Starting phenix.real_space_refine on Tue Oct 27 19:41:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m9a_23721/10_2026/7m9a_23721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m9a_23721/10_2026/7m9a_23721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m9a_23721/10_2026/7m9a_23721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m9a_23721/10_2026/7m9a_23721.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m9a_23721/10_2026/7m9a_23721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m9a_23721/10_2026/7m9a_23721.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7m9a_23721/10_2026/7m9a_23721.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m9a_23721/10_2026/7m9a_23721.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 74 5.49 5 S 96 5.16 5 C 16294 2.51 5 N 4756 2.21 5 O 4919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26139 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "F" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2060 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2054 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2058 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2062 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 247} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "M" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 567 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "N" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 540 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.01, per 1000 atoms: 0.23 Number of scatterers: 26139 At special positions: 0 Unit cell: (144.97, 144.97, 171.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 74 15.00 O 4919 8.00 N 4756 7.00 C 16294 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 943.1 milliseconds 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5784 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 12 sheets defined 63.6% alpha, 6.4% beta 24 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 removed outlier: 3.504A pdb=" N LEU A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 53 Processing helix chain 'A' and resid 65 through 75 removed outlier: 3.537A pdb=" N ASP A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 121 through 136 removed outlier: 3.527A pdb=" N LYS A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 164 removed outlier: 4.237A pdb=" N ASP A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 183 removed outlier: 3.513A pdb=" N ASP A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 200 through 216 Processing helix chain 'A' and resid 226 through 238 removed outlier: 3.893A pdb=" N ILE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 259 Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.564A pdb=" N ALA A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 29 Processing helix chain 'B' and resid 36 through 53 Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.569A pdb=" N TYR B 75 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 121 through 136 Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 150 through 151 No H-bonds generated for 'chain 'B' and resid 150 through 151' Processing helix chain 'B' and resid 152 through 164 removed outlier: 4.130A pdb=" N ASP B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 removed outlier: 3.802A pdb=" N ASP B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 3.878A pdb=" N LEU B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 188' Processing helix chain 'B' and resid 200 through 215 removed outlier: 3.532A pdb=" N PHE B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 238 removed outlier: 4.779A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 258 Processing helix chain 'B' and resid 264 through 275 removed outlier: 3.961A pdb=" N LEU B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 29 Processing helix chain 'C' and resid 36 through 53 Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.741A pdb=" N HIS C 77 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.616A pdb=" N LEU C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 136 Processing helix chain 'C' and resid 146 through 149 Processing helix chain 'C' and resid 150 through 164 removed outlier: 3.980A pdb=" N ALA C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 removed outlier: 3.979A pdb=" N ALA C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.562A pdb=" N LEU C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE C 190 " --> pdb=" O VAL C 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 190' Processing helix chain 'C' and resid 200 through 215 Processing helix chain 'C' and resid 226 through 238 Processing helix chain 'C' and resid 240 through 259 removed outlier: 4.035A pdb=" N GLU C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 247 " --> pdb=" O ARG C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 275 Processing helix chain 'D' and resid 20 through 30 removed outlier: 3.614A pdb=" N GLU D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 53 Processing helix chain 'D' and resid 65 through 78 removed outlier: 3.517A pdb=" N HIS D 77 " --> pdb=" O TYR D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 121 through 137 Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 173 through 181 removed outlier: 3.580A pdb=" N ASP D 177 " --> pdb=" O THR D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 Processing helix chain 'D' and resid 200 through 215 Processing helix chain 'D' and resid 226 through 238 removed outlier: 3.729A pdb=" N ARG D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 258 Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'E' and resid 20 through 29 Processing helix chain 'E' and resid 36 through 53 Processing helix chain 'E' and resid 65 through 77 removed outlier: 3.710A pdb=" N HIS E 77 " --> pdb=" O TYR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 121 through 136 removed outlier: 3.866A pdb=" N CYS E 136 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 149 Processing helix chain 'E' and resid 153 through 164 removed outlier: 3.530A pdb=" N VAL E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 removed outlier: 3.740A pdb=" N ALA E 178 " --> pdb=" O ASP E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 Processing helix chain 'E' and resid 200 through 215 Processing helix chain 'E' and resid 226 through 238 removed outlier: 4.454A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 258 Processing helix chain 'E' and resid 264 through 275 Processing helix chain 'F' and resid 20 through 29 removed outlier: 3.934A pdb=" N LEU F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS F 29 " --> pdb=" O ILE F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 53 removed outlier: 3.555A pdb=" N ASP F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 77 removed outlier: 3.690A pdb=" N HIS F 77 " --> pdb=" O TYR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 121 through 136 removed outlier: 3.509A pdb=" N ASP F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR F 129 " --> pdb=" O PHE F 125 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS F 136 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 164 removed outlier: 3.865A pdb=" N ALA F 155 " --> pdb=" O PRO F 151 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 182 removed outlier: 3.740A pdb=" N ASP F 177 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 201 through 215 Processing helix chain 'F' and resid 226 through 238 Processing helix chain 'F' and resid 240 through 257 Processing helix chain 'F' and resid 264 through 275 Processing helix chain 'G' and resid 20 through 29 Processing helix chain 'G' and resid 36 through 53 Processing helix chain 'G' and resid 65 through 77 removed outlier: 3.551A pdb=" N ARG G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS G 77 " --> pdb=" O TYR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 121 through 136 removed outlier: 3.535A pdb=" N CYS G 136 " --> pdb=" O VAL G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 174 through 183 removed outlier: 3.955A pdb=" N ALA G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL G 179 " --> pdb=" O ARG G 175 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP G 183 " --> pdb=" O VAL G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 190 Processing helix chain 'G' and resid 200 through 215 Processing helix chain 'G' and resid 226 through 238 