Starting phenix.real_space_refine on Fri Jul 3 15:53:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zsi_60416/07_2026/8zsi_60416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zsi_60416/07_2026/8zsi_60416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zsi_60416/07_2026/8zsi_60416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zsi_60416/07_2026/8zsi_60416.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zsi_60416/07_2026/8zsi_60416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zsi_60416/07_2026/8zsi_60416.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 16 5.49 5 S 44 5.16 5 C 9466 2.51 5 N 2410 2.21 5 O 2804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14740 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "B" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "C" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "D" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "E" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2160 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "F" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2160 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "G" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2160 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "H" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2160 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Y43': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Y43': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Y43': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Y43': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.03, per 1000 atoms: 0.21 Number of scatterers: 14740 At special positions: 0 Unit cell: (165.87, 151.32, 80.51, 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 44 16.00 P 16 15.00 O 2804 8.00 N 2410 7.00 C 9466 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: 1.21 Conformation dependent library (CDL) restraints added in 533.1 milliseconds 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3344 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 50.3% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 3.734A pdb=" N ILE A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 58 removed outlier: 3.687A pdb=" N LEU A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 removed outlier: 4.016A pdb=" N PHE A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.932A pdb=" N SER A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.564A pdb=" N ASP A 143 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N CYS A 144 " --> pdb=" O GLN A 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 140 through 144' Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.970A pdb=" N GLY A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 182 Processing helix chain 'B' and resid 9 through 20 removed outlier: 3.735A pdb=" N ILE B 13 " --> pdb=" O ASN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 removed outlier: 3.688A pdb=" N LEU B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 89 removed outlier: 4.016A pdb=" N PHE B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.932A pdb=" N SER B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 95' Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.564A pdb=" N ASP B 143 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N CYS B 144 " --> pdb=" O GLN B 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 140 through 144' Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.970A pdb=" N GLY B 159 " --> pdb=" O PHE B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 182 Processing helix chain 'C' and resid 10 through 20 removed outlier: 3.585A pdb=" N LYS C 14 " --> pdb=" O ARG C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 removed outlier: 3.658A pdb=" N LEU C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 removed outlier: 3.702A pdb=" N PHE C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 4.052A pdb=" N SER C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU C 96 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 144 removed outlier: 3.924A pdb=" N CYS C 144 " --> pdb=" O GLN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 removed outlier: 3.983A pdb=" N GLY C 159 " --> pdb=" O PHE C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.702A pdb=" N ASN C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 164 " --> pdb=" O ARG C 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 160 through 164' Processing helix chain 'C' and resid 166 through 182 Processing helix chain 'D' and resid 9 through 20 removed outlier: 3.735A pdb=" N ILE D 13 " --> pdb=" O ASN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 removed outlier: 3.687A pdb=" N LEU D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 removed outlier: 4.017A pdb=" N PHE D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.932A pdb=" N SER D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN D 95 " --> pdb=" O ASP D 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 90 through 95' Processing helix chain 'D' and resid 140 through 144 removed outlier: 3.564A pdb=" N ASP D 143 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N CYS D 144 " --> pdb=" O GLN D 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 140 through 144' Processing helix chain 'D' and resid 154 through 159 removed outlier: 3.970A pdb=" N GLY D 159 " --> pdb=" O PHE D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 182 Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.660A pdb=" N LYS E 10 " --> pdb=" O ALA E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.559A pdb=" N LEU E 33 " --> pdb=" O SER E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 49 removed outlier: 3.537A pdb=" N ARG E 49 " --> pdb=" O PRO E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 66 removed outlier: 4.833A pdb=" N TYR E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 80 removed outlier: 4.175A pdb=" N TRP E 74 " --> pdb=" O PRO E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 88 Processing helix chain 'E' and resid 89 through 98 Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.512A pdb=" N THR E 114 " --> pdb=" O ARG E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 3.589A pdb=" N ILE E 132 " --> pdb=" O SER E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'E' and resid 170 through 180 removed outlier: 3.583A pdb=" N LYS E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER E 178 " --> pdb=" O ILE E 174 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 180 " --> pdb=" O PHE E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 211 removed outlier: 3.816A pdb=" N PHE E 201 " --> pdb=" O ILE E 197 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS