468 (t0) cc_final: 0.7141 (t0) REVERT: C 159 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6392 (tp30) REVERT: C 179 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8484 (mp) REVERT: C 221 MET cc_start: 0.7000 (tpp) cc_final: 0.6716 (mpp) REVERT: C 229 MET cc_start: 0.7310 (ppp) cc_final: 0.7071 (ppp) REVERT: C 253 LYS cc_start: 0.7924 (tptt) cc_final: 0.7610 (tttt) REVERT: C 265 TYR cc_start: 0.7157 (p90) cc_final: 0.6432 (p90) REVERT: C 304 MET cc_start: 0.7223 (ttt) cc_final: 0.6995 (ttm) REVERT: D 23 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7953 (mtm-85) REVERT: D 253 LYS cc_start: 0.7469 (tptt) cc_final: 0.6865 (tppt) REVERT: D 290 PHE cc_start: 0.8306 (m-80) cc_final: 0.7989 (m-80) REVERT: E 40 ARG cc_start: 0.7763 (ptt90) cc_final: 0.7179 (ptt90) REVERT: E 159 GLU cc_start: 0.7493 (tp30) cc_final: 0.7085 (tp30) REVERT: E 244 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7235 (mt-10) REVERT: E 253 LYS cc_start: 0.7877 (tttt) cc_final: 0.7660 (tttt) REVERT: E 255 ASN cc_start: 0.8180 (t0) cc_final: 0.7960 (t0) REVERT: E 290 PHE cc_start: 0.8052 (m-10) cc_final: 0.7637 (m-80) REVERT: E 309 GLU cc_start: 0.5984 (OUTLIER) cc_final: 0.5448 (tm-30) REVERT: E 318 TYR cc_start: 0.7352 (t80) cc_final: 0.7067 (t80) REVERT: F 36 ASP cc_start: 0.7765 (t0) cc_final: 0.7457 (t0) REVERT: F 48 LEU cc_start: 0.8625 (mm) cc_final: 0.8366 (mp) REVERT: F 111 ASP cc_start: 0.7322 (t0) cc_final: 0.7122 (t0) REVERT: F 203 LYS cc_start: 0.8492 (tppt) cc_final: 0.8282 (mmtp) REVERT: F 206 TYR cc_start: 0.7783 (p90) cc_final: 0.7550 (p90) REVERT: F 228 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6852 (tm-30) REVERT: F 318 TYR cc_start: 0.8144 (t80) cc_final: 0.7924 (t80) REVERT: G 51 ASN cc_start: 0.7559 (t0) cc_final: 0.7357 (t0) REVERT: G 63 ASN cc_start: 0.7370 (t0) cc_final: 0.7059 (t0) REVERT: G 172 GLU cc_start: 0.7144 (tp30) cc_final: 0.6886 (tp30) REVERT: G 176 ARG cc_start: 0.8153 (ttm170) cc_final: 0.7798 (ttm170) REVERT: G 190 LEU cc_start: 0.6947 (mp) cc_final: 0.6740 (tt) REVERT: G 210 LEU cc_start: 0.8360 (mt) cc_final: 0.8127 (tp) REVERT: G 229 ASP cc_start: 0.7730 (m-30) cc_final: 0.7460 (m-30) REVERT: G 262 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6744 (tm-30) REVERT: G 265 ARG cc_start: 0.7907 (ttp-110) cc_final: 0.7592 (ttp-110) REVERT: G 266 LYS cc_start: 0.8587 (mttm) cc_final: 0.8235 (mttm) REVERT: G 272 ARG cc_start: 0.8263 (ttm110) cc_final: 0.7939 (ttm170) REVERT: G 307 VAL cc_start: 0.8717 (m) cc_final: 0.8511 (p) REVERT: G 322 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6595 (mtm) REVERT: H 1 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.6126 (mpp) REVERT: H 126 LYS cc_start: 0.8305 (ttmm) cc_final: 0.7945 (ttmm) REVERT: I 165 LYS cc_start: 0.7865 (mmmt) cc_final: 0.7598 (mmmt) outliers start: 107 outliers final: 48 residues processed: 798 average time/residue: 0.1463 time to fit residues: 181.4360 Evaluate side-chains 776 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 717 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 322 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 164 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 223 optimal weight: 0.0370 chunk 142 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN D 256 ASN E 18 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN F 256 ASN H 12 ASN H 99 GLN H 237 ASN I 53 HIS I 106 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.093049 restraints weight = 40138.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.095979 restraints weight = 17055.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.097801 restraints weight = 9241.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.098995 restraints weight = 5966.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099753 restraints weight = 4371.701| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 22155 Z= 0.255 Angle : 0.697 8.207 30349 Z= 0.374 Chirality : 0.046 0.315 3476 Planarity : 0.006 0.083 3676 Dihedral : 15.692 179.486 3786 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 6.11 % Allowed : 24.57 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.15), residues: 2596 helix: -0.48 (0.18), residues: 758 sheet: -0.23 (0.26), residues: 423 loop : -2.07 (0.14), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 37 TYR 0.035 0.002 TYR E 224 PHE 0.025 0.003 PHE B 243 TRP 0.032 0.002 TRP D 149 HIS 0.008 0.001 HIS G 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.26 (22155) covalent geometry : angle 0.69728 / 0.37 (30349) hydrogen bonds : bond 0.05462 / 3.68 ( 595) hydrogen bonds : angle 5.40010 / 3.71 ( 1650) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 750 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.7420 (t80) cc_final: 0.7173 (t80) REVERT: A 244 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6597 (mt-10) REVERT: A 253 LYS cc_start: 0.7887 (tttp) cc_final: 0.7669 (tttt) REVERT: A 318 TYR cc_start: 0.8045 (t80) cc_final: 0.7454 (t80) REVERT: A 328 MET cc_start: 0.7442 (mtp) cc_final: 0.6994 (mtp) REVERT: B 39 LYS cc_start: 0.8140 (ptpt) cc_final: 0.7890 (ptpp) REVERT: B 55 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7514 (tp) REVERT: B 139 VAL cc_start: 0.8161 (t) cc_final: 0.7907 (p) REVERT: B 144 ASN cc_start: 0.8288 (p0) cc_final: 0.8072 (p0) REVERT: B 167 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7646 (tttm) REVERT: B 184 GLU cc_start: 0.7605 (mp0) cc_final: 0.7357 (mp0) REVERT: B 216 LYS cc_start: 0.8616 (tttt) cc_final: 0.8294 (tttm) REVERT: B 217 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8243 (pt) REVERT: B 221 MET cc_start: 0.7174 (mmm) cc_final: 0.6959 (mmm) REVERT: B 265 TYR cc_start: 0.7685 (p90) cc_final: 0.7279 (p90) REVERT: B 267 ASP cc_start: 0.6843 (p0) cc_final: 0.6036 (p0) REVERT: B 273 PHE cc_start: 0.8405 (p90) cc_final: 0.8022 (p90) REVERT: B 278 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6630 (mt-10) REVERT: C 89 ASP cc_start: 0.7849 (p0) cc_final: 0.7347 (p0) REVERT: C 90 THR cc_start: 0.8170 (m) cc_final: 0.7924 (m) REVERT: C 106 MET cc_start: 0.7844 (tpp) cc_final: 0.7456 (tpp) REVERT: C 111 ASP cc_start: 0.7573 (t0) cc_final: 0.7214 (t0) REVERT: C 120 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: C 159 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6479 (tm-30) REVERT: C 179 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8579 (mp) REVERT: