Starting phenix.real_space_refine on Wed Mar 4 16:25:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ssp_25412/03_2026/7ssp_25412.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ssp_25412/03_2026/7ssp_25412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ssp_25412/03_2026/7ssp_25412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ssp_25412/03_2026/7ssp_25412.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ssp_25412/03_2026/7ssp_25412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ssp_25412/03_2026/7ssp_25412.map" } resolution = 3.5 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5175 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 6909 2.51 5 N 1912 2.21 5 O 2040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10930 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1433 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1436 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1433 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1433 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1298 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1299 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1299 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1299 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.62, per 1000 atoms: 0.24 Number of scatterers: 10930 At special positions: 0 Unit cell: (98.04, 108.3, 96.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 2040 8.00 N 1912 7.00 C 6909 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: 0.85 Conformation dependent library (CDL) restraints added in 566.3 milliseconds 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2616 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 73.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 93 through 108 removed outlier: 3.594A pdb=" N LEU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 117 through 125 removed outlier: 4.037A pdb=" N ILE A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 166 Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 199 through 207 removed outlier: 3.878A pdb=" N ALA A 203 " --> pdb=" O HIS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 230 removed outlier: 4.148A pdb=" N TYR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 259 removed outlier: 3.684A pdb=" N THR A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 244 " --> pdb=" O TRP A 240 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 266 through 282 removed outlier: 4.668A pdb=" N ASP A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 108 removed outlier: 3.994A pdb=" N ARG B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 removed outlier: 4.381A pdb=" N ILE B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 127 No H-bonds generated for 'chain 'B' and resid 125 through 127' Processing helix chain 'B' and resid 144 through 169 removed outlier: 4.057A pdb=" N LEU B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 191 Processing helix chain 'B' and resid 199 through 207 removed outlier: 3.871A pdb=" N ALA B 203 " --> pdb=" O HIS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 230 Processing helix chain 'B' and resid 238 through 259 removed outlier: 3.694A pdb=" N THR B 242 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG B 244 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 266 through 282 removed outlier: 4.908A pdb=" N ASP B 279 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 108 removed outlier: 3.893A pdb=" N ARG C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 125 through 127 No H-bonds generated for 'chain 'C' and resid 125 through 127' Processing helix chain 'C' and resid 142 through 166 removed outlier: 4.083A pdb=" N ILE C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 191 Processing helix chain 'C' and resid 199 through 207 removed outlier: 3.879A pdb=" N ALA C 203 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 229 Processing helix chain 'C' and resid 238 through 259 removed outlier: 3.636A pdb=" N THR C 242 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 243 " --> pdb=" O ASN C 239 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG C 244 " --> pdb=" O TRP C 240 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 266 through 282 removed outlier: 4.824A pdb=" N ASP C 279 " --> pdb=" O ASN C 275 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 280 " --> pdb=" O ARG C 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 109 removed outlier: 3.832A pdb=" N ARG D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 4.264A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 166 removed outlier: 4.326A pdb=" N ILE D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 191 Processing helix chain 'D' and resid 199 through 207 removed outlier: 3.854A pdb=" N ALA D 203 " --> pdb=" O HIS D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 230 removed outlier: 4.131A pdb=" N TYR D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 259 removed outlier: 3.678A pdb=" N THR D 242 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG D 243 " --> pdb=" O ASN D 239 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG D 244 " --> pdb=" O TRP D 240 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE D 250 " --> pdb=" O MET D 246 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR