Starting phenix.real_space_refine on Mon Sep 14 11:49:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m9c_23723/09_2026/7m9c_23723.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m9c_23723/09_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_23723/09_2026/7m9c_23723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m9c_23723/09_2026/7m9c_23723.map" model { file = "/net/cci-nas-00/data/ceres_data/7m9c_23723/09_2026/7m9c_23723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m9c_23723/09_2026/7m9c_23723.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7m9c_23723/09_2026/7m9c_23723.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m9c_23723/09_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 5.98, per 1000 atoms: 0.20 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: 2.24 Conformation dependent library (CDL) restraints added in 989.6 milliseconds 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: 3.53 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: 6.20 Time building geometry restraints manager: 3.01 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=" C3' DT N 29 " pdb=" C2' DT N 29 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DA M 21 " pdb=" C2' DA M 21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DT N 11 " pdb=" C2' DT N 11 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DT N 17 " pdb=" C2' DT N 17 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 ... (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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.990 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 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= 0.268 Angle : 0.663 27.016 42181 Z= 0.426 Chirality : 0.045 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/Z covalent geometry : bond 0.00305 / 0.22 (31132) covalent geometry : angle 0.66328 / 0.43 (42181) hydrogen bonds : bond 0.15126 / 9.93 ( 1579) hydrogen bonds : angle 6.03836 / 4.38 ( 4611) Misc. bond : bond 0.19393 / 10.21 ( 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 : 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7213 (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: 0.7202 (p0) REVERT: C 173 THR cc_start: 0.8137 (p) cc_final: 0.7597 (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: 0.8231 (mp) REVERT: D 247 ILE cc_start: 0.8791 (mt) cc_final: 0.8292 (mm) REVERT: E 113 LEU cc_start: 0.9336 (mt) cc_final: 0.9121 (mp) REVERT: E 144 ASP cc_start: 0.8395 (t70) cc_final: 0.6869 (t0) REVERT: E 159 ASP cc_start: 0.7550 (m-30) cc_final: 0.6633 (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: 0.9271 (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: 0.8127 (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: 0.7014 (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: 0.8582 (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: 0.8578 (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: 0.6927 (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: 0.7655 (t0) REVERT: K 156 ASP cc_start: 0.8611 (m-30) cc_final: 0.7537 (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: 0.7190 (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: 0.7747 (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: 0.2193 time to fit residues: 607.3016 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 : 1.158 ------------------------------------------------------------------------------- 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... 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 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 L 193 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.092705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066235 restraints weight = 119341.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.068601 restraints weight = 65038.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.070187 restraints weight = 43148.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.071213 restraints weight = 32377.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.071895 restraints weight = 26677.090| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 31134 Z= 0.191 Angle : 0.778 10.486 42181 Z= 0.403 Chirality : 0.046 0.280 4756 Planarity : 0.006 0.086 5084 Dihedral : 16.193 178.579 4907 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.07 % Favored : 97.90 % Rotamer: Outliers : 0.54 % Allowed : 3.36 % Favored : 96.10 % 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: 0.64 (0.14), residues: 3570 helix: 0.59 (0.11), residues: 2042 sheet: 0.88 (0.26), residues: 358 loop : 0.25 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 126 TYR 0.024 0.002 TYR G 75 PHE 0.021 0.002 PHE O 204 TRP 0.031 0.003 TRP G 211 HIS 0.017 0.001 HIS P 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (31132) covalent geometry : angle 0.77758 / 0.40 (42181) hydrogen bonds : bond 0.06077 / 4.02 ( 1579) hydrogen bonds : angle 5.07597 / 3.68 ( 4611) Misc. bond : bond 0.00220 / 0.12 ( 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 1208 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 