removed outlier: 3.904A pdb=" N ARG G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 258 Processing helix chain 'G' and resid 264 through 275 removed outlier: 3.907A pdb=" N GLN G 269 " --> pdb=" O LYS G 265 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU G 270 " --> pdb=" O ALA G 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL G 271 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 272 " --> pdb=" O LEU G 268 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS G 273 " --> pdb=" O GLN G 269 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU G 274 " --> pdb=" O GLU G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 30 removed outlier: 3.515A pdb=" N GLU H 24 " --> pdb=" O TRP H 20 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 53 removed outlier: 3.822A pdb=" N GLY H 48 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS H 49 " --> pdb=" O TRP H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 77 removed outlier: 3.685A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS H 77 " --> pdb=" O TYR H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 121 through 136 removed outlier: 3.520A pdb=" N CYS H 136 " --> pdb=" O VAL H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 165 removed outlier: 3.553A pdb=" N GLY H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 183 removed outlier: 3.673A pdb=" N ALA H 178 " --> pdb=" O ASP H 174 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP H 183 " --> pdb=" O VAL H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 Processing helix chain 'H' and resid 200 through 215 Processing helix chain 'H' and resid 226 through 238 removed outlier: 3.756A pdb=" N ARG H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 259 removed outlier: 4.186A pdb=" N LEU H 256 " --> pdb=" O ALA H 252 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER H 257 " --> pdb=" O ILE H 253 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 275 removed outlier: 3.553A pdb=" N VAL H 271 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS H 273 " --> pdb=" O GLN H 269 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 30 Processing helix chain 'I' and resid 36 through 53 Processing helix chain 'I' and resid 65 through 77 removed outlier: 4.099A pdb=" N HIS I 77 " --> pdb=" O TYR I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 113 Processing helix chain 'I' and resid 121 through 136 Processing helix chain 'I' and resid 145 through 149 Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 173 through 181 removed outlier: 3.761A pdb=" N ASP I 177 " --> pdb=" O THR I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 190 Processing helix chain 'I' and resid 200 through 215 removed outlier: 3.657A pdb=" N GLN I 213 " --> pdb=" O GLU I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 238 removed outlier: 3.505A pdb=" N ILE I 232 " --> pdb=" O GLU I 228 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER I 235 " --> pdb=" O ARG I 231 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA I 236 " --> pdb=" O ILE I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 258 Processing helix chain 'I' and resid 264 through 275 Processing helix chain 'J' and resid 20 through 30 Processing helix chain 'J' and resid 36 through 53 Processing helix chain 'J' and resid 65 through 77 Processing helix chain 'J' and resid 101 through 113 removed outlier: 3.535A pdb=" N LEU J 113 " --> pdb=" O ILE J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 136 Processing helix chain 'J' and resid 145 through 149 Processing helix chain 'J' and resid 150 through 164 removed outlier: 3.867A pdb=" N PHE J 154 " --> pdb=" O LYS J 150 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA J 155 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP J 156 " --> pdb=" O GLU J 152 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP J 159 " --> pdb=" O ALA J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 181 removed outlier: 4.177A pdb=" N ASP J 177 " --> pdb=" O THR J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 Processing helix chain 'J' and resid 200 through 215 Processing helix chain 'J' and resid 226 through 238 removed outlier: 3.555A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 258 Processing helix chain 'J' and resid 264 through 273 removed outlier: 3.654A pdb=" N ALA J 272 " --> pdb=" O LEU J 268 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS J 273 " --> pdb=" O GLN J 269 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 29 Processing helix chain 'K' and resid 36 through 53 Processing helix chain 'K' and resid 65 through 77 removed outlier: 3.709A pdb=" N ARG K 74 " --> pdb=" O CYS K 70 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS K 77 " --> pdb=" O TYR K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 113 removed outlier: 3.585A pdb=" N LEU K 113 " --> pdb=" O ILE K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 136 Processing helix chain 'K' and resid 145 through 149 Processing helix chain 'K' and resid 152 through 164 removed outlier: 4.444A pdb=" N ASP K 156 " --> pdb=" O GLU K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 181 removed outlier: 3.684A pdb=" N ASP K 177 " --> pdb=" O THR K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 190 Processing helix chain 'K' and resid 200 through 216 Processing helix chain 'K' and resid 226 through 238 Processing helix chain 'K' and resid 240 through 258 removed outlier: 4.372A pdb=" N GLU K 246 " --> pdb=" O GLY K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 275 removed outlier: 3.640A pdb=" N TYR K 275 " --> pdb=" O VAL K 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 30 Processing helix chain 'L' and resid 36 through 53 Processing helix chain 'L' and resid 65 through 77 removed outlier: 3.613A pdb=" N ARG L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS L 77 " --> pdb=" O TYR L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 113 Processing helix chain 'L' and resid 121 through 136 Processing helix chain 'L' and resid 145 through 149 Processing helix chain 'L' and resid 150 through 164 Processing helix chain 'L' and resid 175 through 181 Processing helix chain 'L' and resid 183 through 190 Processing helix chain 'L' and resid 201 through 215 Processing helix chain 'L' and resid 226 through 238 removed outlier: 4.376A pdb=" N ILE L 232 " --> pdb=" O GLU L 228 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU L 233 " --> pdb=" O MET L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 258 Processing helix chain 'L' and resid 264 through 275 removed outlier: 3.646A pdb=" N VAL L 271 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA L 272 " --> pdb=" O LEU L 268 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS L 273 " --> pdb=" O GLN L 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.311A pdb=" N VAL A 92 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.437A pdb=" N VAL B 92 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N CYS B 56 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLY B 172 " --> pdb=" O CYS B 56 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL B 58 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.671A pdb=" N VAL C 92 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASP C 144 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE C 94 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 141 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL C 171 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 143 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 170 " --> pdb=" O CYS C 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.315A pdb=" N VAL D 92 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP D 144 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE D 94 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU D 141 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL D 171 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE D 143 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N CYS D 56 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N GLY D 172 " --> pdb=" O CYS D 56 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL D 58 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.458A pdb=" N VAL E 92 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASP E 144 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE E 94 " --> pdb=" O ASP