C 229 MET cc_start: 0.7304 (ppp) cc_final: 0.7069 (ppp) REVERT: C 252 GLN cc_start: 0.8350 (pm20) cc_final: 0.7866 (pm20) REVERT: C 265 TYR cc_start: 0.7190 (p90) cc_final: 0.6542 (p90) REVERT: C 270 THR cc_start: 0.8261 (p) cc_final: 0.7833 (t) REVERT: C 304 MET cc_start: 0.7221 (ttt) cc_final: 0.6996 (ttm) REVERT: D 20 SER cc_start: 0.7566 (p) cc_final: 0.7280 (p) REVERT: D 77 GLN cc_start: 0.7347 (tt0) cc_final: 0.7107 (tt0) REVERT: E 40 ARG cc_start: 0.8243 (ptt90) cc_final: 0.7496 (ptt90) REVERT: E 159 GLU cc_start: 0.7201 (tp30) cc_final: 0.6910 (tp30) REVERT: E 309 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5666 (tm-30) REVERT: E 318 TYR cc_start: 0.7441 (t80) cc_final: 0.7151 (t80) REVERT: F 36 ASP cc_start: 0.7846 (t0) cc_final: 0.7643 (t0) REVERT: F 48 LEU cc_start: 0.8659 (mm) cc_final: 0.8386 (mp) REVERT: F 89 ASP cc_start: 0.7884 (p0) cc_final: 0.7286 (p0) REVERT: F 140 ASN cc_start: 0.7973 (t0) cc_final: 0.7721 (m-40) REVERT: F 228 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6957 (tm-30) REVERT: F 320 MET cc_start: 0.7216 (mmt) cc_final: 0.6917 (mmt) REVERT: G 63 ASN cc_start: 0.7597 (t0) cc_final: 0.7302 (t0) REVERT: G 172 GLU cc_start: 0.7216 (tp30) cc_final: 0.6836 (tp30) REVERT: G 176 ARG cc_start: 0.8240 (ttm170) cc_final: 0.7972 (ttm170) REVERT: G 229 ASP cc_start: 0.7723 (m-30) cc_final: 0.7345 (m-30) REVERT: G 262 GLU cc_start: 0.7629 (mm-30) cc_final: 0.6965 (tm-30) REVERT: G 265 ARG cc_start: 0.8019 (ttp-110) cc_final: 0.7762 (ttp-110) REVERT: G 266 LYS cc_start: 0.8787 (mttm) cc_final: 0.8250 (mttm) REVERT: G 307 VAL cc_start: 0.8756 (m) cc_final: 0.8531 (p) REVERT: H 126 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7903 (ttmm) REVERT: H 150 THR cc_start: 0.8942 (t) cc_final: 0.8687 (m) REVERT: I 77 LEU cc_start: 0.6415 (mm) cc_final: 0.6146 (mt) REVERT: I 113 ARG cc_start: 0.7875 (mtt90) cc_final: 0.7671 (mtm110) REVERT: I 165 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7847 (mmmm) outliers start: 127 outliers final: 65 residues processed: 809 average time/residue: 0.1550 time to fit residues: 194.2666 Evaluate side-chains 797 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 724 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 256 ASN Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 126 LYS Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 39 PHE Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 155 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 100 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN D 26 ASN E 18 ASN E 140 ASN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN G 170 ASN G 319 ASN H 20 ASN H 21 ASN H 208 GLN I 136 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.092764 restraints weight = 40298.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.095712 restraints weight = 17027.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097526 restraints weight = 9126.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.098701 restraints weight = 5855.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099443 restraints weight = 4281.074| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22155 Z= 0.216 Angle : 0.658 8.114 30349 Z= 0.350 Chirality : 0.045 0.315 3476 Planarity : 0.005 0.101 3676 Dihedral : 15.606 179.510 3784 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 6.06 % Allowed : 25.72 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.15), residues: 2596 helix: -0.27 (0.18), residues: 760 sheet: -0.18 (0.27), residues: 413 loop : -2.02 (0.14), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 150 TYR 0.019 0.002 TYR D 265 PHE 0.029 0.002 PHE D 37 TRP 0.020 0.002 TRP D 149 HIS 0.009 0.001 HIS G 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (22155) covalent geometry : angle 0.65797 / 0.35 (30349) hydrogen bonds : bond 0.04938 / 3.33 ( 595) hydrogen bonds : angle 5.26356 / 3.60 ( 1650) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 725 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LYS cc_start: 0.8608 (mtpp) cc_final: 0.8252 (tttm) REVERT: A 178 ASN cc_start: 0.7961 (m-40) cc_final: 0.7461 (p0) REVERT: A 253 LYS cc_start: 0.7887 (tttp) cc_final: 0.7661 (tttt) REVERT: A 318 TYR cc_start: 0.8056 (t80) cc_final: 0.7482 (t80) REVERT: B 52 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8392 (ttmm) REVERT: B 55 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7512 (tp) REVERT: B 139 VAL cc_start: 0.8157 (t) cc_final: 0.7846 (p) REVERT: B 144 ASN cc_start: 0.8344 (p0) cc_final: 0.8115 (p0) REVERT: B 184 GLU cc_start: 0.7584 (mp0) cc_final: 0.7343 (mp0) REVERT: B 216 LYS cc_start: 0.8574 (tttt) cc_final: 0.8256 (tttm) REVERT: B 217 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8296 (pt) REVERT: B 221 MET cc_start: 0.7265 (mmm) cc_final: 0.6994 (mmm) REVERT: B 253 LYS cc_start: 0.8121 (tppt) cc_final: 0.7703 (tppt) REVERT: B 265 TYR cc_start: 0.7635 (p90) cc_final: 0.7426 (p90) REVERT: B 271 TYR cc_start: 0.8227 (m-10) cc_final: 0.7946 (m-10) REVERT: B 272 GLU cc_start: 0.6873 (mp0) cc_final: 0.6634 (mp0) REVERT: B 273 PHE cc_start: 0.8384 (p90) cc_final: 0.8033 (p90) REVERT: B 278 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6605 (mt-10) REVERT: C 89 ASP cc_start: 0.7834 (p0) cc_final: 0.7314 (p0) REVERT: C 90 THR cc_start: 0.8188 (m) cc_final: 0.7946 (m) REVERT: C 111 ASP cc_start: 0.7568 (t0) cc_final: 0.7203 (t0) REVERT: C 120 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: C 140 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7705 (t0) REVERT: C 156 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6942 (mt-10) REVERT: C 159 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6437 (tm-30) REVERT: C 179 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8531 (mp) REVERT: C 229 MET cc_start: 0.7273 (ppp) cc_final: 0.7039 (ppp) REVERT: C 265 TYR cc_start: 0.7273 (p90) cc_final: 0.6656 (p90) REVERT: C 270 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7885 (t) REVERT: C 304 MET cc_start: 0.7220 (ttt) cc_final: 0.6995 (ttm) REVERT: C 320 MET cc_start: 0.7413 (mmm) cc_final: 0.6970 (mmm) REVERT: D 20 SER cc_start: 0.7553 (p) cc_final: 0.7271 (p) REVERT: D 91 LEU cc_start: 0.8105 (tt) cc_final: 0.7827 (tp) REVERT: D 153 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8581 (mmtm) REVERT: D 278 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6728 (mt-10) REVERT: E 40 ARG