E 206 " --> pdb=" O TYR E 202 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU E 207 " --> pdb=" O LYS E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 217 Processing helix chain 'E' and resid 228 through 235 removed outlier: 3.562A pdb=" N GLU E 232 " --> pdb=" O ASN E 228 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU E 233 " --> pdb=" O PRO E 229 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE E 234 " --> pdb=" O ILE E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 239 removed outlier: 3.757A pdb=" N ARG E 239 " --> pdb=" O GLU E 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 236 through 239' Processing helix chain 'E' and resid 249 through 263 removed outlier: 3.687A pdb=" N ASN E 260 " --> pdb=" O GLU E 256 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE E 261 " --> pdb=" O PHE E 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 11 removed outlier: 3.612A pdb=" N LYS F 9 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS F 10 " --> pdb=" O ALA F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.732A pdb=" N VAL F 21 " --> pdb=" O GLY F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 42 Processing helix chain 'F' and resid 44 through 50 removed outlier: 3.758A pdb=" N ARG F 49 " --> pdb=" O PRO F 45 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 66 Processing helix chain 'F' and resid 68 through 80 removed outlier: 3.516A pdb=" N TRP F 74 " --> pdb=" O PRO F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 88 removed outlier: 3.528A pdb=" N LYS F 88 " --> pdb=" O ASP F 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 88' Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'F' and resid 110 through 119 removed outlier: 3.563A pdb=" N THR F 114 " --> pdb=" O ARG F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 134 Processing helix chain 'F' and resid 158 through 165 Processing helix chain 'F' and resid 170 through 175 removed outlier: 3.678A pdb=" N LYS F 175 " --> pdb=" O PRO F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 212 removed outlier: 3.579A pdb=" N LYS F 203 " --> pdb=" O LEU F 199 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS F 206 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU F 207 " --> pdb=" O LYS F 203 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP F 208 " --> pdb=" O LEU F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 217 Processing helix chain 'F' and resid 228 through 238 removed outlier: 3.863A pdb=" N GLU F 232 " --> pdb=" O ASN F 228 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU F 233 " --> pdb=" O PRO F 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE F 234 " --> pdb=" O ILE F 230 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN F 237 " --> pdb=" O GLU F 233 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TRP F 238 " --> pdb=" O ILE F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'G' and resid 2 through 11 removed outlier: 3.543A pdb=" N LYS G 9 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS G 10 " --> pdb=" O ALA G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 22 Processing helix chain 'G' and resid 29 through 42 Processing helix chain 'G' and resid 44 through 49 removed outlier: 3.631A pdb=" N ARG G 49 " --> pdb=" O PRO G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 66 Processing helix chain 'G' and resid 68 through 80 removed outlier: 3.892A pdb=" N TRP G 74 " --> pdb=" O PRO G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 88 Processing helix chain 'G' and resid 89 through 98 Processing helix chain 'G' and resid 110 through 119 removed outlier: 3.570A pdb=" N THR G 114 " --> pdb=" O ARG G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 134 Processing helix chain 'G' and resid 160 through 165 Processing helix chain 'G' and resid 170 through 175 Processing helix chain 'G' and resid 194 through 199 removed outlier: 3.796A pdb=" N ILE G 197 " --> pdb=" O ASP G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 212 removed outlier: 4.012A pdb=" N LYS G 206 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G 207 " --> pdb=" O LYS G 203 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP G 208 " --> pdb=" O LEU G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 217 Processing helix chain 'G' and resid 228 through 238 removed outlier: 4.167A pdb=" N GLU G 232 " --> pdb=" O ASN G 228 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU G 233 " --> pdb=" O PRO G 229 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE G 234 " --> pdb=" O ILE G 230 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN G 237 " --> pdb=" O GLU G 233 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TRP G 238 " --> pdb=" O ILE G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 258 Processing helix chain 'G' and resid 258 through 263 removed outlier: 3.767A pdb=" N VAL G 262 " --> pdb=" O LEU G 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 8 Processing helix chain 'H' and resid 18 through 24 removed outlier: 4.112A pdb=" N SER H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN H 24 " --> pdb=" O GLY H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 Processing helix chain 'H' and resid 44 through 50 removed outlier: 3.611A pdb=" N ARG H 49 " --> pdb=" O PRO H 45 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR H 50 " --> pdb=" O ASP H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 66 removed outlier: 5.145A pdb=" N TYR H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 80 removed outlier: 3.607A pdb=" N TRP H 74 " --> pdb=" O PRO H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 88 removed outlier: 3.613A pdb=" N LYS H 88 " --> pdb=" O ASP H 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 85 through 88' Processing helix chain 'H' and resid 89 through 98 Processing helix chain 'H' and resid 110 through 119 removed outlier: 3.508A pdb=" N THR H 114 " --> pdb=" O ARG H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 133 removed outlier: 3.592A pdb=" N ILE H 132 " --> pdb=" O SER H 128 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA H 133 " --> pdb=" O VAL H 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 128 through 133' Processing helix chain 'H' and resid 160 through 165 removed outlier: 3.977A pdb=" N GLN H 164 " --> pdb=" O THR H 160 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG H 165 " --> pdb=" O SER H 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 160 through 165' Processing helix chain 'H' and resid 170 through 180 removed outlier: 3.503A pdb=" N PHE H 176 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER H 178 " --> pdb=" O ILE H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 211 