E 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.434A pdb=" N VAL F 92 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU F 141 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL F 171 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE F 143 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG F 57 " --> pdb=" O LEU F 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.498A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU G 141 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL G 171 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE G 143 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ARG G 57 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 91 through 94 removed outlier: 6.687A pdb=" N VAL H 92 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASP H 144 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE H 94 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 91 through 94 removed outlier: 6.453A pdb=" N VAL I 92 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N CYS I 56 " --> pdb=" O LEU I 170 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLY I 172 " --> pdb=" O CYS I 56 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL I 58 " --> pdb=" O GLY I 172 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU I 194 " --> pdb=" O ARG I 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 91 through 94 removed outlier: 6.425A pdb=" N VAL J 92 " --> pdb=" O ILE J 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 91 through 94 removed outlier: 6.608A pdb=" N VAL K 92 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU K 141 " --> pdb=" O VAL K 169 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL K 171 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE K 143 " --> pdb=" O VAL K 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 91 through 94 removed outlier: 6.286A pdb=" N VAL L 92 " --> pdb=" O ILE L 142 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU L 141 " --> pdb=" O VAL L 169 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL L 171 " --> pdb=" O LEU L 141 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE L 143 " --> pdb=" O VAL L 171 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N CYS L 56 " --> pdb=" O LEU L 170 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N GLY L 172 " --> pdb=" O CYS L 56 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL L 58 " --> pdb=" O GLY L 172 " (cutoff:3.500A) 1307 hydrogen bonds defined for protein. 3861 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7507 1.34 - 1.45: 3784 1.45 - 1.57: 15093 1.57 - 1.69: 136 1.69 - 1.81: 144 Bond restraints: 26664 Sorted by residual: bond pdb=" N PRO K 90 " pdb=" CD PRO K 90 " ideal model delta sigma weight residual 1.473 1.554 -0.081 1.40e-02 5.10e+03 3.38e+01 bond pdb=" C3' DA M 21 " pdb=" C2' DA M 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT N 25 " pdb=" C2' DT N 25 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DT N 9 " pdb=" C2' DT N 9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.84e+00 bond pdb=" C3' DT N 3 " pdb=" C2' DT N 3 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.81e+00 ... (remaining 26659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.41: 36070 5.41 - 10.82: 50 10.82 - 16.23: 4 16.23 - 21.65: 3 21.65 - 27.06: 2 Bond angle restraints: 36129 Sorted by residual: angle pdb=" N ASP C 174 " pdb=" CA ASP C 174 " pdb=" C ASP C 174 " ideal model delta sigma weight residual 114.75 98.32 16.43 1.26e+00 6.30e-01 1.70e+02 angle pdb=" N ARG C 85 " pdb=" CA ARG C 85 " pdb=" C ARG C 85 " ideal model delta sigma weight residual 109.81 136.87 -27.06 2.21e+00 2.05e-01 1.50e+02 angle pdb=" N THR C 173 " pdb=" CA THR C 173 " pdb=" C THR C 173 " ideal model delta sigma weight residual 110.56 132.86 -22.30 1.94e+00 2.66e-01 1.32e+02 angle pdb=" N LYS C 217 " pdb=" CA LYS C 217 " pdb=" C LYS C 217 " ideal model delta sigma weight residual 109.96 92.97 16.99 1.49e+00 4.50e-01 1.30e+02 angle pdb=" N ARG C 85 " pdb=" CA ARG C 85 " pdb=" CB ARG C 85 " ideal model delta sigma weight residual 110.37 92.04 18.33 1.78e+00 3.16e-01 1.06e+02 ... (remaining 36124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 15972 35.09 - 70.17: 434 70.17 - 105.26: 13 105.26 - 140.34: 9 140.34 - 175.43: 6 Dihedral angle restraints: 16434 sinusoidal: 7494 harmonic: 8940 Sorted by residual: dihedral pdb=" O2A ADP L 301 " pdb=" O3A ADP L 301 " pdb=" PA ADP L 301 " pdb=" PB ADP L 301 " ideal model delta sinusoidal sigma weight residual -60.00 115.43 -175.43 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP J 301 " pdb=" O3A ADP J 301 " pdb=" PA ADP J 301 " pdb=" PB ADP J 301 " ideal model delta sinusoidal sigma weight residual 300.00 128.25 171.75 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP K 301 " pdb=" O3A ADP K 301 " pdb=" PB ADP K 301 " pdb=" PA ADP K 301 " ideal model delta sinusoidal sigma weight residual -60.00 101.86 -161.86 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 16431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 4056 0.160 - 0.319: 13 0.319 - 0.479: 1 0.479 - 0.638: 1 0.638 - 0.798: 1 Chirality restraints: 4072 Sorted by residual: chirality pdb=" CA THR C 173 " pdb=" N THR C 173 " pdb=" C THR C 173 " pdb=" CB THR C 173 " both_signs ideal model delta sigma weight residual False 2.53 1.73 0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" CA ARG C 85 " pdb=" N ARG C 85 " pdb=" C ARG C 85 " pdb=" CB ARG C 85 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.02e+00 chirality pdb=" CA GLN C 81 " pdb=" N GLN C 81 " pdb=" C GLN C 81 " pdb=" CB GLN C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 4069 not shown) Planarity restraints: 4356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 85 " -0.044 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO C 86 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 86 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 86 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 85 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO D 86 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 86 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 86 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 85 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO H 86 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 86 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 86 " 0.024 5.00e-02 4.00e+02 ... (remaining 4353 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 6 2.08 - 2.79: 5324 2.79 - 3.49: 35087 3.49 - 4.20: 57982 4.20 - 4.90: 102352 Nonbonded interactions: 200751 Sorted by model distance: nonbonded pdb=" OE2 GLU A 212 " pdb=" OG SER A 222 " model vdw 1.381 3.040 nonbonded pdb=" OE1 GLU C 212 " pdb=" CB LEU C 224 " model vdw 1.821 3.440 nonbonded pdb=" NE ARG F 53 " pdb=" OE2 GLU F 139 " model vdw 2.046 3.120 nonbonded pdb=" O VAL K 89 " pdb=" N VAL K 138 " model vdw 2.059 3.120 nonbonded pdb=" OE1 GLU E 61 " pdb=" OH TYR E 240 " model vdw 2.063 3.040 ... (remaining 200746 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'B' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'C' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'D' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'E' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'F' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 118 or (resid 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 216 or (resid 217 and (name N or name CA or name C or name O or name \ CB )) or resid 218 through 224 or (resid 225 and (name N or name CA or name C or \ name O or name CB )) or resid 226 through 275)) selection = (chain 'G' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'H' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 211 or ( \ resid 212 and (name N or name CA or name C or name O or name CB )) or resid 213 \ through 275)) selection = (chain 'I' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) selection = (chain 'J' and (resid 19 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 118 or (resid 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 216 o \ r (resid 217 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 18 through 224 or (resid 225 and (name N or name CA or name C or name O or name \ CB )) or resid 226 through 275)) selection = (chain 'K' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 118 or (resid 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 