cc_start: 0.8237 (ptt90) cc_final: 0.7832 (ptt90) REVERT: E 159 GLU cc_start: 0.7258 (tp30) cc_final: 0.6971 (tp30) REVERT: E 244 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7220 (mt-10) REVERT: E 253 LYS cc_start: 0.8213 (tttt) cc_final: 0.7927 (tttt) REVERT: E 309 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.5679 (tm-30) REVERT: E 318 TYR cc_start: 0.7428 (t80) cc_final: 0.7215 (t80) REVERT: F 48 LEU cc_start: 0.8628 (mm) cc_final: 0.8377 (mp) REVERT: F 89 ASP cc_start: 0.7902 (p0) cc_final: 0.7352 (p0) REVERT: F 104 GLU cc_start: 0.7168 (mp0) cc_final: 0.6876 (mp0) REVERT: F 153 LYS cc_start: 0.8403 (mmmm) cc_final: 0.8130 (mtpp) REVERT: F 191 GLU cc_start: 0.7744 (tp30) cc_final: 0.7508 (tp30) REVERT: F 228 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6986 (tm-30) REVERT: F 315 ASP cc_start: 0.7718 (m-30) cc_final: 0.7337 (t0) REVERT: F 320 MET cc_start: 0.7239 (mmt) cc_final: 0.7009 (mmt) REVERT: G 63 ASN cc_start: 0.7633 (t0) cc_final: 0.7327 (t0) REVERT: G 172 GLU cc_start: 0.7146 (tp30) cc_final: 0.6820 (tp30) REVERT: G 176 ARG cc_start: 0.8265 (ttm170) cc_final: 0.7933 (ttm170) REVERT: G 229 ASP cc_start: 0.7773 (m-30) cc_final: 0.7337 (m-30) REVERT: G 262 GLU cc_start: 0.7626 (mm-30) cc_final: 0.6927 (tm-30) REVERT: G 265 ARG cc_start: 0.8018 (ttp-110) cc_final: 0.7790 (ttp-110) REVERT: G 266 LYS cc_start: 0.8837 (mttm) cc_final: 0.8251 (mttm) REVERT: G 307 VAL cc_start: 0.8794 (m) cc_final: 0.8560 (p) REVERT: H 126 LYS cc_start: 0.8360 (ttmm) cc_final: 0.7907 (ttmm) REVERT: H 222 PHE cc_start: 0.8495 (m-80) cc_final: 0.8283 (m-10) REVERT: I 77 LEU cc_start: 0.6710 (mm) cc_final: 0.6490 (mt) REVERT: I 113 ARG cc_start: 0.7839 (mtt90) cc_final: 0.7628 (mtm110) outliers start: 126 outliers final: 78 residues processed: 783 average time/residue: 0.1327 time to fit residues: 161.4547 Evaluate side-chains 803 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 717 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 39 PHE Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 155 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 211 optimal weight: 0.4980 chunk 164 optimal weight: 0.6980 chunk 212 optimal weight: 0.8980 chunk 186 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 231 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN D 140 ASN E 18 ASN E 140 ASN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 HIS H 12 ASN H 20 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.107058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.093163 restraints weight = 39940.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096185 restraints weight = 16969.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098064 restraints weight = 9191.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099260 restraints weight = 5956.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.100055 restraints weight = 4385.696| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22155 Z= 0.155 Angle : 0.630 8.406 30349 Z= 0.333 Chirality : 0.043 0.314 3476 Planarity : 0.005 0.087 3676 Dihedral : 15.556 179.010 3782 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.58 % Allowed : 26.39 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 2596 helix: -0.09 (0.18), residues: 768 sheet: -0.27 (0.26), residues: 435 loop : -1.96 (0.14), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 150 TYR 0.033 0.001 TYR D 224 PHE 0.030 0.002 PHE B 243 TRP 0.013 0.001 TRP C 149 HIS 0.010 0.001 HIS G 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (22155) covalent geometry : angle 0.62957 / 0.33 (30349) hydrogen bonds : bond 0.04591 / 3.11 ( 595) hydrogen bonds : angle 5.12082 / 3.49 ( 1650) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 720 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8165 (ptt-90) cc_final: 0.7792 (ptt90) REVERT: A 104 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 318 TYR cc_start: 0.7990 (t80) cc_final: 0.7471 (t80) REVERT: A 328 MET cc_start: 0.7286 (tpp) cc_final: 0.6771 (mtp) REVERT: B 55 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7517 (tp) REVERT: B 216 LYS cc_start: 0.8549 (tttt) cc_final: 0.8208 (tttm) REVERT: B 217 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8294 (pt) REVERT: B 221 MET cc_start: 0.7315 (mmm) cc_final: 0.7076 (mmm) REVERT: B 265 TYR cc_start: 0.7587 (p90) cc_final: 0.7344 (p90) REVERT: B 271 TYR cc_start: 0.8024 (m-10) cc_final: 0.7647 (m-10) REVERT: B 272 GLU cc_start: 0.6803 (mp0) cc_final: 0.6598 (mp0) REVERT: B 278 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6610 (mt-10) REVERT: C 89 ASP cc_start: 0.7865 (p0) cc_final: 0.7374 (p0) REVERT: C 111 ASP cc_start: 0.7528 (t0) cc_final: 0.7162 (t0) REVERT: C 120 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: C 159 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6447 (tm-30) REVERT: C 179 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8515 (mp) REVERT: C 199 THR cc_start: 0.7962 (t) cc_final: 0.7712 (m) REVERT: C 229 MET cc_start: 0.7247 (ppp) cc_final: 0.7022 (ppp) REVERT: C 253 LYS cc_start: 0.8079 (tptt) cc_final: 0.7700 (tttt) REVERT: C 265 TYR cc_start: 0.7281 (p90) cc_final: 0.6783 (p90) REVERT: C 270 THR cc_start: 0.8259 (p) cc_final: 0.7845 (t) REVERT: C 304 MET cc_start: 0.7198 (ttt) cc_final: 0.6983 (ttm) REVERT: C 320 MET cc_start: 0.7406 (mmm) cc_final: 0.6868 (mmm) REVERT: D 20 SER cc_start: 0.7532 (p) cc_final: 0.7220 (p) REVERT: D 153 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8584 (mmtm) REVERT: D 273 PHE cc_start: 0.8275 (p90) cc_final: 0.8049 (p90) REVERT: E 36 ASP cc_start: 0.7757 (t0) cc_final: 0.7552 (t0) REVERT: E 159 GLU cc_start: 0.7290 (tp30) cc_final: 0.6927 (tp30) REVERT: E 244 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7255 (mt-10) REVERT: E 253 LYS cc_start: 0.8203 (tttt) cc_final: 0.7924 (tttt) REVERT: E 309 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5652 (tm-30) REVERT: E 318 TYR cc_start: 0.7460 (t80) cc_final: 0.7231 (t80) REVERT: F 48 LEU cc_start: 0.8627 (mm) cc_final: 0.8370 (mp) REVERT: F 89 ASP cc_start: 0.7949 (p0) cc_final: 0.7310 (p0) REVERT: F 104 GLU cc_start: 0.7138 (mp0) cc_final: 0.6844 (mp0) REVERT: F 106 MET cc_start: 0.7356 (mmm) cc_final: 0.7035 (mmm) REVERT: F 140 ASN cc_start: 0.8173 (t0) cc_final: 0.7854 (t0) REVERT: F 153 LYS cc_start: 0.8407 (mmmm) cc_final: 0.8183 (mtpp) REVERT: F 191 GLU cc_start: 0.7732 (tp30) cc_final: 0.7509 (tp30) REVERT: F 228 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6978 (tm-30) REVERT: F 284 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7646 (mtt90) REVERT: F 315 ASP cc_start: 0.7687 (m-30) cc_final: 0.7288 (t0) REVERT: F 320 MET cc_start: 0.7235 (mmt) cc_final: 0.7016 (mmt) REVERT: G 63 ASN cc_start: 0.7631 (t0) cc_final: 0.7362 (t0) REVERT: G 172 GLU cc_start: 0.7147 (tp30) cc_final: 0.6799 (tp30) REVERT: G 176 ARG cc_start: 0.8307 (ttm170) cc_final: 0.8018 (ttm170) REVERT: G 229 ASP cc_start: 0.7781 (m-30) cc_final: 0.7353 (m-30) REVERT: G 262 GLU cc_start: 0.7629 (mm-30) cc_final: 0.6877 (tm-30) REVERT: G 265 ARG cc_start: 0.8044 (ttp-110) cc_final: 0.7821 (ttp-110) REVERT: G 266 LYS cc_start: 0.8798 (mttm) cc_final: 0.8126 (mttm) REVERT: G 307 VAL cc_start: 0.8779 (m) cc_final: 0.8544 (p) REVERT: H 126 LYS cc_start: 0.8375 (ttmm) cc_final: 0.7919 (ttmm) REVERT: H 176 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8343 (tt) REVERT: H 222 PHE cc_start: 0.8475 (m-80) cc_final: 0.8257 (m-10) REVERT: I 113 ARG cc_start: 0.7828 (mtt90) cc_final: 0.7598 (mtm110) outliers start: 116 outliers final: 75 residues processed: 773 average time/residue: 0.1488 time to fit residues: 178.0836 Evaluate side-chains 785 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 703 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 252 GLN Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 39 PHE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 164 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 92 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 160 optimal weight: 0.0000 chunk 147 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN E 18 ASN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS G 304 HIS H 21 ASN H 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.092171 restraints weight = 40185.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095068 restraints weight = 17015.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096875 restraints weight = 9201.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098015 restraints weight = 5941.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.098767 restraints weight = 4375.176| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22155 Z= 0.204 Angle : 0.639 7.568 30349 Z= 0.342 Chirality : 0.044 0.319 3476 Planarity : 0.005 0.051 3676 Dihedral : 15.526 179.263 3782 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 6.15 % Allowed : 27.02 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.16), residues: 2596 helix: -0.00 (0.18), residues: 768 sheet: -0.21 (0.26), residues: 440 loop : -1.93 (0.15), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 150 TYR 0.025 0.002 TYR D 125 PHE 0.023 0.002 PHE B 243 TRP 0.017 0.002 TRP D 149 HIS 0.009 0.001 HIS G 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (22155) covalent geometry : angle 0.63935 / 0.34 (30349) hydrogen bonds : bond 0.04670 / 3.16 ( 595) hydrogen bonds : angle 5.07649 / 3.47 ( 1650) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 744 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8214 (ptt-90) cc_final: 0.7757 (ptt90) REVERT: A 104 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7323 (mm-30) REVERT: A 175 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8238 (tttm) REVERT: A 318 TYR cc_start: 0.8031 (t80) cc_final: 0.7491 (t80) REVERT: B 52 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8407 (ttmm) REVERT: B 55 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7527 (tp) REVERT: B 183 VAL cc_start: 0.8170 (p) cc_final: 0.7921 (t) REVERT: B 184 GLU cc_start: 0.7414 (mp0) cc_final: 0.7117 (mp0) REVERT: B 216 LYS cc_start: 0.8540 (tttt) cc_final: 0.8264 (tttm) REVERT: B 217 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8288 (pt) REVERT: B 242 LYS cc_start: 0.8555 (ttpp) cc_final: 0.8095 (ttmm) REVERT: B 253 LYS cc_start: 0.8169 (tppt) cc_final: 0.7759 (tppt) REVERT: B 265 TYR cc_start: 0.7652 (p90) cc_final: 0.7411 (p90) REVERT: B 278 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6618 (mt-10) REVERT: C 89 ASP cc_start: 0.7861 (p0) cc_final: 0.7333 (p0) REVERT: C 111 ASP cc_start: 0.7525 (t0) cc_final: 0.7262 (t0) REVERT: C 120 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7909 (tm-30) REVERT: C 140 ASN cc_start: 0.7812 (t0) cc_final: 0.7495 (t0) REVERT: C 156 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6984 (mt-10) REVERT: C 159 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6483 (tm-30) REVERT: C 199 THR cc_start: 0.7961 (t) cc_final: 0.7742 (m) REVERT: C 229 MET cc_start: 0.7263 (ppp) cc_final: 0.7033 (ppp) REVERT: C 265 TYR cc_start: 0.7332 (p90) cc_final: 0.6831 (p90) REVERT: C 270 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.7885 (t) REVERT: C 309 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6666 (tm-30) REVERT: C 320 MET cc_start: 0.7519 (mmm) cc_final: 0.6929 (mmm) REVERT: D 20 SER cc_start: 0.7588 (p) cc_final: 0.7302 (p) REVERT: D 272 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6643 (mm-30) REVERT: E 159 GLU cc_start: 0.7271 (tp30) cc_final: 0.6812 (tp30) REVERT: E 172 PHE cc_start: 0.7534 (m-10) cc_final: 0.7313 (m-10) REVERT: E 173 ASN cc_start: 0.8283 (t0) cc_final: 0.8030 (t0) REVERT: E 253 LYS cc_start: 0.8277 (tttt) cc_final: 0.8020 (tttt) REVERT: E 309 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.5642 (tm-30) REVERT: F 21 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.6920 (m-80) REVERT: F 48 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8350 (mp) REVERT: F 89 ASP cc_start: 0.7987 (p0) cc_final: 0.7305 (p0) REVERT: F 104 GLU cc_start: 0.7225 (mp0) cc_final: 0.6930 (mp0) REVERT: F 106 MET cc_start: 0.7419 (mmm) cc_final: 0.6938 (mmm) REVERT: F 111 ASP cc_start: 0.7381 (t0) cc_final: 0.7094 (t0) REVERT: F 140 ASN cc_start: 0.8183 (t0) cc_final: 0.7876 (t0) REVERT: F 153 LYS cc_start: 0.8326 (mmmm) cc_final: 0.8125 (mtpp) REVERT: F 191 GLU cc_start: 0.7711 (tp30) cc_final: 0.7490 (tp30) REVERT: F 228 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7041 (tm-30) REVERT: F 284 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7660 (mtt90) REVERT: F 315 ASP cc_start: 0.7658 (m-30) cc_final: 0.7274 (t0) REVERT: F 320 MET cc_start: 0.7293 (mmt) cc_final: 0.7075 (mmt) REVERT: G 17 GLU cc_start: 0.8080 (pp20) cc_final: 0.7755 (pp20) REVERT: G 172 GLU cc_start: 0.7135 (tp30) cc_final: 0.6823 (tp30) REVERT: G 175 ASP cc_start: 0.7829 (m-30) cc_final: 0.7549 (t0) REVERT: G 229 ASP cc_start: 0.7781 (m-30) cc_final: 0.7439 (m-30) REVERT: G 262 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7044 (tm-30) REVERT: G 265 ARG cc_start: 0.8070 (ttp-110) cc_final: 0.7864 (ttp-110) REVERT: G 307 VAL cc_start: 0.8786 (m) cc_final: 0.8567 (p) REVERT: H 17 ASN cc_start: 0.8297 (t0) cc_final: 0.8072 (t0) REVERT: H 126 LYS cc_start: 0.8402 (ttmm) cc_final: 0.7953 (ttmm) REVERT: H 166 ASN cc_start: 0.8163 (m110) cc_final: 0.7819 (t0) REVERT: H 222 PHE cc_start: 0.8516 (m-80) cc_final: 0.8244 (m-10) REVERT: I 113 ARG cc_start: 0.7819 (mtt90) cc_final: 0.7564 (mtm110) outliers start: 128 outliers final: 80 residues processed: 803 average time/residue: 0.1516 time to fit residues: 189.3082 Evaluate side-chains 823 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 734 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 157 SER Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 304 HIS Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 39 PHE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 164 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 123 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS H 12 ASN H 21 ASN H 99 GLN H 166 ASN I 136 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.092281 restraints weight = 39889.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095167 restraints weight = 16921.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096967 restraints weight = 9186.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.098113 restraints weight = 5959.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.098836 restraints weight = 4392.539| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22155 Z= 0.191 Angle : 0.648 8.113 30349 Z= 0.345 Chirality : 0.044 0.314 3476 Planarity : 0.005 0.052 3676 Dihedral : 15.493 178.985 3777 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.48 % Allowed : 27.88 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.16), residues: 2596 helix: 0.08 (0.19), residues: 769 sheet: -0.24 (0.25), residues: 447 loop : -1.90 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 284 TYR 0.027 0.002 TYR D 224 PHE 0.033 0.002 PHE B 243 TRP 0.016 0.001 TRP D 33 HIS 0.017 0.001 HIS G 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (22155) covalent geometry : angle 0.64751 / 0.35 (30349) hydrogen bonds : bond 0.04631 / 3.14 ( 595) hydrogen bonds : angle 5.04690 / 3.46 ( 1650) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 726 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8221 (ptt-90) cc_final: 0.7888 (ptt90) REVERT: A 104 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7363 (mm-30) REVERT: A 106 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7359 (tpp) REVERT: A 108 SER cc_start: 0.8350 (m) cc_final: 0.7693 (p) REVERT: A 175 LYS cc_start: 0.8588 (mtpp) cc_final: 0.8258 (tttm) REVERT: A 309 GLU cc_start: 0.7717 (pm20) cc_final: 0.7479 (pm20) REVERT: A 318 TYR cc_start: 0.8002 (t80) cc_final: 0.7544 (t80) REVERT: A 320 MET cc_start: 0.7755 (tpp) cc_final: 0.6996 (mpp) REVERT: B 35 THR cc_start: 0.7801 (t) cc_final: 0.7228 (p) REVERT: B 55 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7529 (tp) REVERT: B 90 THR cc_start: 0.8381 (m) cc_final: 0.7910 (p) REVERT: B 109 CYS cc_start: 0.7400 (t) cc_final: 0.7089 (t) REVERT: B 184 GLU cc_start: 0.7400 (mp0) cc_final: 0.7076 (mp0) REVERT: B 217 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8275 (pt) REVERT: B 242 LYS cc_start: 0.8551 (ttpp) cc_final: 0.8113 (ttmm) REVERT: B 265 TYR cc_start: 0.7671 (p90) cc_final: 0.7429 (p90) REVERT: B 278 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6627 (mt-10) REVERT: C 89 ASP cc_start: 0.7862 (p0) cc_final: 0.7322 (p0) REVERT: C 107 TYR cc_start: 0.7685 (t80) cc_final: 0.7387 (t80) REVERT: C 111 ASP cc_start: 0.7467 (t0) cc_final: 0.7210 (t0) REVERT: C 120 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7952 (tm-30) REVERT: C 156 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.7007 (mt-10) REVERT: C 159 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6440 (tm-30) REVERT: C 229 MET cc_start: 0.7273 (ppp) cc_final: 0.7060 (ppp) REVERT: C 252 GLN cc_start: 0.8309 (pm20) cc_final: 0.7939 (pm20) REVERT: C 270 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.7912 (t) REVERT: C 309 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: C 320 MET cc_start: 0.7555 (mmm) cc_final: 0.6905 (mmm) REVERT: D 20 SER cc_start: 0.7632 (p) cc_final: 0.7347 (p) REVERT: D 224 TYR cc_start: 0.7690 (m-10) cc_final: 0.7398 (m-10) REVERT: D 272 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6707 (mm-30) REVERT: E 159 GLU cc_start: 0.7248 (tp30) cc_final: 0.6842 (tp30) REVERT: E 253 LYS cc_start: 0.8287 (tttt) cc_final: 0.7998 (tttt) REVERT: E 309 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5672 (tm-30) REVERT: F 21 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7101 (m-80) REVERT: F 51 ASP cc_start: 0.7479 (t0) cc_final: 0.7267 (t0) REVERT: F 89 ASP cc_start: 0.7974 (p0) cc_final: 0.7328 (p0) REVERT: F 104 GLU cc_start: 0.7232 (mp0) cc_final: 0.6921 (mp0) REVERT: F 106 MET cc_start: 0.7382 (mmm) cc_final: 0.7135 (mmm) REVERT: F 140 ASN cc_start: 0.8154 (t0) cc_final: 0.7863 (t0) REVERT: F 191 GLU cc_start: 0.7703 (tp30) cc_final: 0.7502 (tp30) REVERT: F 228 GLU cc_start: 0.7353 (tm-30) cc_final: 0.7049 (tm-30) REVERT: G 17 GLU cc_start: 0.8165 (pp20) cc_final: 0.7840 (pp20) REVERT: G 172 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6739 (tp30) REVERT: G 175 ASP cc_start: 0.7825 (m-30) cc_final: 0.7530 (t0) REVERT: G 176 ARG cc_start: 0.8303 (ttm170) cc_final: 0.7860 (ttm170) REVERT: G 229 ASP cc_start: 0.7812 (m-30) cc_final: 0.7460 (m-30) REVERT: G 262 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7050 (tm-30) REVERT: H 126 LYS cc_start: 0.8402 (ttmm) cc_final: 0.7959 (ttmm) REVERT: I 113 ARG cc_start: 0.7809 (mtt90) cc_final: 0.7529 (mtm110) outliers start: 114 outliers final: 83 residues processed: 777 average time/residue: 0.1463 time to fit residues: 176.1559 Evaluate side-chains 804 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 711 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 39 PHE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 164 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 151 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 192 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 254 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 HIS H 12 ASN H 21 ASN H 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.106020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.092655 restraints weight = 39876.