Starting phenix.real_space_refine on Fri Mar 6 10:34:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m9c_23723/03_2026/7m9c_23723.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m9c_23723/03_2026/7m9c_23723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m9c_23723/03_2026/7m9c_23723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m9c_23723/03_2026/7m9c_23723.map" model { file = "/net/cci-nas-00/data/ceres_data/7m9c_23723/03_2026/7m9c_23723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m9c_23723/03_2026/7m9c_23723.cif" } resolution = 4.2 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= 0.002 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 86 5.49 5 S 112 5.16 5 C 19026 2.51 5 N 5552 2.21 5 O 5741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30517 Number of models: 1 Model: "" Number of chains: 26 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: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 693 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain breaks: 1 Chain: "N" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 660 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain breaks: 1 Chain: "O" 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: "P" 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: 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: 7.03, per 1000 atoms: 0.23 Number of scatterers: 30517 At special positions: 0 Unit cell: (195.51, 144.97, 172.9, 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 112 16.00 P 86 15.00 O 5741 8.00 N 5552 7.00 C 19026 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.3 seconds 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6748 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 14 sheets defined 63.3% alpha, 6.4% beta 30 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 removed outlier: 3.505A 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: 3.538A 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: 3.528A 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: 3.680A pdb=" N GLU A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 183 removed outlier: 3.514A 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: 3.565A 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: 3.570A 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: 3.742A 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: 3.868A pdb=" N ASP C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 removed outlier: 3.980A pdb=" N ALA C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.561A 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: 4.036A pdb=" N GLU C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.787A 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: 3.581A 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: 3.728A 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: 3.554A pdb=" N ASP F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 77 removed outlier: 3.691A 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: 3.510A pdb=" N ASP F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR F 129 " --> pdb=" O PHE F 125 " (cutoff:3.500A) removed outlier: 3.559A 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: 4.016A 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: 3.920A 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: 3.552A 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: 4.694A 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: 3.908A 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: 3.586A pdb=" N VAL G 271 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 3.582A 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: 4.278A 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: 3.900A 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: 3.519A 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: 4.063A 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: 4.187A pdb=" N LEU H 256 " --> pdb=" O ALA H 252 " (cutoff:3.500A) removed outlier: 4.288A 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: 3.767A 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: 3.659A 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: 3.760A 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: 3.656A 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: 3.979A pdb=" N ALA J 155 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 3.884A 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: 3.921A pdb=" N ARG K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 3.767A 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: 3.683A 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: 4.371A 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: 3.612A 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: 3.645A pdb=" N VAL L 271 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA L 272 " --> pdb=" O LEU L 268 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS L 273 " --> pdb=" O GLN L 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 29 removed outlier: 3.504A pdb=" N LEU O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 53 Processing helix chain 'O' and resid 65 through 75 removed outlier: 3.537A pdb=" N ASP O 71 " --> pdb=" O THR O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 113 Processing helix chain 'O' and resid 121 through 136 removed outlier: 3.528A pdb=" N LYS O 134 " --> pdb=" O ILE O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 164 removed outlier: 4.237A pdb=" N ASP O 156 " --> pdb=" O GLU O 152 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP O 159 " --> pdb=" O ALA O 155 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU O 162 " --> pdb=" O ARG O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 183 removed outlier: 3.514A pdb=" N ASP O 183 " --> pdb=" O VAL O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 188 Processing helix chain 'O' and resid 200 through 216 Processing helix chain 'O' and resid 226 through 238 removed outlier: 3.893A pdb=" N ILE O 232 " --> pdb=" O GLU O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 240 through 259 Processing helix chain 'O' and resid 264 through 272 removed outlier: 3.564A pdb=" N ALA O 272 " --> pdb=" O LEU O 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 29 Processing helix chain 'P' and resid 36 through 53 Processing helix chain 'P' and resid 65 through 77 removed outlier: 3.551A pdb=" N ARG P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS P 77 " --> pdb=" O TYR P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 113 Processing helix chain 'P' and resid 121 through 136 removed outlier: 3.535A pdb=" N CYS P 136 " --> pdb=" O VAL P 132 " (cutoff:3.500A) Processing helix chain 'P' and resid 153 through 164 Processing helix chain 'P' and resid 174 through 183 removed outlier: 3.955A pdb=" N ALA P 178 " --> pdb=" O ASP P 174 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL P 179 " --> pdb=" O ARG P 175 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP P 183 " --> pdb=" O VAL P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 190 Processing helix chain 'P' and resid 200 through 215 Processing helix chain 'P' and resid 226 through 238 removed outlier: 3.904A pdb=" N ARG P 231 " --> pdb=" O LYS P 227 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE P 232 " --> pdb=" O GLU P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 240 through 258 Processing helix chain 'P' and resid 264 through 275 removed outlier: 3.907A pdb=" N GLN P 269 " --> pdb=" O LYS P 265 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU P 270 " --> pdb=" O ALA P 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL P 271 " --> pdb=" O VAL P 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA P 272 " --> pdb=" O LEU P 268 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS P 273 " --> pdb=" O GLN P 269 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU P 274 " --> pdb=" O GLU P 270 " (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: 6.438A 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: 5.744A 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: 6.496A 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: 6.314A 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: 7.551A 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: 6.167A 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: 6.767A pdb=" N LEU G 141 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 7.694A 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: 7.447A pdb=" N ASP H 144 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.997A 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: 6.454A 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: 5.707A pdb=" N VAL I 58 " --> pdb=" O GLY I 172 " (cutoff:3.500A) removed outlier: 3.745A 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: 6.424A 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: 6.609A 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: 7.387A 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: 6.543A 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) Processing sheet with id=AB4, first strand: chain 'O' and resid 91 through 94 removed outlier: 6.311A pdb=" N VAL O 92 " --> pdb=" O ILE O 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 91 through 94 removed outlier: 6.497A pdb=" N VAL P 92 " --> pdb=" O ILE P 142 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU P 141 " --> pdb=" O VAL P 169 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL P 171 " --> pdb=" O LEU P 141 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE P 143 " --> pdb=" O VAL P 171 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ARG P 57 " --> pdb=" O LEU P 194 " (cutoff:3.500A) 1519 hydrogen bonds defined for protein. 4491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 5.05 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8097 1.33 - 1.45: 4985 1.45 - 1.57: 17724 1.57 - 1.69: 158 1.69 - 1.81: 168 Bond restraints: 31132 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 3.37e+01 bond pdb=" N LYS D 78 " pdb=" CA LYS D 78 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.41e-02 5.03e+03 4.28e+00 bond pdb=" CA LYS D 78 " pdb=" C LYS D 78 " ideal model delta sigma weight residual 1.524 1.548 -0.024 1.26e-02 6.30e+03 3.73e+00 bond pdb=" CB CYS H 56 " pdb=" SG CYS H 56 " ideal model delta sigma weight residual 1.808 1.761 0.047 3.30e-02 9.18e+02 1.99e+00 bond pdb=" C3' DT N -1 " pdb=" O3' DT N -1 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.60e+00 ... (remaining 31127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.40: 42116 5.40 - 10.81: 56 10.81 - 16.21: 4 16.21 - 21.61: 3 21.61 - 27.02: 2 Bond angle restraints: 42181 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 98.31 16.44 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 109.81 136.83 -27.02 2.21e+00 2.05e-01 1.49e+02 angle pdb=" N THR C 173 " pdb=" CA THR C 173 " pdb=" C THR C 173 " ideal model delta sigma weight residual 110.56 132.84 -22.28 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 92.95 17.01 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 92.02 18.35 1.78e+00 3.16e-01 1.06e+02 ... (remaining 42176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 18644 35.09 - 70.18: 516 70.18 - 105.27: 15 105.27 - 140.36: 10 140.36 - 175.45: 5 Dihedral angle restraints: 19190 sinusoidal: 8760 harmonic: 10430 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 -60.00 115.45 -175.45 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 -60.00 101.89 -161.89 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 19187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 4735 0.160 - 0.319: 18 0.319 - 0.478: 1 0.478 - 0.638: 1 0.638 - 0.797: 1 Chirality restraints: 4756 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 8.94e+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 3.45e+00 ... (remaining 4753 not shown) Planarity restraints: 5084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 85 " -0.045 5.00e-02 4.00e+02 6.62e-02 7.02e+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 4.55e-02 3.31e+00 pdb=" N PRO D 86 " 0.079 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 4.29e-02 2.94e+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 5081 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 20 2.06 - 2.77: 4920 2.77 - 3.48: 41379 3.48 - 4.19: 68508 4.19 - 4.90: 120906 Nonbonded interactions: 235733 Sorted by model distance: nonbonded pdb=" CE1 HIS G 97 " pdb=" CZ ARG P 126 " model vdw 1.350 3.490 nonbonded pdb=" OE2 GLU O 212 " pdb=" OG SER O 222 " model vdw 1.381 3.040 nonbonded pdb=" OE2 GLU A 212 " pdb=" OG SER A 222 " model vdw 1.381 3.040 nonbonded pdb=" CE1 HIS G 97 " pdb=" NE ARG P 126 " model vdw 1.485 3.340 nonbonded pdb=" OD2 ASP F 124 " pdb=" NZ LYS G 119 " model vdw 1.589 3.120 ... (remaining 235728 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)) selection = (chain 'O' 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 'P' 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: 1.480 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: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 29.040 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 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 0.274 31134 Z= 0.218 Angle : 0.642 27.016 42181 Z= 0.372 Chirality : 0.043 0.797 4756 Planarity : 0.004 0.066 5084 Dihedral : 15.012 175.446 12442 Min Nonbonded Distance : 1.350 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.58 % Favored : 97.34 % Rotamer: Outliers : 0.10 % Allowed : 3.39 % Favored : 96.52 % Cbeta Deviations : 0.12 % 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: 0.09 (0.13), residues: 3570 helix: 0.20 (0.10), residues: 2100 sheet: 0.58 (0.33), residues: 238 loop : -0.00 (0.17), residues: 1232 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 P 196 TRP 0.015 0.001 TRP K 20 HIS 0.005 0.001 HIS K 77 Details of bonding type rmsd covalent geometry : bond 0.00271 (31132) covalent geometry : angle 0.64208 (42181) hydrogen bonds : bond 0.15126 ( 1579) hydrogen bonds : angle 6.03836 ( 4611) Misc. bond : bond 0.19393 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1833 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1830 time to evaluate : 0.900 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.9264 (mt) cc_final: 0.9056 (mt) REVERT: A 89 VAL cc_start: 0.7979 (t) cc_final: 0.7758 (t) REVERT: A 104 ASP cc_start: 0.8568 (m-30) cc_final: 0.8322 (m-30) REVERT: A 112 TYR cc_start: 0.8861 (t80) cc_final: 0.8412 (t80) REVERT: A 149 LEU cc_start: 0.9303 (tp) cc_final: 0.8973 (tp) REVERT: A 168 VAL cc_start: 0.9056 (t) cc_final: 0.8738 (p) REVERT: A 190 PHE cc_start: 0.8245 (m-80) cc_final: 0.7666 (m-80) REVERT: B 62 SER cc_start: 0.8494 (p) cc_final: 0.7702 (p) REVERT: B 156 ASP cc_start: 0.7629 (m-30) cc_final: 0.7212 (m-30) REVERT: C 25 ILE cc_start: 0.9110 (mt) cc_final: 0.8766 (pt) REVERT: C 147 ASP cc_start: 0.7574 (m-30) cc_final: 0.7201 (p0) REVERT: C 173 THR cc_start: 0.8137 (p) cc_final: 