211 o \ r (resid 212 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 13 through 216 or (resid 217 and (name N or name CA or name C or name O or name \ CB )) or resid 218 through 224 or (resid 225 and (name N or name CA or name C or \ name O or name CB )) or resid 226 through 275)) selection = (chain 'L' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 75 or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or resid 77 through 80 or (resid 81 and ( \ name N or name CA or name C or name O or name CB )) or resid 82 through 118 or ( \ resid 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ through 211 or (resid 212 and (name N or name CA or name C or name O or name CB \ )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C or na \ me O or name CB )) or resid 218 through 224 or (resid 225 and (name N or name CA \ or name C or name O or name CB )) or resid 226 through 275)) } 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 25.340 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 26665 Z= 0.210 Angle : 0.677 27.056 36129 Z= 0.428 Chirality : 0.045 0.798 4072 Planarity : 0.004 0.066 4356 Dihedral : 15.027 175.428 10650 Min Nonbonded Distance : 1.381 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 0.11 % Allowed : 3.69 % Favored : 96.20 % Cbeta Deviations : 0.14 % 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: 0.14 (0.14), residues: 3060 helix: 0.25 (0.11), residues: 1810 sheet: 0.73 (0.36), residues: 204 loop : -0.05 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 243 TYR 0.011 0.001 TYR J 93 PHE 0.008 0.001 PHE G 196 TRP 0.015 0.001 TRP K 20 HIS 0.005 0.001 HIS K 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.21 (26664) covalent geometry : angle 0.67711 / 0.43 (36129) hydrogen bonds : bond 0.15822 / 10.29 ( 1355) hydrogen bonds : angle 6.09391 / 4.44 ( 3957) Misc. bond : bond 0.00167 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 913 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.0946 (ttt) cc_final: 0.0699 (tpp) REVERT: B 25 ILE cc_start: 0.5586 (mm) cc_final: 0.5237 (pt) REVERT: B 55 SER cc_start: 0.8339 (m) cc_final: 0.8068 (p) REVERT: B 67 THR cc_start: 0.5079 (m) cc_final: 0.4373 (m) REVERT: B 100 CYS cc_start: 0.7608 (t) cc_final: 0.7241 (t) REVERT: B 171 VAL cc_start: 0.8377 (t) cc_final: 0.8144 (p) REVERT: C 55 SER cc_start: 0.9379 (m) cc_final: 0.8967 (t) REVERT: C 156 ASP cc_start: 0.8016 (m-30) cc_final: 0.7787 (m-30) REVERT: C 159 ASP cc_start: 0.7625 (m-30) cc_final: 0.7161 (m-30) REVERT: C 163 ASP cc_start: 0.7943 (m-30) cc_final: 0.7677 (m-30) REVERT: D 85 ARG cc_start: 0.5851 (ttp-110) cc_final: 0.4836 (ptt180) REVERT: D 123 SER cc_start: 0.8602 (m) cc_final: 0.8252 (p) REVERT: E 114 LYS cc_start: 0.8723 (mttt) cc_final: 0.8336 (mmtt) REVERT: E 153 THR cc_start: 0.8754 (p) cc_final: 0.8374 (t) REVERT: E 204 PHE cc_start: 0.8867 (t80) cc_final: 0.8656 (t80) REVERT: E 205 LYS cc_start: 0.7412 (mtmt) cc_final: 0.6622 (ptmm) REVERT: E 268 LEU cc_start: 0.8931 (tp) cc_final: 0.8456 (tp) REVERT: F 104 ASP cc_start: 0.7730 (m-30) cc_final: 0.7191 (t70) REVERT: F 157 VAL cc_start: 0.9137 (t) cc_final: 0.8831 (p) REVERT: F 207 THR cc_start: 0.8420 (m) cc_final: 0.8010 (p) REVERT: F 211 TRP cc_start: 0.7363 (m100) cc_final: 0.6930 (m100) REVERT: F 275 TYR cc_start: 0.2682 (t80) cc_final: 0.1720 (t80) REVERT: G 75 TYR cc_start: 0.6351 (m-10) cc_final: 0.5951 (m-10) REVERT: G 88 THR cc_start: 0.6973 (m) cc_final: 0.6334 (t) REVERT: G 142 ILE cc_start: 0.8844 (mm) cc_final: 0.8435 (mm) REVERT: H 104 ASP cc_start: 0.7941 (m-30) cc_final: 0.7323 (t0) REVERT: H 271 VAL cc_start: 0.8111 (t) cc_final: 0.7685 (t) REVERT: I 59 VAL cc_start: 0.8845 (t) cc_final: 0.8612 (m) REVERT: I 210 MET cc_start: 0.8123 (ttp) cc_final: 0.7779 (ttm) REVERT: J 139 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7649 (mt-10) REVERT: K 99 LYS cc_start: 0.8485 (mttt) cc_final: 0.8196 (tppt) REVERT: K 114 LYS cc_start: 0.8338 (mttt) cc_final: 0.8122 (mmtt) REVERT: K 156 ASP cc_start: 0.6588 (m-30) cc_final: 0.6197 (m-30) REVERT: K 176 LEU cc_start: 0.8222 (tp) cc_final: 0.7889 (tp) REVERT: L 38 GLN cc_start: 0.7186 (mm-40) cc_final: 0.6743 (pt0) REVERT: L 41 THR cc_start: 0.5684 (m) cc_final: 0.4986 (m) REVERT: L 42 LEU cc_start: 0.6904 (tp) cc_final: 0.6448 (tp) REVERT: L 99 LYS cc_start: 0.7243 (mttt) cc_final: 0.7009 (ttmm) REVERT: L 153 THR cc_start: 0.6974 (m) cc_final: 0.6759 (m) REVERT: L 229 MET cc_start: 0.3616 (mtt) cc_final: 0.2618 (mmp) REVERT: L 274 GLU cc_start: 0.4948 (tt0) cc_final: 0.4644 (tp30) outliers start: 3 outliers final: 0 residues processed: 916 average time/residue: 0.2154 time to fit residues: 286.3955 Evaluate side-chains 406 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN C 77 HIS ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 GLN D 269 GLN E 213 GLN F 223 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 ASN K 185 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.172265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140571 restraints weight = 41888.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.140709 restraints weight = 74107.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.142303 restraints weight = 58198.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.142613 restraints weight = 35486.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.145739 restraints weight = 29357.775| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26665 Z= 0.163 Angle : 0.708 9.723 36129 Z= 0.355 Chirality : 0.043 0.238 4072 Planarity : 0.005 0.072 4356 Dihedral : 16.124 174.910 4195 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.99 % Favored : 97.94 % Rotamer: Outliers : 2.87 % Allowed : 10.93 % Favored : 86.20 % 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: 1.22 (0.15), residues: 3060 helix: 1.05 (0.12), residues: 1851 sheet: 1.45 (0.30), residues: 292 loop : 0.31 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 189 TYR 0.028 0.002 TYR G 73 PHE 0.019 0.002 PHE F 204 TRP 0.020 0.002 TRP J 45 HIS 0.006 0.001 HIS D 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (26664) covalent geometry : angle 0.70760 / 0.36 (36129) hydrogen bonds : bond 0.06105 / 4.15 ( 1355) hydrogen bonds : angle 4.76793 / 3.46 ( 3957) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 454 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.2988 (mmp-170) cc_final: 0.2275 (mmp-170) REVERT: A 210 MET cc_start: 0.1447 (ttt) cc_final: 0.1078 (tpp) REVERT: A 245 ASP cc_start: 0.3298 (m-30) cc_final: 0.2829 (m-30) REVERT: B 38 GLN cc_start: 0.6863 (tp40) cc_final: 0.6208 (mm-40) REVERT: C 55 SER cc_start: 0.9350 (m) cc_final: 0.9060 (t) REVERT: C 85 ARG cc_start: 0.5431 (OUTLIER) cc_final: 0.5115 (ptt90) REVERT: C 159 ASP cc_start: 0.7125 (m-30) cc_final: 0.6731 (m-30) REVERT: D 273 LYS cc_start: 0.8373 (mttt) cc_final: 0.8129 (mtmm) REVERT: E 114 LYS cc_start: 0.8569 (mttt) cc_final: 0.8337 (mmtt) REVERT: F 78 LYS cc_start: 0.7907 (mttp) cc_final: 0.7420 (mmmt) REVERT: F 244 LEU cc_start: 0.9161 (tp) cc_final: 0.8815 (tp) REVERT: G 70 CYS cc_start: 0.6883 (t) cc_final: 0.5805 (t) REVERT: G 71 ASP cc_start: 0.5719 (t0) cc_final: 0.4182 (t0) REVERT: G 75 TYR cc_start: 0.6261 (m-10) cc_final: 0.5897 (m-10) REVERT: G 77 HIS cc_start: 0.6551 (m-70) cc_final: 0.6303 (m-70) REVERT: I 59 VAL cc_start: 0.8716 (t) cc_final: 0.8330 (m) REVERT: K 73 TYR cc_start: 0.8913 (t80) cc_final: 0.8608 (t80) REVERT: K 176 LEU cc_start: 0.8161 (tp) cc_final: 0.7753 (tp) REVERT: L 24 GLU cc_start: 0.4319 (tp30) cc_final: 0.4092 (tp30) REVERT: L 38 GLN cc_start: 0.7089 (mm-40) cc_final: 0.6688 (pt0) REVERT: L 104 ASP cc_start: 0.7884 (m-30) cc_final: 0.6711 (t0) REVERT: L 224 LEU cc_start: 0.4977 (mt) cc_final: 0.4640 (pt) outliers start: 77 outliers final: 47 residues processed: 509 average time/residue: 0.1850 time to fit residues: 143.0708 Evaluate side-chains 388 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 340 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 CYS Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 157 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [259, 92, 269, 4, 224, 157, 190, 71, 117, 155, 110] chunk 259 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 224 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 97 HIS ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN E 213 GLN H 185 GLN J 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.167797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136702 restraints weight = 42039.