D 254 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 266 through 282 removed outlier: 4.832A pdb=" N ASP D 279 " --> pdb=" O ASN D 275 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 280 " --> pdb=" O ARG D 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 74 removed outlier: 3.728A pdb=" N ILE E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE E 53 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 105 removed outlier: 3.930A pdb=" N ILE E 83 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE E 104 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 130 through 155 removed outlier: 3.971A pdb=" N ALA E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR E 138 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR E 155 " --> pdb=" O ASN E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 180 Processing helix chain 'E' and resid 197 through 205 Processing helix chain 'E' and resid 208 through 217 removed outlier: 3.643A pdb=" N SER E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU E 215 " --> pdb=" O ILE E 211 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 74 removed outlier: 4.456A pdb=" N ARG F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE F 52 " --> pdb=" O ALA F 48 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE F 53 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 104 removed outlier: 3.633A pdb=" N ILE F 83 " --> pdb=" O VAL F 79 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS F 85 " --> pdb=" O PRO F 81 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET F 86 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.520A pdb=" N ALA F 124 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 155 removed outlier: 3.825A pdb=" N VAL F 139 " --> pdb=" O MET F 135 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR F 155 " --> pdb=" O ASN F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 180 Processing helix chain 'F' and resid 195 through 217 removed outlier: 3.564A pdb=" N LEU F 199 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY F 206 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE F 211 " --> pdb=" O CYS F 207 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR F 212 " --> pdb=" O ARG F 208 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG F 216 " --> pdb=" O TYR F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 74 removed outlier: 3.688A pdb=" N ILE G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 104 removed outlier: 3.718A pdb=" N ILE G 83 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE G 104 " --> pdb=" O LEU G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 124 Processing helix chain 'G' and resid 136 through 155 removed outlier: 3.626A pdb=" N THR G 155 " --> pdb=" O ASN G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 180 Processing helix chain 'G' and resid 195 through 217 removed outlier: 3.586A pdb=" N LEU G 199 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY G 206 " --> pdb=" O ILE G 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE G 211 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 74 removed outlier: 3.818A pdb=" N ILE H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE H 53 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 104 removed outlier: 3.756A pdb=" N ILE H 83 " --> pdb=" O VAL H 79 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE H 104 " --> pdb=" O LEU H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 124 Processing helix chain 'H' and resid 137 through 155 removed outlier: 3.614A pdb=" N THR H 155 " --> pdb=" O ASN H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 180 Processing helix chain 'H' and resid 195 through 217 removed outlier: 3.801A pdb=" N LEU H 199 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS H 200 " --> pdb=" O TYR H 196 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER H 201 " --> pdb=" O ALA H 197 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY H 206 " --> pdb=" O ILE H 202 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE H 211 " --> pdb=" O CYS H 207 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU H 215 " --> pdb=" O ILE H 211 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG H 216 " --> pdb=" O TYR H 212 " (cutoff:3.500A) 667 hydrogen bonds defined for protein. 1980 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: 1.36 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3676 1.34 - 1.46: 2044 1.46 - 1.58: 5292 1.58 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 11138 Sorted by residual: bond pdb=" CB VAL G 55 " pdb=" CG2 VAL G 55 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.77e+00 bond pdb=" C ILE C 194 " pdb=" N PRO C 195 " ideal model delta sigma weight residual 1.335 1.351 -0.015 1.30e-02 5.92e+03 1.39e+00 bond pdb=" CA LYS G 131 " pdb=" C LYS G 131 " ideal model delta sigma weight residual 1.523 1.504 0.020 1.80e-02 3.09e+03 1.18e+00 bond pdb=" CB VAL H 55 " pdb=" CG2 VAL H 55 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.73e-01 bond pdb=" N GLN B 172 " pdb=" CA GLN B 172 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.15e-02 7.56e+03 8.40e-01 ... (remaining 11133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 14679 1.66 - 3.32: 333 3.32 - 4.98: 47 4.98 - 6.64: 17 6.64 - 8.30: 2 