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.095535 restraints weight = 16876.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.097345 restraints weight = 9110.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098483 restraints weight = 5854.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.099235 restraints weight = 4313.847| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22155 Z= 0.168 Angle : 0.637 8.715 30349 Z= 0.339 Chirality : 0.043 0.315 3476 Planarity : 0.005 0.054 3676 Dihedral : 15.463 178.936 3777 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.29 % Allowed : 28.37 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.16), residues: 2596 helix: 0.14 (0.19), residues: 769 sheet: -0.22 (0.25), residues: 446 loop : -1.86 (0.15), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 284 TYR 0.020 0.001 TYR A 125 PHE 0.035 0.002 PHE B 243 TRP 0.014 0.001 TRP D 149 HIS 0.010 0.001 HIS G 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (22155) covalent geometry : angle 0.63704 / 0.34 (30349) hydrogen bonds : bond 0.04488 / 3.04 ( 595) hydrogen bonds : angle 5.00458 / 3.43 ( 1650) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 723 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8213 (ptt-90) cc_final: 0.7864 (ptt90) REVERT: A 104 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7398 (mm-30) REVERT: A 175 LYS cc_start: 0.8572 (mtpp) cc_final: 0.8225 (tttp) REVERT: A 242 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7732 (tttt) REVERT: A 304 MET cc_start: 0.6937 (ttm) cc_final: 0.6721 (ttm) REVERT: A 318 TYR cc_start: 0.7977 (t80) cc_final: 0.7521 (t80) REVERT: A 320 MET cc_start: 0.7730 (tpp) cc_final: 0.6942 (mpp) REVERT: A 328 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.7128 (mtm) REVERT: B 35 THR cc_start: 0.7772 (t) cc_final: 0.7301 (p) REVERT: B 55 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7525 (tp) REVERT: B 90 THR cc_start: 0.8383 (m) cc_final: 0.7920 (p) REVERT: B 184 GLU cc_start: 0.7415 (mp0) cc_final: 0.7125 (mp0) REVERT: B 242 LYS cc_start: 0.8550 (ttpp) cc_final: 0.8115 (ttmm) REVERT: B 265 TYR cc_start: 0.7640 (p90) cc_final: 0.7335 (p90) REVERT: B 278 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6681 (mt-10) REVERT: C 89 ASP cc_start: 0.7875 (p0) cc_final: 0.7321 (p0) REVERT: C 90 THR cc_start: 0.8198 (m) cc_final: 0.7954 (m) REVERT: C 111 ASP cc_start: 0.7430 (t0) cc_final: 0.7211 (t0) REVERT: C 120 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: C 156 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6981 (mt-10) REVERT: C 159 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6421 (tm-30) REVERT: C 179 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8328 (mp) REVERT: C 185 ASP cc_start: 0.7179 (p0) cc_final: 0.6759 (p0) REVERT: C 229 MET cc_start: 0.7287 (ppp) cc_final: 0.7081 (ppp) REVERT: C 252 GLN cc_start: 0.8368 (pm20) cc_final: 0.7971 (pm20) REVERT: C 270 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.7893 (t) REVERT: C 309 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6709 (tm-30) REVERT: C 320 MET cc_start: 0.7561 (mmm) cc_final: 0.6961 (mmm) REVERT: D 20 SER cc_start: 0.7609 (p) cc_final: 0.7347 (p) REVERT: D 272 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6695 (mm-30) REVERT: D 290 PHE cc_start: 0.8537 (m-80) cc_final: 0.8305 (m-80) REVERT: E 18 ASN cc_start: 0.7607 (t0) cc_final: 0.7145 (t0) REVERT: E 159 GLU cc_start: 0.7210 (tp30) cc_final: 0.6826 (tp30) REVERT: E 253 LYS cc_start: 0.8266 (tttt) cc_final: 0.8045 (tttt) REVERT: E 309 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5671 (tm-30) REVERT: F 21 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.6821 (m-80) REVERT: F 89 ASP cc_start: 0.7986 (p0) cc_final: 0.7305 (p0) REVERT: F 104 GLU cc_start: 0.7223 (mp0) cc_final: 0.6919 (mp0) REVERT: F 106 MET cc_start: 0.7388 (mmm) cc_final: 0.6935 (mmm) REVERT: F 140 ASN cc_start: 0.8150 (t0) cc_final: 0.7937 (t0) REVERT: F 228 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7027 (tm-30) REVERT: F 291 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8054 (mtt180) REVERT: F 315 ASP cc_start: 0.7601 (m-30) cc_final: 0.7228 (t0) REVERT: G 17 GLU cc_start: 0.8091 (pp20) cc_final: 0.7783 (pp20) REVERT: G 89 PRO cc_start: 0.8714 (Cg_endo) cc_final: 0.8477 (Cg_exo) REVERT: G 129 ARG cc_start: 0.6611 (ttt90) cc_final: 0.6009 (ttt90) REVERT: G 172 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6731 (tp30) REVERT: G 175 ASP cc_start: 0.7819 (m-30) cc_final: 0.7542 (t0) REVERT: G 176 ARG cc_start: 0.8302 (ttm170) cc_final: 0.7824 (ttm170) REVERT: G 215 LEU cc_start: 0.8143 (mm) cc_final: 0.7927 (mp) REVERT: G 229 ASP cc_start: 0.7799 (m-30) cc_final: 0.7446 (m-30) REVERT: G 262 GLU cc_start: 0.7520 (mm-30) cc_final: 0.6957 (tm-30) REVERT: G 266 LYS cc_start: 0.8914 (mttm) cc_final: 0.8303 (mttm) REVERT: H 17 ASN cc_start: 0.8291 (t0) cc_final: 0.8051 (t0) REVERT: H 126 LYS cc_start: 0.8403 (ttmm) cc_final: 0.7924 (ttmm) REVERT: H 166 ASN cc_start: 0.8197 (m-40) cc_final: 0.7839 (t0) REVERT: H 222 PHE cc_start: 0.8610 (m-80) cc_final: 0.8324 (m-10) REVERT: I 113 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7508 (mtm110) outliers start: 110 outliers final: 81 residues processed: 770 average time/residue: 0.1542 time to fit residues: 183.0635 Evaluate side-chains 810 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 718 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 252 GLN Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 157 SER Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 39 PHE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 164 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 126 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 258 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 5 optimal weight: 0.0170 chunk 172 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 304 HIS H 12 ASN H 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.106850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.093469 restraints weight = 39906.