1191 time to evaluate : 1.185 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: 0.9251 (tp) cc_final: 0.8652 (tp) REVERT: A 44 ASP cc_start: 0.9425 (p0) cc_final: 0.9149 (p0) REVERT: A 75 TYR cc_start: 0.8785 (m-80) cc_final: 0.8484 (m-80) REVERT: A 103 LYS cc_start: 0.8991 (tttt) cc_final: 0.8734 (tttp) REVERT: A 113 LEU cc_start: 0.9540 (mt) cc_final: 0.9338 (tt) REVERT: A 115 TYR cc_start: 0.8838 (m-10) cc_final: 0.8599 (m-10) REVERT: A 133 LEU cc_start: 0.9749 (mt) cc_final: 0.9546 (mt) REVERT: A 149 LEU cc_start: 0.9654 (tp) cc_final: 0.9291 (tp) REVERT: A 154 PHE cc_start: 0.9299 (m-80) cc_final: 0.9045 (m-80) REVERT: A 168 VAL cc_start: 0.9369 (t) cc_final: 0.9044 (p) REVERT: A 183 ASP cc_start: 0.8614 (t0) cc_final: 0.8286 (t70) REVERT: A 203 ASP cc_start: 0.9562 (m-30) cc_final: 0.9289 (t0) REVERT: A 214 MET cc_start: 0.9490 (mmp) cc_final: 0.9282 (ttm) REVERT: B 42 LEU cc_start: 0.9854 (tp) cc_final: 0.9588 (tp) REVERT: B 46 LEU cc_start: 0.9720 (mt) cc_final: 0.9455 (mt) REVERT: B 75 TYR cc_start: 0.8344 (m-80) cc_final: 0.8038 (m-80) REVERT: B 97 HIS cc_start: 0.7407 (p90) cc_final: 0.7174 (p90) REVERT: B 207 THR cc_start: 0.9632 (p) cc_final: 0.9418 (p) REVERT: B 210 MET cc_start: 0.9568 (mtt) cc_final: 0.9354 (ttt) REVERT: B 223 ASN cc_start: 0.9316 (t0) cc_final: 0.8807 (t0) REVERT: C 46 LEU cc_start: 0.9844 (mt) cc_final: 0.9632 (mt) REVERT: C 99 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8526 (tptp) REVERT: C 173 THR cc_start: 0.9148 (p) cc_final: 0.8603 (p) REVERT: C 210 MET cc_start: 0.9034 (tpt) cc_final: 0.8163 (tpt) REVERT: C 213 GLN cc_start: 0.9366 (tm-30) cc_final: 0.8785 (tm-30) REVERT: C 214 MET cc_start: 0.9416 (tpp) cc_final: 0.9026 (mpp) REVERT: C 223 ASN cc_start: 0.9166 (t0) cc_final: 0.8867 (t0) REVERT: C 229 MET cc_start: 0.9015 (mpp) cc_final: 0.8763 (mmm) REVERT: C 233 LEU cc_start: 0.9641 (mt) cc_final: 0.9427 (mt) REVERT: C 247 ILE cc_start: 0.9722 (mt) cc_final: 0.8390 (mt) REVERT: C 250 GLU cc_start: 0.9379 (tp30) cc_final: 0.9031 (tp30) REVERT: D 38 GLN cc_start: 0.9140 (mt0) cc_final: 0.8640 (mt0) REVERT: D 42 LEU cc_start: 0.9735 (tp) cc_final: 0.9434 (tp) REVERT: D 46 LEU cc_start: 0.9743 (mt) cc_final: 0.9533 (mm) REVERT: D 63 ARG cc_start: 0.8737 (mmp-170) cc_final: 0.8511 (mmm160) REVERT: D 140 MET cc_start: 0.8952 (ptm) cc_final: 0.8742 (ttp) REVERT: D 152 GLU cc_start: 0.8643 (tp30) cc_final: 0.8398 (tm-30) REVERT: D 159 ASP cc_start: 0.9054 (m-30) cc_final: 0.8810 (m-30) REVERT: D 163 ASP cc_start: 0.9227 (m-30) cc_final: 0.8967 (m-30) REVERT: D 210 MET cc_start: 0.9662 (tpt) cc_final: 0.9080 (tpp) REVERT: D 211 TRP cc_start: 0.8689 (t-100) cc_final: 0.8313 (t60) REVERT: D 269 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8948 (pp30) REVERT: D 275 TYR cc_start: 0.7068 (m-10) cc_final: 0.6836 (m-10) REVERT: E 46 LEU cc_start: 0.9722 (mt) cc_final: 0.9480 (mt) REVERT: E 99 LYS cc_start: 0.9231 (mmmt) cc_final: 0.9001 (mmmt) REVERT: E 104 ASP cc_start: 0.8636 (t70) cc_final: 0.7714 (t0) REVERT: E 132 VAL cc_start: 0.9747 (t) cc_final: 0.9545 (t) REVERT: E 144 ASP cc_start: 0.8441 (t70) cc_final: 0.8234 (t0) REVERT: E 163 ASP cc_start: 0.8822 (m-30) cc_final: 0.7685 (m-30) REVERT: E 183 ASP cc_start: 0.9263 (t0) cc_final: 0.8746 (t70) REVERT: E 199 LEU cc_start: 0.8631 (tp) cc_final: 0.8057 (tp) REVERT: E 210 MET cc_start: 0.9702 (ttt) cc_final: 0.9386 (ttt) REVERT: E 216 LEU cc_start: 0.9277 (tp) cc_final: 0.9034 (tt) REVERT: E 246 GLU cc_start: 0.9278 (tm-30) cc_final: 0.9067 (tm-30) REVERT: E 247 ILE cc_start: 0.9681 (mt) cc_final: 0.9372 (mt) REVERT: E 275 TYR cc_start: 0.5253 (m-10) cc_final: 0.4256 (m-10) REVERT: F 42 LEU cc_start: 0.9248 (mt) cc_final: 0.8958 (mt) REVERT: F 92 VAL cc_start: 0.9862 (t) cc_final: 0.9467 (m) REVERT: F 144 ASP cc_start: 0.8818 (t70) cc_final: 0.8150 (t0) REVERT: F 168 VAL cc_start: 0.9525 (t) cc_final: 0.9229 (m) REVERT: F 190 PHE cc_start: 0.9466 (m-80) cc_final: 0.9107 (m-80) REVERT: F 199 LEU cc_start: 0.7955 (tp) cc_final: 0.7102 (tp) REVERT: F 210 MET cc_start: 0.9659 (mtm) cc_final: 0.9228 (mtt) REVERT: F 229 MET cc_start: 0.9445 (mtp) cc_final: 0.9156 (mtp) REVERT: F 241 ILE cc_start: 0.9697 (pt) cc_final: 0.9496 (pt) REVERT: F 246 GLU cc_start: 0.8998 (pp20) cc_final: 0.8683 (pp20) REVERT: G 88 THR cc_start: 0.9123 (m) cc_final: 0.8895 (p) REVERT: G 174 ASP cc_start: 0.8579 (p0) cc_final: 0.8106 (p0) REVERT: G 190 PHE cc_start: 0.9386 (m-80) cc_final: 0.8718 (m-10) REVERT: G 250 GLU cc_start: 0.9314 (tp30) cc_final: 0.8845 (tp30) REVERT: H 54 LYS cc_start: 0.9168 (tttm) cc_final: 0.8853 (pptt) REVERT: H 103 LYS cc_start: 0.9280 (tttt) cc_final: 0.8917 (pttt) REVERT: H 127 ASP cc_start: 0.9084 (m-30) cc_final: 0.8870 (m-30) REVERT: H 145 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7852 (pp20) REVERT: H 153 THR cc_start: 0.9558 (m) cc_final: 0.9216 (m) REVERT: H 156 ASP cc_start: 0.9394 (m-30) cc_final: 0.8916 (m-30) REVERT: H 176 LEU cc_start: 0.9472 (tp) cc_final: 0.9253 (tt) REVERT: H 189 ARG cc_start: 0.9043 (tpt170) cc_final: 0.8700 (tpt90) REVERT: H 204 PHE cc_start: 0.9476 (t80) cc_final: 0.9252 (t80) REVERT: H 210 MET cc_start: 0.9302 (ptp) cc_final: 0.9039 (ptp) REVERT: I 54 LYS cc_start: 0.9300 (mtpp) cc_final: 0.9050 (ttpp) REVERT: I 93 TYR cc_start: 0.9146 (t80) cc_final: 0.8792 (t80) REVERT: I 127 ASP cc_start: 0.9324 (p0) cc_final: 0.9089 (p0) REVERT: I 210 MET cc_start: 0.9170 (tmm) cc_final: 0.8738 (tmm) REVERT: I 224 LEU cc_start: 0.9546 (mt) cc_final: 0.9330 (mt) REVERT: I 233 LEU cc_start: 0.9767 (tp) cc_final: 0.9438 (pp) REVERT: I 268 LEU cc_start: 0.9800 (tt) cc_final: 0.9584 (tp) REVERT: J 28 LEU cc_start: 0.9730 (mt) cc_final: 0.9435 (mt) REVERT: J 103 LYS cc_start: 0.9148 (tttt) cc_final: 0.8874 (tttp) REVERT: J 142 ILE cc_start: 0.9381 (mm) cc_final: 0.9147 (tp) REVERT: J 144 ASP cc_start: 0.8236 (t0) cc_final: 0.7460 (p0) REVERT: J 162 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8480 (mm-30) REVERT: J 176 LEU cc_start: 0.9483 (mp) cc_final: 0.9114 (mt) REVERT: J 185 GLN cc_start: 0.8864 (tp-100) cc_final: 0.8063 (tp-100) REVERT: J 210 MET cc_start: 0.9655 (mtm) cc_final: 0.9107 (mtt) REVERT: J 232 ILE cc_start: 0.9486 (mm) cc_final: 0.9003 (tt) REVERT: J 248 LEU cc_start: 0.9662 (mt) cc_final: 0.9286 (mt) REVERT: J 253 ILE cc_start: 0.9678 (pt) cc_final: 0.9385 (mm) REVERT: K 46 LEU cc_start: 0.9589 (mt) cc_final: 0.9361 (mt) REVERT: K 54 LYS cc_start: 0.9422 (tppt) cc_final: 0.9112 (tptp) REVERT: K 145 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7827 (mm-30) REVERT: K 149 LEU cc_start: 0.9653 (tp) cc_final: 0.9330 (tp) REVERT: K 156 ASP cc_start: 0.9279 (m-30) cc_final: 0.8791 (m-30) REVERT: K 158 ARG cc_start: 0.8798 (ptt90) cc_final: 0.8257 (ttp80) REVERT: K 162 GLU cc_start: 0.8938 (mm-30) cc_final: 0.7957 (mm-30) REVERT: K 240 TYR cc_start: 0.8722 (m-80) cc_final: 0.7311 (m-10) REVERT: K 254 ARG cc_start: 0.9129 (ttp-170) cc_final: 0.8799 (ptm160) REVERT: L 100 CYS cc_start: 0.7233 (t) cc_final: 0.5396 (t) REVERT: L 124 ASP cc_start: 0.9320 (m-30) cc_final: 0.9006 (m-30) REVERT: L 166 ILE cc_start: 0.8256 (mt) cc_final: 0.7837 (mm) REVERT: L 184 GLU cc_start: 0.8813 (mp0) cc_final: 0.8327 (mp0) REVERT: L 215 VAL cc_start: 0.9510 (t) cc_final: 0.9043 (t) REVERT: L 223 ASN cc_start: 0.9129 (t0) cc_final: 0.8873 (t0) REVERT: L 240 TYR cc_start: 0.8928 (m-10) cc_final: 0.8346 (m-80) REVERT: L 270 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: O 46 LEU cc_start: 0.9652 (mt) cc_final: 0.9399 (mt) REVERT: O 71 ASP cc_start: 0.9449 (p0) cc_final: 0.9077 (p0) REVERT: O 94 ILE cc_start: 0.8652 (mt) cc_final: 0.8436 (mm) REVERT: O 106 PHE cc_start: 0.9170 (m-80) cc_final: 0.8576 (m-80) REVERT: O 115 TYR cc_start: 0.8865 (m-80) cc_final: 0.8457 (m-10) REVERT: O 147 ASP cc_start: 0.8877 (p0) cc_final: 0.8567 (t0) REVERT: O 158 ARG cc_start: 0.9219 (tpt-90) cc_final: 0.8440 (tpt-90) REVERT: O 183 ASP cc_start: 0.9220 (t0) cc_final: 0.8786 (t70) REVERT: O 185 GLN cc_start: 0.9593 (tm-30) cc_final: 0.9255 (tm-30) REVERT: O 232 ILE cc_start: 0.8733 (mt) cc_final: 0.8504 (pt) REVERT: O 240 TYR cc_start: 0.9334 (m-80) cc_final: 0.9123 (m-80) REVERT: P 42 LEU cc_start: 0.9272 (mt) cc_final: 0.9056 (mt) REVERT: P 73 TYR cc_start: 0.8795 (t80) cc_final: 0.8553 (t80) REVERT: P 127 ASP cc_start: 0.9427 (m-30) cc_final: 0.9208 (m-30) REVERT: P 144 ASP cc_start: 0.8715 (t0) cc_final: 0.8259 (t0) REVERT: P 154 PHE cc_start: 0.9638 (m-10) cc_final: 0.9274 (m-80) REVERT: P 164 LEU cc_start: 0.8828 (mm) cc_final: 0.8561 (mm) REVERT: P 214 MET cc_start: 0.8602 (mtm) cc_final: 0.8292 (mpp) REVERT: P 240 TYR cc_start: 0.9688 (m-80) cc_final: 0.9464 (m-80) REVERT: P 263 ILE cc_start: 0.5379 (mp) cc_final: 0.5096 (mp) outliers start: 17 outliers final: 2 residues processed: 1199 average time/residue: 0.1895 time to fit residues: 358.2512 Evaluate side-chains 832 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 828 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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: 5.9990 chunk 226 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 335 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 300 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 310 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN A 213 GLN B 38 GLN B 185 GLN D 213 GLN ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 HIS J 185 GLN K 38 GLN ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 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 = 0.3624 r_free = 0.3624 target = 0.088697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.063038 restraints weight = 123535.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.065136 restraints weight = 69036.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.066524 restraints weight = 46677.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.067466 restraints weight = 35549.