Bond angle restraints: 15078 Sorted by residual: angle pdb=" N ALA E 124 " pdb=" CA ALA E 124 " pdb=" C ALA E 124 " ideal model delta sigma weight residual 114.56 108.60 5.96 1.27e+00 6.20e-01 2.20e+01 angle pdb=" N ALA G 124 " pdb=" CA ALA G 124 " pdb=" C ALA G 124 " ideal model delta sigma weight residual 114.56 108.66 5.90 1.27e+00 6.20e-01 2.16e+01 angle pdb=" N ALA F 124 " pdb=" CA ALA F 124 " pdb=" C ALA F 124 " ideal model delta sigma weight residual 114.56 108.73 5.83 1.27e+00 6.20e-01 2.11e+01 angle pdb=" N ALA H 124 " pdb=" CA ALA H 124 " pdb=" C ALA H 124 " ideal model delta sigma weight residual 114.56 108.75 5.81 1.27e+00 6.20e-01 2.09e+01 angle pdb=" N VAL H 117 " pdb=" CA VAL H 117 " pdb=" C VAL H 117 " ideal model delta sigma weight residual 113.42 108.52 4.90 1.17e+00 7.31e-01 1.76e+01 ... (remaining 15073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5958 17.79 - 35.58: 622 35.58 - 53.38: 116 53.38 - 71.17: 11 71.17 - 88.96: 11 Dihedral angle restraints: 6718 sinusoidal: 2702 harmonic: 4016 Sorted by residual: dihedral pdb=" CA GLU G 165 " pdb=" C GLU G 165 " pdb=" N GLU G 166 " pdb=" CA GLU G 166 " ideal model delta harmonic sigma weight residual 180.00 155.14 24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA GLU H 165 " pdb=" C GLU H 165 " pdb=" N GLU H 166 " pdb=" CA GLU H 166 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA GLU F 165 " pdb=" C GLU F 165 " pdb=" N GLU F 166 " pdb=" CA GLU F 166 " ideal model delta harmonic sigma weight residual 180.00 155.19 24.81 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 6715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1011 0.029 - 0.058: 494 0.058 - 0.087: 145 0.087 - 0.117: 40 0.117 - 0.146: 6 Chirality restraints: 1696 Sorted by residual: chirality pdb=" CA MET C 281 " pdb=" N MET C 281 " pdb=" C MET C 281 " pdb=" CB MET C 281 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA PRO E 81 " pdb=" N PRO E 81 " pdb=" C PRO E 81 " pdb=" CB PRO E 81 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA PRO G 81 " pdb=" N PRO G 81 " pdb=" C PRO G 81 " pdb=" CB PRO G 81 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 1693 not shown) Planarity restraints: 1940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 144 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.73e+00 pdb=" C GLU A 144 " -0.038 2.00e-02 2.50e+03 pdb=" O GLU A 144 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 145 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 112 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 111 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 112 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " -0.026 5.00e-02 4.00e+02 ... (remaining 1937 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2038 2.77 - 3.30: 10425 3.30 - 3.83: 16849 3.83 - 4.37: 18638 4.37 - 4.90: 32859 Nonbonded interactions: 80809 Sorted by model distance: nonbonded pdb=" OD2 ASP D 233 " pdb=" NH1 ARG D 244 " model vdw 2.232 3.120 nonbonded pdb=" OD2 ASP B 233 " pdb=" NH1 ARG B 244 " model vdw 2.236 3.120 nonbonded pdb=" OD2 ASP A 233 " pdb=" NH1 ARG A 244 " model vdw 2.310 3.120 nonbonded pdb=" O SER B 143 " pdb=" OG SER B 143 " model vdw 2.311 3.040 nonbonded pdb=" OD1 ASP D 233 " pdb=" NH1 ARG D 243 " model vdw 2.333 3.120 ... (remaining 80804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 93 through 127 or (resid 141 and (name N or name CA or nam \ e C or name O or name CB )) or resid 142 through 284)) selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 45 through 100 or (resid 101 and (name N or name CA or nam \ e C or name O or name CB )) or resid 102 through 217)) selection = (chain 'F' and (resid 45 through 161 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB )) or resid 163 through 217)) selection = (chain 'G' and (resid 45 through 161 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB )) or resid 163 through 217)) selection = (chain 'H' and (resid 45 through 161 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB )) or resid 163 through 217)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.460 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 0.004 0.044 11138 Z= 0.161 Angle : 0.626 8.298 15078 Z= 0.370 Chirality : 0.037 0.146 1696 Planarity : 0.005 0.053 1940 Dihedral : 14.584 88.962 4102 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.20), residues: 1344 helix: -1.28 (0.15), residues: 1000 sheet: None (None), residues: 0 loop : -4.52 (0.25), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 216 TYR 0.011 0.001 TYR G 212 PHE 0.010 0.001 PHE C 110 TRP 0.008 0.001 TRP H 115 HIS 0.006 0.001 HIS E 147 Details of bonding type rmsd covalent geometry : bond 0.00354 (11138) covalent geometry : angle 0.62629 (15078) hydrogen bonds : bond 0.15023 ( 667) hydrogen bonds : angle 5.87648 ( 1980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.438 Fit side-chains REVERT: A 226 ASP cc_start: 0.7551 (m-30) cc_final: 0.7260 (m-30) REVERT: A 266 PHE cc_start: 0.7627 (m-80) cc_final: 0.7421 (m-80) REVERT: B 163 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6987 (tt0) REVERT: B 202 ARG cc_start: 0.7747 (tmt-80) cc_final: 0.7399 (tpt90) REVERT: C 159 ARG cc_start: 0.7450 (ttp-110) cc_final: 0.7075 (ttm-80) REVERT: C 167 LEU cc_start: 0.8274 (tp) cc_final: 0.8051 (tt) REVERT: C 202 ARG cc_start: 0.7749 (tmt-80) cc_final: 0.7450 (tpt90) REVERT: C 226 ASP cc_start: 0.7462 (m-30) cc_final: 0.7138 (m-30) REVERT: C 281 MET cc_start: 0.6922 (tpp) cc_final: 0.6527 (mmp) REVERT: D 119 GLU cc_start: 0.6020 (tm-30) cc_final: 0.5620 (tm-30) REVERT: D 226 ASP cc_start: 0.7512 (m-30) cc_final: 0.7253 (m-30) REVERT: D 266 PHE cc_start: 0.7658 (m-80) cc_final: 0.7437 (m-80) REVERT: D 281 MET cc_start: 0.6674 (mmm) cc_final: 0.6317 (mmp) REVERT: E 67 TYR cc_start: 0.8693 (m-10) cc_final: 0.7824 (m-10) REVERT: E 101 MET cc_start: 0.8400 (ttm) cc_final: 0.8057 (ttp) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.1351 time to fit residues: 47.7466 Evaluate side-chains 209 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 overall best weight: 0.