0.7598 (p) REVERT: C 253 ILE cc_start: 0.9111 (mt) cc_final: 0.8834 (mm) REVERT: D 28 LEU cc_start: 0.8571 (mt) cc_final: 0.8232 (mp) REVERT: D 247 ILE cc_start: 0.8791 (mt) cc_final: 0.8291 (mm) REVERT: E 113 LEU cc_start: 0.9336 (mt) cc_final: 0.9120 (mp) REVERT: E 144 ASP cc_start: 0.8395 (t70) cc_final: 0.6868 (t0) REVERT: E 159 ASP cc_start: 0.7550 (m-30) cc_final: 0.6630 (m-30) REVERT: E 203 ASP cc_start: 0.7615 (m-30) cc_final: 0.7412 (m-30) REVERT: E 207 THR cc_start: 0.8804 (m) cc_final: 0.8598 (m) REVERT: E 247 ILE cc_start: 0.9552 (mt) cc_final: 0.9010 (mt) REVERT: E 253 ILE cc_start: 0.9376 (mt) cc_final: 0.9070 (pt) REVERT: F 168 VAL cc_start: 0.9476 (t) cc_final: 0.9272 (m) REVERT: F 190 PHE cc_start: 0.7986 (m-80) cc_final: 0.7759 (m-80) REVERT: F 207 THR cc_start: 0.8449 (m) cc_final: 0.8120 (m) REVERT: G 154 PHE cc_start: 0.8387 (m-80) cc_final: 0.8129 (m-80) REVERT: G 190 PHE cc_start: 0.8480 (m-80) cc_final: 0.8164 (m-80) REVERT: H 103 LYS cc_start: 0.9250 (tttt) cc_final: 0.8981 (pttt) REVERT: H 156 ASP cc_start: 0.8063 (m-30) cc_final: 0.7811 (m-30) REVERT: H 176 LEU cc_start: 0.9346 (tp) cc_final: 0.9113 (tt) REVERT: H 189 ARG cc_start: 0.8619 (tpt170) cc_final: 0.8098 (tpt90) REVERT: H 245 ASP cc_start: 0.8037 (t70) cc_final: 0.7506 (t0) REVERT: I 147 ASP cc_start: 0.7974 (m-30) cc_final: 0.7770 (p0) REVERT: I 176 LEU cc_start: 0.9460 (tp) cc_final: 0.9125 (tp) REVERT: I 188 GLU cc_start: 0.7056 (tp30) cc_final: 0.6518 (tp30) REVERT: I 194 LEU cc_start: 0.9380 (mt) cc_final: 0.8486 (mt) REVERT: I 203 ASP cc_start: 0.7310 (m-30) cc_final: 0.7013 (m-30) REVERT: I 247 ILE cc_start: 0.9040 (mt) cc_final: 0.8798 (tp) REVERT: J 103 LYS cc_start: 0.8831 (tttt) cc_final: 0.8581 (tttm) REVERT: J 105 LEU cc_start: 0.9520 (tp) cc_final: 0.9194 (tp) REVERT: J 123 SER cc_start: 0.9103 (p) cc_final: 0.8579 (p) REVERT: J 138 VAL cc_start: 0.9357 (t) cc_final: 0.9037 (p) REVERT: J 144 ASP cc_start: 0.7134 (t0) cc_final: 0.6928 (t0) REVERT: K 49 LYS cc_start: 0.9166 (mmtm) cc_final: 0.8515 (mmmt) REVERT: K 108 LYS cc_start: 0.9153 (mttm) cc_final: 0.8918 (mttt) REVERT: K 144 ASP cc_start: 0.8064 (t0) cc_final: 0.7656 (t0) REVERT: K 156 ASP cc_start: 0.8611 (m-30) cc_final: 0.7538 (m-30) REVERT: K 247 ILE cc_start: 0.8935 (mt) cc_final: 0.8620 (tp) REVERT: L 100 CYS cc_start: 0.7734 (t) cc_final: 0.7192 (t) REVERT: L 166 ILE cc_start: 0.6801 (mt) cc_final: 0.6566 (pt) REVERT: O 46 LEU cc_start: 0.8225 (mt) cc_final: 0.7957 (mt) REVERT: O 86 PRO cc_start: 0.6670 (Cg_exo) cc_final: 0.6257 (Cg_endo) REVERT: O 232 ILE cc_start: 0.7454 (mt) cc_final: 0.6559 (pt) REVERT: P 42 LEU cc_start: 0.7346 (mt) cc_final: 0.7080 (mt) REVERT: P 106 PHE cc_start: 0.8523 (m-80) cc_final: 0.7748 (m-80) REVERT: P 190 PHE cc_start: 0.7237 (m-80) cc_final: 0.6934 (m-80) outliers start: 3 outliers final: 2 residues processed: 1832 average time/residue: 0.2271 time to fit residues: 621.9679 Evaluate side-chains 911 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 909 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 7.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 223 ASN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 GLN I 213 GLN J 77 HIS L 193 HIS ** P 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.092499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.066310 restraints weight = 119204.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.068634 restraints weight = 64854.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.070192 restraints weight = 42962.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.071191 restraints weight = 32193.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.071824 restraints weight = 26457.964| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31134 Z= 0.176 Angle : 0.751 9.301 42181 Z= 0.388 Chirality : 0.045 0.276 4756 Planarity : 0.006 0.058 5084 Dihedral : 16.112 178.660 4907 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.07 % Favored : 97.90 % Rotamer: Outliers : 0.58 % Allowed : 3.29 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.14), residues: 3570 helix: 0.66 (0.11), residues: 2054 sheet: 0.89 (0.26), residues: 358 loop : 0.25 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 126 TYR 0.026 0.002 TYR G 75 PHE 0.021 0.002 PHE J 204 TRP 0.031 0.003 TRP I 45 HIS 0.024 0.001 HIS P 43 Details of bonding type rmsd covalent geometry : bond 0.00387 (31132) covalent geometry : angle 0.75108 (42181) hydrogen bonds : bond 0.05453 ( 1579) hydrogen bonds : angle 4.96898 ( 4611) Misc. bond : bond 0.00389 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 1188 time to evaluate : 1.246 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: 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: 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 36 LEU cc_start: 0.9230 (tp) cc_final: 0.8665 (tp) REVERT: A 43 HIS cc_start: 0.9049 (m90) cc_final: 0.8843 (m90) REVERT: A 44 ASP cc_start: 0.9427 (p0) cc_final: 0.9142 (p0) REVERT: A 75 TYR cc_start: 0.8811 (m-80) cc_final: 0.8487 (m-80) REVERT: A 103 LYS cc_start: 0.8996 (tttt) cc_final: 0.8744 (tttp) REVERT: A 113 LEU cc_start: 0.9575 (mt) cc_final: 0.9218 (tt) REVERT: A 133 LEU cc_start: 0.9756 (mt) cc_final: 0.9550 (mt) REVERT: A 136 CYS cc_start: 0.8364 (m) cc_final: 0.7968 (m) REVERT: A 149 LEU cc_start: 0.9667 (tp) cc_final: 0.9326 (tp) REVERT: A 154 PHE cc_start: 0.9320 (m-80) cc_final: 0.9041 (m-80) REVERT: A 162 GLU cc_start: 0.8822 (pp20) cc_final: 0.8263 (pp20) REVERT: A 168 VAL cc_start: 0.9354 (t) cc_final: 0.9091 (p) REVERT: A 183 ASP cc_start: 0.8605 (t0) cc_final: 0.8277 (t0) REVERT: A 203 ASP cc_start: 0.9574 (m-30) cc_final: 0.9313 (t0) REVERT: A 246 GLU cc_start: 0.9629 (mp0) cc_final: 0.9424 (mp0) REVERT: B 42 LEU cc_start: 0.9853 (tp) cc_final: 0.9585 (tp) REVERT: B 46 LEU cc_start: 0.9714 (mt) cc_final: 0.9511 (mt) REVERT: B 75 TYR cc_start: 0.8339 (m-80) cc_final: 0.8019 (m-80) REVERT: B 97 HIS cc_start: 0.7394 (p90) cc_final: 0.7178 (p90) REVERT: B 207 THR cc_start: 0.9638 (p) cc_final: 0.9423 (p) REVERT: B 210 MET cc_start: 0.9589 (mtt) cc_final: 0.9315 (ttt) REVERT: B 223 ASN cc_start: 0.9352 (t0) cc_final: 0.8847 (t0) REVERT: C 99 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8574 (tptp) REVERT: C 173 THR cc_start: 0.9126 (p) cc_final: 0.8635 (p) REVERT: C 210 MET cc_start: 0.9093 (tpt) cc_final: 0.8224 (tpt) REVERT: C 213 GLN cc_start: 0.9381 (tm-30) cc_final: 0.8779 (tm-30) REVERT: C 214 MET cc_start: 0.9435 (tpp) cc_final: 0.9023 (mpp) REVERT: C 223 ASN cc_start: 0.9238 (t0) cc_final: 0.8926 (t0) REVERT: C 229 MET cc_start: 0.8973 (mpp) cc_final: 0.8726 (mmm) REVERT: C 233 LEU cc_start: 0.9641 (mt) cc_final: 0.9424 (mt) REVERT: C 247 ILE cc_start: 0.9726 (mt) cc_final: 0.8399 (mt) REVERT: C 250 GLU cc_start: 0.9392 (tp30) cc_final: 0.9033 (tp30) REVERT: C 269 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8893 (mp10) REVERT: D 38 GLN cc_start: 0.9074 (mt0) cc_final: 0.8530 (mt0) REVERT: D 42 LEU cc_start: 0.9740 (tp) cc_final: 0.9457 (tp) REVERT: D 63 ARG cc_start: 0.8789 (mmp-170) cc_final: 0.8554 (mmm160) REVERT: D 152 GLU cc_start: 0.8675 (tp30) cc_final: 0.8401 (tm-30) REVERT: D 159 ASP cc_start: 0.9057 (m-30) cc_final: 0.8812 (m-30) REVERT: D 163 ASP cc_start: 0.9237 (m-30) cc_final: 0.8976 (m-30) REVERT: D 210 MET cc_start: 0.9658 (tpt) cc_final: 0.9006 (tpp) REVERT: D 211 TRP cc_start: 0.8777 (t-100) cc_final: 0.8275 (t60) REVERT: D 229 MET cc_start: 0.8771 (mtp) cc_final: 0.8295 (mmt) REVERT: D 247 ILE cc_start: 0.9421 (mt) cc_final: 0.9149 (mm) REVERT: D 248 LEU cc_start: 0.9732 (mt) cc_final: 0.9437 (mt) REVERT: D 269 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8926 (pp30) REVERT: E 46 LEU cc_start: 0.9736 (mt) cc_final: 0.9481 (mt) REVERT: E 47 ASP cc_start: 0.9467 (t0) cc_final: 0.9152 (m-30) REVERT: E 104 ASP cc_start: 0.8661 (t70) cc_final: 0.7737 (t0) REVERT: E 144 ASP cc_start: 0.8463 (t70) cc_final: 0.8244 (t0) REVERT: E 163 ASP cc_start: 0.8778 (m-30) cc_final: 0.7666 (m-30) REVERT: E 183 ASP cc_start: 0.9258 (t0) cc_final: 0.8839 (t70) REVERT: E 199 LEU cc_start: 0.8638 (tp) cc_final: 0.8043 (tp) REVERT: E 204 PHE cc_start: 0.9282 (t80) cc_final: 0.9071 (t80) REVERT: E 210 MET cc_start: 0.9676 (ttt) cc_final: 0.9327 (ttt) REVERT: E 216 LEU cc_start: 0.9290 (tp) cc_final: 0.8737 (tt) REVERT: E 246 GLU cc_start: 0.9292 (tm-30) cc_final: 0.9060 (tm-30) REVERT: E 247 ILE cc_start: 0.9678 (mt) cc_final: 0.9369 (mt) REVERT: E 275 TYR cc_start: 0.5265 (m-10) cc_final: 0.4136 (m-10) REVERT: F 42 LEU cc_start: 0.9260 (mt) cc_final: 0.8945 (mt) REVERT: F 92 VAL cc_start: 0.9862 (t) cc_final: 0.9614 (p) REVERT: F 114 LYS cc_start: 0.9665 (mmtm) cc_final: 0.9439 (mmmm) REVERT: F 144 ASP cc_start: 0.8829 (t70) cc_final: 0.8150 (t0) REVERT: F 168 VAL cc_start: 0.9497 (t) cc_final: 0.9176 (m) REVERT: F 190 PHE cc_start: 0.9477 (m-80) cc_final: 0.9037 (m-80) REVERT: F 199 LEU cc_start: 0.7930 (tp) cc_final: 0.6999 (tp) REVERT: F 210 MET cc_start: 0.9652 (mtm) cc_final: 0.9324 (mtp) REVERT: F 229 MET cc_start: 0.9427 (mtp) cc_final: 0.9152 (mtp) REVERT: F 246 GLU cc_start: 0.9007 (pp20) cc_final: 0.8729 (pp20) REVERT: G 88 THR cc_start: 0.9139 (m) cc_final: 0.8912 (p) REVERT: G 112 TYR cc_start: 0.8873 (t80) cc_final: 0.8581 (t80) REVERT: G 140 MET cc_start: 0.9214 (ttm) cc_final: 0.8706 (mtm) REVERT: G 144 ASP cc_start: 0.8121 (m-30) cc_final: 0.7834 (m-30) REVERT: G 174 ASP cc_start: 0.8614 (p0) cc_final: 0.8114 (p0) REVERT: G 250 GLU cc_start: 0.9301 (tp30) cc_final: 0.8849 (tp30) REVERT: H 38 GLN cc_start: 0.9238 (tp40) cc_final: 0.8874 (tp40) REVERT: H 54 LYS cc_start: 0.9162 (tttm) cc_final: 0.8838 (pptt) REVERT: H 56 CYS cc_start: 0.8363 (m) cc_final: 0.5806 (m) REVERT: H 103 LYS cc_start: 0.9242 (tttt) cc_final: 0.8899 (pttm) REVERT: H 127 ASP cc_start: 0.9090 (m-30) cc_final: 0.8877 (m-30) REVERT: H 145 GLU cc_start: 0.8499 (tm-30) cc_final: 0.7994 (pp20) REVERT: H 153 THR cc_start: 0.9566 (m) cc_final: 0.9223 (m) REVERT: H 156 ASP cc_start: 0.9402 (m-30) cc_final: 0.8734 (m-30) REVERT: H 159 ASP cc_start: 0.8652 (m-30) cc_final: 0.8089 (m-30) REVERT: H 176 LEU cc_start: 0.9478 (tp) cc_final: 0.9252 (tt) REVERT: H 189 ARG cc_start: 0.9067 (tpt170) cc_final: 0.8667 (tpt170) REVERT: H 204 PHE cc_start: 0.9478 (t80) cc_final: 0.9259 (t80) REVERT: I 93 TYR cc_start: 0.9180 (t80) cc_final: 0.8815 (t80) REVERT: I 127 ASP cc_start: 0.9329 (p0) cc_final: 0.9091 (p0) REVERT: I 185 GLN cc_start: 0.9209 (mt0) cc_final: 0.8413 (mp10) REVERT: I 210 MET cc_start: 0.9181 (tmm) cc_final: 0.8731 (tmm) REVERT: I 224 LEU cc_start: 0.9562 (mt) cc_final: 0.9346 (mt) REVERT: I 233 LEU cc_start: 0.9774 (tp) cc_final: 0.9442 (pp) REVERT: I 268 LEU cc_start: 0.9788 (tt) cc_final: 0.9552 (tp) REVERT: J 28 LEU cc_start: 0.9731 (mt) cc_final: 0.9446 (mt) REVERT: J 47 ASP cc_start: 0.9556 (t70) cc_final: 0.9344 (m-30) REVERT: J 103 LYS cc_start: 0.9162 (tttt) cc_final: 0.8894 (tttp) REVERT: J 139 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8681 (mp0) REVERT: J 144 ASP cc_start: 0.8241 (t0) cc_final: 0.7509 (p0) REVERT: J 162 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8489 (mm-30) REVERT: J 176 LEU cc_start: 0.9503 (mp) cc_final: 0.9119 (mt) REVERT: J 185 GLN cc_start: 0.8858 (tp-100) cc_final: 0.8101 (tp40) REVERT: J 210 MET cc_start: 0.9680 (mtm) cc_final: 0.9119 (mtt) REVERT: J 224 LEU cc_start: 0.9392 (mt) cc_final: 0.9176 (mt) REVERT: J 232 ILE cc_start: 0.9495 (mm) cc_final: 0.9004 (tt) REVERT: J 248 LEU cc_start: 0.9663 (mt) cc_final: 0.9275 (mt) REVERT: J 253 ILE cc_start: 0.9679 (pt) cc_final: 0.9410 (mm) REVERT: J 274 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: K 37 GLN cc_start: 0.9045 (pm20) cc_final: 0.8094 (pm20) REVERT: K 46 LEU cc_start: 0.9617 (mt) cc_final: 0.9400 (mt) REVERT: K 54 LYS cc_start: 0.9414 (tppt) cc_final: 0.9100 (tptp) REVERT: K 63 ARG cc_start: 0.8677 (mmp80) cc_final: 0.8432 (mmm160) REVERT: K 107 LYS cc_start: 0.9509 (ttmm) cc_final: 0.9249 (tptt) REVERT: K 111 GLU cc_start: 0.8211 (pp20) cc_final: 0.7941 (pp20) REVERT: K 145 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7849 (mm-30) REVERT: K 149 LEU cc_start: 0.9653 (tp) cc_final: 0.9322 (tp) REVERT: K 156 ASP cc_start: 0.9267 (m-30) cc_final: 0.8742 (m-30) REVERT: K 158 ARG cc_start: 0.8818 (ptt90) cc_final: 0.8255 (ttp80) REVERT: K 162 GLU cc_start: 0.8894 (mm-30) cc_final: 0.7890 (mm-30) REVERT: K 240 TYR cc_start: 0.8703 (m-80) cc_final: 0.7277 (m-10) REVERT: K 254 ARG cc_start: 0.9162 (ttp-170) cc_final: 0.8873 (ptm160) REVERT: L 100 CYS cc_start: 0.7215 (t) cc_final: 0.5351 (t) REVERT: L 124 ASP cc_start: 0.9326 (m-30) cc_final: 0.9015 (m-30) REVERT: L 145 GLU cc_start: 0.8920 (mp0) cc_final: 0.8720 (mp0) REVERT: L 166 ILE cc_start: 0.8369 (mt) cc_final: 0.8005 (mm) REVERT: L 184 GLU cc_start: 0.8940 (mp0) cc_final: 0.8321 (mp0) REVERT: L 215 VAL cc_start: 0.9508 (t) cc_final: 0.9249 (p) REVERT: L 223 ASN cc_start: 0.9149 (t0) cc_final: 0.8895 (t0) REVERT: L 240 TYR cc_start: 0.8935 (m-10) cc_final: 0.8345 (m-80) REVERT: L 270 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8480 (mp0) REVERT: O 46 LEU cc_start: 0.9663 (mt) cc_final: 0.9408 (mt) REVERT: O 71 ASP cc_start: 0.9459 (p0) cc_final: 0.8962 (p0) REVERT: O 75 TYR cc_start: 0.9024 (m-80) cc_final: 0.8817 (m-80) REVERT: O 97 HIS cc_start: 0.9225 (t-90) cc_final: 0.8871 (t-90) REVERT: O 106 PHE cc_start: 0.9154 (m-80) cc_final: 0.8539 (m-80) REVERT: O 115 TYR cc_start: 0.8873 (m-80) cc_final: 0.8434 (m-10) REVERT: O 144 ASP cc_start: 0.7393 (t70) cc_final: 0.5239 (t0) REVERT: O 147 ASP cc_start: 0.8892 (p0) cc_final: 0.8571 (t0) REVERT: O 158 ARG cc_start: 0.9235 (tpt-90) cc_final: 0.8484 (tpt-90) REVERT: O 183 ASP cc_start: 0.9186 (t0) cc_final: 0.8747 (t70) REVERT: O 185 GLN cc_start: 0.9602 (tm-30) cc_final: 0.9258 (tm-30) REVERT: O 232 ILE cc_start: 0.8794 (mt) cc_final: 0.8559 (pt) REVERT: P 42 LEU cc_start: 0.9252 (mt) cc_final: 0.9036 (mt) REVERT: P 73 TYR cc_start: 0.8791 (t80) cc_final: 0.8502 (t80) REVERT: P 127 ASP cc_start: 0.9426 (m-30) cc_final: 0.9199 (m-30) REVERT: P 144 ASP cc_start: 0.8711 (t0) cc_final: 0.8252 (t0) REVERT: P 154 PHE cc_start: 0.9639 (m-10) cc_final: 0.9268 (m-80) REVERT: P 164 LEU cc_start: 0.8815 (mm) cc_final: 0.8559 (mm) REVERT: P 214 MET cc_start: 0.8655 (mtm) cc_final: 0.8392 (mtp) REVERT: P 240 TYR cc_start: 0.9708 (m-80) cc_final: 0.9453 (m-80) REVERT: P 263 ILE cc_start: 0.5762 (mp) cc_final: 0.5489 (mp) outliers start: 18 outliers final: 2 residues processed: 1197 average time/residue: 0.2088 time to fit residues: 389.9624 Evaluate side-chains 848 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 842 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 3 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 335 optimal weight: 8.9990 chunk 112 optimal weight: 0.6980 chunk 118 optimal weight: 8.9990 chunk 300 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 237 optimal weight: 6.9990 chunk 310 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 HIS ** C 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 GLN ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 185 GLN ** P 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.088432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.062492 restraints weight = 123364.