removed outlier: 3.762A pdb=" N PHE H 201 " --> pdb=" O ILE H 197 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR H 202 " --> pdb=" O ARG H 198 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS H 203 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS H 206 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU H 207 " --> pdb=" O LYS H 203 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU H 210 " --> pdb=" O LYS H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 217 Processing helix chain 'H' and resid 229 through 232 Processing helix chain 'H' and resid 233 through 238 removed outlier: 3.803A pdb=" N TRP H 238 " --> pdb=" O ILE H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 263 removed outlier: 3.545A pdb=" N GLU H 256 " --> pdb=" O GLU H 252 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN H 260 " --> pdb=" O GLU H 256 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHE H 261 " --> pdb=" O PHE H 257 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU H 263 " --> pdb=" O LYS H 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 31 removed outlier: 7.353A pdb=" N ILE A 3 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N SER A 30 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE A 5 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N PHE A 62 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG A 4 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N GLU A 64 " --> pdb=" O ARG A 4 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE A 6 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N THR A 66 " --> pdb=" O ILE A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 31 removed outlier: 7.354A pdb=" N ILE B 3 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N SER B 30 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE B 5 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N PHE B 62 " --> pdb=" O ASN B 2 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ARG B 4 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N GLU B 64 " --> pdb=" O ARG B 4 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE B 6 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N THR B 66 " --> pdb=" O ILE B 6 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 26 through 31 removed outlier: 7.058A pdb=" N ILE C 3 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N SER C 30 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE C 5 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N PHE C 62 " --> pdb=" O ASN C 2 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG C 4 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLU C 64 " --> pdb=" O ARG C 4 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE C 6 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N THR C 66 " --> pdb=" O ILE C 6 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 26 through 31 removed outlier: 7.353A pdb=" N ILE D 3 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N SER D 30 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE D 5 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N PHE D 62 " --> pdb=" O ASN D 2 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG D 4 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N GLU D 64 " --> pdb=" O ARG D 4 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE D 6 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N THR D 66 " --> pdb=" O ILE D 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 123 through 126 removed outlier: 6.388A pdb=" N ILE E 124 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LYS E 144 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE E 126 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL E 13 " --> pdb=" O ILE E 102 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N TYR E 104 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU E 15 " --> pdb=" O TYR E 104 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE E 14 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 123 through 126 removed outlier: 7.640A pdb=" N VAL F 13 " --> pdb=" O ILE F 102 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N TYR F 104 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU F 15 " --> pdb=" O TYR F 104 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE F 14 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL F 185 " --> pdb=" O TYR F 221 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 123 through 126 removed outlier: 7.523A pdb=" N VAL G 13 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N TYR G 104 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU G 15 " --> pdb=" O TYR G 104 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE G 14 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE G 188 " --> pdb=" O ILE G 14 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE G 16 " --> pdb=" O ILE G 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 123 through 126 removed outlier: 6.169A pdb=" N ILE H 124 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LYS H 144 " --> pdb=" O ILE H 124 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE H 126 " --> pdb=" O LYS H 144 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL H 13 " --> pdb=" O ILE H 102 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N TYR H 104 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU H 15 " --> pdb=" O TYR H 104 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE H 14 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL H 185 " --> pdb=" O TYR H 221 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N PHE H 223 " --> pdb=" O VAL H 185 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE H 187 " --> pdb=" O PHE H 223 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE H 222 " --> pdb=" O ILE H 243 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2702 1.32 - 1.45: 4096 1.45 - 1.57: 8169 1.57 - 1.70: 33 1.70 - 1.83: 80 Bond restraints: 15080 Sorted by residual: bond pdb=" CAB Y43 C 201 " pdb=" CAC Y43 C 201 " ideal model delta sigma weight residual 1.524 1.217 0.307 2.00e-02 2.50e+03 2.35e+02 bond pdb=" CAB Y43 A 201 " pdb=" CAC Y43 A 201 " ideal model delta sigma weight residual 1.524 1.219 0.305 2.00e-02 2.50e+03 2.33e+02 bond pdb=" CAB Y43 B 201 " pdb=" CAC Y43 B 201 " ideal model delta sigma weight residual 1.524 1.221 0.303 2.00e-02 2.50e+03 2.30e+02 bond pdb=" CAB Y43 D 201 " pdb=" CAC Y43 D 201 " ideal model delta sigma weight residual 1.524 1.222 0.302 2.00e-02 2.50e+03 2.28e+02 bond pdb=" C6 Y43 D 201 " pdb=" O6 Y43 D 201 " ideal model delta sigma weight residual 1.221 1.401 -0.180 2.00e-02 2.50e+03 8.13e+01 ... (remaining 15075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 19669 3.43 - 6.87: 610 6.87 - 10.30: 