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN E 70 GLN E 148 HIS F 70 GLN G 70 GLN H 70 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.170255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.146040 restraints weight = 13672.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.147636 restraints weight = 10724.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148516 restraints weight = 9237.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.149478 restraints weight = 8429.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.149478 restraints weight = 7904.614| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11138 Z= 0.115 Angle : 0.557 8.080 15078 Z= 0.284 Chirality : 0.035 0.132 1696 Planarity : 0.005 0.066 1940 Dihedral : 3.925 20.757 1488 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.87 % Allowed : 8.96 % Favored : 90.17 % 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: -0.59 (0.24), residues: 1344 helix: 0.71 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -3.81 (0.28), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 159 TYR 0.013 0.001 TYR G 212 PHE 0.009 0.001 PHE B 266 TRP 0.008 0.001 TRP H 115 HIS 0.005 0.001 HIS H 147 Details of bonding type rmsd covalent geometry : bond 0.00232 (11138) covalent geometry : angle 0.55688 (15078) hydrogen bonds : bond 0.03889 ( 667) hydrogen bonds : angle 3.34581 ( 1980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 211 time to evaluate : 0.451 Fit side-chains REVERT: A 164 GLU cc_start: 0.7487 (tm-30) cc_final: 0.6815 (tt0) REVERT: A 226 ASP cc_start: 0.7442 (m-30) cc_final: 0.7216 (m-30) REVERT: B 163 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7106 (pt0) REVERT: B 202 ARG cc_start: 0.7787 (tmt-80) cc_final: 0.7459 (tpt90) REVERT: B 227 MET cc_start: 0.8193 (ttp) cc_final: 0.7903 (ttp) REVERT: C 110 PHE cc_start: 0.5703 (p90) cc_final: 0.5331 (p90) REVERT: C 199 HIS cc_start: 0.7381 (m90) cc_final: 0.7102 (m90) REVERT: C 202 ARG cc_start: 0.7822 (tmt-80) cc_final: 0.7505 (tpt90) REVERT: C 226 ASP cc_start: 0.7358 (m-30) cc_final: 0.7124 (m-30) REVERT: C 281 MET cc_start: 0.6823 (tpp) cc_final: 0.6507 (tpp) REVERT: D 226 ASP cc_start: 0.7414 (m-30) cc_final: 0.7180 (m-30) REVERT: D 281 MET cc_start: 0.6914 (mmm) cc_final: 0.6570 (mmp) REVERT: E 67 TYR cc_start: 0.8517 (m-10) cc_final: 0.7788 (m-10) REVERT: F 67 TYR cc_start: 0.8541 (m-10) cc_final: 0.7846 (m-10) REVERT: G 67 TYR cc_start: 0.8597 (m-10) cc_final: 0.7801 (m-10) REVERT: H 67 TYR cc_start: 0.8602 (m-10) cc_final: 0.7730 (m-10) REVERT: H 208 ARG cc_start: 0.7199 (tmt170) cc_final: 0.6125 (ttp80) outliers start: 10 outliers final: 9 residues processed: 219 average time/residue: 0.1335 time to fit residues: 38.4741 Evaluate side-chains 201 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.0980 chunk 64 optimal weight: 0.0970 chunk 72 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 169 GLN B 229 HIS B 275 ASN C 275 ASN D 275 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.160846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.134629 restraints weight = 13773.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.137681 restraints weight = 8766.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139700 restraints weight = 6580.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.140960 restraints weight = 5477.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.141887 restraints weight = 4877.249| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11138 Z= 0.103 Angle : 0.526 7.291 15078 Z= 0.265 Chirality : 0.035 0.203 1696 Planarity : 0.005 0.063 1940 Dihedral : 3.595 19.273 1488 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.70 % Allowed : 12.53 % Favored : 86.77 % 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: 0.52 (0.25), residues: 1344 helix: 1.50 (0.18), residues: 1004 sheet: None (None), residues: 0 loop : -3.36 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 159 TYR 0.006 0.001 TYR H 212 PHE 0.009 0.001 PHE B 266 TRP 0.007 0.001 TRP H 115 HIS 0.005 0.001 HIS E 147 Details of bonding type rmsd covalent geometry : bond 0.00212 (11138) covalent geometry : angle 0.52616 (15078) hydrogen bonds : bond 0.03435 ( 667) hydrogen bonds : angle 2.87430 ( 1980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 201 time to evaluate : 0.340 Fit side-chains REVERT: A 114 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7270 (t-90) REVERT: A 164 GLU cc_start: 0.7536 (tm-30) cc_final: 0.6852 (tt0) REVERT: B 159 ARG cc_start: 0.7231 (ttm-80) cc_final: 