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.064629 restraints weight = 67282.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066070 restraints weight = 44798.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.067026 restraints weight = 33887.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.067615 restraints weight = 28037.296| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31134 Z= 0.200 Angle : 0.714 9.423 42181 Z= 0.369 Chirality : 0.043 0.278 4756 Planarity : 0.005 0.098 5084 Dihedral : 15.952 174.048 4907 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.02 % Favored : 97.93 % Rotamer: Outliers : 0.42 % Allowed : 3.29 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.14), residues: 3570 helix: 0.76 (0.11), residues: 2156 sheet: 1.13 (0.26), residues: 358 loop : 0.43 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 158 TYR 0.028 0.002 TYR F 240 PHE 0.029 0.002 PHE L 154 TRP 0.037 0.002 TRP P 211 HIS 0.011 0.002 HIS P 43 Details of bonding type rmsd covalent geometry : bond 0.00425 (31132) covalent geometry : angle 0.71359 (42181) hydrogen bonds : bond 0.04573 ( 1579) hydrogen bonds : angle 4.84299 ( 4611) Misc. bond : bond 0.00178 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 1024 time to evaluate : 1.235 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.9486 (mp10) cc_final: 0.9194 (mp10) REVERT: A 43 HIS cc_start: 0.9248 (m90) cc_final: 0.8973 (m90) REVERT: A 75 TYR cc_start: 0.8828 (m-80) cc_final: 0.8608 (m-80) REVERT: A 94 ILE cc_start: 0.9542 (pt) cc_final: 0.9133 (pt) REVERT: A 103 LYS cc_start: 0.9120 (tttt) cc_final: 0.8871 (tttp) REVERT: A 113 LEU cc_start: 0.9671 (mt) cc_final: 0.9312 (tt) REVERT: A 136 CYS cc_start: 0.8514 (m) cc_final: 0.8094 (m) REVERT: A 154 PHE cc_start: 0.9512 (m-80) cc_final: 0.9028 (m-80) REVERT: A 158 ARG cc_start: 0.9001 (ttp80) cc_final: 0.8655 (ttp80) REVERT: A 168 VAL cc_start: 0.9416 (t) cc_final: 0.9136 (p) REVERT: A 183 ASP cc_start: 0.8695 (t0) cc_final: 0.8333 (t70) REVERT: B 75 TYR cc_start: 0.8344 (m-80) cc_final: 0.8004 (m-80) REVERT: B 97 HIS cc_start: 0.7426 (p90) cc_final: 0.6657 (p-80) REVERT: B 111 GLU cc_start: 0.9182 (tp30) cc_final: 0.8870 (tp30) REVERT: B 159 ASP cc_start: 0.8995 (m-30) cc_final: 0.8674 (m-30) REVERT: B 223 ASN cc_start: 0.9417 (t0) cc_final: 0.8969 (t0) REVERT: C 46 LEU cc_start: 0.9869 (mt) cc_final: 0.9612 (mt) REVERT: C 98 GLN cc_start: 0.9160 (tp-100) cc_final: 0.8900 (tp-100) REVERT: C 99 LYS cc_start: 0.9175 (mmmt) cc_final: 0.8755 (tptp) REVERT: C 185 GLN cc_start: 0.9289 (mt0) cc_final: 0.8772 (mp10) REVERT: C 188 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8764 (tp30) REVERT: C 223 ASN cc_start: 0.9246 (t0) cc_final: 0.8962 (t0) REVERT: C 250 GLU cc_start: 0.9358 (tp30) cc_final: 0.8776 (tp30) REVERT: D 42 LEU cc_start: 0.9792 (tp) cc_final: 0.9583 (tp) REVERT: D 54 LYS cc_start: 0.9038 (tttt) cc_final: 0.7949 (ttmt) REVERT: D 152 GLU cc_start: 0.8673 (tp30) cc_final: 0.8468 (tm-30) REVERT: D 156 ASP cc_start: 0.9300 (m-30) cc_final: 0.9066 (m-30) REVERT: D 159 ASP cc_start: 0.8869 (m-30) cc_final: 0.8664 (m-30) REVERT: D 163 ASP cc_start: 0.9216 (m-30) cc_final: 0.8908 (m-30) REVERT: D 176 LEU cc_start: 0.9597 (tp) cc_final: 0.9242 (tp) REVERT: D 180 ILE cc_start: 0.9381 (mt) cc_final: 0.9131 (mt) REVERT: D 210 MET cc_start: 0.9652 (tpt) cc_final: 0.9417 (mtt) REVERT: D 211 TRP cc_start: 0.8761 (t-100) cc_final: 0.8142 (t60) REVERT: D 247 ILE cc_start: 0.9598 (mt) cc_final: 0.9352 (mm) REVERT: D 248 LEU cc_start: 0.9727 (mt) cc_final: 0.8998 (mt) REVERT: D 275 TYR cc_start: 0.7465 (m-10) cc_final: 0.6722 (m-10) REVERT: E 42 LEU cc_start: 0.9803 (tp) cc_final: 0.9554 (tp) REVERT: E 46 LEU cc_start: 0.9757 (mt) cc_final: 0.9501 (mt) REVERT: E 47 ASP cc_start: 0.9372 (t0) cc_final: 0.9127 (m-30) REVERT: E 99 LYS cc_start: 0.9535 (mtpp) cc_final: 0.9304 (mmmt) REVERT: E 100 CYS cc_start: 0.8548 (t) cc_final: 0.8210 (t) REVERT: E 104 ASP cc_start: 0.8707 (t70) cc_final: 0.7856 (t0) REVERT: E 107 LYS cc_start: 0.9250 (tttp) cc_final: 0.8937 (ttmm) REVERT: E 108 LYS cc_start: 0.9547 (mttm) cc_final: 0.9199 (mmmm) REVERT: E 139 GLU cc_start: 0.8970 (mp0) cc_final: 0.8595 (pm20) REVERT: E 140 MET cc_start: 0.8963 (ttm) cc_final: 0.8577 (tpp) REVERT: E 159 ASP cc_start: 0.9022 (t0) cc_final: 0.7420 (t0) REVERT: E 163 ASP cc_start: 0.8558 (m-30) cc_final: 0.7104 (m-30) REVERT: E 183 ASP cc_start: 0.9346 (t0) cc_final: 0.8737 (t70) REVERT: E 185 GLN cc_start: 0.8965 (mp10) cc_final: 0.8755 (mp10) REVERT: E 199 LEU cc_start: 0.8576 (tp) cc_final: 0.8171 (tp) REVERT: E 210 MET cc_start: 0.9605 (ttt) cc_final: 0.9348 (ttt) REVERT: E 246 GLU cc_start: 0.9236 (tm-30) cc_final: 0.8911 (tm-30) REVERT: F 27 ARG cc_start: 0.8986 (ttp-110) cc_final: 0.8781 (ptp-170) REVERT: F 111 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8893 (tm-30) REVERT: F 114 LYS cc_start: 0.9694 (mmtm) cc_final: 0.9466 (mmmm) REVERT: F 144 ASP cc_start: 0.9057 (t70) cc_final: 0.8357 (t0) REVERT: F 145 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8777 (mt-10) REVERT: F 170 LEU cc_start: 0.9625 (mt) cc_final: 0.9245 (mt) REVERT: F 190 PHE cc_start: 0.9502 (m-80) cc_final: 0.9053 (m-80) REVERT: F 199 LEU cc_start: 0.7918 (tp) cc_final: 0.7435 (tp) REVERT: F 210 MET cc_start: 0.9583 (mtm) cc_final: 0.9303 (mtp) REVERT: F 229 MET cc_start: 0.9426 (mtp) cc_final: 0.9139 (mtt) REVERT: F 238 GLU cc_start: 0.8248 (pp20) cc_final: 0.6553 (pp20) REVERT: F 240 TYR cc_start: 0.8911 (m-10) cc_final: 0.8452 (m-10) REVERT: G 75 TYR cc_start: 0.8586 (m-10) cc_final: 0.8112 (m-10) REVERT: G 154 PHE cc_start: 0.9148 (m-80) cc_final: 0.8881 (m-80) REVERT: G 174 ASP cc_start: 0.8675 (p0) cc_final: 0.8317 (p0) REVERT: G 190 PHE cc_start: 0.9282 (m-80) cc_final: 0.8736 (m-10) REVERT: G 250 GLU cc_start: 0.9287 (tp30) cc_final: 0.8580 (tp30) REVERT: H 100 CYS cc_start: 0.9254 (t) cc_final: 0.9045 (t) REVERT: H 103 LYS cc_start: 0.9358 (tttt) cc_final: 0.9005 (pttt) REVERT: H 144 ASP cc_start: 0.8585 (t0) cc_final: 0.8181 (t0) REVERT: H 176 LEU cc_start: 0.9547 (tp) cc_final: 0.9332 (tt) REVERT: H 183 ASP cc_start: 0.8633 (m-30) cc_final: 0.7915 (t70) REVERT: H 185 GLN cc_start: 0.9276 (mt0) cc_final: 0.9035 (mm110) REVERT: H 189 ARG cc_start: 0.9196 (tpt170) cc_final: 0.8752 (tpt170) REVERT: H 223 ASN cc_start: 0.9312 (t0) cc_final: 0.8827 (t0) REVERT: I 93 TYR cc_start: 0.9235 (t80) cc_final: 0.8934 (t80) REVERT: I 158 ARG cc_start: 0.9100 (ptm-80) cc_final: 0.8806 (tmm-80) REVERT: I 185 GLN cc_start: 0.9125 (mt0) cc_final: 0.8480 (mp10) REVERT: I 210 MET cc_start: 0.9200 (tmm) cc_final: 0.8925 (tmm) REVERT: I 211 TRP cc_start: 0.9388 (t-100) cc_final: 0.9031 (t60) REVERT: I 224 LEU cc_start: 0.9578 (mt) cc_final: 0.9229 (mt) REVERT: I 233 LEU cc_start: 0.9835 (tp) cc_final: 0.9496 (pp) REVERT: J 103 LYS cc_start: 0.9319 (tttt) cc_final: 0.9054 (tttp) REVERT: J 111 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8739 (tm-30) REVERT: J 115 TYR cc_start: 0.9048 (m-80) cc_final: 0.8752 (m-10) REVERT: J 127 ASP cc_start: 0.9150 (m-30) cc_final: 0.8837 (m-30) REVERT: J 139 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8820 (mp0) REVERT: J 144 ASP cc_start: 0.8326 (t0) cc_final: 0.7646 (p0) REVERT: J 162 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8455 (mm-30) REVERT: J 177 ASP cc_start: 0.9450 (p0) cc_final: 0.9206 (p0) REVERT: J 180 ILE cc_start: 0.9548 (mt) cc_final: 0.9341 (mt) REVERT: J 187 LEU cc_start: 0.9061 (mt) cc_final: 0.8829 (mt) REVERT: J 210 MET cc_start: 0.9704 (mtm) cc_final: 0.9179 (mtt) REVERT: K 54 LYS cc_start: 0.9442 (tppt) cc_final: 0.9204 (tptp) REVERT: K 116 ARG cc_start: 0.8679 (mmp80) cc_final: 0.7758 (mmp80) REVERT: K 124 ASP cc_start: 0.9466 (m-30) cc_final: 0.9257 (m-30) REVERT: K 127 ASP cc_start: 0.9330 (m-30) cc_final: 0.9129 (m-30) REVERT: K 129 THR cc_start: 0.9724 (m) cc_final: 0.9401 (p) REVERT: K 145 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7920 (mm-30) REVERT: K 158 ARG cc_start: 0.8742 (ptt90) cc_final: 0.8460 (ttp80) REVERT: K 159 ASP cc_start: 0.9228 (t70) cc_final: 0.8869 (t70) REVERT: K 162 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8228 (mm-30) REVERT: K 163 ASP cc_start: 0.8893 (m-30) cc_final: 0.8622 (m-30) REVERT: K 223 ASN cc_start: 0.9584 (m110) cc_final: 0.9371 (m110) REVERT: K 248 LEU cc_start: 0.9754 (mt) cc_final: 0.9404 (mt) REVERT: K 254 ARG cc_start: 0.9075 (ttp-170) cc_final: 0.8768 (ptm160) REVERT: L 38 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8671 (pm20) REVERT: L 63 ARG cc_start: 0.9482 (mmp80) cc_final: 0.9131 (mmm160) REVERT: L 100 CYS cc_start: 0.6911 (t) cc_final: 0.5417 (t) REVERT: L 124 ASP cc_start: 0.9392 (m-30) cc_final: 0.9095 (m-30) REVERT: L 184 GLU cc_start: 0.8852 (mp0) cc_final: 0.8648 (mp0) REVERT: L 213 GLN cc_start: 0.8570 (pp30) cc_final: 0.8071 (pp30) REVERT: L 215 VAL cc_start: 0.9680 (t) cc_final: 0.9004 (t) REVERT: L 240 TYR cc_start: 0.8847 (m-10) cc_final: 0.8336 (m-80) REVERT: L 269 GLN cc_start: 0.9396 (pp30) cc_final: 0.8758 (pp30) REVERT: O 46 LEU cc_start: 0.9689 (mt) cc_final: 0.9459 (mt) REVERT: O 71 ASP cc_start: 0.9496 (p0) cc_final: 0.9081 (p0) REVERT: O 107 LYS cc_start: 0.9779 (tttm) cc_final: 0.9551 (tttm) REVERT: O 130 ILE cc_start: 0.9857 (pt) cc_final: 0.9550 (pt) REVERT: O 134 LYS cc_start: 0.9521 (ptpp) cc_final: 0.9140 (tptp) REVERT: O 147 ASP cc_start: 0.8799 (p0) cc_final: 0.8247 (t0) REVERT: O 158 ARG cc_start: 0.9341 (tpt-90) cc_final: 0.8733 (tpt-90) REVERT: O 166 ILE cc_start: 0.9200 (mt) cc_final: 0.8925 (mm) REVERT: O 183 ASP cc_start: 0.9082 (t0) cc_final: 0.8535 (t0) REVERT: O 185 GLN cc_start: 0.9624 (tm-30) cc_final: 0.9384 (tm-30) REVERT: P 56 CYS cc_start: 0.9247 (p) cc_final: 0.8778 (p) REVERT: P 113 LEU cc_start: 0.9630 (tt) cc_final: 0.9341 (tt) REVERT: P 115 TYR cc_start: 0.8306 (m-10) cc_final: 0.8075 (m-10) REVERT: P 127 ASP cc_start: 0.9432 (m-30) cc_final: 0.9197 (m-30) REVERT: P 144 ASP cc_start: 0.8814 (t0) cc_final: 0.8598 (t0) REVERT: P 171 VAL cc_start: 0.7735 (t) cc_final: 0.7429 (p) REVERT: P 214 MET cc_start: 0.8661 (mtm) cc_final: 0.8011 (ptm) outliers start: 13 outliers final: 3 residues processed: 1031 average time/residue: 0.2028 time to fit residues: 330.0929 Evaluate side-chains 776 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 773 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 39 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 323 optimal weight: 0.9980 chunk 287 optimal weight: 1.9990 chunk 314 optimal weight: 7.9990 chunk 156 optimal weight: 0.0870 chunk 97 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN P 97 HIS P 185 GLN ** P 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.089104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.062918 restraints weight = 121435.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065124 restraints weight = 66033.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.066615 restraints weight = 43913.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.067584 restraints weight = 33068.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.068195 restraints weight = 27295.652| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.6348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31134 Z= 0.147 Angle : 0.682 8.291 42181 Z= 0.348 Chirality : 0.043 0.282 4756 Planarity : 0.004 0.050 5084 Dihedral : 15.770 175.648 4907 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.35 % Favored : 97.59 % Rotamer: Outliers : 0.22 % Allowed : 2.30 % Favored : 97.48 % 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: 1.14 (0.14), residues: 3570 helix: 0.98 (0.11), residues: 2060 sheet: 1.32 (0.27), residues: 358 loop : 0.40 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 63 TYR 0.018 0.002 TYR L 75 PHE 0.030 0.002 PHE O 106 TRP 0.035 0.002 TRP P 211 HIS 0.015 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00325 (31132) covalent geometry : angle 0.68230 (42181) hydrogen bonds : bond 0.04297 ( 1579) hydrogen bonds : angle 4.68844 ( 4611) Misc. bond : bond 0.00234 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 989 time to evaluate : 1.173 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: 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: 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 36 LEU cc_start: 0.9492 (tp) cc_final: 0.8832 (tp) REVERT: A 38 GLN cc_start: 0.9513 (mp10) cc_final: 0.8964 (mp10) REVERT: A 43 HIS cc_start: 0.9243 (m90) cc_final: 0.8833 (m-70) REVERT: A 46 LEU cc_start: 0.9800 (mt) cc_final: 0.9597 (mt) REVERT: A 70 CYS cc_start: 0.9551 (m) cc_final: 0.9306 (p) REVERT: A 75 TYR cc_start: 0.8958 (m-80) cc_final: 0.8707 (m-80) REVERT: A 93 TYR cc_start: 0.8823 (t80) cc_final: 0.8513 (t80) REVERT: A 94 ILE cc_start: 0.9355 (pt) cc_final: 0.9124 (pt) REVERT: A 113 LEU cc_start: 0.9676 (mt) cc_final: 0.9308 (tt) REVERT: A 131 GLU cc_start: 0.9326 (tt0) cc_final: 0.8866 (pt0) REVERT: A 136 CYS cc_start: 0.8364 (m) cc_final: 0.8019 (m) REVERT: A 140 MET cc_start: 0.9208 (ttm) cc_final: 0.9004 (ttp) REVERT: A 154 PHE cc_start: 0.9512 (m-80) cc_final: 0.9055 (m-80) REVERT: A 156 ASP cc_start: 0.9230 (m-30) cc_final: 0.9027 (m-30) REVERT: A 158 ARG cc_start: 0.8961 (ttp80) cc_final: 0.8256 (ttp80) REVERT: A 168 VAL cc_start: 0.9344 (t) cc_final: 0.9112 (p) REVERT: A 183 ASP cc_start: 0.8649 (t0) cc_final: 0.8284 (t70) REVERT: A 210 MET cc_start: 0.9471 (ptp) cc_final: 0.9145 (ptp) REVERT: A 214 MET cc_start: 0.9545 (mmp) cc_final: 0.9238 (mmm) REVERT: B 75 TYR cc_start: 0.8356 (m-80) cc_final: 0.8018 (m-80) REVERT: B 111 GLU cc_start: 0.9172 (tp30) cc_final: 0.8804 (tp30) REVERT: B 159 ASP cc_start: 0.9028 (m-30) cc_final: 0.8681 (m-30) REVERT: B 210 MET cc_start: 0.9643 (ttt) cc_final: 0.9080 (mtt) REVERT: B 214 MET cc_start: 0.9515 (mmp) cc_final: 0.8950 (mtt) REVERT: B 216 LEU cc_start: 0.9304 (mp) cc_final: 0.8759 (tp) REVERT: B 218 LEU cc_start: 0.8736 (mt) cc_final: 0.8438 (mt) REVERT: B 223 ASN cc_start: 0.9459 (t0) cc_final: 0.8744 (t0) REVERT: B 229 MET cc_start: 0.9164 (mpp) cc_final: 0.8774 (pmm) REVERT: C 46 LEU cc_start: 0.9849 (mt) cc_final: 0.9647 (mt) REVERT: C 98 GLN cc_start: 0.9234 (tp-100) cc_final: 0.9027 (tp-100) REVERT: C 99 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8724 (tptp) REVERT: C 154 PHE cc_start: 0.8652 (m-80) cc_final: 0.8340 (m-10) REVERT: C 183 ASP cc_start: 0.9434 (t0) cc_final: 0.9231 (t0) REVERT: C 185 GLN cc_start: 0.9398 (mt0) cc_final: 0.8843 (mp10) REVERT: C 223 ASN cc_start: 0.9285 (t0) cc_final: 0.8919 (t0) REVERT: C 247 ILE cc_start: 0.9644 (mt) cc_final: 0.9253 (mt) REVERT: C 250 GLU cc_start: 0.9380 (tp30) cc_final: 0.8784 (tp30) REVERT: D 38 GLN cc_start: 0.8823 (mt0) cc_final: 0.8618 (tt0) REVERT: D 54 LYS cc_start: 0.8931 (tttt) cc_final: 0.8603 (ttmt) REVERT: D 152 GLU cc_start: 0.8655 (tp30) cc_final: 0.8438 (tm-30) REVERT: D 163 ASP cc_start: 0.9219 (m-30) cc_final: 0.8947 (m-30) REVERT: D 176 LEU cc_start: 0.9462 (tp) cc_final: 0.9238 (tp) REVERT: D 180 ILE cc_start: 0.9380 (mt) cc_final: 0.9107 (mt) REVERT: D 194 LEU cc_start: 0.8736 (tt) cc_final: 0.8415 (tt) REVERT: D 211 TRP cc_start: 0.8678 (t-100) cc_final: 0.8157 (t-100) REVERT: D 229 MET cc_start: 0.8743 (mtt) cc_final: 0.8322 (mmt) REVERT: D 246 GLU cc_start: 0.8504 (pp20) cc_final: 0.8197 (pp20) REVERT: D 247 ILE cc_start: 0.9479 (mt) cc_final: 0.9055 (mm) REVERT: D 248 LEU cc_start: 0.9750 (mt) cc_final: 0.9330 (mp) REVERT: E 42 LEU cc_start: 0.9815 (tp) cc_final: 0.9572 (tt) REVERT: E 46 LEU cc_start: 0.9790 (mt) cc_final: 0.9523 (mt) REVERT: E 99 LYS cc_start: 0.9533 (mtpp) cc_final: 0.9291 (mmmt) REVERT: E 100 CYS cc_start: 0.8532 (t) cc_final: 0.8231 (t) REVERT: E 104 ASP cc_start: 0.8708 (t70) cc_final: 0.7858 (t0) REVERT: E 139 GLU cc_start: 0.8860 (mp0) cc_final: 0.8351 (pm20) REVERT: E 162 GLU cc_start: 0.8316 (pp20) cc_final: 0.8033 (pp20) REVERT: E 183 ASP cc_start: 0.9356 (t0) cc_final: 0.9046 (t70) REVERT: E 199 LEU cc_start: 0.8556 (tp) cc_final: 0.8243 (tp) REVERT: E 210 MET cc_start: 0.9617 (ttt) cc_final: 0.9334 (ttt) REVERT: E 253 ILE cc_start: 0.9713 (tt) cc_final: 0.9435 (pt) REVERT: E 275 TYR cc_start: 0.5647 (m-10) cc_final: 0.5180 (m-10) REVERT: F 111 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8813 (tm-30) REVERT: F 144 ASP cc_start: 0.9036 (t70) cc_final: 0.8273 (t0) REVERT: F 145 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8763 (mt-10) REVERT: F 170 LEU cc_start: 0.9613 (mt) cc_final: 0.9243 (mt) REVERT: F 190 PHE cc_start: 0.9502 (m-80) cc_final: 0.8904 (m-10) REVERT: F 199 LEU cc_start: 0.7867 (tp) cc_final: 0.7415 (tp) REVERT: F 210 MET cc_start: 0.9578 (mtm) cc_final: 0.9273 (mtp) REVERT: F 229 MET cc_start: 0.9405 (mtp) cc_final: 0.9168 (mtp) REVERT: F 246 GLU cc_start: 0.9058 (pp20) cc_final: 0.8825 (pp20) REVERT: G 75 TYR cc_start: 0.8571 (m-10) cc_final: 0.8068 (m-10) REVERT: G 174 ASP cc_start: 0.8661 (p0) cc_final: 0.8270 (p0) REVERT: G 190 PHE cc_start: 0.9244 (m-80) cc_final: 0.8943 (m-10) REVERT: G 210 MET cc_start: 0.9410 (mmp) cc_final: 0.9200 (mmm) REVERT: G 214 MET cc_start: 0.9613 (mpp) cc_final: 0.9384 (mpp) REVERT: G 250 GLU cc_start: 0.9256 (tp30) cc_final: 0.8680 (tp30) REVERT: H 103 LYS cc_start: 0.9284 (tttt) cc_final: 0.8993 (pttt) REVERT: H 127 ASP cc_start: 0.9031 (m-30) cc_final: 0.8821 (m-30) REVERT: H 139 GLU cc_start: 0.8656 (mp0) cc_final: 0.8225 (tt0) REVERT: H 144 ASP cc_start: 0.8465 (t0) cc_final: 0.8059 (t0) REVERT: H 159 ASP cc_start: 0.8385 (m-30) cc_final: 0.7980 (m-30) REVERT: H 176 LEU cc_start: 0.9527 (tp) cc_final: 0.9273 (tt) REVERT: H 183 ASP cc_start: 0.8654 (m-30) cc_final: 0.7909 (t70) REVERT: H 189 ARG cc_start: 0.9140 (tpt170) cc_final: 0.8746 (tpt170) REVERT: H 210 MET cc_start: 0.9487 (ptp) cc_final: 0.9124 (ptp) REVERT: H 223 ASN cc_start: 0.9328 (t0) cc_final: 0.8889 (t0) REVERT: I 93 TYR cc_start: 0.9164 (t80) cc_final: 0.8792 (t80) REVERT: I 139 GLU cc_start: 0.9044 (mp0) cc_final: 0.8836 (mp0) REVERT: I 158 ARG cc_start: 0.9125 (ptm-80) cc_final: 0.8918 (tmm-80) REVERT: I 185 GLN cc_start: 0.9208 (mt0) cc_final: 0.8496 (mp10) REVERT: I 210 MET cc_start: 0.9192 (tmm) cc_final: 0.8920 (tmm) REVERT: I 211 TRP cc_start: 0.9360 (t-100) cc_final: 0.9071 (t60) REVERT: I 224 LEU cc_start: 0.9557 (mt) cc_final: 0.9206 (mt) REVERT: I 233 LEU cc_start: 0.9832 (tp) cc_final: 0.9561 (pp) REVERT: I 244 LEU cc_start: 0.9691 (pp) cc_final: 0.9477 (pp) REVERT: J 97 HIS cc_start: 0.7535 (p90) cc_final: 0.7290 (p90) REVERT: J 100 CYS cc_start: 0.9240 (t) cc_final: 0.7842 (p) REVERT: J 103 LYS cc_start: 0.9273 (tttt) cc_final: 0.9008 (tttp) REVERT: J 111 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8774 (tm-30) REVERT: J 144 ASP cc_start: 0.8196 (t0) cc_final: 0.7910 (p0) REVERT: J 149 LEU cc_start: 0.9524 (mp) cc_final: 0.8956 (mt) REVERT: J 159 ASP cc_start: 0.9429 (t70) cc_final: 0.9060 (t0) REVERT: J 162 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8357 (mm-30) REVERT: J 177 ASP cc_start: 0.9357 (p0) cc_final: 0.9144 (p0) REVERT: J 210 MET cc_start: 0.9684 (mtm) cc_final: 0.9204 (mtt) REVERT: J 229 MET cc_start: 0.9383 (mmt) cc_final: 0.9072 (mmm) REVERT: K 54 LYS cc_start: 0.9461 (tppt) cc_final: 0.9177 (tptp) REVERT: K 92 VAL cc_start: 0.9757 (t) cc_final: 0.9476 (m) REVERT: K 116 ARG cc_start: 0.8661 (mmp80) cc_final: 0.8092 (mmp80) REVERT: K 129 THR cc_start: 0.9750 (m) cc_final: 0.9425 (p) REVERT: K 145 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7872 (mm-30) REVERT: K 159 ASP cc_start: 0.9221 (t70) cc_final: 0.8872 (t0) REVERT: K 162 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8320 (mm-30) REVERT: K 163 ASP cc_start: 0.8929 (m-30) cc_final: 0.8417 (m-30) REVERT: K 174 ASP cc_start: 0.9344 (p0) cc_final: 0.9034 (p0) REVERT: K 223 ASN cc_start: 0.9592 (m110) cc_final: 0.9200 (m110) REVERT: K 229 MET cc_start: 0.8770 (mmp) cc_final: 0.8542 (mtt) REVERT: K 254 ARG cc_start: 0.9098 (ttp-170) cc_final: 0.8724 (ptm160) REVERT: K 268 LEU cc_start: 0.9436 (mt) cc_final: 0.9182 (mt) REVERT: K 271 VAL cc_start: 0.9507 (t) cc_final: 0.9283 (m) REVERT: L 38 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8475 (pm20) REVERT: L 63 ARG cc_start: 0.9449 (mmp80) cc_final: 0.9138 (mmm160) REVERT: L 70 CYS cc_start: 0.9718 (t) cc_final: 0.9498 (p) REVERT: L 100 CYS cc_start: 0.6778 (t) cc_final: 0.5395 (t) REVERT: L 104 ASP cc_start: 0.8624 (t0) cc_final: 0.8364 (t0) REVERT: L 124 ASP cc_start: 0.9391 (m-30) cc_final: 0.9097 (m-30) REVERT: L 213 GLN cc_start: 0.8620 (pp30) cc_final: 0.8123 (pp30) REVERT: L 215 VAL cc_start: 0.9669 (t) cc_final: 0.9357 (t) REVERT: L 223 ASN cc_start: 0.9421 (t0) cc_final: 0.9199 (p0) REVERT: L 240 TYR cc_start: 0.8840 (m-10) cc_final: 0.8324 (m-80) REVERT: L 269 GLN cc_start: 0.9307 (pp30) cc_final: 0.8962 (pp30) REVERT: L 270 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8670 (mp0) REVERT: O 42 LEU cc_start: 0.9658 (mm) cc_final: 0.9450 (mm) REVERT: O 77 HIS cc_start: 0.8436 (m-70) cc_final: 0.8220 (m90) REVERT: O 106 PHE cc_start: 0.9451 (m-80) cc_final: 0.8929 (m-80) REVERT: O 107 LYS cc_start: 0.9780 (tttm) cc_final: 0.9401 (tttm) REVERT: O 111 GLU cc_start: 0.9482 (mt-10) cc_final: 0.9186 (mt-10) REVERT: O 134 LYS cc_start: 0.9499 (ptpp) cc_final: 0.9152 (tptp) REVERT: O 158 ARG cc_start: 0.9227 (tpt-90) cc_final: 0.8251 (tpt170) REVERT: O 180 ILE cc_start: 0.9547 (pt) cc_final: 0.9337 (pt) REVERT: O 183 ASP cc_start: 0.9059 (t0) cc_final: 0.8424 (t0) REVERT: O 185 GLN cc_start: 0.9657 (tm-30) cc_final: 0.9138 (tm-30) REVERT: O 240 TYR cc_start: 0.9241 (m-80) cc_final: 0.8929 (m-80) REVERT: P 113 LEU cc_start: 0.9621 (tt) cc_final: 0.9202 (tt) REVERT: P 115 TYR cc_start: 0.8227 (m-10) cc_final: 0.7975 (m-10) REVERT: P 127 ASP cc_start: 0.9407 (m-30) cc_final: 0.9153 (m-30) REVERT: P 144 ASP cc_start: 0.8838 (t0) cc_final: 0.8582 (t0) REVERT: P 154 PHE cc_start: 0.9621 (m-10) cc_final: 0.9143 (m-80) REVERT: P 168 VAL cc_start: 0.9207 (t) cc_final: 0.8886 (t) REVERT: P 176 LEU cc_start: 0.9593 (tp) cc_final: 0.9358 (pp) REVERT: P 214 MET cc_start: 0.8701 (mtm) cc_final: 0.8011 (ptm) REVERT: P 229 MET cc_start: 0.0718 (mtt) cc_final: -0.0143 (mtt) outliers start: 7 outliers final: 3 residues processed: 993 average time/residue: 0.1989 time to fit residues: 313.3174 Evaluate side-chains 763 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 759 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 351 optimal weight: 30.0000 chunk 56 optimal weight: 3.9990 chunk 316 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 298 optimal weight: 20.0000 chunk 294 optimal weight: 0.9980 chunk 168 optimal weight: 8.9990 chunk 227 optimal weight: 1.9990 chunk 317 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN A 213 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 HIS ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 HIS P 185 GLN ** P 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.086069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.060272 restraints weight = 124168.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.062343 restraints weight = 68421.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.063713 restraints weight = 45928.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.064630 restraints weight = 34934.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.065183 restraints weight = 29008.578| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.6820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31134 Z= 0.198 Angle : 0.685 8.530 42181 Z= 0.352 Chirality : 0.042 0.202 4756 Planarity : 0.004 0.050 5084 Dihedral : 15.587 177.675 4907 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.21 % Favored : 97.73 % Rotamer: Outliers : 0.13 % Allowed : 2.14 % Favored : 97.73 % 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: 1.11 (0.14), residues: 3570 helix: 0.96 (0.11), residues: 2134 sheet: 1.26 (0.27), residues: 358 loop : 0.32 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 175 TYR 0.055 0.002 TYR K 240 PHE 0.021 0.002 PHE O 106 TRP 0.047 0.002 TRP G 211 HIS 0.008 0.001 HIS K 193 Details of bonding type rmsd covalent geometry : bond 0.00423 (31132) covalent geometry : angle 0.68478 (42181) hydrogen bonds : bond 0.04387 ( 1579) hydrogen bonds : angle 4.72838 ( 4611) Misc. bond : bond 0.00237 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 934 time to evaluate : 1.130 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: 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: 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 36 LEU cc_start: 0.9529 (tp) cc_final: 0.8840 (tp) REVERT: A 38 GLN cc_start: 0.9545 (mp10) cc_final: 0.9050 (mp10) REVERT: A 43 HIS cc_start: 0.9301 (m90) cc_final: 0.8931 (m-70) REVERT: A 46 LEU cc_start: 0.9814 (mt) cc_final: 0.9572 (mt) REVERT: A 70 CYS cc_start: 0.9555 (m) cc_final: 0.9257 (p) REVERT: A 75 TYR cc_start: 0.8893 (m-80) cc_final: 0.8585 (m-80) REVERT: A 93 TYR cc_start: 0.9126 (t80) cc_final: 0.8679 (t80) REVERT: A 111 GLU cc_start: 0.9503 (tm-30) cc_final: 0.9293 (tm-30) REVERT: A 113 LEU cc_start: 0.9659 (mt) cc_final: 0.9336 (tt) REVERT: A 140 MET cc_start: 0.9265 (ttm) cc_final: 0.8766 (ttp) REVERT: A 149 LEU cc_start: 0.9697 (tp) cc_final: 0.9350 (tp) REVERT: A 154 PHE cc_start: 0.9533 (m-80) cc_final: 0.8907 (m-80) REVERT: A 168 VAL cc_start: 0.9375 (t) cc_final: 0.9171 (p) REVERT: A 183 ASP cc_start: 0.8755 (t0) cc_final: 0.8389 (t70) REVERT: A 214 MET cc_start: 0.9540 (mmp) cc_final: 0.9241 (mmm) REVERT: B 54 LYS cc_start: 0.9022 (tptp) cc_final: 0.8745 (tptp) REVERT: B 61 GLU cc_start: 0.8712 (mp0) cc_final: 0.8258 (pm20) REVERT: B 75 TYR cc_start: 0.8384 (m-80) cc_final: 0.8052 (m-80) REVERT: B 111 GLU cc_start: 0.9216 (tp30) cc_final: 0.8868 (tp30) REVERT: B 159 ASP cc_start: 0.8932 (m-30) cc_final: 0.8575 (m-30) REVERT: B 214 MET cc_start: 0.9514 (mmp) cc_final: 0.9257 (mmm) REVERT: B 216 LEU cc_start: 0.9270 (mp) cc_final: 0.8714 (tp) REVERT: B 218 LEU cc_start: 0.8841 (mt) cc_final: 0.8516 (mt) REVERT: B 223 ASN cc_start: 0.9552 (t0) cc_final: 0.8961 (t0) REVERT: B 229 MET cc_start: 0.9177 (mpp) cc_final: 0.8831 (pmm) REVERT: C 46 LEU cc_start: 0.9867 (mt) cc_final: 0.9642 (mt) REVERT: C 99 LYS cc_start: 0.9175 (mmmt) cc_final: 0.8960 (tptp) REVERT: C 185 GLN cc_start: 0.9188 (mt0) cc_final: 0.8678 (mp10) REVERT: C 223 ASN cc_start: 0.9378 (t0) cc_final: 0.9071 (t0) REVERT: C 246 GLU cc_start: 0.8835 (pm20) cc_final: 0.8325 (pm20) REVERT: C 250 GLU cc_start: 0.9362 (tp30) cc_final: 0.8879 (tp30) REVERT: D 131 GLU cc_start: 0.9186 (tt0) cc_final: 0.8874 (tm-30) REVERT: D 152 GLU cc_start: 0.8817 (tp30) cc_final: 0.8589 (tm-30) REVERT: D 156 ASP cc_start: 0.9228 (m-30) cc_final: 0.8703 (m-30) REVERT: D 159 ASP cc_start: 0.8874 (m-30) cc_final: 0.8669 (m-30) REVERT: D 163 ASP cc_start: 0.9183 (m-30) cc_final: 0.8862 (m-30) REVERT: D 176 LEU cc_start: 0.9496 (tp) cc_final: 0.9248 (tp) REVERT: D 180 ILE cc_start: 0.9427 (mt) cc_final: 0.9127 (mt) REVERT: D 210 MET cc_start: 0.9388 (mtm) cc_final: 0.9050 (ptp) REVERT: D 211 TRP cc_start: 0.8837 (t-100) cc_final: 0.8395 (t60) REVERT: D 229 MET cc_start: 0.8745 (mtt) cc_final: 0.8295 (mmt) REVERT: E 42 LEU cc_start: 0.9807 (tp) cc_final: 0.9544 (tt) REVERT: E 46 LEU cc_start: 0.9824 (mt) cc_final: 0.9521 (mt) REVERT: E 47 ASP cc_start: 0.9421 (t0) cc_final: 0.9211 (m-30) REVERT: E 97 HIS cc_start: 0.8254 (m-70) cc_final: 0.8033 (m90) REVERT: E 98 GLN cc_start: 0.8820 (mm110) cc_final: 0.8556 (mm110) REVERT: E 99 LYS cc_start: 0.9540 (mtpp) cc_final: 0.9282 (mmmt) REVERT: E 104 ASP cc_start: 0.8638 (t70) cc_final: 0.7939 (t0) REVERT: E 119 LYS cc_start: 0.8935 (mmtt) cc_final: 0.7608 (mmtm) REVERT: E 139 GLU cc_start: 0.8965 (mp0) cc_final: 0.8664 (mp0) REVERT: E 159 ASP cc_start: 0.8332 (t0) cc_final: 0.7666 (t0) REVERT: E 163 ASP cc_start: 0.8018 (m-30) cc_final: 0.7648 (m-30) REVERT: E 183 ASP cc_start: 0.9342 (t0) cc_final: 0.8556 (t70) REVERT: E 185 GLN cc_start: 0.9081 (mp10) cc_final: 0.8880 (mp10) REVERT: E 199 LEU cc_start: 0.8641 (tp) cc_final: 0.8352 (tp) REVERT: E 210 MET cc_start: 0.9580 (ttt) cc_final: 0.9274 (ttt) REVERT: E 240 TYR cc_start: 0.9132 (m-10) cc_final: 0.8919 (m-10) REVERT: E 253 ILE cc_start: 0.9706 (tt) cc_final: 0.9412 (pt) REVERT: F 144 ASP cc_start: 0.9086 (t70) cc_final: 0.8160 (t0) REVERT: F 145 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8703 (mt-10) REVERT: F 170 LEU cc_start: 0.9635 (mt) cc_final: 0.9278 (mt) REVERT: F 190 PHE cc_start: 0.9531 (m-80) cc_final: 0.9070 (m-10) REVERT: F 210 MET cc_start: 0.9551 (mtm) cc_final: 0.9207 (mtt) REVERT: F 229 MET cc_start: 0.9366 (mtp) cc_final: 0.9103 (mtt) REVERT: G 75 TYR cc_start: 0.8660 (m-10) cc_final: 0.8194 (m-10) REVERT: G 140 MET cc_start: 0.8802 (ttm) cc_final: 0.8469 (mtm) REVERT: G 154 PHE cc_start: 0.9188 (m-80) cc_final: 0.8926 (m-80) REVERT: G 170 LEU cc_start: 0.9655 (mm) cc_final: 0.9253 (mm) REVERT: G 174 ASP cc_start: 0.8816 (p0) cc_final: 0.8361 (p0) REVERT: G 190 PHE cc_start: 0.9277 (m-80) cc_final: 0.8883 (m-10) REVERT: G 250 GLU cc_start: 0.9353 (tp30) cc_final: 0.8662 (tp30) REVERT: H 103 LYS cc_start: 0.9403 (tttt) cc_final: 0.9082 (pttt) REVERT: H 127 ASP cc_start: 0.9007 (m-30) cc_final: 0.8795 (m-30) REVERT: H 144 ASP cc_start: 0.8436 (t0) cc_final: 0.8123 (t0) REVERT: H 176 LEU cc_start: 0.9584 (tp) cc_final: 0.9311 (tt) REVERT: H 183 ASP cc_start: 0.8720 (m-30) cc_final: 0.7829 (t70) REVERT: H 189 ARG cc_start: 0.9183 (tpt170) cc_final: 0.8879 (mmm-85) REVERT: H 210 MET cc_start: 0.9485 (ptp) cc_final: 0.9188 (ptp) REVERT: H 223 ASN cc_start: 0.9377 (t0) cc_final: 0.9013 (t0) REVERT: I 93 TYR cc_start: 0.9150 (t80) cc_final: 0.8730 (t80) REVERT: I 185 GLN cc_start: 0.9232 (mt0) cc_final: 0.8464 (mp10) REVERT: I 210 MET cc_start: 0.9195 (tmm) cc_final: 0.8824 (tmm) REVERT: I 224 LEU cc_start: 0.9584 (mt) cc_final: 