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096380 restraints weight = 16760.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098184 restraints weight = 8981.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099342 restraints weight = 5749.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.100079 restraints weight = 4201.165| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22155 Z= 0.146 Angle : 0.652 10.111 30349 Z= 0.343 Chirality : 0.043 0.314 3476 Planarity : 0.005 0.053 3676 Dihedral : 15.424 178.869 3775 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.62 % Allowed : 29.28 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.16), residues: 2596 helix: 0.26 (0.19), residues: 762 sheet: -0.20 (0.25), residues: 436 loop : -1.82 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 103 TYR 0.034 0.001 TYR D 224 PHE 0.038 0.002 PHE B 243 TRP 0.015 0.001 TRP D 149 HIS 0.011 0.001 HIS G 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (22155) covalent geometry : angle 0.65248 / 0.34 (30349) hydrogen bonds : bond 0.04385 / 2.97 ( 595) hydrogen bonds : angle 4.93426 / 3.38 ( 1650) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 716 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7383 (mm-30) REVERT: A 108 SER cc_start: 0.8410 (m) cc_final: 0.7797 (p) REVERT: A 242 LYS cc_start: 0.7993 (ttpt) cc_final: 0.7704 (tttt) REVERT: A 318 TYR cc_start: 0.7928 (t80) cc_final: 0.7483 (t80) REVERT: A 320 MET cc_start: 0.7697 (tpp) cc_final: 0.6902 (mpp) REVERT: B 35 THR cc_start: 0.7769 (t) cc_final: 0.7337 (p) REVERT: B 55 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7537 (tp) REVERT: B 90 THR cc_start: 0.8381 (m) cc_final: 0.7918 (p) REVERT: B 184 GLU cc_start: 0.7394 (mp0) cc_final: 0.7075 (mp0) REVERT: B 242 LYS cc_start: 0.8548 (ttpp) cc_final: 0.8103 (ttmm) REVERT: B 265 TYR cc_start: 0.7559 (p90) cc_final: 0.7296 (p90) REVERT: B 278 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6690 (mt-10) REVERT: B 324 ILE cc_start: 0.7894 (mp) cc_final: 0.7611 (mt) REVERT: C 89 ASP cc_start: 0.7895 (p0) cc_final: 0.7321 (p0) REVERT: C 90 THR cc_start: 0.8187 (m) cc_final: 0.7921 (m) REVERT: C 111 ASP cc_start: 0.7361 (t0) cc_final: 0.7150 (t0) REVERT: C 156 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6921 (mt-10) REVERT: C 159 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6386 (tm-30) REVERT: C 179 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8308 (mp) REVERT: C 185 ASP cc_start: 0.7219 (p0) cc_final: 0.6807 (p0) REVERT: C 252 GLN cc_start: 0.8359 (pm20) cc_final: 0.7995 (pm20) REVERT: C 270 THR cc_start: 0.8271 (p) cc_final: 0.7869 (t) REVERT: C 309 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6675 (tm-30) REVERT: C 320 MET cc_start: 0.7589 (mmm) cc_final: 0.6975 (mmm) REVERT: D 20 SER cc_start: 0.7615 (p) cc_final: 0.7334 (p) REVERT: D 272 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6714 (mm-30) REVERT: D 290 PHE cc_start: 0.8517 (m-80) cc_final: 0.8295 (m-80) REVERT: E 18 ASN cc_start: 0.7641 (t0) cc_final: 0.7365 (t0) REVERT: E 36 ASP cc_start: 0.7612 (t0) cc_final: 0.7277 (t0) REVERT: E 159 GLU cc_start: 0.7214 (tp30) cc_final: 0.6850 (tp30) REVERT: E 253 LYS cc_start: 0.8264 (tttt) cc_final: 0.8026 (tttt) REVERT: E 309 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5640 (tm-30) REVERT: F 21 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.6827 (m-80) REVERT: F 89 ASP cc_start: 0.7989 (p0) cc_final: 0.7314 (p0) REVERT: F 104 GLU cc_start: 0.7230 (mp0) cc_final: 0.6917 (mp0) REVERT: F 106 MET cc_start: 0.7372 (mmm) cc_final: 0.6938 (mmm) REVERT: F 228 GLU cc_start: 0.7363 (tm-30) cc_final: 0.7031 (tm-30) REVERT: F 315 ASP cc_start: 0.7597 (m-30) cc_final: 0.7230 (t0) REVERT: G 17 GLU cc_start: 0.8135 (pp20) cc_final: 0.7824 (pp20) REVERT: G 129 ARG cc_start: 0.6526 (ttt90) cc_final: 0.5998 (ttt90) REVERT: G 172 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6734 (tp30) REVERT: G 175 ASP cc_start: 0.7846 (m-30) cc_final: 0.7582 (t0) REVERT: G 176 ARG cc_start: 0.8303 (ttm170) cc_final: 0.7802 (ttm170) REVERT: G 201 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7489 (ttp80) REVERT: G 229 ASP cc_start: 0.7813 (m-30) cc_final: 0.7451 (m-30) REVERT: G 262 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7025 (tm-30) REVERT: G 265 ARG cc_start: 0.7988 (ttp-110) cc_final: 0.7730 (ttp-110) REVERT: G 266 LYS cc_start: 0.8918 (mttm) cc_final: 0.8290 (mttm) REVERT: H 17 ASN cc_start: 0.8231 (t0) cc_final: 0.8009 (t0) REVERT: H 126 LYS cc_start: 0.8430 (ttmm) cc_final: 0.7956 (ttmm) REVERT: H 166 ASN cc_start: 0.8190 (m-40) cc_final: 0.7855 (t0) REVERT: H 222 PHE cc_start: 0.8643 (m-80) cc_final: 0.8235 (m-80) REVERT: I 113 ARG cc_start: 0.7789 (mtt90) cc_final: 0.7485 (mtm110) outliers start: 96 outliers final: 72 residues processed: 752 average time/residue: 0.1387 time to fit residues: 161.9777 Evaluate side-chains 791 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 712 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain G residue 304 HIS Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 39 PHE Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 164 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 64 optimal weight: 0.2980 chunk 263 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 202 optimal weight: 0.0000 chunk 101 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 181 optimal weight: 0.0980 chunk 245 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.107617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094237 restraints weight = 40082.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097144 restraints weight = 16922.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.098966 restraints weight = 9099.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.100112 restraints weight = 5828.