0.6902 (ttm-80) REVERT: B 164 GLU cc_start: 0.7620 (tm-30) cc_final: 0.6962 (tt0) REVERT: B 202 ARG cc_start: 0.7589 (tmt-80) cc_final: 0.7283 (tpt90) REVERT: B 227 MET cc_start: 0.8138 (ttp) cc_final: 0.7807 (ttp) REVERT: C 159 ARG cc_start: 0.7223 (ttm-80) cc_final: 0.6855 (ttm-80) REVERT: C 202 ARG cc_start: 0.7677 (tmt-80) cc_final: 0.7324 (tpt90) REVERT: C 281 MET cc_start: 0.6881 (tpp) cc_final: 0.6675 (tpp) REVERT: E 67 TYR cc_start: 0.8568 (m-10) cc_final: 0.7915 (m-10) REVERT: F 67 TYR cc_start: 0.8539 (m-10) cc_final: 0.7869 (m-10) REVERT: F 151 ASN cc_start: 0.7660 (t0) cc_final: 0.7380 (t0) REVERT: G 67 TYR cc_start: 0.8594 (m-10) cc_final: 0.7876 (m-10) REVERT: G 150 ASN cc_start: 0.6871 (m-40) cc_final: 0.6581 (m-40) REVERT: G 151 ASN cc_start: 0.7727 (t0) cc_final: 0.7482 (t0) REVERT: H 67 TYR cc_start: 0.8624 (m-10) cc_final: 0.7923 (m-10) REVERT: H 150 ASN cc_start: 0.6903 (m-40) cc_final: 0.6625 (m-40) REVERT: H 151 ASN cc_start: 0.7754 (t0) cc_final: 0.7453 (t0) REVERT: H 208 ARG cc_start: 0.6915 (tmt170) cc_final: 0.5655 (ttp80) outliers start: 8 outliers final: 6 residues processed: 209 average time/residue: 0.1350 time to fit residues: 37.1886 Evaluate side-chains 201 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 194 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 229 HIS B 275 ASN D 275 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.153031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.124834 restraints weight = 13888.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127839 restraints weight = 9066.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.129817 restraints weight = 6929.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.130874 restraints weight = 5849.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.131612 restraints weight = 5307.700| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11138 Z= 0.117 Angle : 0.537 8.275 15078 Z= 0.270 Chirality : 0.036 0.195 1696 Planarity : 0.005 0.058 1940 Dihedral : 3.573 19.461 1488 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.87 % Allowed : 14.53 % Favored : 84.60 % 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: 0.87 (0.25), residues: 1344 helix: 1.66 (0.17), residues: 1028 sheet: None (None), residues: 0 loop : -3.25 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 159 TYR 0.019 0.001 TYR G 212 PHE 0.010 0.001 PHE B 266 TRP 0.005 0.001 TRP B 228 HIS 0.004 0.001 HIS G 147 Details of bonding type rmsd covalent geometry : bond 0.00264 (11138) covalent geometry : angle 0.53722 (15078) hydrogen bonds : bond 0.04145 ( 667) hydrogen bonds : angle 2.83546 ( 1980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 203 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7703 (tm-30) cc_final: 0.6812 (tt0) REVERT: A 208 MET cc_start: 0.8068 (ttm) cc_final: 0.7823 (mtt) REVERT: B 164 GLU cc_start: 0.7717 (tm-30) cc_final: 0.6913 (tt0) REVERT: B 202 ARG cc_start: 0.7718 (tmt-80) cc_final: 0.7407 (tpt-90) REVERT: B 208 MET cc_start: 0.8081 (ttm) cc_final: 0.7790 (mtt) REVERT: B 226 ASP cc_start: 0.7848 (m-30) cc_final: 0.7639 (m-30) REVERT: B 227 MET cc_start: 0.8184 (ttp) cc_final: 0.7908 (ttp) REVERT: C 202 ARG cc_start: 0.7735 (tmt-80) cc_final: 0.7435 (tpt90) REVERT: C 208 MET cc_start: 0.8122 (ttm) cc_final: 0.7817 (mtt) REVERT: C 265 ASP cc_start: 0.7282 (p0) cc_final: 0.7020 (t0) REVERT: D 208 MET cc_start: 0.8136 (ttm) cc_final: 0.7876 (mtt) REVERT: E 67 TYR cc_start: 0.8655 (m-10) cc_final: 0.7998 (m-10) REVERT: E 135 MET cc_start: 0.7578 (mmp) cc_final: 0.7236 (mmt) REVERT: F 151 ASN cc_start: 0.7798 (t0) cc_final: 0.7557 (t0) REVERT: F 208 ARG cc_start: 0.6946 (tmt170) cc_final: 0.5525 (ttp80) REVERT: G 67 TYR cc_start: 0.8674 (m-10) cc_final: 0.8013 (m-10) REVERT: G 151 ASN cc_start: 0.7793 (t0) cc_final: 0.7577 (t0) REVERT: G 208 ARG cc_start: 0.6771 (tmt170) cc_final: 0.5529 (ttp80) REVERT: H 67 TYR cc_start: 0.8699 (m-10) cc_final: 0.7980 (m-10) REVERT: H 151 ASN cc_start: 0.7824 (t0) cc_final: 0.7582 (t0) REVERT: H 208 ARG cc_start: 0.6998 (tmt170) cc_final: 0.5734 (ttp80) outliers start: 10 outliers final: 9 residues processed: 212 average time/residue: 0.1273 time to fit residues: 35.4567 Evaluate side-chains 198 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 3.9990 chunk 114 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS B 229 HIS C 275 ASN D 229 HIS E 148 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.148204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119896 restraints weight = 13767.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122769 restraints weight = 8917.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124452 restraints weight = 6835.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125742 restraints weight = 5869.