0.9160 (mt) REVERT: I 229 MET cc_start: 0.8933 (mmp) cc_final: 0.8591 (mmm) REVERT: J 97 HIS cc_start: 0.7748 (p90) cc_final: 0.7454 (p90) REVERT: J 99 LYS cc_start: 0.9570 (mmmm) cc_final: 0.9255 (mmmm) REVERT: J 100 CYS cc_start: 0.9233 (t) cc_final: 0.8305 (p) REVERT: J 103 LYS cc_start: 0.9309 (tttt) cc_final: 0.8911 (tppt) REVERT: J 127 ASP cc_start: 0.9125 (m-30) cc_final: 0.8896 (m-30) REVERT: J 149 LEU cc_start: 0.9564 (mp) cc_final: 0.9113 (mp) REVERT: J 162 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8365 (mm-30) REVERT: J 210 MET cc_start: 0.9687 (mtm) cc_final: 0.9397 (mtp) REVERT: J 229 MET cc_start: 0.9402 (mmt) cc_final: 0.9102 (mmm) REVERT: K 54 LYS cc_start: 0.9410 (tppt) cc_final: 0.9007 (mmmt) REVERT: K 92 VAL cc_start: 0.9765 (t) cc_final: 0.9461 (m) REVERT: K 116 ARG cc_start: 0.8686 (mmp80) cc_final: 0.8166 (mmp80) REVERT: K 124 ASP cc_start: 0.9499 (m-30) cc_final: 0.9213 (m-30) REVERT: K 129 THR cc_start: 0.9748 (m) cc_final: 0.9436 (p) REVERT: K 145 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7902 (mm-30) REVERT: K 162 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8515 (mm-30) REVERT: K 210 MET cc_start: 0.9100 (mtm) cc_final: 0.8864 (mtt) REVERT: K 223 ASN cc_start: 0.9603 (m110) cc_final: 0.9263 (m110) REVERT: K 229 MET cc_start: 0.8868 (mmp) cc_final: 0.8615 (mtt) REVERT: L 38 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8587 (pm20) REVERT: L 63 ARG cc_start: 0.9502 (mmp80) cc_final: 0.9120 (mmm160) REVERT: L 70 CYS cc_start: 0.9718 (t) cc_final: 0.9473 (p) REVERT: L 93 TYR cc_start: 0.8842 (t80) cc_final: 0.8606 (t80) REVERT: L 100 CYS cc_start: 0.6386 (t) cc_final: 0.5386 (t) REVERT: L 104 ASP cc_start: 0.8653 (t0) cc_final: 0.8442 (t0) REVERT: L 124 ASP cc_start: 0.9399 (m-30) cc_final: 0.9130 (m-30) REVERT: L 131 GLU cc_start: 0.9318 (tt0) cc_final: 0.8956 (pt0) REVERT: L 215 VAL cc_start: 0.9734 (t) cc_final: 0.8991 (t) REVERT: L 223 ASN cc_start: 0.9445 (t0) cc_final: 0.9178 (p0) REVERT: L 240 TYR cc_start: 0.8910 (m-10) cc_final: 0.8364 (m-80) REVERT: L 269 GLN cc_start: 0.9178 (pp30) cc_final: 0.8935 (pp30) REVERT: O 108 LYS cc_start: 0.9613 (mtpt) cc_final: 0.9282 (pttm) REVERT: O 134 LYS cc_start: 0.9460 (ptpp) cc_final: 0.9131 (tptp) REVERT: O 147 ASP cc_start: 0.8800 (p0) cc_final: 0.7887 (t0) REVERT: O 183 ASP cc_start: 0.9096 (t0) cc_final: 0.8494 (t0) REVERT: O 185 GLN cc_start: 0.9444 (tm-30) cc_final: 0.8774 (tm-30) REVERT: O 240 TYR cc_start: 0.9222 (m-80) cc_final: 0.8787 (m-80) REVERT: P 56 CYS cc_start: 0.9222 (p) cc_final: 0.8399 (p) REVERT: P 113 LEU cc_start: 0.9634 (tt) cc_final: 0.9177 (tt) REVERT: P 115 TYR cc_start: 0.8499 (m-10) cc_final: 0.8223 (m-10) REVERT: P 127 ASP cc_start: 0.9413 (m-30) cc_final: 0.9149 (m-30) REVERT: P 144 ASP cc_start: 0.8597 (t0) cc_final: 0.8116 (t0) REVERT: P 154 PHE cc_start: 0.9640 (m-10) cc_final: 0.9387 (m-80) REVERT: P 164 LEU cc_start: 0.8796 (mm) cc_final: 0.8461 (mm) REVERT: P 168 VAL cc_start: 0.9377 (t) cc_final: 0.8969 (t) REVERT: P 214 MET cc_start: 0.8720 (mtm) cc_final: 0.8158 (ptm) REVERT: P 229 MET cc_start: 0.0839 (mtt) cc_final: 0.0241 (mtt) outliers start: 4 outliers final: 3 residues processed: 937 average time/residue: 0.1940 time to fit residues: 288.4427 Evaluate side-chains 733 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 730 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 195 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 295 optimal weight: 7.9990 chunk 255 optimal weight: 1.9990 chunk 321 optimal weight: 4.9990 chunk 93 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 194 optimal weight: 0.0770 chunk 76 optimal weight: 5.9990 chunk 281 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN B 185 GLN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN I 22 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 185 GLN L 38 GLN O 38 GLN P 97 HIS P 185 GLN ** P 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.086474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.060552 restraints weight = 124131.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.062674 restraints weight = 68196.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.064076 restraints weight = 45666.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065044 restraints weight = 34669.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.065640 restraints weight = 28592.573| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.7059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31134 Z= 0.150 Angle : 0.672 8.765 42181 Z= 0.344 Chirality : 0.042 0.223 4756 Planarity : 0.004 0.075 5084 Dihedral : 15.437 179.789 4907 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.70 % Rotamer: Outliers : 0.06 % Allowed : 1.79 % Favored : 98.15 % 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: 1.13 (0.14), residues: 3570 helix: 1.05 (0.11), residues: 2098 sheet: 1.30 (0.27), residues: 358 loop : 0.19 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 158 TYR 0.026 0.001 TYR G 93 PHE 0.029 0.002 PHE O 106 TRP 0.045 0.002 TRP G 211 HIS 0.015 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00331 (31132) covalent geometry : angle 0.67236 (42181) hydrogen bonds : bond 0.04143 ( 1579) hydrogen bonds : angle 4.66240 ( 4611) Misc. bond : bond 0.00286 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 937 time to evaluate : 1.186 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: 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: 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 36 LEU cc_start: 0.9489 (tp) cc_final: 0.8879 (tp) REVERT: A 38 GLN cc_start: 0.9558 (mp10) cc_final: 0.9077 (mp10) REVERT: A 43 HIS cc_start: 0.9324 (m90) cc_final: 0.8949 (m-70) REVERT: A 46 LEU cc_start: 0.9812 (mt) cc_final: 0.9594 (mt) REVERT: A 70 CYS cc_start: 0.9504 (m) cc_final: 0.9200 (p) REVERT: A 93 TYR cc_start: 0.9202 (t80) cc_final: 0.8766 (t80) REVERT: A 111 GLU cc_start: 0.9514 (tm-30) cc_final: 0.9290 (tm-30) REVERT: A 113 LEU cc_start: 0.9665 (mt) cc_final: 0.9320 (tt) REVERT: A 140 MET cc_start: 0.9220 (ttm) cc_final: 0.8765 (ttp) REVERT: A 149 LEU cc_start: 0.9659 (tp) cc_final: 0.9326 (tp) REVERT: A 154 PHE cc_start: 0.9519 (m-80) cc_final: 0.8948 (m-80) REVERT: A 158 ARG cc_start: 0.9064 (ttp80) cc_final: 0.8737 (ttp80) REVERT: A 162 GLU cc_start: 0.8701 (pp20) cc_final: 0.8029 (pp20) REVERT: A 168 VAL cc_start: 0.9363 (t) cc_final: 0.9161 (p) REVERT: A 183 ASP cc_start: 0.8606 (t0) cc_final: 0.8222 (t70) REVERT: A 210 MET cc_start: 0.9520 (ptp) cc_final: 0.9251 (ptp) REVERT: A 214 MET cc_start: 0.9504 (mmp) cc_final: 0.9207 (mmm) REVERT: A 246 GLU cc_start: 0.9550 (OUTLIER) cc_final: 0.9297 (pm20) REVERT: A 250 GLU cc_start: 0.9650 (tp30) cc_final: 0.9382 (pt0) REVERT: B 61 GLU cc_start: 0.8677 (mp0) cc_final: 0.8296 (pm20) REVERT: B 75 TYR cc_start: 0.8365 (m-80) cc_final: 0.7992 (m-80) REVERT: B 111 GLU cc_start: 0.9157 (tp30) cc_final: 0.8792 (tp30) REVERT: B 159 ASP cc_start: 0.8794 (m-30) cc_final: 0.8491 (m-30) REVERT: B 210 MET cc_start: 0.9605 (ttt) cc_final: 0.9086 (mtt) REVERT: B 214 MET cc_start: 0.9495 (mmp) cc_final: 0.8985 (mtt) REVERT: B 216 LEU cc_start: 0.9198 (mp) cc_final: 0.8635 (tp) REVERT: B 218 LEU cc_start: 0.8808 (mt) cc_final: 0.8522 (mt) REVERT: B 223 ASN cc_start: 0.9561 (t0) cc_final: 0.8958 (t0) REVERT: B 229 MET cc_start: 0.9157 (mpp) cc_final: 0.8815 (pmm) REVERT: C 99 LYS cc_start: 0.9214 (mmmt) cc_final: 0.8967 (tptp) REVERT: C 144 ASP cc_start: 0.7842 (p0) cc_final: 0.7591 (p0) REVERT: C 166 ILE cc_start: 0.9503 (mt) cc_final: 0.9287 (mm) REVERT: C 173 THR cc_start: 0.8334 (p) cc_final: 0.8001 (t) REVERT: C 185 GLN cc_start: 0.9370 (mt0) cc_final: 0.8778 (mp10) REVERT: C 223 ASN cc_start: 0.9405 (t0) cc_final: 0.9144 (t0) REVERT: C 247 ILE cc_start: 0.9568 (mt) cc_final: 0.8875 (mt) REVERT: C 250 GLU cc_start: 0.9392 (tp30) cc_final: 0.8885 (tp30) REVERT: D 99 LYS cc_start: 0.9352 (mptt) cc_final: 0.8729 (tptt) REVERT: D 156 ASP cc_start: 0.9163 (m-30) cc_final: 0.8737 (m-30) REVERT: D 176 LEU cc_start: 0.9460 (tp) cc_final: 0.9200 (tp) REVERT: D 180 ILE cc_start: 0.9379 (mt) cc_final: 0.9105 (mt) REVERT: D 210 MET cc_start: 0.9401 (mtm) cc_final: 0.9143 (mtt) REVERT: D 211 TRP cc_start: 0.8714 (t-100) cc_final: 0.8161 (t60) REVERT: D 229 MET cc_start: 0.8756 (mtt) cc_final: 0.8326 (mmt) REVERT: D 247 ILE cc_start: 0.9484 (mm) cc_final: 0.9242 (mm) REVERT: E 47 ASP cc_start: 0.9413 (t0) cc_final: 0.9207 (m-30) REVERT: E 98 GLN cc_start: 0.8772 (mm110) cc_final: 0.8505 (mm110) REVERT: E 99 LYS cc_start: 0.9546 (mtpp) cc_final: 0.9270 (mmmt) REVERT: E 104 ASP cc_start: 0.8615 (t70) cc_final: 0.8009 (t0) REVERT: E 127 ASP cc_start: 0.9114 (t70) cc_final: 0.8821 (t0) REVERT: E 139 GLU cc_start: 0.8993 (mp0) cc_final: 0.8737 (mp0) REVERT: E 159 ASP cc_start: 0.8482 (t0) cc_final: 0.7888 (t0) REVERT: E 163 ASP cc_start: 0.8052 (m-30) cc_final: 0.7713 (m-30) REVERT: E 183 ASP cc_start: 0.9414 (t0) cc_final: 0.8994 (t70) REVERT: E 185 GLN cc_start: 0.9030 (mp10) cc_final: 0.8826 (mp10) REVERT: E 199 LEU cc_start: 0.8566 (tp) cc_final: 0.8255 (tp) REVERT: E 210 MET cc_start: 0.9567 (ttt) cc_final: 0.9059 (ttt) REVERT: E 213 GLN cc_start: 0.8956 (pp30) cc_final: 0.8621 (pp30) REVERT: E 253 ILE cc_start: 0.9693 (tt) cc_final: 0.9400 (pt) REVERT: F 111 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8879 (tm-30) REVERT: F 119 LYS cc_start: 0.8830 (mptt) cc_final: 0.8609 (mmtt) REVERT: F 125 PHE cc_start: 0.9070 (t80) cc_final: 0.8835 (t80) REVERT: F 144 ASP cc_start: 0.9061 (t70) cc_final: 0.8113 (t0) REVERT: F 145 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8670 (mt-10) REVERT: F 170 LEU cc_start: 0.9674 (mt) cc_final: 0.9347 (mt) REVERT: F 190 PHE cc_start: 0.9510 (m-80) cc_final: 0.9052 (m-10) REVERT: F 199 LEU cc_start: 0.8295 (tp) cc_final: 0.7898 (tp) REVERT: F 210 MET cc_start: 0.9546 (mtm) cc_final: 0.9237 (mtp) REVERT: F 229 MET cc_start: 0.9353 (mtp) cc_final: 0.9127 (mtp) REVERT: F 246 GLU cc_start: 0.9022 (pp20) cc_final: 0.8773 (pp20) REVERT: G 75 TYR cc_start: 0.8643 (m-10) cc_final: 0.8153 (m-10) REVERT: G 140 MET cc_start: 0.8675 (ttm) cc_final: 0.8454 (mtm) REVERT: G 154 PHE cc_start: 0.9162 (m-80) cc_final: 0.8858 (m-80) REVERT: G 159 ASP cc_start: 0.9308 (t70) cc_final: 0.8400 (t70) REVERT: G 170 LEU cc_start: 0.9709 (mm) cc_final: 0.9479 (mm) REVERT: G 174 ASP cc_start: 0.8811 (p0) cc_final: 0.8350 (p0) REVERT: G 175 ARG cc_start: 0.8610 (mmp80) cc_final: 0.8401 (mmm160) REVERT: G 246 GLU cc_start: 0.9300 (pt0) cc_final: 0.9011 (pp20) REVERT: G 250 GLU cc_start: 0.9298 (tp30) cc_final: 0.8700 (tp30) REVERT: H 103 LYS cc_start: 0.9353 (tttt) cc_final: 0.9055 (pttt) REVERT: H 162 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8613 (mm-30) REVERT: H 176 LEU cc_start: 0.9591 (tp) cc_final: 0.9327 (tt) REVERT: H 183 ASP cc_start: 0.8565 (m-30) cc_final: 0.7635 (t70) REVERT: H 189 ARG cc_start: 0.9153 (tpt170) cc_final: 0.8849 (mmm-85) REVERT: H 210 MET cc_start: 0.9449 (ptp) cc_final: 0.9125 (ptp) REVERT: H 223 ASN cc_start: 0.9456 (t0) cc_final: 0.9131 (t0) REVERT: I 93 TYR cc_start: 0.9083 (t80) cc_final: 0.8747 (t80) REVERT: I 139 GLU cc_start: 0.9004 (mp0) cc_final: 0.8671 (mp0) REVERT: I 185 GLN cc_start: 0.9215 (mt0) cc_final: 0.8475 (mp10) REVERT: I 210 MET cc_start: 0.9218 (tmm) cc_final: 0.8859 (tmm) REVERT: I 224 LEU cc_start: 0.9570 (mt) cc_final: 0.9111 (mt) REVERT: I 233 LEU cc_start: 0.9860 (tp) cc_final: 0.9581 (pp) REVERT: J 93 TYR cc_start: 0.9036 (t80) cc_final: 0.8763 (t80) REVERT: J 97 HIS cc_start: 0.7704 (p90) cc_final: 0.7497 (p90) REVERT: J 99 LYS cc_start: 0.9539 (mmmm) cc_final: 0.9233 (mmmm) REVERT: J 111 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8877 (tm-30) REVERT: J 127 ASP cc_start: 0.9093 (m-30) cc_final: 0.8853 (m-30) REVERT: J 139 GLU cc_start: 0.9069 (mp0) cc_final: 0.8474 (mp0) REVERT: J 159 ASP cc_start: 0.9296 (t70) cc_final: 0.9063 (t0) REVERT: J 162 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8265 (mm-30) REVERT: J 185 GLN cc_start: 0.9585 (mm110) cc_final: 0.9304 (mm110) REVERT: J 187 LEU cc_start: 0.8843 (mt) cc_final: 0.8636 (mt) REVERT: J 210 MET cc_start: 0.9676 (mtm) cc_final: 0.9363 (mtp) REVERT: J 229 MET cc_start: 0.9400 (mmt) cc_final: 0.9107 (mmm) REVERT: K 46 LEU cc_start: 0.9742 (mt) cc_final: 0.9538 (mt) REVERT: K 54 LYS cc_start: 0.9463 (tppt) cc_final: 0.8972 (mmmt) REVERT: K 92 VAL cc_start: 0.9734 (t) cc_final: 0.9482 (m) REVERT: K 116 ARG cc_start: 0.8700 (mmp80) cc_final: 0.8180 (mmp80) REVERT: K 124 ASP cc_start: 0.9510 (m-30) cc_final: 0.9280 (m-30) REVERT: K 129 THR cc_start: 0.9722 (m) cc_final: 0.9411 (p) REVERT: K 140 MET cc_start: 0.8993 (ttp) cc_final: 0.8552 (ttp) REVERT: K 145 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7878 (mm-30) REVERT: K 162 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8492 (mm-30) REVERT: K 210 MET cc_start: 0.9236 (mtm) cc_final: 0.8854 (mtt) REVERT: K 214 MET cc_start: 0.9309 (mtm) cc_final: 0.9100 (mtp) REVERT: K 223 ASN cc_start: 0.9604 (m110) cc_final: 0.9397 (m110) REVERT: L 37 GLN cc_start: 0.9540 (pm20) cc_final: 0.9303 (pm20) REVERT: L 38 GLN cc_start: 0.9008 (mm110) cc_final: 0.8706 (pm20) REVERT: L 63 ARG cc_start: 0.9394 (mmp80) cc_final: 0.9022 (mmm160) REVERT: L 70 CYS cc_start: 0.9710 (t) cc_final: 0.9486 (p) REVERT: L 93 TYR cc_start: 0.8852 (t80) cc_final: 0.8385 (t80) REVERT: L 100 CYS cc_start: 0.6392 (t) cc_final: 0.4854 (t) REVERT: L 104 ASP cc_start: 0.8627 (t0) cc_final: 0.8350 (t0) REVERT: L 124 ASP cc_start: 0.9348 (m-30) cc_final: 0.9105 (m-30) REVERT: L 131 GLU cc_start: 0.9312 (tt0) cc_final: 0.8925 (pt0) REVERT: L 215 VAL cc_start: 0.9737 (t) cc_final: 0.9061 (t) REVERT: L 240 TYR cc_start: 0.8875 (m-10) cc_final: 0.8345 (m-80) REVERT: L 269 GLN cc_start: 0.9208 (pp30) cc_final: 0.8966 (pp30) REVERT: O 106 PHE cc_start: 0.9438 (m-80) cc_final: 0.9100 (m-80) REVERT: O 124 ASP cc_start: 0.9637 (m-30) cc_final: 0.9418 (m-30) REVERT: O 183 ASP cc_start: 0.9115 (t0) cc_final: 0.8552 (t70) REVERT: O 240 TYR cc_start: 0.9209 (m-80) cc_final: 0.8754 (m-80) REVERT: P 56 CYS cc_start: 0.9140 (p) cc_final: 0.8439 (p) REVERT: P 127 ASP cc_start: 0.9354 (m-30) cc_final: 0.9079 (m-30) REVERT: P 144 ASP cc_start: 0.8722 (t0) cc_final: 0.8208 (t0) REVERT: P 168 VAL cc_start: 0.9202 (t) cc_final: 0.8815 (t) REVERT: P 190 PHE cc_start: 0.9259 (m-80) cc_final: 0.8919 (m-80) REVERT: P 214 MET cc_start: 0.8794 (mtm) cc_final: 0.8207 (ptm) REVERT: P 229 MET cc_start: 0.0924 (mtt) cc_final: 0.0328 (mtt) outliers start: 2 outliers final: 0 residues processed: 938 average time/residue: 0.2001 time to fit residues: 297.8073 Evaluate side-chains 725 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 724 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 323 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 234 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 336 optimal weight: 20.0000 chunk 232 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN P 97 HIS P 185 GLN ** P 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.085472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.059513 restraints weight = 125734.