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.138707 restraints weight = 79236.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.138904 restraints weight = 52347.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.139679 restraints weight = 33938.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141341 restraints weight = 26883.230| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26665 Z= 0.180 Angle : 0.674 14.626 36129 Z= 0.339 Chirality : 0.043 0.189 4072 Planarity : 0.005 0.064 4356 Dihedral : 16.163 176.895 4195 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.35 % Favored : 97.58 % Rotamer: Outliers : 3.51 % Allowed : 13.02 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.15), residues: 3060 helix: 1.29 (0.12), residues: 1796 sheet: 1.12 (0.37), residues: 202 loop : 0.19 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 85 TYR 0.019 0.001 TYR G 73 PHE 0.027 0.002 PHE J 204 TRP 0.036 0.002 TRP L 211 HIS 0.005 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (26664) covalent geometry : angle 0.67427 / 0.34 (36129) hydrogen bonds : bond 0.05754 / 3.92 ( 1355) hydrogen bonds : angle 4.53168 / 3.28 ( 3957) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 375 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.3275 (mmp-170) cc_final: 0.2623 (mmp-170) REVERT: A 141 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7011 (tp) REVERT: A 210 MET cc_start: 0.1503 (ttt) cc_final: 0.1031 (tpp) REVERT: A 245 ASP cc_start: 0.3428 (m-30) cc_final: 0.2914 (m-30) REVERT: B 38 GLN cc_start: 0.6853 (tp40) cc_final: 0.6428 (mm-40) REVERT: B 152 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6734 (tm-30) REVERT: C 55 SER cc_start: 0.9358 (m) cc_final: 0.9094 (t) REVERT: D 116 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.8001 (ttm110) REVERT: D 256 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8667 (mp) REVERT: D 273 LYS cc_start: 0.8515 (mttt) cc_final: 0.8212 (mtmm) REVERT: F 78 LYS cc_start: 0.7811 (mttp) cc_final: 0.7379 (mmmt) REVERT: F 207 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7791 (p) REVERT: F 210 MET cc_start: 0.7458 (tpp) cc_final: 0.6992 (tpp) REVERT: F 244 LEU cc_start: 0.9139 (tp) cc_final: 0.8898 (tp) REVERT: G 175 ARG cc_start: 0.7726 (mmm-85) cc_final: 0.7225 (tpp80) REVERT: I 59 VAL cc_start: 0.8741 (t) cc_final: 0.8230 (m) REVERT: I 229 MET cc_start: 0.6454 (mmp) cc_final: 0.6100 (mmp) REVERT: I 275 TYR cc_start: 0.7334 (m-10) cc_final: 0.6813 (m-80) REVERT: K 73 TYR cc_start: 0.8994 (t80) cc_final: 0.8736 (t80) REVERT: K 176 LEU cc_start: 0.8289 (tp) cc_final: 0.7777 (tp) REVERT: L 38 GLN cc_start: 0.7169 (mm-40) cc_final: 0.6713 (pt0) REVERT: L 104 ASP cc_start: 0.7943 (m-30) cc_final: 0.6983 (t0) outliers start: 94 outliers final: 63 residues processed: 448 average time/residue: 0.1687 time to fit residues: 119.4740 Evaluate side-chains 392 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 325 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain H residue 56 CYS Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 157 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [141, 186, 134, 47, 227, 195, 14, 161, 228, 32, 197] chunk 141 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 228 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN H 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.166037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134253 restraints weight = 41852.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.135735 restraints weight = 83424.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.136724 restraints weight = 55824.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.137220 restraints weight = 35995.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138802 restraints weight = 28356.072| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26665 Z= 0.180 Angle : 0.654 12.882 36129 Z= 0.328 Chirality : 0.043 0.187 4072 Planarity : 0.004 0.061 4356 Dihedral : 16.092 176.951 4195 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.25 % Favored : 97.68 % Rotamer: Outliers : 3.62 % Allowed : 14.36 % Favored : 82.02 % 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: 1.35 (0.15), residues: 3060 helix: 1.44 (0.12), residues: 1786 sheet: 0.91 (0.36), residues: 204 loop : 0.08 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 50 TYR 0.024 0.002 TYR G 93 PHE 0.018 0.002 PHE F 204 TRP 0.038 0.002 TRP L 211 HIS 0.004 0.001 HIS D 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (26664) covalent geometry : angle 0.65403 / 0.33 (36129) hydrogen bonds : bond 0.05430 / 3.70 ( 1355) hydrogen bonds : angle 4.40806 / 3.18 ( 3957) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 349 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.6939 (m90) cc_final: 0.6457 (m-70) REVERT: A 210 MET cc_start: 0.1737 (ttt) cc_final: 0.1094 (tpp) REVERT: A 245 ASP cc_start: 0.3401 (m-30) cc_final: 0.2872 (m-30) REVERT: B 152 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6721 (tm-30) REVERT: B 248 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7257 (mp) REVERT: C 85 ARG cc_start: 0.5415 (OUTLIER) cc_final: 0.5203 (ptt90) REVERT: C 257 SER cc_start: 0.8004 (p) cc_final: 0.7460 (t) REVERT: D 81 GLN cc_start: 0.7067 (pt0) cc_final: 0.6847 (pp30) REVERT: D 116 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8035 (ttm110) REVERT: D 256 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8698 (mp) REVERT: D 273 LYS cc_start: 0.8599 (mttt) cc_final: 0.8271 (mtmm) REVERT: E 61 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7127 (mm-30) REVERT: F 78 LYS cc_start: 0.7825 (mttp) cc_final: 0.7296 (mmmt) REVERT: G 175 ARG cc_start: 0.7708 (mmm-85) cc_final: 0.7224 (tpp80) REVERT: G 210 MET cc_start: 0.7565 (mpp) cc_final: 0.7070 (mpp) REVERT: G 214 MET cc_start: 0.5071 (mmp) cc_final: 0.3949 (tpt) REVERT: I 119 LYS cc_start: 0.8410 (mmtm) cc_final: 0.8172 (mmtm) REVERT: I 226 SER cc_start: 0.7278 (OUTLIER) cc_final: 0.6451 (m) REVERT: I 229 MET cc_start: 0.6429 (mmp) cc_final: 0.5961 (mmp) REVERT: I 233 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8437 (tp) REVERT: K 73 TYR cc_start: 0.9060 (t80) cc_final: 0.8812 (t80) REVERT: K 176 LEU cc_start: 0.8279 (tp) cc_final: 0.7767 (tp) REVERT: L 38 GLN cc_start: 0.7329 (mm-40) cc_final: 0.6733 (pt0) REVERT: L 104 ASP cc_start: 0.7931 (m-30) cc_final: 0.7202 (t0) outliers start: 97 outliers final: 69 residues processed: 432 average time/residue: 0.1696 time to fit residues: 116.0477 Evaluate side-chains 384 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 308 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain G residue 56 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain H residue 56 CYS Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 180 ILE Chi-restraints excluded: chain L residue 267 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [150, 269, 217, 219, 145, 181, 53, 195, 295, 125, 210] chunk 150 optimal weight: 10.0000 chunk 269 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 219 optimal weight: 0.0970 chunk 145 optimal weight: 9.9990 chunk 181 optimal weight: 0.0050 chunk 53 optimal weight: 7.9990 chunk 195 optimal weight: 7.9990 chunk 295 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 210 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.167545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.136220 restraints weight = 41403.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.137086 restraints weight = 79416.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138515 restraints weight = 56487.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.138858 restraints weight = 35161.