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.068055 restraints weight = 29575.536| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31134 Z= 0.216 Angle : 0.755 10.126 42181 Z= 0.391 Chirality : 0.044 0.289 4756 Planarity : 0.006 0.079 5084 Dihedral : 16.122 170.473 4907 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.79 % Rotamer: Outliers : 0.45 % Allowed : 3.36 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3570 helix: 0.72 (0.11), residues: 2144 sheet: 0.94 (0.26), residues: 358 loop : 0.32 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 126 TYR 0.021 0.002 TYR F 240 PHE 0.026 0.002 PHE L 196 TRP 0.035 0.002 TRP P 211 HIS 0.012 0.002 HIS P 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.22 (31132) covalent geometry : angle 0.75475 / 0.39 (42181) hydrogen bonds : bond 0.05200 / 3.42 ( 1579) hydrogen bonds : angle 4.99170 / 3.61 ( 4611) Misc. bond : bond 0.00275 / 0.14 ( 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 1020 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1006 time to evaluate : 1.403 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: A 36 LEU cc_start: 0.9517 (tp) cc_final: 0.9077 (tp) REVERT: A 38 GLN cc_start: 0.9470 (mp10) cc_final: 0.9162 (mp10) REVERT: A 43 HIS cc_start: 0.9148 (m90) cc_final: 0.8811 (m90) REVERT: A 46 LEU cc_start: 0.9822 (mt) cc_final: 0.9599 (mt) REVERT: A 75 TYR cc_start: 0.8668 (m-80) cc_final: 0.8409 (m-80) REVERT: A 94 ILE cc_start: 0.9559 (pt) cc_final: 0.9286 (pt) REVERT: A 103 LYS cc_start: 0.9155 (tttt) cc_final: 0.8895 (tttp) REVERT: A 113 LEU cc_start: 0.9622 (mt) cc_final: 0.9336 (tt) REVERT: A 136 CYS cc_start: 0.8421 (m) cc_final: 0.8185 (m) REVERT: A 149 LEU cc_start: 0.9675 (tp) cc_final: 0.9366 (tp) REVERT: A 154 PHE cc_start: 0.9539 (m-80) cc_final: 0.9068 (m-80) REVERT: A 158 ARG cc_start: 0.9006 (ttp80) cc_final: 0.8786 (ttp80) REVERT: A 168 VAL cc_start: 0.9446 (t) cc_final: 0.9205 (p) REVERT: A 183 ASP cc_start: 0.8805 (t0) cc_final: 0.8443 (t70) REVERT: B 75 TYR cc_start: 0.8238 (m-80) cc_final: 0.7948 (m-80) REVERT: B 97 HIS cc_start: 0.7442 (p90) cc_final: 0.6728 (p-80) REVERT: B 159 ASP cc_start: 0.8874 (m-30) cc_final: 0.8600 (m-30) REVERT: B 223 ASN cc_start: 0.9347 (t0) cc_final: 0.8883 (t0) REVERT: C 46 LEU cc_start: 0.9856 (mt) cc_final: 0.9591 (mt) REVERT: C 98 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8844 (tp-100) REVERT: C 99 LYS cc_start: 0.9093 (mmmt) cc_final: 0.8802 (tptp) REVERT: C 159 ASP cc_start: 0.8745 (m-30) cc_final: 0.8527 (m-30) REVERT: C 183 ASP cc_start: 0.9445 (t0) cc_final: 0.9106 (t0) REVERT: C 185 GLN cc_start: 0.9267 (mt0) cc_final: 0.8875 (mp10) REVERT: C 188 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8720 (tp30) REVERT: C 210 MET cc_start: 0.8997 (tpt) cc_final: 0.7999 (tpt) REVERT: C 213 GLN cc_start: 0.9285 (tm-30) cc_final: 0.8647 (tm-30) REVERT: C 214 MET cc_start: 0.9344 (tpp) cc_final: 0.9043 (mpp) REVERT: C 215 VAL cc_start: 0.9168 (t) cc_final: 0.8825 (t) REVERT: C 223 ASN cc_start: 0.9156 (t0) cc_final: 0.8849 (t0) REVERT: C 246 GLU cc_start: 0.8095 (pp20) cc_final: 0.7710 (pp20) REVERT: C 247 ILE cc_start: 0.9235 (mt) cc_final: 0.8748 (mt) REVERT: C 250 GLU cc_start: 0.9322 (tp30) cc_final: 0.8854 (tp30) REVERT: C 254 ARG cc_start: 0.8817 (ttp-170) cc_final: 0.8292 (ttp-170) REVERT: C 269 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8900 (mp10) REVERT: D 42 LEU cc_start: 0.9698 (tp) cc_final: 0.9457 (tp) REVERT: D 54 LYS cc_start: 0.9085 (tttt) cc_final: 0.8189 (ttmt) REVERT: D 139 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8452 (tt0) REVERT: D 163 ASP cc_start: 0.9152 (m-30) cc_final: 0.8876 (m-30) REVERT: D 176 LEU cc_start: 0.9610 (tp) cc_final: 0.9252 (tp) REVERT: D 180 ILE cc_start: 0.9418 (mt) cc_final: 0.9082 (mt) REVERT: D 211 TRP cc_start: 0.8656 (t-100) cc_final: 0.8159 (t60) REVERT: D 229 MET cc_start: 0.8691 (mtt) cc_final: 0.8214 (mmt) REVERT: D 248 LEU cc_start: 0.9758 (mt) cc_final: 0.9537 (mt) REVERT: E 42 LEU cc_start: 0.9763 (tp) cc_final: 0.9496 (tp) REVERT: E 46 LEU cc_start: 0.9731 (mt) cc_final: 0.9415 (mt) REVERT: E 47 ASP cc_start: 0.9410 (t0) cc_final: 0.9062 (m-30) REVERT: E 100 CYS cc_start: 0.8543 (t) cc_final: 0.8298 (t) REVERT: E 104 ASP cc_start: 0.8491 (t70) cc_final: 0.7666 (t0) REVERT: E 107 LYS cc_start: 0.9230 (tttp) cc_final: 0.8909 (ttmm) REVERT: E 108 LYS cc_start: 0.9546 (mttm) cc_final: 0.9309 (mmmm) REVERT: E 159 ASP cc_start: 0.8860 (t0) cc_final: 0.8638 (t0) REVERT: E 183 ASP cc_start: 0.9356 (t0) cc_final: 0.8885 (t70) REVERT: E 199 LEU cc_start: 0.8538 (tp) cc_final: 0.8264 (tp) REVERT: E 210 MET cc_start: 0.9666 (ttt) cc_final: 0.9246 (ttt) REVERT: E 246 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8905 (tm-30) REVERT: F 144 ASP cc_start: 0.9006 (t70) cc_final: 0.8342 (t0) REVERT: F 145 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8713 (mt-10) REVERT: F 168 VAL cc_start: 0.9491 (t) cc_final: 0.9122 (m) REVERT: F 170 LEU cc_start: 0.9707 (mt) cc_final: 0.9373 (mt) REVERT: F 190 PHE cc_start: 0.9475 (m-80) cc_final: 0.8854 (m-80) REVERT: F 199 LEU cc_start: 0.7897 (tp) cc_final: 0.7534 (tp) REVERT: F 210 MET cc_start: 0.9530 (mtm) cc_final: 0.9265 (mtp) REVERT: F 212 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: F 229 MET cc_start: 0.9431 (mtp) cc_final: 0.9139 (mtp) REVERT: F 240 TYR cc_start: 0.8849 (m-10) cc_final: 0.8279 (m-10) REVERT: F 241 ILE cc_start: 0.9710 (pt) cc_final: 0.9502 (pt) REVERT: G 75 TYR cc_start: 0.8474 (m-10) cc_final: 0.8095 (m-10) REVERT: G 140 MET cc_start: 0.9020 (ttm) cc_final: 0.8774 (ttm) REVERT: G 170 LEU cc_start: 0.9686 (mm) cc_final: 0.9268 (mm) REVERT: G 174 ASP cc_start: 0.8419 (p0) cc_final: 0.8134 (p0) REVERT: G 190 PHE cc_start: 0.9161 (m-80) cc_final: 0.8604 (m-10) REVERT: G 250 GLU cc_start: 0.9299 (tp30) cc_final: 0.8595 (tp30) REVERT: H 103 LYS cc_start: 0.9392 (tttt) cc_final: 0.8997 (pttt) REVERT: H 156 ASP cc_start: 0.9326 (m-30) cc_final: 0.9107 (m-30) REVERT: H 176 LEU cc_start: 0.9534 (tp) cc_final: 0.9333 (tt) REVERT: H 185 GLN cc_start: 0.9257 (mt0) cc_final: 0.8950 (mm-40) REVERT: H 189 ARG cc_start: 0.9144 (tpt170) cc_final: 0.8754 (tpt170) REVERT: H 223 ASN cc_start: 0.9197 (t0) cc_final: 0.8677 (t0) REVERT: I 93 TYR cc_start: 0.9244 (t80) cc_final: 0.8955 (t80) REVERT: I 158 ARG cc_start: 0.9062 (ptm-80) cc_final: 0.8516 (tmm-80) REVERT: I 185 GLN cc_start: 0.9037 (mt0) cc_final: 0.8422 (mp10) REVERT: I 210 MET cc_start: 0.9164 (tmm) cc_final: 0.8774 (tmm) REVERT: I 211 TRP cc_start: 0.9342 (t-100) cc_final: 0.8996 (t-100) REVERT: I 224 LEU cc_start: 0.9561 (mt) cc_final: 0.9248 (mt) REVERT: I 233 LEU cc_start: 0.9817 (tp) cc_final: 0.9463 (pp) REVERT: I 248 LEU cc_start: 0.9750 (mt) cc_final: 0.9519 (mt) REVERT: J 51 LYS cc_start: 0.9480 (mmpt) cc_final: 0.9169 (mmmt) REVERT: J 99 LYS cc_start: 0.9628 (tppt) cc_final: 0.9418 (tppp) REVERT: J 103 LYS cc_start: 0.9277 (tttt) cc_final: 0.9033 (tttp) REVERT: J 115 TYR cc_start: 0.8913 (m-80) cc_final: 0.8698 (m-10) REVERT: J 127 ASP cc_start: 0.9048 (m-30) cc_final: 0.8783 (m-30) REVERT: J 144 ASP cc_start: 0.8189 (t0) cc_final: 0.7657 (p0) REVERT: J 162 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8470 (mm-30) REVERT: J 187 LEU cc_start: 0.9107 (mt) cc_final: 0.8865 (mt) REVERT: J 210 MET cc_start: 0.9655 (mtm) cc_final: 0.9000 (mtt) REVERT: J 246 GLU cc_start: 0.9023 (pp20) cc_final: 0.8708 (pp20) REVERT: K 54 LYS cc_start: 0.9458 (tppt) cc_final: 0.9237 (tptp) REVERT: K 129 THR cc_start: 0.9771 (m) cc_final: 0.9485 (p) REVERT: K 145 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7814 (mm-30) REVERT: K 150 LYS cc_start: 0.9049 (tptp) cc_final: 0.8703 (tptp) REVERT: K 158 ARG cc_start: 0.8874 (ptt90) cc_final: 0.8447 (ttp80) REVERT: K 162 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8156 (mm-30) REVERT: K 174 ASP cc_start: 0.9312 (p0) cc_final: 0.8906 (p0) REVERT: K 223 ASN cc_start: 0.9500 (m110) cc_final: 0.9282 (m110) REVERT: K 254 ARG cc_start: 0.9146 (ttp-170) cc_final: 0.8823 (ptm160) REVERT: L 63 ARG cc_start: 0.9437 (mmp80) cc_final: 0.9136 (mmm160) REVERT: L 93 TYR cc_start: 0.8986 (t80) cc_final: 0.8369 (t80) REVERT: L 100 CYS cc_start: 0.7147 (t) cc_final: 0.5818 (t) REVERT: L 124 ASP cc_start: 0.9382 (m-30) cc_final: 0.9081 (m-30) REVERT: L 141 LEU cc_start: 0.9725 (tp) cc_final: 0.9219 (tp) REVERT: L 184 GLU cc_start: 0.8571 (mp0) cc_final: 0.8259 (mp0) REVERT: L 215 VAL cc_start: 0.9484 (t) cc_final: 0.8694 (t) REVERT: L 223 ASN cc_start: 0.9413 (t0) cc_final: 0.9205 (t0) REVERT: L 240 TYR cc_start: 0.8844 (m-10) cc_final: 0.8308 (m-80) REVERT: O 42 LEU cc_start: 0.9673 (mm) cc_final: 0.9420 (mm) REVERT: O 94 ILE cc_start: 0.8844 (mt) cc_final: 0.8616 (mm) REVERT: O 106 PHE cc_start: 0.9245 (m-10) cc_final: 0.8622 (m-80) REVERT: O 107 LYS cc_start: 0.9782 (tttm) cc_final: 0.9542 (tttm) REVERT: O 115 TYR cc_start: 0.8778 (m-80) cc_final: 0.8556 (m-10) REVERT: O 130 ILE cc_start: 0.9849 (pt) cc_final: 0.9482 (pt) REVERT: O 134 LYS cc_start: 0.9501 (pttm) cc_final: 0.9091 (tptp) REVERT: O 147 ASP cc_start: 0.8694 (p0) cc_final: 0.8324 (t0) REVERT: O 158 ARG cc_start: 0.9254 (tpt-90) cc_final: 0.8609 (tpt-90) REVERT: O 183 ASP cc_start: 0.9140 (t0) cc_final: 0.8547 (t0) REVERT: O 185 GLN cc_start: 0.9604 (tm-30) cc_final: 0.9271 (tm-30) REVERT: O 191 ARG cc_start: 0.8880 (mtt-85) cc_final: 0.8256 (ptm160) REVERT: O 240 TYR cc_start: 0.9254 (m-80) cc_final: 0.9029 (m-80) REVERT: P 42 LEU cc_start: 0.9231 (mt) cc_final: 0.9014 (mt) REVERT: P 56 CYS cc_start: 0.9051 (p) cc_final: 0.8730 (p) REVERT: P 73 TYR cc_start: 0.8962 (t80) cc_final: 0.8458 (t80) REVERT: P 113 LEU cc_start: 0.9659 (tt) cc_final: 0.9382 (tt) REVERT: P 115 TYR cc_start: 0.8106 (m-10) cc_final: 0.7803 (m-10) REVERT: P 144 ASP cc_start: 0.8753 (t0) cc_final: 0.8296 (t0) REVERT: P 154 PHE cc_start: 0.9642 (m-10) cc_final: 0.9303 (m-80) REVERT: P 214 MET cc_start: 0.8758 (mtm) cc_final: 0.8041 (ptm) outliers start: 14 outliers final: 5 residues processed: 1017 average time/residue: 0.1888 time to fit residues: 304.0615 Evaluate side-chains 766 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 759 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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: 8.9990 chunk 227 optimal weight: 4.9990 chunk 323 optimal weight: 7.9990 chunk 287 optimal weight: 0.7980 chunk 314 optimal weight: 4.9990 chunk 156 optimal weight: 30.0000 chunk 97 optimal weight: 6.9990 chunk 134 optimal weight: 0.3980 chunk 239 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 GLN J 213 GLN ** K 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.087975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.062467 restraints weight = 123399.