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.126283 restraints weight = 5307.570| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11138 Z= 0.160 Angle : 0.597 8.565 15078 Z= 0.302 Chirality : 0.038 0.209 1696 Planarity : 0.005 0.052 1940 Dihedral : 3.861 19.479 1488 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.74 % Allowed : 13.84 % Favored : 84.42 % 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: 0.91 (0.24), residues: 1344 helix: 1.59 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -2.77 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 159 TYR 0.015 0.001 TYR B 230 PHE 0.015 0.002 PHE B 266 TRP 0.008 0.001 TRP B 116 HIS 0.004 0.001 HIS F 147 Details of bonding type rmsd covalent geometry : bond 0.00383 (11138) covalent geometry : angle 0.59677 (15078) hydrogen bonds : bond 0.05261 ( 667) hydrogen bonds : angle 3.10931 ( 1980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.407 Fit side-chains REVERT: A 164 GLU cc_start: 0.7627 (tm-30) cc_final: 0.6711 (tt0) REVERT: B 164 GLU cc_start: 0.7694 (tm-30) cc_final: 0.6800 (tt0) REVERT: C 114 HIS cc_start: 0.7132 (m-70) cc_final: 0.6832 (t-90) REVERT: C 196 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: C 265 ASP cc_start: 0.7330 (p0) cc_final: 0.7043 (t0) REVERT: E 67 TYR cc_start: 0.8774 (m-10) cc_final: 0.8230 (m-10) REVERT: E 135 MET cc_start: 0.7591 (mmp) cc_final: 0.7298 (mmt) REVERT: F 208 ARG cc_start: 0.6857 (tmt170) cc_final: 0.5377 (ttp80) REVERT: G 208 ARG cc_start: 0.6820 (tmt170) cc_final: 0.5584 (ttp80) REVERT: H 208 ARG cc_start: 0.7057 (tmt170) cc_final: 0.5617 (ttp80) outliers start: 20 outliers final: 15 residues processed: 202 average time/residue: 0.1214 time to fit residues: 32.9191 Evaluate side-chains 192 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Chi-restraints excluded: chain H residue 215 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 23 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 ASN C 275 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.146922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.118438 restraints weight = 13881.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121447 restraints weight = 8861.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123411 restraints weight = 6719.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124405 restraints weight = 5678.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125318 restraints weight = 5163.560| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11138 Z= 0.176 Angle : 0.600 8.246 15078 Z= 0.304 Chirality : 0.039 0.210 1696 Planarity : 0.005 0.049 1940 Dihedral : 3.957 20.464 1488 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.18 % Allowed : 14.88 % Favored : 82.94 % 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: 0.91 (0.24), residues: 1344 helix: 1.57 (0.17), residues: 1028 sheet: None (None), residues: 0 loop : -2.78 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 159 TYR 0.014 0.001 TYR B 230 PHE 0.013 0.002 PHE B 266 TRP 0.008 0.001 TRP B 116 HIS 0.005 0.001 HIS H 147 Details of bonding type rmsd covalent geometry : bond 0.00428 (11138) covalent geometry : angle 0.59990 (15078) hydrogen bonds : bond 0.05253 ( 667) hydrogen bonds : angle 3.12094 ( 1980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.400 Fit side-chains REVERT: A 96 GLU cc_start: 0.6322 (tm-30) cc_final: 0.5967 (tm-30) REVERT: A 164 GLU cc_start: 0.7701 (tm-30) cc_final: 0.6802 (tt0) REVERT: B 164 GLU cc_start: 0.7734 (tm-30) cc_final: 0.6861 (tt0) REVERT: C 144 GLU cc_start: 0.6017 (mt-10) cc_final: 0.5733 (mp0) REVERT: E 135 MET cc_start: 0.7649 (mmp) cc_final: 0.7356 (mmt) REVERT: F 208 ARG cc_start: 0.6937 (tmt170) cc_final: 0.5314 (ttp80) REVERT: G 131 LYS cc_start: 0.7988 (mppt) cc_final: 0.7708 (mppt) REVERT: G 208 ARG cc_start: 0.6905 (tmt170) cc_final: 0.5644 (ttp80) REVERT: H 208 ARG cc_start: 0.6988 (tmt170) cc_final: 0.5583 (ttp80) outliers start: 25 outliers final: 20 residues processed: 202 average time/residue: 0.1258 time to fit residues: 33.9327 Evaluate side-chains 196 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Chi-restraints excluded: chain H residue 215 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 17 optimal weight: 30.0000 chunk 54 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 275 ASN C 275 ASN G 57 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.147093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119014 restraints weight = 13737.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121969 restraints weight = 8894.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123707 restraints weight = 6814.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125090 restraints weight = 5815.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125765 restraints weight = 5231.561| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11138 Z= 0.138 Angle : 0.567 7.953 15078 Z= 0.285 Chirality : 0.037 0.215 1696 Planarity : 0.005 0.049 1940 Dihedral : 3.839 20.209 1488 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.91 % Allowed : 16.10 % Favored : 81.98 % 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: 1.25 (0.24), residues: 1344 helix: 1.80 (0.17), residues: 1028 sheet: None (None), residues: 0 loop : -2.58 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 159 TYR 0.011 0.001 TYR B 230 PHE 0.013 0.001 PHE C 110 TRP 0.008 0.001 TRP F 115 HIS 0.004 0.001 HIS H 147 Details of bonding type rmsd covalent geometry : bond 0.00328 (11138) covalent geometry : angle 0.56740 (15078) hydrogen bonds : bond 0.04603 ( 667) hydrogen bonds : angle 2.97523 ( 1980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7601 (tm-30) cc_final: 0.6751 (tt0) REVERT: B 164 GLU cc_start: 0.7707 (tm-30) cc_final: 0.6868 (tt0) REVERT: C 196 