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.140167 restraints weight = 28610.821| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26665 Z= 0.123 Angle : 0.614 10.845 36129 Z= 0.305 Chirality : 0.041 0.194 4072 Planarity : 0.004 0.057 4356 Dihedral : 15.921 176.045 4195 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.55 % Rotamer: Outliers : 2.80 % Allowed : 15.93 % Favored : 81.28 % 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: 1.59 (0.15), residues: 3060 helix: 1.60 (0.12), residues: 1853 sheet: 1.09 (0.36), residues: 202 loop : 0.14 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 254 TYR 0.019 0.001 TYR G 112 PHE 0.021 0.001 PHE F 204 TRP 0.027 0.001 TRP L 211 HIS 0.002 0.000 HIS D 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (26664) covalent geometry : angle 0.61407 / 0.31 (36129) hydrogen bonds : bond 0.04830 / 3.33 ( 1355) hydrogen bonds : angle 4.22985 / 3.07 ( 3957) Misc. bond : bond 0.00111 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 338 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.6838 (m90) cc_final: 0.6412 (m-70) REVERT: A 63 ARG cc_start: 0.3405 (mmp-170) cc_final: 0.2862 (mmp-170) REVERT: A 210 MET cc_start: 0.1743 (ttt) cc_final: 0.1134 (tpp) REVERT: A 245 ASP cc_start: 0.3395 (m-30) cc_final: 0.2845 (m-30) REVERT: B 104 ASP cc_start: 0.7160 (t70) cc_final: 0.6867 (t0) REVERT: B 152 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7005 (tm-30) REVERT: B 248 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7243 (mp) REVERT: C 85 ARG cc_start: 0.5151 (OUTLIER) cc_final: 0.4778 (ptt90) REVERT: C 175 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7720 (ttm110) REVERT: C 257 SER cc_start: 0.7987 (p) cc_final: 0.7441 (t) REVERT: D 116 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.8178 (ttm110) REVERT: D 273 LYS cc_start: 0.8593 (mttt) cc_final: 0.8246 (mtmm) REVERT: E 61 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7127 (mm-30) REVERT: F 78 LYS cc_start: 0.7796 (mttp) cc_final: 0.7325 (mmmt) REVERT: G 140 MET cc_start: 0.8198 (tpp) cc_final: 0.7846 (mpp) REVERT: G 175 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.7392 (tpp80) REVERT: G 210 MET cc_start: 0.7248 (mpp) cc_final: 0.6957 (mpp) REVERT: G 214 MET cc_start: 0.5185 (mmp) cc_final: 0.4095 (tpt) REVERT: I 59 VAL cc_start: 0.8861 (t) cc_final: 0.8355 (m) REVERT: I 123 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8157 (t) REVERT: I 226 SER cc_start: 0.7119 (OUTLIER) cc_final: 0.6286 (m) REVERT: I 275 TYR cc_start: 0.7240 (m-10) cc_final: 0.6911 (m-80) REVERT: J 119 LYS cc_start: 0.8418 (tppt) cc_final: 0.8045 (mmmt) REVERT: K 176 LEU cc_start: 0.8364 (tp) cc_final: 0.7829 (tp) REVERT: K 185 GLN cc_start: 0.6919 (mp10) cc_final: 0.6604 (mp10) REVERT: L 38 GLN cc_start: 0.7305 (mm-40) cc_final: 0.6733 (pt0) REVERT: L 104 ASP cc_start: 0.7936 (m-30) cc_final: 0.7120 (t0) REVERT: L 229 MET cc_start: 0.4248 (ttt) cc_final: 0.3872 (ppp) REVERT: L 261 LYS cc_start: 0.4995 (tppt) cc_final: 0.4746 (tptt) outliers start: 75 outliers final: 54 residues processed: 399 average time/residue: 0.1750 time to fit residues: 109.2842 Evaluate side-chains 369 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 308 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 CYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 180 ILE Chi-restraints excluded: chain L residue 267 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [18, 267, 17, 295, 108, 78, 107, 296, 214, 48, 119] chunk 18 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 295 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 107 optimal weight: 0.3980 chunk 296 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN G 193 HIS L 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.163468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.131915 restraints weight = 41429.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.133173 restraints weight = 75905.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133880 restraints weight = 56893.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134373 restraints weight = 36224.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135910 restraints weight = 29104.475| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26665 Z= 0.182 Angle : 0.652 11.609 36129 Z= 0.324 Chirality : 0.042 0.210 4072 Planarity : 0.004 0.069 4356 Dihedral : 15.898 177.235 4195 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 3.80 % Allowed : 15.52 % Favored : 80.68 % 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: 1.46 (0.15), residues: 3060 helix: 1.53 (0.12), residues: 1853 sheet: 0.95 (0.37), residues: 202 loop : 0.04 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 182 TYR 0.033 0.002 TYR G 93 PHE 0.019 0.002 PHE F 204 TRP 0.022 0.002 TRP A 45 HIS 0.004 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (26664) covalent geometry : angle 0.65241 / 0.32 (36129) hydrogen bonds : bond 0.05251 / 3.58 ( 1355) hydrogen bonds : angle 4.31543 / 3.12 ( 3957) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 330 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.6755 (m90) cc_final: 0.6272 (m-70) REVERT: A 210 MET cc_start: 0.1170 (ttt) cc_final: 0.0553 (tpp) REVERT: A 245 ASP cc_start: 0.4042 (m-30) cc_final: 0.3587 (m-30) REVERT: B 104 ASP cc_start: 0.7348 (t70) cc_final: 0.7078 (t0) REVERT: B 152 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: B 248 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7409 (mp) REVERT: C 85 ARG cc_start: 0.5574 (OUTLIER) cc_final: 0.5096 (ptt90) REVERT: C 175 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7916 (ttm110) REVERT: C 257 SER cc_start: 0.8017 (p) cc_final: 0.7503 (t) REVERT: D 81 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6541 (tm-30) REVERT: D 116 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8081 (ttm110) REVERT: D 273 LYS cc_start: 0.8668 (mttt) cc_final: 0.8310 (mtmm) REVERT: E 166 ILE cc_start: 0.8144 (mm) cc_final: 0.7931 (tp) REVERT: F 78 LYS cc_start: 0.7778 (mttp) cc_final: 0.7312 (mmmt) REVERT: F 206 ASN cc_start: 0.8117 (t0) cc_final: 0.7877 (t0) REVERT: F 210 MET cc_start: 0.7580 (tpp) cc_final: 0.7141 (tpt) REVERT: G 175 ARG cc_start: 0.7789 (mmm-85) cc_final: 0.7305 (tpp80) REVERT: G 210 MET cc_start: 0.7085 (mpp) cc_final: 0.6211 (mtp) REVERT: G 214 MET cc_start: 0.5294 (mmp) cc_final: 0.4171 (tpt) REVERT: I 123 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8153 (t) REVERT: I 226 SER cc_start: 0.7293 (OUTLIER) cc_final: 0.6408 (m) REVERT: I 229 MET cc_start: 0.6431 (mmp) cc_final: 0.5892 (mmp) REVERT: J 119 LYS cc_start: 0.8386 (tppt) cc_final: 0.7990 (mmmt) REVERT: K 175 ARG cc_start: 0.6494 (mtm180) cc_final: 0.6092 (mtm180) REVERT: K 176 LEU cc_start: 0.8494 (tp) cc_final: 0.8013 (tp) REVERT: L 38 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6757 (pt0) REVERT: L 68 VAL cc_start: 0.7862 (OUTLIER) cc_final: 0.7582 (p) REVERT: L 73 TYR cc_start: 0.7678 (t80) cc_final: 0.7443 (t80) REVERT: L 104 ASP cc_start: 0.7981 (m-30) cc_final: 0.7142 (t0) REVERT: L 261 LYS cc_start: 0.4746 (tppt) cc_final: 0.4468 (tptt) outliers start: 102 outliers final: 77 residues processed: 411 average time/residue: 0.1816 time to fit residues: 116.5493 Evaluate side-chains 391 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 306 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 80 GLN Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 243 ARG Chi-restraints excluded: chain G residue 56 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 93 TYR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 210 MET Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 100 CYS Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 180 ILE Chi-restraints excluded: chain L residue 267 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [291, 18, 37, 187, 66, 245, 102, 129, 281, 5, 208] chunk 291 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 245 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 281 optimal weight: 0.0770 chunk 5 optimal weight: 9.9990 chunk 208 optimal weight: 0.3980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 38 GLN K 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.165544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.134448 restraints weight = 41415.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.136397 restraints weight = 75429.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.136830 restraints weight = 50561.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137173 restraints weight = 35341.