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.064540 restraints weight = 68766.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.065915 restraints weight = 46393.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.066858 restraints weight = 35352.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.067455 restraints weight = 29248.124| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31134 Z= 0.200 Angle : 0.720 10.161 42181 Z= 0.374 Chirality : 0.044 0.290 4756 Planarity : 0.005 0.053 5084 Dihedral : 15.985 174.553 4907 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.21 % Favored : 97.73 % Rotamer: Outliers : 0.10 % Allowed : 2.97 % Favored : 96.93 % 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: 0.97 (0.14), residues: 3570 helix: 0.92 (0.11), residues: 2036 sheet: 1.07 (0.27), residues: 358 loop : 0.25 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG I 63 TYR 0.031 0.002 TYR J 75 PHE 0.019 0.002 PHE P 106 TRP 0.035 0.002 TRP P 211 HIS 0.014 0.002 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (31132) covalent geometry : angle 0.71982 / 0.37 (42181) hydrogen bonds : bond 0.04910 / 3.23 ( 1579) hydrogen bonds : angle 4.95199 / 3.60 ( 4611) Misc. bond : bond 0.00221 / 0.12 ( 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 943 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 940 time to evaluate : 1.154 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: A 43 HIS cc_start: 0.9211 (m90) cc_final: 0.8928 (m-70) REVERT: A 46 LEU cc_start: 0.9824 (mt) cc_final: 0.9600 (mt) REVERT: A 86 PRO cc_start: 0.8839 (Cg_exo) cc_final: 0.8560 (Cg_endo) REVERT: A 113 LEU cc_start: 0.9659 (mt) cc_final: 0.9305 (tt) REVERT: A 136 CYS cc_start: 0.8376 (m) cc_final: 0.7731 (m) REVERT: A 140 MET cc_start: 0.9188 (ttm) cc_final: 0.8834 (ttp) REVERT: A 154 PHE cc_start: 0.9559 (m-80) cc_final: 0.9098 (m-80) REVERT: A 168 VAL cc_start: 0.9434 (t) cc_final: 0.9218 (p) REVERT: A 183 ASP cc_start: 0.8616 (t0) cc_final: 0.8276 (t70) REVERT: B 75 TYR cc_start: 0.8282 (m-80) cc_final: 0.7989 (m-80) REVERT: B 159 ASP cc_start: 0.8769 (m-30) cc_final: 0.8458 (m-30) REVERT: B 210 MET cc_start: 0.9643 (ttt) cc_final: 0.9077 (mtt) REVERT: B 214 MET cc_start: 0.9476 (mmp) cc_final: 0.8979 (mtt) REVERT: B 216 LEU cc_start: 0.9124 (mp) cc_final: 0.8714 (tp) REVERT: B 218 LEU cc_start: 0.8793 (mt) cc_final: 0.8433 (mt) REVERT: B 223 ASN cc_start: 0.9378 (t0) cc_final: 0.8705 (t0) REVERT: B 229 MET cc_start: 0.9035 (mpp) cc_final: 0.8676 (pmm) REVERT: C 46 LEU cc_start: 0.9843 (mt) cc_final: 0.9613 (mt) REVERT: C 51 LYS cc_start: 0.9637 (mmtt) cc_final: 0.9433 (mmmm) REVERT: C 93 TYR cc_start: 0.8590 (t80) cc_final: 0.8301 (t80) REVERT: C 98 GLN cc_start: 0.9113 (tp-100) cc_final: 0.8831 (tp-100) REVERT: C 99 LYS cc_start: 0.9112 (mmmt) cc_final: 0.8904 (tptp) REVERT: C 144 ASP cc_start: 0.7102 (p0) cc_final: 0.6882 (p0) REVERT: C 215 VAL cc_start: 0.9192 (t) cc_final: 0.8872 (t) REVERT: C 223 ASN cc_start: 0.9225 (t0) cc_final: 0.8852 (t0) REVERT: C 246 GLU cc_start: 0.8134 (pp20) cc_final: 0.7738 (pp20) REVERT: C 247 ILE cc_start: 0.9219 (mt) cc_final: 0.8682 (mt) REVERT: C 250 GLU cc_start: 0.9293 (tp30) cc_final: 0.8747 (tp30) REVERT: C 254 ARG cc_start: 0.8880 (ttp-170) cc_final: 0.8240 (ttp-170) REVERT: D 42 LEU cc_start: 0.9776 (tp) cc_final: 0.9567 (tt) REVERT: D 54 LYS cc_start: 0.8972 (tttt) cc_final: 0.8694 (ttmt) REVERT: D 159 ASP cc_start: 0.8881 (m-30) cc_final: 0.8642 (m-30) REVERT: D 163 ASP cc_start: 0.9176 (m-30) cc_final: 0.8949 (m-30) REVERT: D 176 LEU cc_start: 0.9459 (tp) cc_final: 0.9219 (tp) REVERT: D 180 ILE cc_start: 0.9373 (mt) cc_final: 0.9107 (mt) REVERT: D 184 GLU cc_start: 0.9277 (pm20) cc_final: 0.8775 (pm20) REVERT: D 211 TRP cc_start: 0.8603 (t-100) cc_final: 0.8133 (t60) REVERT: D 229 MET cc_start: 0.8659 (mtt) cc_final: 0.8091 (mmt) REVERT: E 42 LEU cc_start: 0.9781 (tp) cc_final: 0.9540 (tt) REVERT: E 46 LEU cc_start: 0.9707 (mt) cc_final: 0.9432 (mt) REVERT: E 104 ASP cc_start: 0.8554 (t70) cc_final: 0.7708 (t0) REVERT: E 159 ASP cc_start: 0.8739 (t0) cc_final: 0.8517 (t0) REVERT: E 163 ASP cc_start: 0.8498 (m-30) cc_final: 0.8185 (m-30) REVERT: E 171 VAL cc_start: 0.9568 (t) cc_final: 0.9087 (m) REVERT: E 183 ASP cc_start: 0.9381 (t0) cc_final: 0.8912 (t70) REVERT: E 199 LEU cc_start: 0.8532 (tp) cc_final: 0.8221 (tp) REVERT: E 210 MET cc_start: 0.9681 (ttt) cc_final: 0.8590 (tpt) REVERT: E 214 MET cc_start: 0.8912 (mmp) cc_final: 0.8543 (mmm) REVERT: E 253 ILE cc_start: 0.9686 (tt) cc_final: 0.9416 (pt) REVERT: F 42 LEU cc_start: 0.9149 (mt) cc_final: 0.8944 (mt) REVERT: F 114 LYS cc_start: 0.9717 (mmtt) cc_final: 0.9502 (mmmm) REVERT: F 144 ASP cc_start: 0.9017 (t70) cc_final: 0.8270 (t0) REVERT: F 145 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8766 (mt-10) REVERT: F 170 LEU cc_start: 0.9684 (mt) cc_final: 0.9259 (mt) REVERT: F 175 ARG cc_start: 0.8595 (tpt170) cc_final: 0.8270 (tpm170) REVERT: F 190 PHE cc_start: 0.9487 (m-80) cc_final: 0.8914 (m-10) REVERT: F 199 LEU cc_start: 0.7942 (tp) cc_final: 0.7437 (tp) REVERT: F 210 MET cc_start: 0.9538 (mtm) cc_final: 0.9199 (mtp) REVERT: F 229 MET cc_start: 0.9432 (mtp) cc_final: 0.9181 (mtp) REVERT: F 271 VAL cc_start: 0.9229 (t) cc_final: 0.8476 (t) REVERT: G 75 TYR cc_start: 0.8542 (m-10) cc_final: 0.8104 (m-10) REVERT: G 154 PHE cc_start: 0.9023 (m-80) cc_final: 0.8774 (m-80) REVERT: G 174 ASP cc_start: 0.8581 (p0) cc_final: 0.8285 (p0) REVERT: G 210 MET cc_start: 0.8661 (ttt) cc_final: 0.8451 (mmp) REVERT: G 214 MET cc_start: 0.9587 (mpp) cc_final: 0.9371 (mpp) REVERT: G 250 GLU cc_start: 0.9286 (tp30) cc_final: 0.8731 (tp30) REVERT: H 103 LYS cc_start: 0.9403 (tttt) cc_final: 0.9035 (pttt) REVERT: H 176 LEU cc_start: 0.9541 (tp) cc_final: 0.9302 (tt) REVERT: H 183 ASP cc_start: 0.8690 (m-30) cc_final: 0.7964 (t70) REVERT: H 189 ARG cc_start: 0.9204 (tpt170) cc_final: 0.8846 (mmm-85) REVERT: H 223 ASN cc_start: 0.9268 (t0) cc_final: 0.8790 (t0) REVERT: I 53 ARG cc_start: 0.8682 (mmt90) cc_final: 0.8400 (mmm-85) REVERT: I 93 TYR cc_start: 0.9216 (t80) cc_final: 0.8893 (t80) REVERT: I 139 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8498 (mm-30) REVERT: I 158 ARG cc_start: 0.9145 (ptm-80) cc_final: 0.8844 (tmm-80) REVERT: I 185 GLN cc_start: 0.9164 (mt0) cc_final: 0.8404 (mp10) REVERT: I 210 MET cc_start: 0.9139 (tmm) cc_final: 0.8874 (tmm) REVERT: I 224 LEU cc_start: 0.9482 (mt) cc_final: 0.9181 (mt) REVERT: I 229 MET cc_start: 0.8859 (mmp) cc_final: 0.8406 (mmm) REVERT: J 47 ASP cc_start: 0.9554 (t70) cc_final: 0.9240 (m-30) REVERT: J 99 LYS cc_start: 0.9613 (tppt) cc_final: 0.9382 (tppp) REVERT: J 100 CYS cc_start: 0.9266 (t) cc_final: 0.8365 (p) REVERT: J 103 LYS cc_start: 0.9331 (tttt) cc_final: 0.8967 (tppt) REVERT: J 115 TYR cc_start: 0.8958 (m-80) cc_final: 0.8684 (m-10) REVERT: J 127 ASP cc_start: 0.9087 (m-30) cc_final: 0.8883 (m-30) REVERT: J 144 ASP cc_start: 0.8233 (t0) cc_final: 0.7748 (p0) REVERT: J 149 LEU cc_start: 0.9527 (mp) cc_final: 0.9175 (mp) REVERT: J 162 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8436 (mm-30) REVERT: J 177 ASP cc_start: 0.9393 (p0) cc_final: 0.9156 (p0) REVERT: J 210 MET cc_start: 0.9654 (mtm) cc_final: 0.9381 (mtp) REVERT: J 229 MET cc_start: 0.9215 (mmt) cc_final: 0.9007 (mmm) REVERT: J 246 GLU cc_start: 0.9027 (pp20) cc_final: 0.8739 (pp20) REVERT: K 54 LYS cc_start: 0.9458 (tppt) cc_final: 0.9038 (mmmt) REVERT: K 129 THR cc_start: 0.9780 (m) cc_final: 0.9494 (p) REVERT: K 145 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7846 (mm-30) REVERT: K 158 ARG cc_start: 0.8815 (ptt90) cc_final: 0.8502 (ttp80) REVERT: K 162 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8251 (mm-30) REVERT: K 223 ASN cc_start: 0.9513 (m110) cc_final: 0.9292 (m110) REVERT: K 254 ARG cc_start: 0.9068 (ttp-170) cc_final: 0.8783 (ptm160) REVERT: L 63 ARG cc_start: 0.9440 (mmp80) cc_final: 0.9143 (mmm160) REVERT: L 93 TYR cc_start: 0.8893 (t80) cc_final: 0.8270 (t80) REVERT: L 100 CYS cc_start: 0.6990 (t) cc_final: 0.5123 (t) REVERT: L 124 ASP cc_start: 0.9395 (m-30) cc_final: 0.9106 (m-30) REVERT: L 141 LEU cc_start: 0.9708 (tp) cc_final: 0.9243 (tp) REVERT: L 184 GLU cc_start: 0.8656 (mp0) cc_final: 0.8405 (mp0) REVERT: L 213 GLN cc_start: 0.8532 (pp30) cc_final: 0.7909 (pp30) REVERT: L 215 VAL cc_start: 0.9515 (t) cc_final: 0.8707 (t) REVERT: L 223 ASN cc_start: 0.9427 (t0) cc_final: 0.9190 (t0) REVERT: L 240 TYR cc_start: 0.8853 (m-10) cc_final: 0.8372 (m-80) REVERT: O 104 ASP cc_start: 0.9490 (m-30) cc_final: 0.9111 (m-30) REVERT: O 130 ILE cc_start: 0.9860 (pt) cc_final: 0.9585 (pt) REVERT: O 134 LYS cc_start: 0.9498 (pttm) cc_final: 0.9134 (tptp) REVERT: O 158 ARG cc_start: 0.9308 (tpt-90) cc_final: 0.8348 (tpt-90) REVERT: O 166 ILE cc_start: 0.9232 (mt) cc_final: 0.9007 (mm) REVERT: O 183 ASP cc_start: 0.9151 (t0) cc_final: 0.8608 (t0) REVERT: O 185 GLN cc_start: 0.9611 (tm-30) cc_final: 0.9276 (tm-30) REVERT: O 191 ARG cc_start: 0.8914 (mtt-85) cc_final: 0.8294 (ptm160) REVERT: P 56 CYS cc_start: 0.9097 (p) cc_final: 0.8443 (p) REVERT: P 113 LEU cc_start: 0.9630 (tt) cc_final: 0.9096 (tt) REVERT: P 115 TYR cc_start: 0.8329 (m-10) cc_final: 0.7967 (m-10) REVERT: P 144 ASP cc_start: 0.8812 (t0) cc_final: 0.8573 (t0) REVERT: P 168 VAL cc_start: 0.9378 (t) cc_final: 0.9112 (t) REVERT: P 189 ARG cc_start: 0.9270 (tpm170) cc_final: 0.8847 (tpp80) REVERT: P 210 MET cc_start: 0.7941 (mtm) cc_final: 0.7741 (mtp) REVERT: P 214 MET cc_start: 0.8765 (mtm) cc_final: 0.8122 (ptm) REVERT: P 229 MET cc_start: 0.0855 (mtt) cc_final: -0.0056 (mtt) outliers start: 3 outliers final: 1 residues processed: 942 average time/residue: 0.1931 time to fit residues: 291.2989 Evaluate side-chains 731 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 730 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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: 4.9990 chunk 56 optimal weight: 6.9990 chunk 316 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 298 optimal weight: 9.9990 chunk 294 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 317 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN L 38 GLN O 38 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.087495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.062060 restraints weight = 124457.