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.7310 (m-80) REVERT: E 67 TYR cc_start: 0.8751 (m-10) cc_final: 0.8226 (m-10) REVERT: E 135 MET cc_start: 0.7624 (mmp) cc_final: 0.7309 (mmt) REVERT: F 208 ARG cc_start: 0.6880 (tmt170) cc_final: 0.5172 (ttp80) REVERT: G 208 ARG cc_start: 0.6857 (tmt170) cc_final: 0.5586 (ttp80) REVERT: H 208 ARG cc_start: 0.6945 (tmt170) cc_final: 0.5440 (ttp80) outliers start: 22 outliers final: 15 residues processed: 189 average time/residue: 0.1147 time to fit residues: 29.8648 Evaluate side-chains 185 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Chi-restraints excluded: chain H residue 215 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 40 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 111 optimal weight: 0.2980 chunk 113 optimal weight: 0.0980 chunk 56 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 ASN G 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123712 restraints weight = 13632.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126792 restraints weight = 8740.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128836 restraints weight = 6648.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.129948 restraints weight = 5612.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130522 restraints weight = 5081.576| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11138 Z= 0.096 Angle : 0.522 9.961 15078 Z= 0.258 Chirality : 0.035 0.218 1696 Planarity : 0.004 0.050 1940 Dihedral : 3.534 18.856 1488 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.13 % Allowed : 17.32 % Favored : 81.55 % 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: 1.83 (0.25), residues: 1344 helix: 2.23 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -2.66 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 159 TYR 0.009 0.001 TYR H 212 PHE 0.014 0.001 PHE C 110 TRP 0.011 0.001 TRP G 115 HIS 0.004 0.001 HIS G 147 Details of bonding type rmsd covalent geometry : bond 0.00209 (11138) covalent geometry : angle 0.52183 (15078) hydrogen bonds : bond 0.03125 ( 667) hydrogen bonds : angle 2.66661 ( 1980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 159 ARG cc_start: 0.7335 (ttm-80) cc_final: 0.6830 (ttm-80) REVERT: A 164 GLU cc_start: 0.7528 (tm-30) cc_final: 0.6753 (tt0) REVERT: A 226 ASP cc_start: 0.7825 (m-30) cc_final: 0.7552 (m-30) REVERT: B 159 ARG cc_start: 0.7342 (ttm-80) cc_final: 0.6809 (ttm-80) REVERT: B 164 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6796 (tt0) REVERT: C 159 ARG cc_start: 0.7289 (ttm-80) cc_final: 0.6829 (ttm-80) REVERT: C 164 GLU cc_start: 0.7296 (tp30) cc_final: 0.6493 (tt0) REVERT: C 196 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: C 216 SER cc_start: 0.8533 (t) cc_final: 0.8221 (m) REVERT: C 226 ASP cc_start: 0.7768 (m-30) cc_final: 0.7497 (m-30) REVERT: D 159 ARG cc_start: 0.7295 (ttm-80) cc_final: 0.6788 (ttm-80) REVERT: D 283 MET cc_start: 0.5367 (mmt) cc_final: 0.5152 (mmt) REVERT: E 67 TYR cc_start: 0.8649 (m-10) cc_final: 0.8194 (m-10) REVERT: E 71 MET cc_start: 0.8215 (tpp) cc_final: 0.7953 (tpt) REVERT: E 135 MET cc_start: 0.7538 (mmp) cc_final: 0.7236 (mmt) REVERT: F 67 TYR cc_start: 0.8626 (m-10) cc_final: 0.8227 (m-10) REVERT: F 208 ARG cc_start: 0.6883 (tmt170) cc_final: 0.5243 (ttp80) REVERT: G 71 MET cc_start: 0.8189 (tpp) cc_final: 0.7957 (tpt) REVERT: G 208 ARG cc_start: 0.6792 (tmt170) cc_final: 0.5615 (ttp80) REVERT: H 67 TYR cc_start: 0.8714 (m-10) cc_final: 0.8281 (m-10) REVERT: H 208 ARG cc_start: 0.6954 (tmt170) cc_final: 0.5669 (ttp80) outliers start: 13 outliers final: 7 residues processed: 189 average time/residue: 0.1072 time to fit residues: 28.2526 Evaluate side-chains 180 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 178 GLU Chi-restraints excluded: chain H residue 215 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 106 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 chunk 95 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 78 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127271 restraints weight = 13369.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.130435 restraints weight = 8471.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.132531 restraints weight = 6390.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.133854 restraints weight = 5351.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134609 restraints weight = 4788.907| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11138 Z= 0.096 Angle : 0.523 8.432 15078 Z= 0.258 Chirality : 0.035 0.209 1696 Planarity : 0.004 0.050 1940 Dihedral : 3.423 18.604 1488 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.96 % Allowed : 17.67 % Favored : 81.38 % 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: 2.21 (0.25), residues: 1344 helix: 2.47 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -2.29 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 159 TYR 0.006 0.001 TYR B 230 PHE 0.016 0.001 PHE C 110 TRP 0.008 0.001 TRP F 115 HIS 0.004 0.001 HIS E 147 Details of bonding type rmsd covalent geometry : bond 0.00210 (11138) covalent geometry : angle 0.52252 (15078) hydrogen bonds : bond 0.03223 ( 667) hydrogen bonds : angle 2.60714 ( 1980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 159 ARG cc_start: 0.7377 (ttm-80) cc_final: 0.6866 (ttm-80) REVERT: A 