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.139188 restraints weight = 27838.073| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26665 Z= 0.120 Angle : 0.600 10.507 36129 Z= 0.298 Chirality : 0.041 0.200 4072 Planarity : 0.004 0.067 4356 Dihedral : 15.708 176.596 4195 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 2.95 % Allowed : 16.26 % Favored : 80.79 % 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: 1.64 (0.15), residues: 3060 helix: 1.67 (0.12), residues: 1853 sheet: 0.96 (0.36), residues: 202 loop : 0.12 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 158 TYR 0.021 0.001 TYR G 93 PHE 0.017 0.001 PHE F 204 TRP 0.035 0.002 TRP L 211 HIS 0.002 0.000 HIS D 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (26664) covalent geometry : angle 0.60041 / 0.30 (36129) hydrogen bonds : bond 0.04646 / 3.19 ( 1355) hydrogen bonds : angle 4.13840 / 3.00 ( 3957) Misc. bond : bond 0.00100 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 327 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.7025 (m90) cc_final: 0.6655 (m-70) REVERT: A 210 MET cc_start: 0.1618 (ttt) cc_final: 0.0857 (tpp) REVERT: A 245 ASP cc_start: 0.3971 (m-30) cc_final: 0.3574 (m-30) REVERT: B 104 ASP cc_start: 0.7216 (t70) cc_final: 0.6968 (t0) REVERT: B 152 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: B 248 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7365 (mp) REVERT: C 85 ARG cc_start: 0.5427 (OUTLIER) cc_final: 0.4960 (ptt90) REVERT: C 175 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7766 (ttm110) REVERT: C 229 MET cc_start: 0.7272 (mmp) cc_final: 0.6659 (mmt) REVERT: C 257 SER cc_start: 0.7997 (p) cc_final: 0.7444 (t) REVERT: D 31 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7661 (ptpp) REVERT: D 116 ARG cc_start: 0.8454 (ttm-80) cc_final: 0.8200 (ttm110) REVERT: D 273 LYS cc_start: 0.8651 (mttt) cc_final: 0.8264 (mtmm) REVERT: E 166 ILE cc_start: 0.8239 (mm) cc_final: 0.8020 (tp) REVERT: F 78 LYS cc_start: 0.7751 (mttp) cc_final: 0.7314 (mmmt) REVERT: F 206 ASN cc_start: 0.8031 (t0) cc_final: 0.7804 (t0) REVERT: G 175 ARG cc_start: 0.7766 (mmm-85) cc_final: 0.7523 (tpp80) REVERT: G 210 MET cc_start: 0.6950 (mpp) cc_final: 0.6166 (mtp) REVERT: G 214 MET cc_start: 0.5354 (mmp) cc_final: 0.4281 (tpt) REVERT: H 140 MET cc_start: 0.8568 (ttm) cc_final: 0.8300 (ttm) REVERT: I 123 SER cc_start: 0.8670 (OUTLIER) cc_final: 0.8113 (t) REVERT: I 226 SER cc_start: 0.7263 (OUTLIER) cc_final: 0.6408 (m) REVERT: J 119 LYS cc_start: 0.8369 (tppt) cc_final: 0.8143 (mmmt) REVERT: K 175 ARG cc_start: 0.6449 (mtm180) cc_final: 0.6006 (mtm180) REVERT: K 176 LEU cc_start: 0.8480 (tp) cc_final: 0.8064 (tp) REVERT: K 231 ARG cc_start: 0.7708 (tpp-160) cc_final: 0.7386 (tpt90) REVERT: L 38 GLN cc_start: 0.7369 (mm-40) cc_final: 0.6751 (pt0) REVERT: L 68 VAL cc_start: 0.7840 (OUTLIER) cc_final: 0.7589 (p) REVERT: L 104 ASP cc_start: 0.7943 (m-30) cc_final: 0.7079 (t0) REVERT: L 261 LYS cc_start: 0.4752 (tppt) cc_final: 0.4482 (tptt) outliers start: 79 outliers final: 61 residues processed: 389 average time/residue: 0.1763 time to fit residues: 106.5064 Evaluate side-chains 374 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 305 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 243 ARG Chi-restraints excluded: chain G residue 56 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 93 TYR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 140 MET Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 153 THR Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 267 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [285, 74, 135, 274, 56, 3, 174, 233, 157, 129, 85] chunk 285 optimal weight: 0.6980 chunk 74 optimal weight: 0.0050 chunk 135 optimal weight: 0.5980 chunk 274 optimal weight: 0.0030 chunk 56 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 174 optimal weight: 0.0170 chunk 233 optimal weight: 1.9990 chunk 157 optimal weight: 0.0670 chunk 129 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.167839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.136448 restraints weight = 41386.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.136551 restraints weight = 71775.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.137970 restraints weight = 58251.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138210 restraints weight = 35829.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.140530 restraints weight = 30014.985| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26665 Z= 0.106 Angle : 0.591 10.490 36129 Z= 0.293 Chirality : 0.040 0.208 4072 Planarity : 0.004 0.046 4356 Dihedral : 15.434 173.693 4195 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.32 % Favored : 97.58 % Rotamer: Outliers : 2.39 % Allowed : 17.23 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.15), residues: 3060 helix: 1.76 (0.12), residues: 1864 sheet: 1.06 (0.36), residues: 204 loop : 0.22 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 258 TYR 0.015 0.001 TYR G 112 PHE 0.029 0.001 PHE C 204 TRP 0.030 0.002 TRP L 211 HIS 0.002 0.000 HIS D 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (26664) covalent geometry : angle 0.59122 / 0.29 (36129) hydrogen bonds : bond 0.04072 / 2.81 ( 1355) hydrogen bonds : angle 4.02578 / 2.93 ( 3957) Misc. bond : bond 0.00145 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 333 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.4921 (OUTLIER) cc_final: 0.4583 (mp) REVERT: A 43 HIS cc_start: 0.6987 (m90) cc_final: 0.6685 (m-70) REVERT: A 210 MET cc_start: 0.1101 (ttt) cc_final: 0.0780 (tpp) REVERT: A 245 ASP cc_start: 0.4011 (m-30) cc_final: 0.3582 (m-30) REVERT: B 104 ASP cc_start: 0.7138 (t70) cc_final: 0.6897 (t0) REVERT: B 152 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: C 175 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7646 (ttm110) REVERT: D 81 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.6425 (tm-30) REVERT: D 273 LYS cc_start: 0.8773 (mttt) cc_final: 0.8396 (mtmm) REVERT: E 230 LEU cc_start: 0.8135 (tt) cc_final: 0.7670 (mt) REVERT: F 78 LYS cc_start: 0.7730 (mttp) cc_final: 0.7290 (mmmt) REVERT: F 206 ASN cc_start: 0.8070 (t0) cc_final: 0.7756 (t0) REVERT: F 207 THR cc_start: 0.8160 (p) cc_final: 0.7821 (p) REVERT: G 140 MET cc_start: 0.8242 (tpp) cc_final: 0.7970 (mpp) REVERT: G 175 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7515 (tpp80) REVERT: G 210 MET cc_start: 0.7555 (mpp) cc_final: 0.6863 (mtp) REVERT: G 214 MET cc_start: 0.5334 (mmp) cc_final: 0.4216 (tpt) REVERT: I 59 VAL cc_start: 0.8828 (t) cc_final: 0.8318 (m) REVERT: I 73 TYR cc_start: 0.9017 (t80) cc_final: 0.8689 (t80) REVERT: I 226 SER cc_start: 0.7223 (OUTLIER) cc_final: 0.6400 (m) REVERT: K 175 ARG cc_start: 0.6447 (mtm180) cc_final: 0.6003 (mtm180) REVERT: K 176 LEU cc_start: 0.8365 (tp) cc_final: 0.7983 (tp) REVERT: K 231 ARG cc_start: 0.7650 (tpp-160) cc_final: 0.7402 (tpt90) REVERT: K 275 TYR cc_start: 0.5539 (m-80) cc_final: 0.5279 (m-80) REVERT: L 38 GLN cc_start: 0.7323 (mm-40) cc_final: 0.6730 (pt0) outliers start: 64 outliers final: 44 residues processed: 384 average time/residue: 0.1787 time to fit residues: 106.5470 Evaluate side-chains 351 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 302 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 56 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 93 TYR Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 140 MET Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 180 ILE Chi-restraints excluded: chain L residue 267 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [147, 35, 88, 28, 104, 240, 90, 30, 27, 217, 278] chunk 147 optimal weight: 6.9990 chunk 35 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 240 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 278 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN B 185 GLN F 269 GLN H 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.165688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.134403 restraints weight = 41535.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135429 restraints weight = 77705.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.136607 restraints weight = 56883.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.136866 restraints weight = 35536.