86 10.30 - 13.73: 11 13.73 - 17.17: 6 Bond angle restraints: 20382 Sorted by residual: angle pdb=" CA PRO C 103 " pdb=" N PRO C 103 " pdb=" CD PRO C 103 " ideal model delta sigma weight residual 112.00 94.83 17.17 1.40e+00 5.10e-01 1.50e+02 angle pdb=" N GLU H 59 " pdb=" CA GLU H 59 " pdb=" C GLU H 59 " ideal model delta sigma weight residual 111.82 99.83 11.99 1.16e+00 7.43e-01 1.07e+02 angle pdb=" N ILE E 195 " pdb=" CA ILE E 195 " pdb=" C ILE E 195 " ideal model delta sigma weight residual 113.20 105.53 7.67 9.60e-01 1.09e+00 6.38e+01 angle pdb=" N LEU G 55 " pdb=" CA LEU G 55 " pdb=" C LEU G 55 " ideal model delta sigma weight residual 113.15 104.03 9.12 1.19e+00 7.06e-01 5.87e+01 angle pdb=" N LEU H 224 " pdb=" CA LEU H 224 " pdb=" C LEU H 224 " ideal model delta sigma weight residual 110.31 101.70 8.61 1.20e+00 6.94e-01 5.15e+01 ... (remaining 20377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.69: 8647 31.69 - 63.37: 491 63.37 - 95.06: 45 95.06 - 126.74: 3 126.74 - 158.43: 4 Dihedral angle restraints: 9190 sinusoidal: 3990 harmonic: 5200 Sorted by residual: dihedral pdb=" OAN Y43 C 201 " pdb=" OAL Y43 C 201 " pdb=" PAM Y43 C 201 " pdb=" PAI Y43 C 201 " ideal model delta sinusoidal sigma weight residual 19.62 -138.81 158.43 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" OAN Y43 B 201 " pdb=" OAL Y43 B 201 " pdb=" PAM Y43 B 201 " pdb=" PAI Y43 B 201 " ideal model delta sinusoidal sigma weight residual 19.62 -129.35 148.97 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" OAN Y43 D 201 " pdb=" OAL Y43 D 201 " pdb=" PAM Y43 D 201 " pdb=" PAI Y43 D 201 " ideal model delta sinusoidal sigma weight residual 19.62 -129.22 148.84 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 9187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 2160 0.168 - 0.335: 39 0.335 - 0.503: 0 0.503 - 0.670: 0 0.670 - 0.838: 1 Chirality restraints: 2200 Sorted by residual: chirality pdb=" C1B NAD H1001 " pdb=" C2B NAD H1001 " pdb=" N9A NAD H1001 " pdb=" O4B NAD H1001 " both_signs ideal model delta sigma weight residual False 2.35 1.51 0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" CB ILE A 110 " pdb=" CA ILE A 110 " pdb=" CG1 ILE A 110 " pdb=" CG2 ILE A 110 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE D 110 " pdb=" CA ILE D 110 " pdb=" CG1 ILE D 110 " pdb=" CG2 ILE D 110 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 2197 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD H1001 " -0.332 2.00e-02 2.50e+03 2.03e-01 8.27e+02 pdb=" C2N NAD H1001 " 0.353 2.00e-02 2.50e+03 pdb=" C3N NAD H1001 " 0.020 2.00e-02 2.50e+03 pdb=" C4N NAD H1001 " -0.192 2.00e-02 2.50e+03 pdb=" C5N NAD H1001 " -0.039 2.00e-02 2.50e+03 pdb=" C6N NAD H1001 " 0.186 2.00e-02 2.50e+03 pdb=" C7N NAD H1001 " -0.103 2.00e-02 2.50e+03 pdb=" N1N NAD H1001 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD E1001 " -0.218 2.00e-02 2.50e+03 1.57e-01 4.96e+02 pdb=" C2N NAD E1001 " 0.153 2.00e-02 2.50e+03 pdb=" C3N NAD E1001 " -0.031 2.00e-02 2.50e+03 pdb=" C4N NAD E1001 " -0.266 2.00e-02 2.50e+03 pdb=" C5N NAD E1001 " 0.028 2.00e-02 2.50e+03 pdb=" C6N NAD E1001 " 0.221 2.00e-02 2.50e+03 pdb=" C7N NAD E1001 " 0.054 2.00e-02 2.50e+03 pdb=" N1N NAD E1001 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B NAD H1001 " -0.081 2.00e-02 2.50e+03 5.90e-02 9.57e+01 pdb=" C2A NAD H1001 " 0.006 2.00e-02 2.50e+03 pdb=" C4A NAD H1001 " 0.047 2.00e-02 2.50e+03 pdb=" C5A NAD H1001 " 0.090 2.00e-02 2.50e+03 pdb=" C6A NAD H1001 " 0.041 2.00e-02 2.50e+03 pdb=" C8A NAD H1001 " -0.022 2.00e-02 2.50e+03 pdb=" N1A NAD H1001 " -0.014 2.00e-02 2.50e+03 pdb=" N3A NAD H1001 " 0.024 2.00e-02 2.50e+03 pdb=" N6A NAD H1001 " -0.124 2.00e-02 2.50e+03 pdb=" N7A NAD H1001 " 0.051 2.00e-02 2.50e+03 pdb=" N9A NAD H1001 " -0.018 2.00e-02 2.50e+03 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4557 2.79 - 3.31: 12961 3.31 - 3.84: 24244 3.84 - 4.37: 29523 4.37 - 4.90: 49346 Nonbonded interactions: 120631 Sorted by model distance: nonbonded pdb=" CD2 LEU F 192 " pdb=" CD1 LEU F 224 " model vdw 2.258 3.880 nonbonded pdb=" O PHE H 163 " pdb=" N ARG H 165 " model vdw 2.283 3.120 nonbonded pdb=" OH TYR E 108 " pdb=" O VAL E 156 " model vdw 2.289 3.040 nonbonded pdb=" OG SER F 184 " pdb=" O LYS F 219 " model vdw 2.300 3.040 nonbonded pdb=" O SER H 22 " pdb=" N ASN H 24 " model vdw 2.303 3.120 ... (remaining 120626 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 1 through 264) selection = chain 'F' selection = chain 'G' selection = (chain 'H' and resid 1 through 264) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.400 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.307 15080 Z= 0.817 Angle : 1.414 17.168 20382 Z= 0.846 Chirality : 0.063 0.838 2200 Planarity : 0.010 0.203 2562 Dihedral : 18.322 158.426 5846 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 2.25 % Allowed : 10.19 % Favored : 87.56 % Rotamer: Outliers : 4.19 % Allowed : 17.81 % Favored : 78.00 % 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: -4.55 (0.16), residues: 1776 helix: -3.21 (0.14), residues: 696 sheet: -1.64 (0.26), residues: 392 loop : -3.47 (0.19), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 104 TYR 0.032 0.003 TYR B 178 PHE 0.023 0.003 PHE E 201 TRP 0.022 0.002 TRP C 142 HIS 0.008 0.002 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.01279 / 0.82 (15080) covalent geometry : angle 1.41386 / 0.85 (20382) hydrogen bonds : bond 0.24348 / 16.64 ( 534) hydrogen bonds : angle 9.13348 / 6.23 ( 1524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 323 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 21 residues processed: 371 average time/residue: 0.1334 time to fit residues: 70.4088 Evaluate side-chains 202 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 190 TYR Chi-restraints excluded: chain G residue 238 TRP Chi-restraints excluded: chain G residue 260 ASN Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 190 TYR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 256 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN A 163 ASN B 9 ASN B 32 HIS B 89 GLN B 95 GLN B 163 ASN C 11 HIS D 32 HIS D 95 GLN D 163 ASN E 107 ASN ** E 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 GLN F 99 ASN F 107 ASN F 118 ASN F 164 GLN F 237 GLN G 87 ASN H 24 ASN H 107 ASN H 118 ASN H 138 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.083369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.055779 restraints weight = 43173.221| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.88 r_work: 0.2780 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15080 Z= 0.164 Angle : 0.682 7.572 20382 Z= 0.356 Chirality : 0.048 0.170 2200 Planarity : 0.006 0.098 2562 Dihedral : 14.558 179.681 2232 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.52 % Favored : 94.26 % Rotamer: Outliers : 3.75 % Allowed : 18.00 % Favored : 78.25 % 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: -3.13 (0.18), residues: 1776 helix: -1.66 (0.17), residues: 764 sheet: -1.22 (0.27), residues: 384 loop : -2.98 (0.21), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 239 TYR 0.036 0.002 TYR E 162 PHE 0.018 0.001 PHE E 201 TRP 0.018 0.002 TRP H 238 HIS 0.008 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (15080) covalent geometry : angle 0.68236 / 0.36 (20382) hydrogen bonds : bond 0.04542 / 3.10 ( 534) hydrogen bonds : angle 5.58482 / 3.84 ( 1524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 203 time to evaluate : 0.649 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: A 66 THR cc_start: 0.9054 (m) cc_final: 0.8597 (p) REVERT: A 74 ASN cc_start: 0.7890 (t0) cc_final: 0.7621 (t0) REVERT: A 149 ASP cc_start: 0.7069 (m-30) cc_final: 0.6705 (m-30) REVERT: B 158 MET cc_start: 0.8320 (tpp) cc_final: 0.7945 (tpp) REVERT: C 74 ASN cc_start: 0.8269 (t0) cc_final: 0.7899 (t0) REVERT: C 123 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8680 (pm20) REVERT: D 66 THR cc_start: 0.9034 (m) cc_final: 0.8554 (p) REVERT: D 149 ASP cc_start: 0.7022 (m-30) cc_final: 0.6664 (m-30) REVERT: E 75 MET cc_start: 0.9497 (mtp) cc_final: 0.9240 (mtp) REVERT: F 23 MET cc_start: 0.9206 (tmm) cc_final: 0.8713 (ppp) REVERT: F 198 ARG cc_start: 0.8765 (mtp85) cc_final: 0.8153 (mtt180) REVERT: G 239 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7697 (ttm110) outliers start: 60 outliers final: 23 residues processed: 247 average time/residue: 0.1429 time to fit residues: 50.5807 Evaluate side-chains 193 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 238 TRP Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain G residue 190 TYR Chi-restraints excluded: chain G residue 238 TRP Chi-restraints excluded: chain G residue 260 ASN Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 190 TYR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 256 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 28 optimal weight: 30.0000 chunk 31 optimal weight: 40.0000 chunk 100 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN B 9 ASN D 32 HIS F 217 GLN F 237 GLN H 118 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.079875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.052091 restraints weight = 43763.124| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.85 r_work: 0.2690 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15080 Z= 0.212 Angle : 0.657 8.571 20382 Z= 0.339 Chirality : 0.048 0.177 2200 Planarity : 0.005 0.068 2562 Dihedral : 13.835 178.641 2203 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.91 % Favored : 94.03 % Rotamer: Outliers : 3.00 % Allowed : 19.38 % Favored : 77.62 % 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: -2.32 (0.19), residues: 1776 helix: -0.91 (0.18), residues: 788 sheet: -0.94 (0.27), residues: 384 loop : -2.63 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 10 TYR 0.024 0.002 TYR E 162 PHE 0.016 0.002 PHE D 172 TRP 0.018 0.002 TRP E 30 HIS 0.007 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (15080) covalent geometry : angle 0.65691 / 0.34 (20382) hydrogen bonds : bond 0.04393 / 2.99 ( 534) hydrogen bonds : angle 5.12039 / 3.54 ( 1524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 0.616 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: A 66 THR cc_start: 0.9131 (m) cc_final: 0.8594 (p) REVERT: A 74 ASN cc_start: 0.8014 (t0) cc_final: 0.7660 (t0) REVERT: A 82 GLN cc_start: 0.8462 (tm-30) cc_final: 0.7722 (tm-30) REVERT: A 86 ASP cc_start: 0.8978 (t0) cc_final: 0.8583 (m-30) REVERT: A 158 MET cc_start: 0.8590 (tpp) cc_final: 0.7307 (tpp) REVERT: B 74 ASN cc_start: 0.8338 (t0) cc_final: 0.8116 (t0) REVERT: C 69 TYR cc_start: 0.7852 (m-10) cc_final: 0.7614 (m-10) REVERT: C 74 ASN cc_start: 0.8457 (t0) cc_final: 0.7969 (t0) REVERT: D 66 THR cc_start: 0.9102 (m) cc_final: 0.8535 (p) REVERT: D 86 ASP cc_start: 0.8943 (t0) cc_final: 0.8637 (m-30) REVERT: D 109 THR cc_start: 0.8621 (p) cc_final: 0.8275 (p) REVERT: D 158 MET cc_start: 0.8611 (tpp) cc_final: 0.7392 (tpp) REVERT: D 161 ARG cc_start: 0.9158 (ttp-170) cc_final: 0.8954 (ttp80) REVERT: E 239 ARG cc_start: 0.8724 (tpp80) cc_final: 0.8470 (tpp80) REVERT: G 239 ARG cc_start: 0.8339 (ttm110) cc_final: 0.8000 (ttm110) outliers start: 48 outliers final: 31 residues processed: 217 average time/residue: 0.1411 time to fit residues: 44.1303 Evaluate side-chains 197 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain E residue 238 TRP Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 190 TYR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 190 TYR Chi-restraints excluded: chain G residue 238 TRP Chi-restraints excluded: chain G residue 260 ASN Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 190 TYR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 256 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS F 237 GLN H 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.079407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.051494 restraints weight = 43482.895| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.86 r_work: 0.2670 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15080 Z= 0.190 Angle : 0.610 8.491 20382 Z= 0.313 Chirality : 0.046 0.173 2200 Planarity : 0.005 0.053 2562 Dihedral : 13.614 176.341 2203 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.84 % Favored : 95.10 % Rotamer: Outliers : 2.69 % Allowed : 20.25 % Favored : 77.06 % 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: -1.86 (0.20), residues: 1776 helix: -0.50 (0.18), residues: 788 sheet: -0.77 (0.27), residues: 384 loop : -2.39 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 10 TYR 0.016 0.001 TYR E 162 PHE 0.016 0.001 PHE A 172 TRP 0.021 0.002 TRP E 30 HIS 0.005 0.001 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (15080) covalent geometry : angle 0.61018 / 0.31 (20382) hydrogen bonds : bond 0.03859 / 2.63 ( 534) hydrogen bonds : angle 4.82130 / 3.33 ( 1524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.766 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: A 66 THR cc_start: 0.9219 (m) cc_final: 0.8837 (p) REVERT: A 74 ASN cc_start: 0.8205 (t0) cc_final: 0.7784 (t0) REVERT: A 86 ASP cc_start: 0.9091 (t0) cc_final: 0.8694 (m-30) REVERT: A 149 ASP cc_start: 0.7230 (m-30) cc_final: 0.6979 (m-30) REVERT: B 74 ASN cc_start: 0.8414 (t0) cc_final: 0.8110 (t0) REVERT: B 86 ASP cc_start: 0.8701 (m-30) cc_final: 0.8386 (m-30) REVERT: C 1 MET cc_start: 0.7369 (mmp) cc_final: 0.7144 (mmp) REVERT: C 69 TYR cc_start: 0.8001 (m-10) cc_final: 0.7714 (m-10) REVERT: C 74 ASN cc_start: 