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.100845 restraints weight = 4273.364| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22155 Z= 0.133 Angle : 0.646 10.766 30349 Z= 0.340 Chirality : 0.042 0.311 3476 Planarity : 0.005 0.052 3676 Dihedral : 15.404 178.843 3775 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.94 % Allowed : 30.34 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.16), residues: 2596 helix: 0.31 (0.19), residues: 765 sheet: -0.17 (0.26), residues: 437 loop : -1.80 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 284 TYR 0.029 0.001 TYR C 318 PHE 0.040 0.002 PHE B 243 TRP 0.012 0.001 TRP D 149 HIS 0.037 0.001 HIS G 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (22155) covalent geometry : angle 0.64592 / 0.34 (30349) hydrogen bonds : bond 0.04221 / 2.85 ( 595) hydrogen bonds : angle 4.88812 / 3.35 ( 1650) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 713 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7348 (mm-30) REVERT: A 108 SER cc_start: 0.8409 (m) cc_final: 0.7785 (p) REVERT: A 159 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7405 (mt-10) REVERT: A 175 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8230 (tttp) REVERT: A 242 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7681 (tttt) REVERT: A 318 TYR cc_start: 0.7913 (t80) cc_final: 0.7455 (t80) REVERT: A 320 MET cc_start: 0.7672 (tpp) cc_final: 0.6895 (mpp) REVERT: B 35 THR cc_start: 0.7736 (t) cc_final: 0.7320 (p) REVERT: B 55 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7541 (tp) REVERT: B 90 THR cc_start: 0.8359 (m) cc_final: 0.7874 (p) REVERT: B 126 ILE cc_start: 0.8551 (mm) cc_final: 0.8314 (mt) REVERT: B 139 VAL cc_start: 0.8061 (t) cc_final: 0.7769 (p) REVERT: B 183 VAL cc_start: 0.8108 (p) cc_final: 0.7771 (t) REVERT: B 184 GLU cc_start: 0.7326 (mp0) cc_final: 0.7008 (mp0) REVERT: B 242 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8107 (ttmm) REVERT: B 265 TYR cc_start: 0.7517 (p90) cc_final: 0.7244 (p90) REVERT: B 278 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6658 (mt-10) REVERT: B 324 ILE cc_start: 0.7853 (mp) cc_final: 0.7591 (mt) REVERT: C 89 ASP cc_start: 0.7876 (p0) cc_final: 0.7344 (p0) REVERT: C 111 ASP cc_start: 0.7354 (t0) cc_final: 0.7150 (t0) REVERT: C 156 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6828 (mt-10) REVERT: C 159 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6419 (tm-30) REVERT: C 179 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8338 (mp) REVERT: C 185 ASP cc_start: 0.7196 (p0) cc_final: 0.6736 (p0) REVERT: C 252 GLN cc_start: 0.8352 (pm20) cc_final: 0.7977 (pm20) REVERT: C 253 LYS cc_start: 0.8081 (tptt) cc_final: 0.7730 (tttt) REVERT: C 270 THR cc_start: 0.8243 (p) cc_final: 0.7838 (t) REVERT: C 309 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6682 (tm-30) REVERT: C 320 MET cc_start: 0.7588 (mmm) cc_final: 0.6966 (mmm) REVERT: D 20 SER cc_start: 0.7632 (p) cc_final: 0.7380 (p) REVERT: D 272 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6788 (mm-30) REVERT: D 290 PHE cc_start: 0.8505 (m-80) cc_final: 0.8285 (m-80) REVERT: E 18 ASN cc_start: 0.7637 (t0) cc_final: 0.7374 (t0) REVERT: E 36 ASP cc_start: 0.7590 (t0) cc_final: 0.7263 (t0) REVERT: E 159 GLU cc_start: 0.7223 (tp30) cc_final: 0.6870 (tp30) REVERT: E 253 LYS cc_start: 0.8232 (tttt) cc_final: 0.7975 (tttt) REVERT: E 309 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5642 (tm-30) REVERT: F 21 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: F 104 GLU cc_start: 0.7213 (mp0) cc_final: 0.6895 (mp0) REVERT: F 106 MET cc_start: 0.7359 (mmm) cc_final: 0.6933 (mmm) REVERT: F 228 GLU cc_start: 0.7363 (tm-30) cc_final: 0.7022 (tm-30) REVERT: F 315 ASP cc_start: 0.7539 (m-30) cc_final: 0.7182 (t0) REVERT: G 17 GLU cc_start: 0.8088 (pp20) cc_final: 0.7765 (pp20) REVERT: G 89 PRO cc_start: 0.8662 (Cg_endo) cc_final: 0.8402 (Cg_exo) REVERT: G 129 ARG cc_start: 0.6544 (ttt90) cc_final: 0.6014 (ttt90) REVERT: G 172 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6713 (tp30) REVERT: G 175 ASP cc_start: 0.7853 (m-30) cc_final: 0.7583 (t0) REVERT: G 176 ARG cc_start: 0.8300 (ttm170) cc_final: 0.7794 (ttm170) REVERT: G 201 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7475 (ttp80) REVERT: G 229 ASP cc_start: 0.7754 (m-30) cc_final: 0.7418 (m-30) REVERT: G 262 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7052 (tm-30) REVERT: G 265 ARG cc_start: 0.7995 (ttp-110) cc_final: 0.7731 (ttp-110) REVERT: G 266 LYS cc_start: 0.8914 (mttm) cc_final: 0.8278 (mttm) REVERT: H 17 ASN cc_start: 0.8199 (t0) cc_final: 0.7973 (t0) REVERT: H 106 MET cc_start: 0.7375 (ppp) cc_final: 0.6900 (ppp) REVERT: H 126 LYS cc_start: 0.8424 (ttmm) cc_final: 0.7957 (ttmm) REVERT: H 166 ASN cc_start: 0.8179 (m-40) cc_final: 0.7855 (t0) REVERT: I 113 ARG cc_start: 0.7774 (mtt90) cc_final: 0.7477 (mtm110) outliers start: 82 outliers final: 60 residues processed: 747 average time/residue: 0.1512 time to fit residues: 175.1552 Evaluate side-chains 775 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 708 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 296 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 236 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 39 PHE Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 164 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 26 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 169 optimal weight: 4.9990 chunk 220 optimal weight: 0.2980 chunk 121 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 21 ASN H 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.106484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.093167 restraints weight = 40088.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096081 restraints weight = 16781.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.097871 restraints weight = 8990.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099005 restraints weight = 5746.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099758 restraints weight = 4225.655| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22155 Z= 0.172 Angle : 0.660 10.857 30349 Z= 0.347 Chirality : 0.044 0.344 3476 Planarity : 0.005 0.052 3676 Dihedral : 15.352 178.994 3771 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.85 % Allowed : 30.82 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.16), residues: 2596 helix: 0.33 (0.19), residues: 764 sheet: -0.05 (0.26), residues: 426 loop : -1.82 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 284 TYR 0.027 0.001 TYR C 318 PHE 0.039 0.002 PHE B 243 TRP 0.015 0.001 TRP D 149 HIS 0.007 0.001 HIS G 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (22155) covalent geometry : angle 0.66025 / 0.35 (30349) hydrogen bonds : bond 0.04387 / 2.95 ( 595) hydrogen bonds : angle 4.86310 / 3.34 ( 1650) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4359.58 seconds wall clock time: 76 minutes 2.71 seconds (4562.71 seconds total)