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.061580 restraints weight = 69441.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.062958 restraints weight = 46591.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.063854 restraints weight = 35528.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.064459 restraints weight = 29629.110| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.7273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31134 Z= 0.169 Angle : 0.674 7.785 42181 Z= 0.346 Chirality : 0.043 0.341 4756 Planarity : 0.004 0.079 5084 Dihedral : 15.343 178.929 4907 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.41 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: 1.13 (0.14), residues: 3570 helix: 1.09 (0.12), residues: 2096 sheet: 1.17 (0.27), residues: 358 loop : 0.16 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 76 TYR 0.033 0.002 TYR H 75 PHE 0.031 0.002 PHE D 196 TRP 0.045 0.002 TRP G 211 HIS 0.013 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00373 (31132) covalent geometry : angle 0.67359 (42181) hydrogen bonds : bond 0.04247 ( 1579) hydrogen bonds : angle 4.70316 ( 4611) Misc. bond : bond 0.00478 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 904 time to evaluate : 1.189 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: 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: 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 38 GLN cc_start: 0.9569 (mp10) cc_final: 0.9315 (mp10) REVERT: A 43 HIS cc_start: 0.9286 (m90) cc_final: 0.8950 (m-70) REVERT: A 46 LEU cc_start: 0.9822 (mt) cc_final: 0.9583 (mt) REVERT: A 70 CYS cc_start: 0.9520 (m) cc_final: 0.9073 (p) REVERT: A 93 TYR cc_start: 0.9332 (t80) cc_final: 0.8717 (t80) REVERT: A 111 GLU cc_start: 0.9558 (tm-30) cc_final: 0.9317 (tm-30) REVERT: A 113 LEU cc_start: 0.9658 (mt) cc_final: 0.9304 (tt) REVERT: A 140 MET cc_start: 0.9249 (ttm) cc_final: 0.8751 (ttp) REVERT: A 154 PHE cc_start: 0.9548 (m-80) cc_final: 0.9094 (m-80) REVERT: A 158 ARG cc_start: 0.9040 (ttp80) cc_final: 0.8289 (ttp80) REVERT: A 183 ASP cc_start: 0.8660 (t0) cc_final: 0.8259 (t70) REVERT: A 214 MET cc_start: 0.9496 (mmp) cc_final: 0.9224 (mmm) REVERT: A 250 GLU cc_start: 0.9642 (tp30) cc_final: 0.9165 (tp30) REVERT: B 61 GLU cc_start: 0.8669 (mp0) cc_final: 0.8299 (pm20) REVERT: B 75 TYR cc_start: 0.8402 (m-80) cc_final: 0.8009 (m-80) REVERT: B 98 GLN cc_start: 0.9126 (tp40) cc_final: 0.8891 (mm-40) REVERT: B 111 GLU cc_start: 0.9203 (tp30) cc_final: 0.8823 (tp30) REVERT: B 159 ASP cc_start: 0.8738 (m-30) cc_final: 0.8460 (m-30) REVERT: B 216 LEU cc_start: 0.9228 (mp) cc_final: 0.8664 (tp) REVERT: B 218 LEU cc_start: 0.8841 (mt) cc_final: 0.8553 (mt) REVERT: B 223 ASN cc_start: 0.9581 (t0) cc_final: 0.9215 (t0) REVERT: C 46 LEU cc_start: 0.9874 (mt) cc_final: 0.9654 (mt) REVERT: C 95 ARG cc_start: 0.9068 (ttm-80) cc_final: 0.8722 (ttm-80) REVERT: C 99 LYS cc_start: 0.9225 (mmmt) cc_final: 0.8860 (tptp) REVERT: C 140 MET cc_start: 0.8860 (ttm) cc_final: 0.8652 (ttm) REVERT: C 166 ILE cc_start: 0.9502 (mt) cc_final: 0.9277 (mm) REVERT: C 173 THR cc_start: 0.8196 (p) cc_final: 0.7788 (t) REVERT: C 183 ASP cc_start: 0.9441 (t0) cc_final: 0.9203 (t0) REVERT: C 187 LEU cc_start: 0.9217 (mt) cc_final: 0.8842 (mt) REVERT: C 223 ASN cc_start: 0.9377 (t0) cc_final: 0.9139 (t0) REVERT: C 250 GLU cc_start: 0.9393 (tp30) cc_final: 0.8850 (tp30) REVERT: D 99 LYS cc_start: 0.9259 (mmtt) cc_final: 0.8908 (tptp) REVERT: D 163 ASP cc_start: 0.9100 (m-30) cc_final: 0.8803 (m-30) REVERT: D 176 LEU cc_start: 0.9469 (tp) cc_final: 0.9216 (tp) REVERT: D 180 ILE cc_start: 0.9380 (mt) cc_final: 0.9105 (mt) REVERT: D 210 MET cc_start: 0.9405 (mtm) cc_final: 0.9159 (ptp) REVERT: D 211 TRP cc_start: 0.8713 (t-100) cc_final: 0.8207 (t60) REVERT: D 229 MET cc_start: 0.8868 (mtt) cc_final: 0.8356 (mmt) REVERT: E 47 ASP cc_start: 0.9424 (t0) cc_final: 0.9189 (m-30) REVERT: E 97 HIS cc_start: 0.8365 (m-70) cc_final: 0.8155 (m90) REVERT: E 98 GLN cc_start: 0.8787 (mm110) cc_final: 0.8524 (mm110) REVERT: E 99 LYS cc_start: 0.9534 (mtpp) cc_final: 0.9287 (mmmt) REVERT: E 104 ASP cc_start: 0.8662 (t70) cc_final: 0.8033 (t0) REVERT: E 127 ASP cc_start: 0.9025 (t70) cc_final: 0.8824 (t0) REVERT: E 139 GLU cc_start: 0.9042 (mp0) cc_final: 0.8772 (mp0) REVERT: E 159 ASP cc_start: 0.8461 (t0) cc_final: 0.7917 (t0) REVERT: E 163 ASP cc_start: 0.8033 (m-30) cc_final: 0.7714 (m-30) REVERT: E 183 ASP cc_start: 0.9390 (t0) cc_final: 0.8972 (t0) REVERT: E 185 GLN cc_start: 0.8949 (mp10) cc_final: 0.8675 (mp10) REVERT: E 199 LEU cc_start: 0.8625 (tp) cc_final: 0.8187 (tp) REVERT: E 210 MET cc_start: 0.9565 (ttt) cc_final: 0.9070 (ttt) REVERT: E 213 GLN cc_start: 0.8999 (pp30) cc_final: 0.8650 (pp30) REVERT: E 253 ILE cc_start: 0.9706 (tt) cc_final: 0.9408 (pt) REVERT: F 42 LEU cc_start: 0.9369 (mt) cc_final: 0.9120 (mt) REVERT: F 111 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8876 (tm-30) REVERT: F 112 TYR cc_start: 0.9511 (t80) cc_final: 0.9275 (t80) REVERT: F 125 PHE cc_start: 0.9053 (t80) cc_final: 0.8795 (t80) REVERT: F 144 ASP cc_start: 0.9060 (t70) cc_final: 0.8090 (t0) REVERT: F 145 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8665 (mt-10) REVERT: F 170 LEU cc_start: 0.9670 (mt) cc_final: 0.9344 (mt) REVERT: F 190 PHE cc_start: 0.9496 (m-80) cc_final: 0.9111 (m-10) REVERT: F 199 LEU cc_start: 0.8245 (tp) cc_final: 0.7782 (tp) REVERT: F 210 MET cc_start: 0.9549 (mtm) cc_final: 0.9218 (mtt) REVERT: F 229 MET cc_start: 0.9345 (mtp) cc_final: 0.9003 (mtp) REVERT: G 93 TYR cc_start: 0.5756 (m-10) cc_final: 0.5493 (m-10) REVERT: G 127 ASP cc_start: 0.9272 (m-30) cc_final: 0.9067 (m-30) REVERT: G 140 MET cc_start: 0.8747 (ttm) cc_final: 0.8267 (mtm) REVERT: G 154 PHE cc_start: 0.9198 (m-80) cc_final: 0.8829 (m-80) REVERT: G 159 ASP cc_start: 0.8886 (t70) cc_final: 0.8488 (t70) REVERT: G 170 LEU cc_start: 0.9721 (mm) cc_final: 0.9508 (mm) REVERT: G 174 ASP cc_start: 0.8926 (p0) cc_final: 0.8445 (p0) REVERT: G 175 ARG cc_start: 0.8670 (mmp80) cc_final: 0.8429 (mmm160) REVERT: G 210 MET cc_start: 0.9457 (mmp) cc_final: 0.9249 (mmm) REVERT: G 246 GLU cc_start: 0.9315 (pt0) cc_final: 0.9009 (pp20) REVERT: G 250 GLU cc_start: 0.9322 (tp30) cc_final: 0.8649 (tp30) REVERT: H 103 LYS cc_start: 0.9388 (tttt) cc_final: 0.9105 (pttt) REVERT: H 139 GLU cc_start: 0.8972 (mp0) cc_final: 0.8305 (tt0) REVERT: H 162 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8755 (mm-30) REVERT: H 176 LEU cc_start: 0.9598 (tp) cc_final: 0.9350 (tt) REVERT: H 183 ASP cc_start: 0.8787 (m-30) cc_final: 0.7805 (t70) REVERT: H 189 ARG cc_start: 0.9121 (tpt170) cc_final: 0.8729 (mmm-85) REVERT: H 210 MET cc_start: 0.9439 (ptp) cc_final: 0.9172 (ptp) REVERT: H 223 ASN cc_start: 0.9480 (t0) cc_final: 0.9148 (t0) REVERT: I 61 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8688 (tt0) REVERT: I 93 TYR cc_start: 0.9054 (t80) cc_final: 0.8716 (t80) REVERT: I 111 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8631 (tm-30) REVERT: I 139 GLU cc_start: 0.9050 (mp0) cc_final: 0.8839 (mp0) REVERT: I 185 GLN cc_start: 0.9237 (mt0) cc_final: 0.8525 (mp10) REVERT: I 210 MET cc_start: 0.9235 (tmm) cc_final: 0.8863 (tmm) REVERT: I 233 LEU cc_start: 0.9869 (tp) cc_final: 0.9582 (pp) REVERT: J 93 TYR cc_start: 0.9022 (t80) cc_final: 0.8768 (t80) REVERT: J 99 LYS cc_start: 0.9559 (mmmm) cc_final: 0.9189 (mmmm) REVERT: J 103 LYS cc_start: 0.9197 (tttp) cc_final: 0.8787 (tppt) REVERT: J 111 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8923 (tm-30) REVERT: J 119 LYS cc_start: 0.9177 (tptp) cc_final: 0.8943 (tptp) REVERT: J 127 ASP cc_start: 0.9070 (m-30) cc_final: 0.8806 (m-30) REVERT: J 131 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8877 (tm-30) REVERT: J 159 ASP cc_start: 0.9385 (t70) cc_final: 0.9072 (t0) REVERT: J 162 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8374 (mm-30) REVERT: J 185 GLN cc_start: 0.9545 (mm110) cc_final: 0.9262 (mm110) REVERT: J 187 LEU cc_start: 0.8877 (mt) cc_final: 0.8619 (mt) REVERT: J 210 MET cc_start: 0.9692 (mtm) cc_final: 0.9396 (mtp) REVERT: J 229 MET cc_start: 0.9378 (mmt) cc_final: 0.9075 (mmm) REVERT: K 46 LEU cc_start: 0.9733 (mt) cc_final: 0.9517 (mt) REVERT: K 54 LYS cc_start: 0.9440 (tppt) cc_final: 0.8940 (mmmt) REVERT: K 63 ARG cc_start: 0.9240 (mmp-170) cc_final: 0.8984 (mmp-170) REVERT: K 92 VAL cc_start: 0.9742 (t) cc_final: 0.9479 (m) REVERT: K 116 ARG cc_start: 0.8688 (mmp80) cc_final: 0.8172 (mmp80) REVERT: K 124 ASP cc_start: 0.9509 (m-30) cc_final: 0.9287 (m-30) REVERT: K 140 MET cc_start: 0.8993 (ttp) cc_final: 0.8664 (ttp) REVERT: K 145 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7887 (mm-30) REVERT: K 162 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8532 (mm-30) REVERT: K 214 MET cc_start: 0.9325 (mtm) cc_final: 0.9112 (mtp) REVERT: K 223 ASN cc_start: 0.9623 (m110) cc_final: 0.9320 (m110) REVERT: L 38 GLN cc_start: 0.9169 (mm110) cc_final: 0.8647 (pm20) REVERT: L 63 ARG cc_start: 0.9471 (mmp80) cc_final: 0.8905 (mmm160) REVERT: L 93 TYR cc_start: 0.8842 (t80) cc_final: 0.8356 (t80) REVERT: L 124 ASP cc_start: 0.9347 (m-30) cc_final: 0.9113 (m-30) REVERT: L 131 GLU cc_start: 0.9320 (tt0) cc_final: 0.8932 (pt0) REVERT: L 215 VAL cc_start: 0.9779 (t) cc_final: 0.9266 (t) REVERT: L 240 TYR cc_start: 0.8888 (m-10) cc_final: 0.8360 (m-80) REVERT: L 269 GLN cc_start: 0.9202 (pp30) cc_final: 0.8972 (pp30) REVERT: O 77 HIS cc_start: 0.8643 (m-70) cc_final: 0.8402 (m90) REVERT: O 95 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7838 (ttp80) REVERT: O 108 LYS cc_start: 0.9474 (mtpt) cc_final: 0.9195 (pttm) REVERT: O 158 ARG cc_start: 0.9167 (tpt-90) cc_final: 0.8832 (tpt-90) REVERT: O 183 ASP cc_start: 0.9112 (t0) cc_final: 0.8510 (t0) REVERT: O 185 GLN cc_start: 0.9413 (tm-30) cc_final: 0.9135 (tm-30) REVERT: O 240 TYR cc_start: 0.9206 (m-80) cc_final: 0.8875 (m-10) REVERT: P 56 CYS cc_start: 0.9135 (p) cc_final: 0.8442 (p) REVERT: P 113 LEU cc_start: 0.9642 (tt) cc_final: 0.8967 (tt) REVERT: P 115 TYR cc_start: 0.8740 (m-10) cc_final: 0.8470 (m-10) REVERT: P 116 ARG cc_start: 0.8357 (tmm160) cc_final: 0.8155 (tmt170) REVERT: P 127 ASP cc_start: 0.9379 (m-30) cc_final: 0.9161 (m-30) REVERT: P 144 ASP cc_start: 0.8740 (t0) cc_final: 0.8218 (t0) REVERT: P 168 VAL cc_start: 0.9215 (t) cc_final: 0.8848 (t) REVERT: P 190 PHE cc_start: 0.9193 (m-80) cc_final: 0.8669 (m-80) REVERT: P 214 MET cc_start: 0.8806 (mtm) cc_final: 0.8235 (ptm) REVERT: P 229 MET cc_start: 0.0994 (mtt) cc_final: 0.0407 (mtt) outliers start: 0 outliers final: 0 residues processed: 904 average time/residue: 0.1979 time to fit residues: 284.3236 Evaluate side-chains 714 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 714 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 229 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 283 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 chunk 285 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 GLN ** P 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 HIS P 185 GLN ** P 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.086750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.060906 restraints weight = 126344.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.063041 restraints weight = 69093.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.064444 restraints weight = 46137.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.065364 restraints weight = 35007.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.065994 restraints weight = 29123.642| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.7431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31134 Z= 0.144 Angle : 0.677 7.786 42181 Z= 0.348 Chirality : 0.043 0.275 4756 Planarity : 0.004 0.054 5084 Dihedral : 15.225 178.758 4907 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.35 % Favored : 97.59 % Rotamer: Outliers : 0.03 % Allowed : 0.83 % Favored : 99.14 % 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: 1.16 (0.14), residues: 3570 helix: 1.04 (0.12), residues: 2132 sheet: 1.19 (0.28), residues: 358 loop : 0.31 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 116 TYR 0.039 0.002 TYR F 75 PHE 0.031 0.001 PHE O 106 TRP 0.047 0.002 TRP G 211 HIS 0.012 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00317 (31132) covalent geometry : angle 0.67745 (42181) hydrogen bonds : bond 0.04091 ( 1579) hydrogen bonds : angle 4.69115 ( 4611) Misc. bond : bond 0.00774 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 926 time to evaluate : 1.323 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.9298 (m90) cc_final: 0.8945 (m-70) REVERT: A 46 LEU cc_start: 0.9820 (mt) cc_final: 0.9575 (mt) REVERT: A 70 CYS cc_start: 0.9479 (m) cc_final: 0.9011 (p) REVERT: A 75 TYR cc_start: 0.8934 (m-10) cc_final: 0.8666 (m-80) REVERT: A 93 TYR cc_start: 0.9317 (t80) cc_final: 0.8552 (t80) REVERT: A 95 ARG cc_start: 0.8356 (tmt170) cc_final: 0.8153 (tmt170) REVERT: A 111 GLU cc_start: 0.9555 (tm-30) cc_final: 0.9277 (tm-30) REVERT: A 112 TYR cc_start: 0.9221 (t80) cc_final: 0.8953 (t80) REVERT: A 113 LEU cc_start: 0.9651 (mt) cc_final: 0.9306 (tt) REVERT: A 140 MET cc_start: 0.9219 (ttm) cc_final: 0.8828 (ttp) REVERT: A 154 PHE cc_start: 0.9497 (m-80) cc_final: 0.9057 (m-80) REVERT: A 183 ASP cc_start: 0.8726 (t0) cc_final: 0.8306 (t0) REVERT: A 214 MET cc_start: 0.9480 (mmp) cc_final: 0.9202 (mmm) REVERT: A 250 GLU cc_start: 0.9607 (tp30) cc_final: 0.9125 (tp30) REVERT: B 61 GLU cc_start: 0.8675 (mp0) cc_final: 0.8349 (pm20) REVERT: B 75 TYR cc_start: 0.8397 (m-80) cc_final: 0.7980 (m-80) REVERT: B 98 GLN cc_start: 0.9193 (tp40) cc_final: 0.8867 (mm-40) REVERT: B 111 GLU cc_start: 0.9185 (tp30) cc_final: 0.8792 (tp30) REVERT: B 159 ASP cc_start: 0.8741 (m-30) cc_final: 0.8447 (m-30) REVERT: B 223 ASN cc_start: 0.9602 (t0) cc_final: 0.9172 (t0) REVERT: C 46 LEU cc_start: 0.9873 (mt) cc_final: 0.9664 (mt) REVERT: C 95 ARG cc_start: 0.9039 (ttm-80) cc_final: 0.8810 (ttm-80) REVERT: C 99 LYS cc_start: 0.9204 (mmmt) cc_final: 0.8887 (tptp) REVERT: C 156 ASP cc_start: 0.9232 (m-30) cc_final: 0.9003 (m-30) REVERT: C 173 THR cc_start: 0.8198 (p) cc_final: 0.7831 (t) REVERT: C 185 GLN cc_start: 0.9422 (tt0) cc_final: 0.9219 (tp-100) REVERT: C 213 GLN cc_start: 0.9338 (tm-30) cc_final: 0.9121 (tm-30) REVERT: C 223 ASN cc_start: 0.9386 (t0) cc_final: 0.9154 (t0) REVERT: C 247 ILE cc_start: 0.9583 (mt) cc_final: 0.8676 (mt) REVERT: C 250 GLU cc_start: 0.9355 (tp30) cc_final: 0.8860 (tp30) REVERT: D 99 LYS cc_start: 0.9301 (mmtt) cc_final: 0.8836 (tptp) REVERT: D 163 ASP cc_start: 0.9080 (m-30) cc_final: 0.8775 (m-30) REVERT: D 176 LEU cc_start: 0.9483 (tp) cc_final: 0.9244 (tp) REVERT: D 180 ILE cc_start: 0.9385 (mt) cc_final: 0.9111 (mt) REVERT: D 211 TRP cc_start: 0.8697 (t-100) cc_final: 0.8085 (t60) REVERT: D 229 MET cc_start: 0.8908 (mtt) cc_final: 0.8391 (mmt) REVERT: D 246 GLU cc_start: 0.8718 (pp20) cc_final: 