0.8611 (t0) cc_final: 0.8109 (t0) REVERT: D 66 THR cc_start: 0.9098 (m) cc_final: 0.8644 (p) REVERT: D 80 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8506 (tt) REVERT: D 86 ASP cc_start: 0.9029 (t0) cc_final: 0.8584 (m-30) REVERT: D 109 THR cc_start: 0.8445 (p) cc_final: 0.8227 (p) REVERT: D 149 ASP cc_start: 0.7296 (m-30) cc_final: 0.7003 (m-30) REVERT: E 159 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7914 (mp0) REVERT: E 239 ARG cc_start: 0.8728 (tpp80) cc_final: 0.8511 (tpp80) REVERT: H 159 GLU cc_start: 0.8382 (tt0) cc_final: 0.7959 (mm-30) outliers start: 43 outliers final: 32 residues processed: 207 average time/residue: 0.1391 time to fit residues: 41.5245 Evaluate side-chains 190 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain E residue 238 TRP Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 164 GLN Chi-restraints excluded: chain F residue 190 TYR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 190 TYR Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 238 TRP Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 190 TYR Chi-restraints excluded: chain H residue 192 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 89 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS F 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.079012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.050831 restraints weight = 43747.484| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.90 r_work: 0.2652 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15080 Z= 0.191 Angle : 0.602 8.874 20382 Z= 0.307 Chirality : 0.046 0.183 2200 Planarity : 0.004 0.052 2562 Dihedral : 13.371 175.218 2198 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.06 % Allowed : 19.75 % Favored : 77.19 % 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: -1.56 (0.20), residues: 1776 helix: -0.26 (0.18), residues: 788 sheet: -0.63 (0.26), residues: 384 loop : -2.22 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 10 TYR 0.013 0.001 TYR C 178 PHE 0.015 0.001 PHE A 172 TRP 0.020 0.002 TRP E 30 HIS 0.004 0.001 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (15080) covalent geometry : angle 0.60162 / 0.31 (20382) hydrogen bonds : bond 0.03835 / 2.62 ( 534) hydrogen bonds : angle 4.73360 / 3.25 ( 1524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 0.555 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: A 66 THR cc_start: 0.9237 (m) cc_final: 0.8843 (p) REVERT: A 74 ASN cc_start: 0.8411 (t0) cc_final: 0.7880 (t0) REVERT: A 82 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8260 (tm-30) REVERT: A 86 ASP cc_start: 0.9180 (t0) cc_final: 0.8869 (m-30) REVERT: B 69 TYR cc_start: 0.7931 (m-10) cc_final: 0.7670 (m-10) REVERT: B 74 ASN cc_start: 0.8490 (t0) cc_final: 0.8161 (t0) REVERT: C 69 TYR cc_start: 0.8087 (m-10) cc_final: 0.7812 (m-10) REVERT: C 74 ASN cc_start: 0.8756 (t0) cc_final: 0.8262 (t0) REVERT: D 66 THR cc_start: 0.9088 (m) cc_final: 0.8642 (p) REVERT: D 80 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8513 (tt) REVERT: D 86 ASP cc_start: 0.9099 (t0) cc_final: 0.8644 (m-30) REVERT: D 149 ASP cc_start: 0.7271 (m-30) cc_final: 0.7066 (m-30) REVERT: E 239 ARG cc_start: 0.8758 (tpp80) cc_final: 0.8543 (tpp80) REVERT: F 198 ARG cc_start: 0.8883 (mtp85) cc_final: 0.8218 (mtt180) outliers start: 49 outliers final: 36 residues processed: 200 average time/residue: 0.1318 time to fit residues: 37.9953 Evaluate side-chains 189 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain E residue 238 TRP Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 164 GLN Chi-restraints excluded: chain F residue 190 TYR Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 190 TYR Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 238 TRP Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 190 TYR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 195 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 43 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN G 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.079776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.051727 restraints weight = 42821.928| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.86 r_work: 0.2678 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15080 Z= 0.127 Angle : 0.560 8.181 20382 Z= 0.288 Chirality : 0.045 0.172 2200 Planarity : 0.004 0.050 2562 Dihedral : 13.264 171.836 2198 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.50 % Allowed : 20.19 % Favored : 77.31 % 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: -1.32 (0.20), residues: 1776 helix: -0.04 (0.18), residues: 788 sheet: -0.55 (0.26), residues: 384 loop : -2.09 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 10 TYR 0.010 0.001 TYR E 162 PHE 0.015 0.001 PHE A 172 TRP 0.020 0.001 TRP E 30 HIS 0.005 0.001 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15080) covalent geometry : angle 0.55959 / 0.29 (20382) hydrogen bonds : bond 0.03362 / 2.29 ( 534) hydrogen bonds : angle 4.55373 / 3.12 ( 1524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 THR cc_start: 0.9203 (m) cc_final: 0.8827 (p) REVERT: A 74 ASN cc_start: 0.8378 (t0) cc_final: 0.7831 (t0) REVERT: A 82 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8160 (tm-30) REVERT: A 86 ASP cc_start: 0.9196 (t0) cc_final: 0.8866 (m-30) REVERT: B 69 TYR cc_start: 0.7981 (m-10) cc_final: 0.7727 (m-10) REVERT: B 74 ASN cc_start: 0.8522 (t0) cc_final: 0.8178 (t0) REVERT: B 86 ASP cc_start: 0.9191 (t0) cc_final: 0.8646 (m-30) REVERT: C 69 TYR cc_start: 0.8088 (m-10) cc_final: 0.7881 (m-10) REVERT: C 74 ASN cc_start: 0.8788 (t0) cc_final: 0.8292 (t0) REVERT: D 66 THR cc_start: 0.8910 (m) cc_final: 0.8435 (p) REVERT: D 80 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8487 (tt) REVERT: D 86 ASP cc_start: 0.9138 (t0) cc_final: 0.8663 (m-30) REVERT: E 239 ARG cc_start: 0.8773 (tpp80) cc_final: 0.8533 (tpp80) REVERT: F 198 ARG cc_start: 0.8841 (mtp85) cc_final: 0.8158 (mtt180) REVERT: G 239 ARG cc_start: 0.8456 (ttm110) cc_final: 0.8151 (ttm110) REVERT: H 159 GLU cc_start: 0.8399 (tt0) cc_final: 0.8011 (mm-30) outliers start: 40 outliers final: 28 residues processed: 193 average time/residue: 0.1363 time to fit residues: 37.8165 Evaluate side-chains 182 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 238 TRP Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 164 GLN Chi-restraints excluded: chain F residue 190 TYR Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 190 TYR Chi-restraints excluded: chain G residue 238 TRP Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 190 TYR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 195 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 82 