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139203 restraints weight = 29107.554| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 26665 Z= 0.133 Angle : 0.622 11.845 36129 Z= 0.306 Chirality : 0.041 0.274 4072 Planarity : 0.004 0.086 4356 Dihedral : 15.408 171.725 4195 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.45 % Favored : 97.48 % Rotamer: Outliers : 2.57 % Allowed : 17.68 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.15), residues: 3060 helix: 1.80 (0.12), residues: 1852 sheet: 1.08 (0.36), residues: 204 loop : 0.16 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 27 TYR 0.014 0.001 TYR G 93 PHE 0.016 0.001 PHE C 204 TRP 0.038 0.002 TRP L 211 HIS 0.002 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (26664) covalent geometry : angle 0.62237 / 0.31 (36129) hydrogen bonds : bond 0.04354 / 2.98 ( 1355) hydrogen bonds : angle 4.05787 / 2.94 ( 3957) Misc. bond : bond 0.00062 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 325 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.4928 (OUTLIER) cc_final: 0.4584 (mp) REVERT: A 43 HIS cc_start: 0.7060 (m90) cc_final: 0.6710 (m-70) REVERT: A 210 MET cc_start: 0.1746 (ttt) cc_final: 0.1211 (tpp) REVERT: A 245 ASP cc_start: 0.4056 (m-30) cc_final: 0.3662 (m-30) REVERT: B 104 ASP cc_start: 0.7159 (t70) cc_final: 0.6929 (t0) REVERT: B 152 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: C 175 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7841 (ttm110) REVERT: D 81 GLN cc_start: 0.6726 (OUTLIER) cc_final: 0.5978 (tm-30) REVERT: D 273 LYS cc_start: 0.8799 (mttt) cc_final: 0.8423 (mtmm) REVERT: E 230 LEU cc_start: 0.8231 (tt) cc_final: 0.7778 (mt) REVERT: F 78 LYS cc_start: 0.7751 (mttp) cc_final: 0.7278 (mmmt) REVERT: F 206 ASN cc_start: 0.8090 (t0) cc_final: 0.7790 (t0) REVERT: F 207 THR cc_start: 0.8251 (p) cc_final: 0.7932 (p) REVERT: G 210 MET cc_start: 0.7117 (mpp) cc_final: 0.6522 (mtp) REVERT: G 214 MET cc_start: 0.4991 (mmp) cc_final: 0.4137 (tpt) REVERT: I 123 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8127 (t) REVERT: I 226 SER cc_start: 0.7276 (OUTLIER) cc_final: 0.6399 (m) REVERT: K 175 ARG cc_start: 0.6633 (mtm180) cc_final: 0.6130 (mtm180) REVERT: K 176 LEU cc_start: 0.8433 (tp) cc_final: 0.8074 (tp) REVERT: K 231 ARG cc_start: 0.7767 (tpp-160) cc_final: 0.7464 (tpt90) REVERT: L 104 ASP cc_start: 0.7957 (m-30) cc_final: 0.7047 (t0) REVERT: L 173 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.6963 (m) outliers start: 69 outliers final: 54 residues processed: 378 average time/residue: 0.1707 time to fit residues: 101.9672 Evaluate side-chains 370 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 309 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 269 GLN Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 56 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 93 TYR Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 140 MET Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 180 ILE Chi-restraints excluded: chain L residue 267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [74, 229, 102, 161, 256, 129, 278, 203, 43, 282, 208] chunk 74 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 278 optimal weight: 20.0000 chunk 203 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 282 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN F 269 GLN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.164880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.133667 restraints weight = 41286.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.135083 restraints weight = 77994.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.135829 restraints weight = 55165.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136358 restraints weight = 35262.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.137742 restraints weight = 28352.442| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26665 Z= 0.143 Angle : 0.623 10.706 36129 Z= 0.309 Chirality : 0.041 0.242 4072 Planarity : 0.004 0.079 4356 Dihedral : 15.384 170.150 4195 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.25 % Rotamer: Outliers : 2.57 % Allowed : 17.83 % Favored : 79.60 % 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: 1.72 (0.15), residues: 3060 helix: 1.62 (0.12), residues: 1896 sheet: 1.04 (0.29), residues: 314 loop : 0.24 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 231 TYR 0.017 0.001 TYR G 93 PHE 0.019 0.001 PHE C 204 TRP 0.032 0.002 TRP L 211 HIS 0.002 0.001 HIS I 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (26664) covalent geometry : angle 0.62342 / 0.31 (36129) hydrogen bonds : bond 0.04501 / 3.07 ( 1355) hydrogen bonds : angle 4.09008 / 2.96 ( 3957) Misc. bond : bond 0.00053 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 308 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.4947 (OUTLIER) cc_final: 0.4594 (mp) REVERT: A 43 HIS cc_start: 0.7075 (m90) cc_final: 0.6734 (m-70) REVERT: A 210 MET cc_start: 0.1236 (ttt) cc_final: 0.0804 (tpp) REVERT: A 245 ASP cc_start: 0.4103 (m-30) cc_final: 0.3697 (m-30) REVERT: B 104 ASP cc_start: 0.7174 (t70) cc_final: 0.6907 (t0) REVERT: B 152 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7199 (tm-30) REVERT: C 175 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7818 (ttm110) REVERT: D 81 GLN cc_start: 0.6744 (OUTLIER) cc_final: 0.5985 (tm-30) REVERT: D 206 ASN cc_start: 0.7869 (t0) cc_final: 0.7557 (t0) REVERT: D 273 LYS cc_start: 0.8770 (mttt) cc_final: 0.8406 (mtmm) REVERT: E 230 LEU cc_start: 0.8256 (tt) cc_final: 0.7795 (mt) REVERT: F 37 GLN cc_start: 0.7182 (mp10) cc_final: 0.6785 (mp10) REVERT: F 78 LYS cc_start: 0.7746 (mttp) cc_final: 0.7274 (mmmt) REVERT: F 206 ASN cc_start: 0.8130 (t0) cc_final: 0.7794 (t0) REVERT: F 207 THR cc_start: 0.8331 (p) cc_final: 0.8064 (p) REVERT: G 77 HIS cc_start: 0.5949 (m-70) cc_final: 0.5666 (m90) REVERT: G 210 MET cc_start: 0.7048 (mpp) cc_final: 0.6487 (mtp) REVERT: G 214 MET cc_start: 0.4885 (mmp) cc_final: 0.4065 (tpt) REVERT: I 123 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8139 (t) REVERT: I 226 SER cc_start: 0.7408 (OUTLIER) cc_final: 0.6533 (m) REVERT: K 175 ARG cc_start: 0.6722 (mtm180) cc_final: 0.6219 (mtm180) REVERT: K 176 LEU cc_start: 0.8396 (tp) cc_final: 0.8060 (tp) REVERT: L 104 ASP cc_start: 0.7975 (m-30) cc_final: 0.7086 (t0) REVERT: L 173 THR cc_start: 0.7101 (OUTLIER) cc_final: 0.6792 (m) outliers start: 69 outliers final: 57 residues processed: 363 average time/residue: 0.1712 time to fit residues: 97.5586 Evaluate side-chains 363 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 299 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 269 GLN Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 56 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 93 TYR Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 140 MET Chi-restraints excluded: chain I residue 147 ASP Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 223 ASN Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 183 ASP Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 180 ILE Chi-restraints excluded: chain L residue 267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: [233, 280, 138, 64, 205, 57, 74, 273, 279, 70, 127] chunk 233 optimal weight: 0.6980 chunk 280 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 205 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 273 optimal weight: 7.9990 chunk 279 optimal weight: 0.7980 chunk 70 optimal weight: 0.0370 chunk 127 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 269 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.165736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.134116 restraints weight = 41067.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.134614 restraints weight = 71546.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.135771 restraints weight = 57098.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.136143 restraints weight = 35198.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.137686 restraints weight = 29425.300| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26665 Z= 0.117 Angle : 0.615 11.591 36129 Z= 0.303 Chirality : 0.041 0.255 4072 Planarity : 0.004 0.079 4356 Dihedral : 15.322 168.731 4195 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 2.50 % Allowed : 17.98 % Favored : 79.52 % 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: 1.78 (0.15), residues: 3060 helix: 1.67 (0.12), residues: 1896 sheet: 1.09 (0.29), residues: 312 loop : 0.26 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 231 TYR 0.016 0.001 TYR G 93 PHE 0.019 0.001 PHE C 204 TRP 0.033 0.002 TRP L 211 HIS 0.002 0.000 HIS D 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (26664) covalent geometry : angle 0.61528 / 0.30 (36129) hydrogen bonds : bond 0.04279 / 2.93 ( 1355) hydrogen bonds : angle 4.04061 / 2.93 ( 3957) Misc. bond : bond 0.00094 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3906.16 seconds wall clock time: 68 minutes 23.39 seconds (4103.39 seconds total)