0.8258 (pp20) REVERT: D 247 ILE cc_start: 0.9498 (mm) cc_final: 0.8934 (mm) REVERT: E 47 ASP cc_start: 0.9412 (t0) cc_final: 0.9172 (m-30) REVERT: E 98 GLN cc_start: 0.8732 (mm110) cc_final: 0.8497 (mm110) REVERT: E 99 LYS cc_start: 0.9522 (mttm) cc_final: 0.9274 (mmmt) REVERT: E 104 ASP cc_start: 0.8673 (t70) cc_final: 0.8053 (t0) REVERT: E 139 GLU cc_start: 0.9095 (mp0) cc_final: 0.8825 (mp0) REVERT: E 159 ASP cc_start: 0.8442 (t0) cc_final: 0.7950 (t0) REVERT: E 163 ASP cc_start: 0.8009 (m-30) cc_final: 0.7709 (m-30) REVERT: E 183 ASP cc_start: 0.9416 (t0) cc_final: 0.9003 (t0) REVERT: E 185 GLN cc_start: 0.8984 (mp10) cc_final: 0.8721 (mp10) REVERT: E 199 LEU cc_start: 0.8508 (tp) cc_final: 0.8132 (tp) REVERT: E 246 GLU cc_start: 0.8805 (pp20) cc_final: 0.8385 (pp20) REVERT: E 253 ILE cc_start: 0.9684 (tt) cc_final: 0.9398 (pt) REVERT: F 42 LEU cc_start: 0.9401 (mt) cc_final: 0.9184 (mt) REVERT: F 112 TYR cc_start: 0.9488 (t80) cc_final: 0.9271 (t80) REVERT: F 144 ASP cc_start: 0.9030 (t70) cc_final: 0.8058 (t0) REVERT: F 145 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8642 (mt-10) REVERT: F 170 LEU cc_start: 0.9683 (mt) cc_final: 0.9389 (mt) REVERT: F 190 PHE cc_start: 0.9479 (m-80) cc_final: 0.9138 (m-10) REVERT: F 199 LEU cc_start: 0.8301 (tp) cc_final: 0.7861 (tp) REVERT: F 210 MET cc_start: 0.9541 (mtm) cc_final: 0.9259 (mtp) REVERT: F 229 MET cc_start: 0.9360 (mtp) cc_final: 0.9032 (mtp) REVERT: F 246 GLU cc_start: 0.9009 (pp20) cc_final: 0.8747 (pp20) REVERT: G 127 ASP cc_start: 0.9261 (m-30) cc_final: 0.9043 (m-30) REVERT: G 140 MET cc_start: 0.8714 (ttm) cc_final: 0.8037 (mtm) REVERT: G 154 PHE cc_start: 0.9217 (m-80) cc_final: 0.8887 (m-80) REVERT: G 159 ASP cc_start: 0.8855 (t70) cc_final: 0.8401 (t70) REVERT: G 163 ASP cc_start: 0.8556 (m-30) cc_final: 0.8345 (m-30) REVERT: G 174 ASP cc_start: 0.8952 (p0) cc_final: 0.8489 (p0) REVERT: G 175 ARG cc_start: 0.8670 (mmp80) cc_final: 0.8374 (mmm160) REVERT: G 210 MET cc_start: 0.9449 (mmp) cc_final: 0.9201 (mmm) REVERT: G 214 MET cc_start: 0.9731 (mpp) cc_final: 0.9468 (mpp) REVERT: G 246 GLU cc_start: 0.9321 (pt0) cc_final: 0.9001 (pp20) REVERT: G 250 GLU cc_start: 0.9240 (tp30) cc_final: 0.8663 (tp30) REVERT: H 103 LYS cc_start: 0.9320 (tttt) cc_final: 0.9028 (pttm) REVERT: H 127 ASP cc_start: 0.9048 (m-30) cc_final: 0.8834 (m-30) REVERT: H 162 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8728 (mm-30) REVERT: H 176 LEU cc_start: 0.9557 (tp) cc_final: 0.9302 (tt) REVERT: H 183 ASP cc_start: 0.8706 (m-30) cc_final: 0.7831 (t70) REVERT: H 189 ARG cc_start: 0.9181 (tpt170) cc_final: 0.8756 (mmm-85) REVERT: H 210 MET cc_start: 0.9437 (ptp) cc_final: 0.9198 (ptp) REVERT: H 223 ASN cc_start: 0.9508 (t0) cc_final: 0.9233 (t0) REVERT: I 61 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8752 (tt0) REVERT: I 75 TYR cc_start: 0.8567 (m-80) cc_final: 0.8282 (m-80) REVERT: I 139 GLU cc_start: 0.9040 (mp0) cc_final: 0.8822 (mp0) REVERT: I 185 GLN cc_start: 0.9243 (mt0) cc_final: 0.8527 (mp10) REVERT: I 210 MET cc_start: 0.9211 (tmm) cc_final: 0.8874 (tmm) REVERT: I 233 LEU cc_start: 0.9864 (tp) cc_final: 0.9575 (pp) REVERT: J 93 TYR cc_start: 0.9031 (t80) cc_final: 0.8813 (t80) REVERT: J 99 LYS cc_start: 0.9563 (mmmm) cc_final: 0.9199 (mmmm) REVERT: J 100 CYS cc_start: 0.9100 (t) cc_final: 0.8535 (p) REVERT: J 111 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8967 (tm-30) REVERT: J 127 ASP cc_start: 0.9106 (m-30) cc_final: 0.8876 (m-30) REVERT: J 149 LEU cc_start: 0.9531 (mm) cc_final: 0.9027 (mp) REVERT: J 159 ASP cc_start: 0.9363 (t70) cc_final: 0.9065 (t0) REVERT: J 162 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8367 (mm-30) REVERT: J 185 GLN cc_start: 0.9543 (mm110) cc_final: 0.9259 (mm110) REVERT: J 187 LEU cc_start: 0.8856 (mt) cc_final: 0.8575 (mt) REVERT: J 210 MET cc_start: 0.9692 (mtm) cc_final: 0.9343 (mtp) REVERT: J 213 GLN cc_start: 0.9130 (mp10) cc_final: 0.8829 (mp10) REVERT: J 224 LEU cc_start: 0.9382 (mm) cc_final: 0.9111 (pp) REVERT: J 229 MET cc_start: 0.9384 (mmt) cc_final: 0.9078 (mmm) REVERT: K 20 TRP cc_start: 0.8869 (p-90) cc_final: 0.8276 (p-90) REVERT: K 54 LYS cc_start: 0.9441 (tppt) cc_final: 0.8941 (mmmt) REVERT: K 63 ARG cc_start: 0.9200 (mmp-170) cc_final: 0.8912 (mmm160) REVERT: K 92 VAL cc_start: 0.9747 (t) cc_final: 0.9468 (m) REVERT: K 116 ARG cc_start: 0.8675 (mmp80) cc_final: 0.8087 (mmp80) REVERT: K 124 ASP cc_start: 0.9505 (m-30) cc_final: 0.9296 (m-30) REVERT: K 145 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7873 (mm-30) REVERT: K 162 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8626 (mm-30) REVERT: K 210 MET cc_start: 0.9192 (mtm) cc_final: 0.8844 (mtt) REVERT: L 37 GLN cc_start: 0.9585 (pm20) cc_final: 0.9346 (pm20) REVERT: L 38 GLN cc_start: 0.9181 (mm110) cc_final: 0.8752 (pm20) REVERT: L 63 ARG cc_start: 0.9385 (mmp80) cc_final: 0.8897 (mmm160) REVERT: L 124 ASP cc_start: 0.9327 (m-30) cc_final: 0.9104 (m-30) REVERT: L 131 GLU cc_start: 0.9249 (tt0) cc_final: 0.8849 (pt0) REVERT: L 215 VAL cc_start: 0.9793 (t) cc_final: 0.9379 (t) REVERT: L 240 TYR cc_start: 0.8855 (m-10) cc_final: 0.8339 (m-80) REVERT: L 269 GLN cc_start: 0.9184 (pp30) cc_final: 0.8944 (pp30) REVERT: O 77 HIS cc_start: 0.8615 (m-70) cc_final: 0.8390 (m90) REVERT: O 106 PHE cc_start: 0.9611 (m-80) cc_final: 0.9339 (m-80) REVERT: O 111 GLU cc_start: 0.9328 (mt-10) cc_final: 0.9085 (mt-10) REVERT: O 153 THR cc_start: 0.8559 (p) cc_final: 0.8352 (p) REVERT: O 158 ARG cc_start: 0.8954 (tpt-90) cc_final: 0.8579 (tpt-90) REVERT: O 183 ASP cc_start: 0.9119 (t0) cc_final: 0.8486 (t0) REVERT: O 185 GLN cc_start: 0.9459 (tm-30) cc_final: 0.9152 (tm-30) REVERT: O 191 ARG cc_start: 0.9016 (mtt-85) cc_final: 0.8408 (ptm160) REVERT: O 240 TYR cc_start: 0.9209 (m-80) cc_final: 0.8756 (m-80) REVERT: P 37 GLN cc_start: 0.9654 (tm-30) cc_final: 0.9451 (mm-40) REVERT: P 56 CYS cc_start: 0.9145 (p) cc_final: 0.8486 (p) REVERT: P 113 LEU cc_start: 0.9650 (tt) cc_final: 0.8893 (tt) REVERT: P 115 TYR cc_start: 0.8756 (m-10) cc_final: 0.8518 (m-10) REVERT: P 144 ASP cc_start: 0.8779 (t0) cc_final: 0.8231 (t0) REVERT: P 154 PHE cc_start: 0.9592 (m-10) cc_final: 0.9111 (m-10) REVERT: P 168 VAL cc_start: 0.9179 (t) cc_final: 0.8792 (t) REVERT: P 190 PHE cc_start: 0.9177 (m-80) cc_final: 0.8582 (m-80) REVERT: P 214 MET cc_start: 0.8688 (mtm) cc_final: 0.8096 (ptm) REVERT: P 229 MET cc_start: 0.0985 (mtt) cc_final: 0.0386 (mtt) outliers start: 1 outliers final: 1 residues processed: 926 average time/residue: 0.2022 time to fit residues: 296.1763 Evaluate side-chains 729 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 728 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 67 optimal weight: 7.9990 chunk 304 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 288 optimal weight: 0.0570 chunk 158 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 344 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 262 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 269 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 GLN P 97 HIS ** P 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.085646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.059945 restraints weight = 126507.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.062002 restraints weight = 70153.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.063354 restraints weight = 47306.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.064235 restraints weight = 36094.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.064800 restraints weight = 29999.106| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.7619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31134 Z= 0.164 Angle : 0.693 11.784 42181 Z= 0.357 Chirality : 0.043 0.397 4756 Planarity : 0.004 0.066 5084 Dihedral : 15.178 178.551 4907 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.49 % Favored : 97.42 % Rotamer: Outliers : 0.03 % Allowed : 0.58 % Favored : 99.39 % Cbeta Deviations : 0.03 % 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: 1.06 (0.14), residues: 3570 helix: 0.99 (0.11), residues: 2144 sheet: 1.12 (0.28), residues: 358 loop : 0.21 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 158 TYR 0.020 0.001 TYR G 93 PHE 0.022 0.002 PHE O 106 TRP 0.050 0.002 TRP G 211 HIS 0.007 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00361 (31132) covalent geometry : angle 0.69349 (42181) hydrogen bonds : bond 0.04183 ( 1579) hydrogen bonds : angle 4.71309 ( 4611) Misc. bond : bond 0.00039 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 893 time to evaluate : 1.182 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: 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 43 HIS cc_start: 0.9330 (m90) cc_final: 0.8961 (m-70) REVERT: A 46 LEU cc_start: 0.9820 (mt) cc_final: 0.9582 (mt) REVERT: A 70 CYS cc_start: 0.9395 (m) cc_final: 0.8890 (p) REVERT: A 75 TYR cc_start: 0.8933 (m-10) cc_final: 0.8644 (m-80) REVERT: A 93 TYR cc_start: 0.9338 (t80) cc_final: 0.8794 (t80) REVERT: A 111 GLU cc_start: 0.9562 (tm-30) cc_final: 0.9254 (tm-30) REVERT: A 140 MET cc_start: 0.9289 (ttm) cc_final: 0.8988 (ttp) REVERT: A 154 PHE cc_start: 0.9532 (m-80) cc_final: 0.9099 (m-80) REVERT: A 158 ARG cc_start: 0.9050 (ttp80) cc_final: 0.8775 (ttp80) REVERT: A 162 GLU cc_start: 0.8701 (pp20) cc_final: 0.8147 (pp20) REVERT: A 183 ASP cc_start: 0.8778 (t0) cc_final: 0.8427 (t0) REVERT: A 210 MET cc_start: 0.9421 (ptp) cc_final: 0.9210 (ptp) REVERT: A 214 MET cc_start: 0.9475 (mmp) cc_final: 0.9216 (mmm) REVERT: A 250 GLU cc_start: 0.9608 (tp30) cc_final: 0.9125 (tp30) REVERT: B 61 GLU cc_start: 0.8640 (mp0) cc_final: 0.8302 (pm20) REVERT: B 75 TYR cc_start: 0.8407 (m-80) cc_final: 0.7984 (m-80) REVERT: B 98 GLN cc_start: 0.9209 (tp40) cc_final: 0.8864 (mm-40) REVERT: B 111 GLU cc_start: 0.9149 (tp30) cc_final: 0.8782 (tp30) REVERT: B 159 ASP cc_start: 0.8739 (m-30) cc_final: 0.8431 (m-30) REVERT: B 185 GLN cc_start: 0.9360 (tp-100) cc_final: 0.9049 (tp-100) REVERT: B 210 MET cc_start: 0.9578 (ttp) cc_final: 0.9171 (ptp) REVERT: B 214 MET cc_start: 0.9494 (mmp) cc_final: 0.9009 (mtt) REVERT: B 223 ASN cc_start: 0.9606 (t0) cc_final: 0.9208 (t0) REVERT: C 95 ARG cc_start: 0.9055 (ttm-80) cc_final: 0.8796 (ttm-80) REVERT: C 156 ASP cc_start: 0.9182 (m-30) cc_final: 0.8976 (m-30) REVERT: C 173 THR cc_start: 0.8225 (p) cc_final: 0.7845 (t) REVERT: C 183 ASP cc_start: 0.9337 (t0) cc_final: 0.9111 (t0) REVERT: C 187 LEU cc_start: 0.9397 (mt) cc_final: 0.9011 (mt) REVERT: C 213 GLN cc_start: 0.9333 (tm-30) cc_final: 0.9112 (tm-30) REVERT: C 223 ASN cc_start: 0.9391 (t0) cc_final: 0.9173 (t0) REVERT: C 250 GLU cc_start: 0.9382 (tp30) cc_final: 0.8815 (tp30) REVERT: C 263 ILE cc_start: 0.8917 (mm) cc_final: 0.8609 (mm) REVERT: D 54 LYS cc_start: 0.8970 (ttpt) cc_final: 0.8720 (ttpt) REVERT: D 99 LYS cc_start: 0.9332 (mmtt) cc_final: 0.8837 (tptp) REVERT: D 163 ASP cc_start: 0.9074 (m-30) cc_final: 0.8783 (m-30) REVERT: D 176 LEU cc_start: 0.9494 (tp) cc_final: 0.9236 (tp) REVERT: D 180 ILE cc_start: 0.9392 (mt) cc_final: 0.9139 (mt) REVERT: D 211 TRP cc_start: 0.8725 (t-100) cc_final: 0.8100 (t60) REVERT: D 229 MET cc_start: 0.8982 (mtt) cc_final: 0.8442 (mmt) REVERT: D 246 GLU cc_start: 0.8797 (pp20) cc_final: 0.8228 (pp20) REVERT: D 247 ILE cc_start: 0.9528 (mm) cc_final: 0.8972 (mm) REVERT: E 47 ASP cc_start: 0.9418 (t0) cc_final: 0.9183 (m-30) REVERT: E 98 GLN cc_start: 0.8704 (mm110) cc_final: 0.8464 (mm110) REVERT: E 99 LYS cc_start: 0.9455 (mttm) cc_final: 0.9236 (mmmt) REVERT: E 104 ASP cc_start: 0.8674 (t70) cc_final: 0.8018 (t0) REVERT: E 139 GLU cc_start: 0.9054 (mp0) cc_final: 0.8794 (mp0) REVERT: E 159 ASP cc_start: 0.8452 (t0) cc_final: 0.7848 (t0) REVERT: E 163 ASP cc_start: 0.8019 (m-30) cc_final: 0.7669 (m-30) REVERT: E 183 ASP cc_start: 0.9437 (t0) cc_final: 0.9077 (t0) REVERT: E 185 GLN cc_start: 0.9001 (mp10) cc_final: 0.8747 (mp10) REVERT: E 199 LEU cc_start: 0.8522 (tp) cc_final: 0.8054 (tp) REVERT: E 211 TRP cc_start: 0.9078 (t-100) cc_final: 0.8722 (t-100) REVERT: F 42 LEU cc_start: 0.9406 (mt) cc_final: 0.9185 (mt) REVERT: F 144 ASP cc_start: 0.9042 (t70) cc_final: 0.8077 (t0) REVERT: F 145 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8664 (mt-10) REVERT: F 170 LEU cc_start: 0.9682 (mt) cc_final: 0.9409 (mt) REVERT: F 190 PHE cc_start: 0.9490 (m-80) cc_final: 0.9249 (m-10) REVERT: F 199 LEU cc_start: 0.8386 (tp) cc_final: 0.7944 (tp) REVERT: F 210 MET cc_start: 0.9531 (mtm) cc_final: 0.9217 (ptp) REVERT: F 229 MET cc_start: 0.9387 (mtp) cc_final: 0.9056 (mtp) REVERT: F 269 GLN cc_start: 0.9556 (mt0) cc_final: 0.9317 (mp10) REVERT: G 93 TYR cc_start: 0.5699 (m-10) cc_final: 0.5464 (m-10) REVERT: G 127 ASP cc_start: 0.9235 (m-30) cc_final: 0.9023 (m-30) REVERT: G 140 MET cc_start: 0.8607 (ttm) cc_final: 0.8026 (mtm) REVERT: G 154 PHE cc_start: 0.9292 (m-80) cc_final: 0.8940 (m-80) REVERT: G 159 ASP cc_start: 0.8792 (t70) cc_final: 0.8362 (t70) REVERT: G 174 ASP cc_start: 0.8939 (p0) cc_final: 0.8415 (p0) REVERT: G 175 ARG cc_start: 0.8654 (mmp80) cc_final: 0.8372 (mmm160) REVERT: G 210 MET cc_start: 0.9465 (mmp) cc_final: 0.9239 (mmp) REVERT: G 246 GLU cc_start: 0.9304 (pt0) cc_final: 0.8989 (pp20) REVERT: G 250 GLU cc_start: 0.9281 (tp30) cc_final: 0.8570 (tp30) REVERT: H 103 LYS cc_start: 0.9360 (tttt) cc_final: 0.9074 (pttm) REVERT: H 127 ASP cc_start: 0.9054 (m-30) cc_final: 0.8839 (m-30) REVERT: H 162 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8749 (mm-30) REVERT: H 176 LEU cc_start: 0.9572 (tp) cc_final: 0.9320 (tt) REVERT: H 183 ASP cc_start: 0.8673 (m-30) cc_final: 0.7949 (t70) REVERT: H 189 ARG cc_start: 0.9218 (tpt170) cc_final: 0.8843 (mmm-85) REVERT: H 210 MET cc_start: 0.9434 (ptp) cc_final: 0.8913 (ptp) REVERT: H 223 ASN cc_start: 0.9479 (t0) cc_final: 0.9223 (t0) REVERT: I 61 GLU cc_start: 0.9361 (mm-30) cc_final: 0.8738 (tt0) REVERT: I 75 TYR cc_start: 0.8570 (m-80) cc_final: 0.8303 (m-80) REVERT: I 93 TYR cc_start: 0.9102 (t80) cc_final: 0.8608 (t80) REVERT: I 139 GLU cc_start: 0.9048 (mp0) cc_final: 0.8814 (mp0) REVERT: I 185 GLN cc_start: 0.9245 (mt0) cc_final: 0.8492 (mp10) REVERT: I 210 MET cc_start: 0.9206 (tmm) cc_final: 0.8856 (tmm) REVERT: I 233 LEU cc_start: 0.9865 (tp) cc_final: 0.9570 (pp) REVERT: J 99 LYS cc_start: 0.9571 (mmmm) cc_final: 0.9221 (mmmm) REVERT: J 100 CYS cc_start: 0.8942 (t) cc_final: 0.8488 (p) REVERT: J 127 ASP cc_start: 0.9142 (m-30) cc_final: 0.8903 (m-30) REVERT: J 149 LEU cc_start: 0.9487 (mm) cc_final: 0.8940 (mp) REVERT: J 159 ASP cc_start: 0.9387 (t70) cc_final: 0.9056 (t0) REVERT: J 162 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8365 (mm-30) REVERT: J 210 MET cc_start: 0.9700 (mtm) cc_final: 0.9396 (mtp) REVERT: J 229 MET cc_start: 0.9382 (mmt) cc_final: 0.9063 (mmm) REVERT: K 20 TRP cc_start: 0.8969 (p-90) cc_final: 0.8317 (p-90) REVERT: K 54 LYS cc_start: 0.9438 (tppt) cc_final: 0.8968 (mmmt) REVERT: K 63 ARG cc_start: 0.9225 (mmp-170) cc_final: 0.8936 (mmm160) REVERT: K 92 VAL cc_start: 0.9743 (t) cc_final: 0.9526 (m) REVERT: K 116 ARG cc_start: 0.8626 (mmp80) cc_final: 0.8121 (mmp80) REVERT: K 124 ASP cc_start: 0.9532 (m-30) cc_final: 0.9328 (m-30) REVERT: K 140 MET cc_start: 0.8768 (ttp) cc_final: 0.7486 (ttp) REVERT: K 145 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7840 (mm-30) REVERT: K 159 ASP cc_start: 0.9438 (t0) cc_final: 0.9072 (t0) REVERT: K 162 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8664 (mm-30) REVERT: K 163 ASP cc_start: 0.8808 (m-30) cc_final: 0.8525 (m-30) REVERT: K 210 MET cc_start: 0.9214 (mtm) cc_final: 0.8843 (ptp) REVERT: K 254 ARG cc_start: 0.9002 (ptt180) cc_final: 0.8797 (ptt180) REVERT: L 37 GLN cc_start: 0.9593 (pm20) cc_final: 0.9319 (pm20) REVERT: L 38 GLN cc_start: 0.9307 (mm110) cc_final: 0.8901 (pm20) REVERT: L 63 ARG cc_start: 0.9505 (mmp80) cc_final: 0.8981 (mmm160) REVERT: L 124 ASP cc_start: 0.9336 (m-30) cc_final: 0.9072 (m-30) REVERT: L 131 GLU cc_start: 0.9257 (tt0) cc_final: 0.8853 (pt0) REVERT: L 215 VAL cc_start: 0.9812 (t) cc_final: 0.9262 (t) REVERT: L 224 LEU cc_start: 0.9753 (mt) cc_final: 0.9550 (mt) REVERT: L 240 TYR cc_start: 0.8864 (m-10) cc_final: 0.8352 (m-80) REVERT: L 269 GLN cc_start: 0.9213 (pp30) cc_final: 0.8963 (pp30) REVERT: O 71 ASP cc_start: 0.8969 (t0) cc_final: 0.8682 (p0) REVERT: O 106 PHE cc_start: 0.9590 (m-80) cc_final: 0.9316 (m-80) REVERT: O 183 ASP cc_start: 0.9002 (t0) cc_final: 0.8342 (t0) REVERT: O 191 ARG cc_start: 0.8956 (mtt-85) cc_final: 0.8282 (ptm160) REVERT: O 240 TYR cc_start: 0.9176 (m-80) cc_final: 0.8909 (m-10) REVERT: P 56 CYS cc_start: 0.8994 (p) cc_final: 0.8202 (p) REVERT: P 127 ASP cc_start: 0.9401 (m-30) cc_final: 0.9126 (m-30) REVERT: P 140 MET cc_start: 0.9281 (ptm) cc_final: 0.8948 (ptm) REVERT: P 144 ASP cc_start: 0.8852 (t0) cc_final: 0.8356 (t0) REVERT: P 154 PHE cc_start: 0.9611 (m-10) cc_final: 0.9142 (m-10) REVERT: P 168 VAL cc_start: 0.9225 (t) cc_final: 0.8889 (t) REVERT: P 190 PHE cc_start: 0.9209 (m-80) cc_final: 0.8646 (m-80) REVERT: P 214 MET cc_start: 0.8639 (mtm) cc_final: 0.8134 (ptm) REVERT: P 229 MET cc_start: 0.1126 (mtt) cc_final: 0.0574 (mtt) outliers start: 1 outliers final: 0 residues processed: 893 average time/residue: 0.1855 time to fit residues: 265.7841 Evaluate side-chains 718 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 718 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 39 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 208 optimal weight: 0.5980 chunk 293 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 344 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 261 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 GLN C 185 GLN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN H 98 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 GLN P 37 GLN P 97 HIS ** P 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.086281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.060521 restraints weight = 124671.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.062592 restraints weight = 68803.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.063956 restraints weight = 46225.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.064878 restraints weight = 35222.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.065474 restraints weight = 29185.450| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.7724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 31134 Z= 0.144 Angle : 0.700 9.193 42181 Z= 0.357 Chirality : 0.044 0.325 4756 Planarity : 0.004 0.057 5084 Dihedral : 15.088 178.264 4907 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.35 % Favored : 97.48 % Rotamer: Outliers : 0.03 % Allowed : 0.22 % Favored : 99.74 % 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: 1.09 (0.14), residues: 3570 helix: 1.06 (0.12), residues: 2108 sheet: 1.14 (0.28), residues: 358 loop : 0.12 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 158 TYR 0.021 0.001 TYR L 75 PHE 0.030 0.002 PHE O 106 TRP 0.048 0.002 TRP G 211 HIS 0.012 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00322 (31132) covalent geometry : angle 0.70032 (42181) hydrogen bonds : bond 0.04094 ( 1579) hydrogen bonds : angle 4.70248 ( 4611) Misc. bond : bond 0.00144 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 895 time to evaluate : 1.067 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: 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 36 LEU cc_start: 0.9419 (tp) cc_final: 0.9069 (tp) REVERT: A 38 GLN cc_start: 0.9547 (mp10) cc_final: 0.9332 (mp10) REVERT: A 43 HIS cc_start: 0.9338 (m90) cc_final: 0.8981 (m-70) REVERT: A 46 LEU cc_start: 0.9818 (mt) cc_final: 0.9580 (mt) REVERT: A 70 CYS cc_start: 0.9308 (m) cc_final: 0.8868 (p) REVERT: A 93 TYR cc_start: 0.9285 (t80) cc_final: 0.8644 (t80) REVERT: A 95 ARG cc_start: 0.8580 (tmt170) cc_final: 0.8132 (tmt170) REVERT: A 111 GLU cc_start: 0.9511 (tm-30) cc_final: 0.9203 (tm-30) REVERT: A 112 TYR cc_start: 0.9224 (t80) cc_final: 0.8884 (t80) REVERT: A 113 LEU cc_start: 0.9634 (mt) cc_final: 0.9308 (tt) REVERT: A 127 ASP cc_start: 0.9432 (t70) cc_final: 0.9128 (t0) REVERT: A 140 MET cc_start: 0.9243 (ttm) cc_final: 0.8961 (ttp) REVERT: A 149 LEU cc_start: 0.9529 (tp) cc_final: 0.9114 (tp) REVERT: A 154 PHE cc_start: 0.9524 (m-80) cc_final: 0.9088 (m-80) REVERT: A 158 ARG cc_start: 0.9005 (ttp80) cc_final: 0.8739 (ttp80) REVERT: A 162 GLU cc_start: 0.8669 (pp20) cc_final: 0.8083 (pp20) REVERT: A 183 ASP cc_start: 0.8553 (t0) cc_final: 0.8168 (t0) REVERT: A 210 MET cc_start: 0.9430 (ptp) cc_final: 0.9060 (ptp) REVERT: A 211 TRP cc_start: 0.6810 (t-100) cc_final: 0.6534 (t-100) REVERT: A 214 MET cc_start: 0.9458 (mmp) cc_final: 0.9172 (mmm) REVERT: A 222 SER cc_start: 0.9127 (t) cc_final: 0.8858 (t) REVERT: A 229 MET cc_start: 0.9537 (ptp) cc_final: 0.9196 (pmm) REVERT: A 250 GLU cc_start: 0.9589 (tp30) cc_final: 0.9070 (tp30) REVERT: B 61 GLU cc_start: 0.8650 (mp0) cc_final: 0.8346 (pm20) REVERT: B 75 TYR cc_start: 0.8519 (m-80) cc_final: 0.8178 (m-80) REVERT: B 111 GLU cc_start: 0.9107 (tp30) cc_final: 0.8725 (tp30) REVERT: B 159 ASP cc_start: 0.8700 (m-30) cc_final: 0.8427 (m-30) REVERT: B 210 MET cc_start: 0.9583 (ttp) cc_final: 0.9127 (ptp) REVERT: B 214 MET cc_start: 0.9442 (mmp) cc_final: 0.8972 (mtt) REVERT: B 223 ASN cc_start: 0.9619 (t0) cc_final: 0.9276 (t0) REVERT: C 95 ARG cc_start: 0.9051 (ttm-80) cc_final: 0.8807 (ttm-80) REVERT: C 173 THR cc_start: 0.8095 (p) cc_final: 0.7752 (t) REVERT: C 183 ASP cc_start: 0.9422 (t0) cc_final: 0.9174 (t0) REVERT: C 185 GLN cc_start: 0.9173 (tp40) cc_final: 0.8955 (tp40) REVERT: C 187 LEU cc_start: 0.9439 (mt) cc_final: 0.9058 (mt) REVERT: C 250 GLU cc_start: 0.9340 (tp30) cc_final: 0.8793 (tp30) REVERT: D 99 LYS cc_start: 0.9270 (mmtt) cc_final: 0.8776 (tptp) REVERT: D 163 ASP cc_start: 0.9057 (m-30) cc_final: 0.8754 (m-30) REVERT: D 210 MET cc_start: 0.9471 (mtm) cc_final: 0.9260 (ptp) REVERT: D 211 TRP cc_start: 0.8645 (t-100) cc_final: 0.8192 (t60) REVERT: D 229 MET cc_start: 0.8897 (mtt) cc_final: 0.8248 (mmt) REVERT: E 98 GLN cc_start: 0.8692 (mm110) cc_final: 0.8435 (mm110) REVERT: E 99 LYS cc_start: 0.9447 (mttm) cc_final: 0.9226 (mmmt) REVERT: E 104 ASP cc_start: 0.8625 (t70) cc_final: 0.8066 (t0) REVERT: E 139 GLU cc_start: 0.9053 (mp0) cc_final: 0.8798 (mp0) REVERT: E 183 ASP cc_start: 0.9435 (t0) cc_final: 0.9086 (t0) REVERT: E 185 GLN cc_start: 0.9013 (mp10) cc_final: 0.8748 (mp10) REVERT: E 199 LEU cc_start: 0.8520 (tp) cc_final: 0.8136 (tp) REVERT: E 211 TRP cc_start: 0.9048 (t-100) cc_final: 0.8736 (t-100) REVERT: E 253 ILE cc_start: 0.9665 (tt) cc_final: 0.9343 (pt) REVERT: F 42 LEU cc_start: 0.9394 (mt) cc_final: 0.9174 (mt) REVERT: F 144 ASP cc_start: 0.9049 (t70) cc_final: 0.8102 (t0) REVERT: F 145 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8722 (mt-10) REVERT: F 170 LEU cc_start: 0.9675 (mt) cc_final: 0.9401 (mt) REVERT: F 190 PHE cc_start: 0.9470 (m-80) cc_final: 0.9239 (m-10) REVERT: F 199 LEU cc_start: 0.8365 (tp) cc_final: 0.7920 (tp) REVERT: F 210 MET cc_start: 0.9511 (mtm) cc_final: 0.9199 (ptp) REVERT: F 229 MET cc_start: 0.9369 (mtp) cc_final: 0.9021 (mtp) REVERT: F 269 GLN cc_start: 0.9535 (mt0) cc_final: 0.9186 (mt0) REVERT: G 127 ASP cc_start: 0.9229 (m-30) cc_final: 0.9009 (m-30) REVERT: G 140 MET cc_start: 0.8542 (ttm) cc_final: 0.8001 (mtm) REVERT: G 153 THR cc_start: 0.9121 (t) cc_final: 0.8845 (m) REVERT: G 154 PHE cc_start: 0.9276 (m-80) cc_final: 0.8928 (m-80) REVERT: G 159 ASP cc_start: 0.8750 (t70) cc_final: 0.8291 (t70) REVERT: G 163 ASP cc_start: 0.8559 (m-30) cc_final: 0.8354 (m-30) REVERT: G 174 ASP cc_start: 0.8864 (p0) cc_final: 0.8295 (p0) REVERT: G 175 ARG cc_start: 0.8621 (mmp80) cc_final: 0.8291 (mmm160) REVERT: G 246 GLU cc_start: 0.9316 (pt0) cc_final: 0.9003 (pp20) REVERT: G 250 GLU cc_start: 0.9233 (tp30) cc_final: 0.8652 (tp30) REVERT: G 271 VAL cc_start: 0.9246 (t) cc_final: 0.9016 (m) REVERT: H 103 LYS cc_start: 0.9305 (tttt) cc_final: 0.9012 (pttm) REVERT: H 127 ASP cc_start: 0.9026 (m-30) cc_final: 0.8822 (m-30) REVERT: H 176 LEU cc_start: 0.9549 (tp) cc_final: 0.9306 (tt) REVERT: H 183 ASP cc_start: 0.8634 (m-30) cc_final: 0.7964 (t70) REVERT: H 189 ARG cc_start: 0.9236 (tpt170) cc_final: 0.8853 (mmm-85) REVERT: H 210 MET cc_start: 0.9382 (ptp) cc_final: 0.8758 (ptp) REVERT: H 223 ASN cc_start: 0.9438 (t0) cc_final: 0.9169 (t0) REVERT: I 61 GLU cc_start: 0.9384 (mm-30) cc_final: 0.8766 (tt0) REVERT: I 75 TYR cc_start: 0.8560 (m-80) cc_final: 0.8286 (m-80) REVERT: I 93 TYR cc_start: 0.8807 (t80) cc_final: 0.8548 (t80) REVERT: I 111 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8529 (tm-30) REVERT: I 139 GLU cc_start: 0.9011 (mp0) cc_final: 0.8777 (mp0) REVERT: I 185 GLN cc_start: 0.9235 (mt0) cc_final: 0.8512 (mp10) REVERT: I 210 MET cc_start: 0.9215 (tmm) cc_final: 0.8842 (tmm) REVERT: I 233 LEU cc_start: 0.9855 (tp) cc_final: 0.9569 (pp) REVERT: J 97 HIS cc_start: 0.7481 (p90) cc_final: 0.7280 (p-80) REVERT: J 99 LYS cc_start: 0.9564 (mmmm) cc_final: 0.9205 (mmmm) REVERT: J 100 CYS cc_start: 0.8882 (t) cc_final: 0.8419 (p) REVERT: J 149 LEU cc_start: 0.9476 (mm) cc_final: 0.8905 (mp) REVERT: J 159 ASP cc_start: 0.9390 (t70) cc_final: 0.8854 (t0) REVERT: J 162 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8405 (mm-30) REVERT: J 163 ASP cc_start: 0.9315 (t0) cc_final: 0.8919 (p0) REVERT: J 210 MET cc_start: 0.9694 (mtm) cc_final: 0.9312 (mtp) REVERT: J 213 GLN cc_start: 0.9209 (mp10) cc_final: 0.8898 (mp10) REVERT: J 229 MET cc_start: 0.9398 (mmt) cc_final: 0.9090 (mmm) REVERT: K 20 TRP cc_start: 0.8988 (p-90) cc_final: 0.8280 (p-90) REVERT: K 54 LYS cc_start: 0.9447 (tppt) cc_final: 0.8979 (mmmt) REVERT: K 63 ARG cc_start: 0.9225 (mmp-170) cc_final: 0.8887 (mmm160) REVERT: K 116 ARG cc_start: 0.8612 (mmp80) cc_final: 0.8209 (mmp80) REVERT: K 159 ASP cc_start: 0.9403 (t0) cc_final: 0.9013 (t0) REVERT: K 162 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8653 (mm-30) REVERT: K 163 ASP cc_start: 0.8764 (m-30) cc_final: 0.8467 (m-30) REVERT: K 210 MET cc_start: 0.9175 (mtm) cc_final: 0.8855 (mtt) REVERT: L 38 GLN cc_start: 0.9284 (mm110) cc_final: 0.8904 (pm20) REVERT: L 63 ARG cc_start: 0.9452 (mmp80) cc_final: 0.8931 (mmm160) REVERT: L 116 ARG cc_start: 0.8904 (mtp-110) cc_final: 0.8691 (ttm110) REVERT: L 124 ASP cc_start: 0.9326 (m-30) cc_final: 0.9063 (m-30) REVERT: L 131 GLU cc_start: 0.9250 (tt0) cc_final: 0.8831 (pt0) REVERT: L 145 GLU cc_start: 0.7244 (pm20) cc_final: 0.6883 (tp30) REVERT: L 215 VAL cc_start: 0.9811 (t) cc_final: 0.9165 (t) REVERT: L 240 TYR cc_start: 0.8849 (m-10) cc_final: 0.8354 (m-80) REVERT: L 269 GLN cc_start: 0.9169 (pp30) cc_final: 0.8935 (pp30) REVERT: O 71 ASP cc_start: 0.9360 (t0) cc_final: 0.8596 (p0) REVERT: O 104 ASP cc_start: 0.9358 (m-30) cc_final: 0.9124 (m-30) REVERT: O 106 PHE cc_start: 0.9618 (m-80) cc_final: 0.9295 (m-80) REVERT: O 107 LYS cc_start: 0.9453 (mtmm) cc_final: 0.9207 (mttt) REVERT: O 108 LYS cc_start: 0.9483 (mtpt) cc_final: 0.9187 (mtpt) REVERT: O 144 ASP cc_start: 0.7353 (t70) cc_final: 0.6506 (p0) REVERT: O 158 ARG cc_start: 0.9041 (tpt-90) cc_final: 0.8449 (tpp80) REVERT: O 183 ASP cc_start: 0.9036 (t0) cc_final: 0.8237 (t0) REVERT: O 185 GLN cc_start: 0.9542 (tm-30) cc_final: 0.9049 (tm-30) REVERT: O 191 ARG cc_start: 0.9022 (mtt-85) cc_final: 0.8338 (ptm160) REVERT: O 240 TYR cc_start: 0.9155 (m-80) cc_final: 0.8880 (m-10) REVERT: P 37 GLN cc_start: 0.8666 (mp10) cc_final: 0.8429 (mp10) REVERT: P 56 CYS cc_start: 0.8964 (p) cc_final: 0.8164 (p) REVERT: P 116 ARG cc_start: 0.8437 (tmm160) cc_final: 0.8196 (tmt170) REVERT: P 127 ASP cc_start: 0.9390 (m-30) cc_final: 0.9118 (m-30) REVERT: P 144 ASP cc_start: 0.8915 (t0) cc_final: 0.8387 (t0) REVERT: P 154 PHE cc_start: 0.9607 (m-10) cc_final: 0.9386 (m-80) REVERT: P 180 ILE cc_start: 0.9502 (tp) cc_final: 0.9203 (tp) REVERT: P 187 LEU cc_start: 0.9677 (tt) cc_final: 0.9418 (tp) REVERT: P 190 PHE cc_start: 0.9200 (m-80) cc_final: 0.8633 (m-80) REVERT: P 214 MET cc_start: 0.8647 (mtm) cc_final: 0.8161 (ptm) REVERT: P 229 MET cc_start: 0.1094 (mtt) cc_final: 0.0534 (mtt) outliers start: 1 outliers final: 0 residues processed: 895 average time/residue: 0.1875 time to fit residues: 268.4041 Evaluate side-chains 719 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 719 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 147 optimal weight: 0.8980 chunk 203 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 317 optimal weight: 0.9980 chunk 268 optimal weight: 3.9990 chunk 324 optimal weight: 7.9990 chunk 265 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 HIS P 185 GLN ** P 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.086682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.061172 restraints weight = 126764.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.063199 restraints weight = 70900.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.064565 restraints weight = 47926.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.065458 restraints weight = 36511.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066038 restraints weight = 30280.471| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.7879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31134 Z= 0.150 Angle : 0.705 11.953 42181 Z= 0.364 Chirality : 0.044 0.306 4756 Planarity : 0.004 0.073 5084 Dihedral : 15.047 178.442 4907 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.44 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.14), residues: 3570 helix: 1.01 (0.12), residues: 2108 sheet: 1.12 (0.28), residues: 358 loop : 0.09 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 126 TYR 0.030 0.001 TYR A 75 PHE 0.026 0.002 PHE O 106 TRP 0.047 0.002 TRP G 211 HIS 0.014 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00334 (31132) covalent geometry : angle 0.70519 (42181) hydrogen bonds : bond 0.04147 ( 1579) hydrogen bonds : angle 4.74697 ( 4611) Misc. bond : bond 0.00348 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7763.89 seconds wall clock time: 134 minutes 8.73 seconds (8048.73 seconds total)