164 GLU cc_start: 0.7532 (tm-30) cc_final: 0.6840 (tt0) REVERT: B 159 ARG cc_start: 0.7349 (ttm-80) cc_final: 0.6824 (ttm-80) REVERT: B 164 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6789 (tt0) REVERT: C 159 ARG cc_start: 0.7313 (ttm-80) cc_final: 0.6853 (ttm-80) REVERT: C 164 GLU cc_start: 0.7373 (tp30) cc_final: 0.6523 (tt0) REVERT: C 196 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.6830 (m-80) REVERT: C 216 SER cc_start: 0.8520 (t) cc_final: 0.8219 (m) REVERT: D 164 GLU cc_start: 0.7526 (tp30) cc_final: 0.6707 (tt0) REVERT: E 67 TYR cc_start: 0.8623 (m-10) cc_final: 0.8161 (m-10) REVERT: E 71 MET cc_start: 0.8219 (tpp) cc_final: 0.7959 (tpt) REVERT: E 135 MET cc_start: 0.7517 (mmp) cc_final: 0.7202 (mmt) REVERT: F 67 TYR cc_start: 0.8585 (m-10) cc_final: 0.8130 (m-10) REVERT: F 208 ARG cc_start: 0.6834 (tmt170) cc_final: 0.5199 (ttp80) REVERT: G 71 MET cc_start: 0.8250 (tpp) cc_final: 0.8032 (tpt) REVERT: G 208 ARG cc_start: 0.6703 (tmt170) cc_final: 0.5565 (ttp80) REVERT: H 67 TYR cc_start: 0.8703 (m-10) cc_final: 0.8209 (m-10) REVERT: H 71 MET cc_start: 0.8204 (tpp) cc_final: 0.7921 (tpt) REVERT: H 208 ARG cc_start: 0.6913 (tmt170) cc_final: 0.5518 (ttp80) outliers start: 11 outliers final: 8 residues processed: 179 average time/residue: 0.1072 time to fit residues: 26.7654 Evaluate side-chains 177 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Chi-restraints excluded: chain H residue 215 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 99 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122643 restraints weight = 13578.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125778 restraints weight = 8578.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127879 restraints weight = 6463.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.129145 restraints weight = 5410.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.129803 restraints weight = 4857.267| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11138 Z= 0.127 Angle : 0.556 8.041 15078 Z= 0.275 Chirality : 0.037 0.213 1696 Planarity : 0.004 0.050 1940 Dihedral : 3.537 18.599 1488 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.96 % Allowed : 17.58 % Favored : 81.46 % 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: 2.17 (0.25), residues: 1344 helix: 2.47 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -2.09 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 159 TYR 0.011 0.001 TYR B 230 PHE 0.020 0.001 PHE C 110 TRP 0.007 0.001 TRP A 200 HIS 0.004 0.001 HIS F 147 Details of bonding type rmsd covalent geometry : bond 0.00300 (11138) covalent geometry : angle 0.55623 (15078) hydrogen bonds : bond 0.04194 ( 667) hydrogen bonds : angle 2.74060 ( 1980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.6142 (mm-30) cc_final: 0.5707 (mm-30) REVERT: A 164 GLU cc_start: 0.7561 (tm-30) cc_final: 0.6797 (tt0) REVERT: B 164 GLU cc_start: 0.7473 (tm-30) cc_final: 0.6847 (tt0) REVERT: C 164 GLU cc_start: 0.7395 (tp30) cc_final: 0.6503 (tt0) REVERT: C 196 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: D 159 ARG cc_start: 0.7390 (ttm170) cc_final: 0.7118 (ttm-80) REVERT: E 67 TYR cc_start: 0.8709 (m-10) cc_final: 0.8198 (m-10) REVERT: E 135 MET cc_start: 0.7567 (mmp) cc_final: 0.7284 (mmt) REVERT: F 208 ARG cc_start: 0.6786 (tmt170) cc_final: 0.5077 (ttp80) REVERT: G 208 ARG cc_start: 0.6608 (tmt170) cc_final: 0.5415 (ttp80) REVERT: H 208 ARG cc_start: 0.6808 (tmt170) cc_final: 0.5387 (ttp80) outliers start: 11 outliers final: 8 residues processed: 176 average time/residue: 0.1015 time to fit residues: 25.0333 Evaluate side-chains 176 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain C residue 196 TYR Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain H residue 178 GLU Chi-restraints excluded: chain H residue 215 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 94 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 57 optimal weight: 0.0970 chunk 95 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126923 restraints weight = 13445.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130151 restraints weight = 8478.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132295 restraints weight = 6360.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133171 restraints weight = 5315.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.134366 restraints weight = 4850.328| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11138 Z= 0.097 Angle : 0.527 8.506 15078 Z= 0.259 Chirality : 0.035 0.210 1696 Planarity : 0.004 0.049 1940 Dihedral : 3.435 18.528 1488 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.87 % Allowed : 17.84 % Favored : 81.29 % 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: 2.47 (0.25), residues: 1344 helix: 2.65 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -2.16 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 159 TYR 0.006 0.001 TYR B 230 PHE 0.020 0.001 PHE C 110 TRP 0.010 0.001 TRP G 115 HIS 0.004 0.001 HIS E 147 Details of bonding type rmsd covalent geometry : bond 0.00217 (11138) covalent geometry : angle 0.52701 (15078) hydrogen bonds : bond 0.03261 ( 667) hydrogen bonds : angle 2.58724 ( 1980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1595.84 seconds wall clock time: 28 minutes 8.35 seconds (1688.35 seconds total)