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.079704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.052294 restraints weight = 43136.584| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.76 r_work: 0.2687 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15080 Z= 0.138 Angle : 0.580 7.943 20382 Z= 0.299 Chirality : 0.045 0.168 2200 Planarity : 0.004 0.050 2562 Dihedral : 13.133 168.373 2198 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.56 % Allowed : 20.12 % Favored : 77.31 % 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: -1.23 (0.20), residues: 1776 helix: -0.02 (0.18), residues: 796 sheet: -0.46 (0.26), residues: 388 loop : -2.02 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 10 TYR 0.010 0.001 TYR C 178 PHE 0.014 0.001 PHE D 172 TRP 0.023 0.001 TRP E 30 HIS 0.007 0.001 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (15080) covalent geometry : angle 0.58032 / 0.30 (20382) hydrogen bonds : bond 0.03407 / 2.34 ( 534) hydrogen bonds : angle 4.49947 / 3.09 ( 1524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 THR cc_start: 0.9199 (m) cc_final: 0.8829 (p) REVERT: A 74 ASN cc_start: 0.8389 (t0) cc_final: 0.7427 (t0) REVERT: A 82 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8203 (tm-30) REVERT: A 86 ASP cc_start: 0.9204 (t0) cc_final: 0.8881 (m-30) REVERT: A 138 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6626 (mmt180) REVERT: A 160 ASP cc_start: 0.8817 (p0) cc_final: 0.8602 (t70) REVERT: A 161 ARG cc_start: 0.9236 (ttp80) cc_final: 0.9021 (ptt-90) REVERT: B 69 TYR cc_start: 0.8124 (m-10) cc_final: 0.7909 (m-10) REVERT: B 74 ASN cc_start: 0.8567 (t0) cc_final: 0.8204 (t0) REVERT: B 86 ASP cc_start: 0.9182 (t0) cc_final: 0.8736 (m-30) REVERT: B 161 ARG cc_start: 0.9344 (ttp80) cc_final: 0.9005 (ttp80) REVERT: C 74 ASN cc_start: 0.8848 (t0) cc_final: 0.8354 (t0) REVERT: C 97 LEU cc_start: 0.8890 (mt) cc_final: 0.8600 (tp) REVERT: C 140 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.8116 (t80) REVERT: D 66 THR cc_start: 0.8939 (m) cc_final: 0.8502 (p) REVERT: D 80 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8465 (tt) REVERT: D 86 ASP cc_start: 0.9120 (t0) cc_final: 0.8639 (m-30) REVERT: F 190 TYR cc_start: 0.8870 (OUTLIER) cc_final: 0.8540 (t80) REVERT: F 198 ARG cc_start: 0.8853 (mtp85) cc_final: 0.8157 (mtt180) REVERT: H 159 GLU cc_start: 0.8457 (tt0) cc_final: 0.8107 (mm-30) REVERT: H 190 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8092 (t80) REVERT: H 237 GLN cc_start: 0.9342 (tp40) cc_final: 0.9033 (mm-40) outliers start: 41 outliers final: 31 residues processed: 189 average time/residue: 0.1448 time to fit residues: 38.9983 Evaluate side-chains 190 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 238 TRP Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 164 GLN Chi-restraints excluded: chain F residue 190 TYR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 190 TYR Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 238 TRP Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 190 TYR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 195 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 120 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN C 102 ASN C 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.078116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.050734 restraints weight = 43495.318| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 3.76 r_work: 0.2647 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15080 Z= 0.221 Angle : 0.628 7.818 20382 Z= 0.323 Chirality : 0.047 0.173 2200 Planarity : 0.005 0.054 2562 Dihedral : 13.089 167.087 2198 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.00 % Allowed : 20.25 % Favored : 76.75 % 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 (0.20), residues: 1776 helix: -0.08 (0.18), residues: 796 sheet: -0.57 (0.26), residues: 388 loop : -2.07 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 10 TYR 0.012 0.001 TYR C 178 PHE 0.016 0.001 PHE H 201 TRP 0.027 0.001 TRP E 30 HIS 0.004 0.001 HIS D 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (15080) covalent geometry : angle 0.62831 / 0.32 (20382) hydrogen bonds : bond 0.03927 / 2.69 ( 534) hydrogen bonds : angle 4.60430 / 3.16 ( 1524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 THR cc_start: 0.9227 (m) cc_final: 0.8870 (p) REVERT: A 74 ASN cc_start: 0.8451 (t0) cc_final: 0.7957 (t0) REVERT: A 82 GLN cc_start: 0.8602 (tm-30) cc_final: 0.7882 (tm-30) REVERT: A 86 ASP cc_start: 0.9236 (t0) cc_final: 0.8801 (m-30) REVERT: B 74 ASN cc_start: 0.8672 (t0) cc_final: 0.8143 (t0) REVERT: C 74 ASN cc_start: 0.8895 (t0) cc_final: 0.8394 (t0) REVERT: C 97 LEU cc_start: 0.8921 (mt) cc_final: 0.8621 (tp) REVERT: C 140 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8152 (t80) REVERT: D 66 THR cc_start: 0.8981 (m) cc_final: 0.8561 (p) REVERT: D 80 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8580 (tt) REVERT: D 86 ASP cc_start: 0.9148 (t0) cc_final: 0.8666 (m-30) REVERT: E 239 ARG cc_start: 0.8791 (tpp80) cc_final: 0.8534 (tpp80) REVERT: F 190 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8525 (t80) REVERT: F 198 ARG cc_start: 0.8904 (mtp85) cc_final: 0.8317 (mtm180) REVERT: H 159 GLU cc_start: 0.8545 (tt0) cc_final: 0.8235 (mm-30) REVERT: H 190 TYR cc_start: 0.9000 (OUTLIER) cc_final: 0.8169 (t80) REVERT: H 237 GLN cc_start: 0.9391 (tp40) cc_final: 0.9089 (mm-40) outliers start: 48 outliers final: 36 residues processed: 182 average time/residue: 0.1389 time to fit residues: 36.5823 Evaluate side-chains 184 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 237 GLN Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 164 GLN Chi-restraints excluded: chain F residue 190 TYR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 190 TYR Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 238 TRP Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 190 TYR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 195 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 149 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 99 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.079336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.052077 restraints weight = 43016.843| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.73 r_work: 0.2686 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15080 Z= 0.130 Angle : 0.588 9.348 20382 Z= 0.302 Chirality : 0.045 0.187 2200 Planarity : 0.004 0.058 2562 Dihedral : 12.988 167.779 2198 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.38 % Allowed : 20.50 % Favored : 77.12 % 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: -1.14 (0.20), residues: 1776 helix: 0.09 (0.19), residues: 796 sheet: -0.51 (0.26), residues: 388 loop : -1.97 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 10 TYR 0.009 0.001 TYR C 178 PHE 0.014 0.001 PHE B 172 TRP 0.022 0.001 TRP E 30 HIS 0.007 0.001 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (15080) covalent geometry : angle 0.58841 / 0.30 (20382) hydrogen bonds : bond 0.03276 / 2.24 ( 534) hydrogen bonds : angle 4.39862 / 3.01 ( 1524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 THR cc_start: 0.9204 (m) cc_final: 0.8839 (p) REVERT: A 74 ASN cc_start: 0.8420 (t0) cc_final: 0.7940 (t0) REVERT: A 82 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8070 (tm-30) REVERT: A 86 ASP cc_start: 0.9246 (t0) cc_final: 0.8882 (m-30) REVERT: A 138 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.6777 (mmt180) REVERT: A 160 ASP cc_start: 0.8727 (p0) cc_final: 0.8370 (t70) REVERT: B 74 ASN cc_start: 0.8700 (t0) cc_final: 0.8162 (t0) REVERT: C 74 ASN cc_start: 0.8866 (t0) cc_final: 0.8357 (t0) REVERT: C 97 LEU cc_start: 0.8941 (mt) cc_final: 0.8641 (tp) REVERT: C 140 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8147 (t80) REVERT: D 66 THR cc_start: 0.8899 (m) cc_final: 0.8477 (p) REVERT: D 80 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8521 (tt) REVERT: D 82 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7441 (tm-30) REVERT: D 86 ASP cc_start: 0.9146 (t0) cc_final: 0.8656 (m-30) REVERT: E 239 ARG cc_start: 0.8733 (tpp80) cc_final: 0.8407 (tpp80) REVERT: F 190 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.8522 (t80) REVERT: F 198 ARG cc_start: 0.8916 (mtp85) cc_final: 0.8239 (mtt180) REVERT: G 239 ARG cc_start: 0.8492 (ttm110) cc_final: 0.8199 (ttm110) REVERT: H 159 GLU cc_start: 0.8452 (tt0) cc_final: 0.8123 (mm-30) REVERT: H 190 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.8238 (t80) REVERT: H 237 GLN cc_start: 0.9364 (tp40) cc_final: 0.9094 (mm-40) outliers start: 38 outliers final: 32 residues processed: 176 average time/residue: 0.1438 time to fit residues: 36.1918 Evaluate side-chains 181 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 164 GLN Chi-restraints excluded: chain F residue 190 TYR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 190 TYR Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 238 TRP Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 190 TYR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 105 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 145 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.079672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.052457 restraints weight = 42957.299| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.72 r_work: 0.2691 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15080 Z= 0.119 Angle : 0.581 7.894 20382 Z= 0.299 Chirality : 0.045 0.164 2200 Planarity : 0.004 0.062 2562 Dihedral : 12.895 167.711 2198 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.31 % Allowed : 20.31 % Favored : 77.38 % 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: -1.02 (0.20), residues: 1776 helix: 0.20 (0.19), residues: 796 sheet: -0.46 (0.26), residues: 388 loop : -1.93 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 10 TYR 0.009 0.001 TYR C 178 PHE 0.013 0.001 PHE B 172 TRP 0.020 0.001 TRP E 30 HIS 0.005 0.001 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (15080) covalent geometry : angle 0.58057 / 0.30 (20382) hydrogen bonds : bond 0.03183 / 2.18 ( 534) hydrogen bonds : angle 4.33426 / 2.97 ( 1524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 THR cc_start: 0.9181 (m) cc_final: 0.8813 (p) REVERT: A 74 ASN cc_start: 0.8463 (t0) cc_final: 0.7977 (t0) REVERT: A 82 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8023 (tm-30) REVERT: A 86 ASP cc_start: 0.9244 (t0) cc_final: 0.8875 (m-30) REVERT: A 138 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.6771 (mmt180) REVERT: A 160 ASP cc_start: 0.8722 (p0) cc_final: 0.8388 (t70) REVERT: B 74 ASN cc_start: 0.8718 (t0) cc_final: 0.8190 (t0) REVERT: C 74 ASN cc_start: 0.8873 (t0) cc_final: 0.8366 (t0) REVERT: C 97 LEU cc_start: 0.8954 (mt) cc_final: 0.8658 (tp) REVERT: C 140 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8066 (t80) REVERT: D 66 THR cc_start: 0.8905 (m) cc_final: 0.8468 (p) REVERT: D 80 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8512 (tt) REVERT: D 82 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7475 (tm-30) REVERT: D 86 ASP cc_start: 0.9166 (t0) cc_final: 0.8727 (m-30) REVERT: E 239 ARG cc_start: 0.8711 (tpp80) cc_final: 0.8405 (tpp80) REVERT: F 190 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8494 (t80) REVERT: F 198 ARG cc_start: 0.8895 (mtp85) cc_final: 0.8193 (mtt180) REVERT: G 239 ARG cc_start: 0.8484 (ttm110) cc_final: 0.8205 (ttm110) REVERT: H 159 GLU cc_start: 0.8476 (tt0) cc_final: 0.8153 (mm-30) REVERT: H 190 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.8230 (t80) REVERT: H 237 GLN cc_start: 0.9344 (tp40) cc_final: 0.9080 (mm-40) outliers start: 37 outliers final: 29 residues processed: 172 average time/residue: 0.1410 time to fit residues: 35.1655 Evaluate side-chains 179 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 164 GLN Chi-restraints excluded: chain F residue 190 TYR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 190 TYR Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 238 TRP Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 190 TYR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 65 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 159 optimal weight: 0.0370 chunk 87 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 28 optimal weight: 40.0000 chunk 97 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.078404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050814 restraints weight = 43340.325| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.79 r_work: 0.2659 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15080 Z= 0.179 Angle : 0.605 7.921 20382 Z= 0.311 Chirality : 0.046 0.167 2200 Planarity : 0.004 0.061 2562 Dihedral : 12.834 166.314 2198 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.19 % Allowed : 20.56 % Favored : 77.25 % 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: -1.05 (0.20), residues: 1776 helix: 0.19 (0.19), residues: 796 sheet: -0.50 (0.26), residues: 388 loop : -1.92 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 10 TYR 0.013 0.001 TYR A 69 PHE 0.014 0.001 PHE H 201 TRP 0.025 0.001 TRP E 30 HIS 0.006 0.001 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (15080) covalent geometry : angle 0.60512 / 0.31 (20382) hydrogen bonds : bond 0.03542 / 2.43 ( 534) hydrogen bonds : angle 4.41673 / 3.03 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3598.30 seconds wall clock time: 62 minutes 43.10 seconds (3763.10 seconds total)