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.064122 restraints weight = 69595.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.065492 restraints weight = 47088.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.066421 restraints weight = 35947.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.067018 restraints weight = 29800.310| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31134 Z= 0.189 Angle : 0.703 9.661 42181 Z= 0.365 Chirality : 0.044 0.272 4756 Planarity : 0.005 0.066 5084 Dihedral : 15.849 175.908 4907 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.35 % Favored : 97.59 % Rotamer: Outliers : 0.13 % Allowed : 2.24 % Favored : 97.64 % 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: 0.92 (0.14), residues: 3570 helix: 0.81 (0.11), residues: 2132 sheet: 1.09 (0.27), residues: 358 loop : 0.30 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG P 50 TYR 0.029 0.002 TYR K 240 PHE 0.031 0.002 PHE O 106 TRP 0.039 0.002 TRP G 211 HIS 0.015 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (31132) covalent geometry : angle 0.70319 / 0.37 (42181) hydrogen bonds : bond 0.04781 / 3.14 ( 1579) hydrogen bonds : angle 4.96310 / 3.61 ( 4611) Misc. bond : bond 0.00233 / 0.12 ( 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 932 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 928 time to evaluate : 1.196 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: A 36 LEU cc_start: 0.9452 (tp) cc_final: 0.8901 (tp) REVERT: A 38 GLN cc_start: 0.9481 (mp10) cc_final: 0.9162 (mp10) REVERT: A 43 HIS cc_start: 0.9294 (m90) cc_final: 0.8971 (m-70) REVERT: A 46 LEU cc_start: 0.9824 (mt) cc_final: 0.9586 (mt) REVERT: A 75 TYR cc_start: 0.8865 (m-80) cc_final: 0.8579 (m-80) REVERT: A 94 ILE cc_start: 0.9301 (tp) cc_final: 0.9027 (tp) REVERT: A 113 LEU cc_start: 0.9668 (mt) cc_final: 0.9327 (tt) REVERT: A 136 CYS cc_start: 0.8292 (m) cc_final: 0.7873 (m) REVERT: A 140 MET cc_start: 0.9199 (ttm) cc_final: 0.8758 (ttp) REVERT: A 154 PHE cc_start: 0.9574 (m-80) cc_final: 0.9155 (m-80) REVERT: A 183 ASP cc_start: 0.8737 (t0) cc_final: 0.8392 (t70) REVERT: A 230 LEU cc_start: 0.9159 (tt) cc_final: 0.8936 (tt) REVERT: B 75 TYR cc_start: 0.8258 (m-80) cc_final: 0.7950 (m-80) REVERT: B 111 GLU cc_start: 0.9022 (tp30) cc_final: 0.8687 (tp30) REVERT: B 159 ASP cc_start: 0.8728 (m-30) cc_final: 0.8466 (m-30) REVERT: B 210 MET cc_start: 0.9621 (ttt) cc_final: 0.9107 (mtt) REVERT: B 214 MET cc_start: 0.9455 (mmp) cc_final: 0.8975 (mtt) REVERT: B 216 LEU cc_start: 0.9087 (mp) cc_final: 0.8615 (tt) REVERT: B 218 LEU cc_start: 0.8800 (mt) cc_final: 0.8455 (mt) REVERT: B 223 ASN cc_start: 0.9397 (t0) cc_final: 0.8723 (t0) REVERT: B 229 MET cc_start: 0.9008 (mpp) cc_final: 0.8671 (pmm) REVERT: C 46 LEU cc_start: 0.9862 (mt) cc_final: 0.9617 (mt) REVERT: C 147 ASP cc_start: 0.8735 (p0) cc_final: 0.8076 (m-30) REVERT: C 185 GLN cc_start: 0.9101 (mt0) cc_final: 0.8785 (mt0) REVERT: C 215 VAL cc_start: 0.9213 (t) cc_final: 0.8875 (t) REVERT: C 223 ASN cc_start: 0.9217 (t0) cc_final: 0.8867 (t0) REVERT: C 246 GLU cc_start: 0.8176 (pp20) cc_final: 0.7748 (pp20) REVERT: C 247 ILE cc_start: 0.9215 (mt) cc_final: 0.8724 (mt) REVERT: C 250 GLU cc_start: 0.9241 (tp30) cc_final: 0.8732 (tp30) REVERT: C 254 ARG cc_start: 0.8967 (ttp-170) cc_final: 0.8323 (ttp-170) REVERT: D 156 ASP cc_start: 0.9193 (m-30) cc_final: 0.8948 (m-30) REVERT: D 159 ASP cc_start: 0.8970 (m-30) cc_final: 0.8706 (m-30) REVERT: D 163 ASP cc_start: 0.9172 (m-30) cc_final: 0.8851 (m-30) REVERT: D 176 LEU cc_start: 0.9462 (tp) cc_final: 0.9183 (tp) REVERT: D 180 ILE cc_start: 0.9411 (mt) cc_final: 0.9116 (mt) REVERT: D 211 TRP cc_start: 0.8592 (t-100) cc_final: 0.8061 (t60) REVERT: D 246 GLU cc_start: 0.8450 (pp20) cc_final: 0.8086 (pp20) REVERT: D 247 ILE cc_start: 0.9498 (mm) cc_final: 0.8929 (mm) REVERT: E 42 LEU cc_start: 0.9789 (tp) cc_final: 0.9548 (tt) REVERT: E 46 LEU cc_start: 0.9744 (mt) cc_final: 0.9448 (mt) REVERT: E 104 ASP cc_start: 0.8534 (t70) cc_final: 0.7800 (t0) REVERT: E 119 LYS cc_start: 0.8872 (mmtt) cc_final: 0.7490 (mmtm) REVERT: E 159 ASP cc_start: 0.8541 (t0) cc_final: 0.7314 (t0) REVERT: E 163 ASP cc_start: 0.8544 (m-30) cc_final: 0.7355 (m-30) REVERT: E 183 ASP cc_start: 0.9402 (t0) cc_final: 0.8944 (t70) REVERT: E 199 LEU cc_start: 0.8547 (tp) cc_final: 0.8242 (tp) REVERT: E 210 MET cc_start: 0.9676 (ttt) cc_final: 0.8572 (tpt) REVERT: E 214 MET cc_start: 0.8970 (mmp) cc_final: 0.8650 (mmm) REVERT: E 253 ILE cc_start: 0.9699 (tt) cc_final: 0.9412 (pt) REVERT: F 42 LEU cc_start: 0.9193 (mt) cc_final: 0.8952 (mt) REVERT: F 47 ASP cc_start: 0.9347 (t70) cc_final: 0.9082 (t0) REVERT: F 100 CYS cc_start: 0.7542 (m) cc_final: 0.7201 (m) REVERT: F 144 ASP cc_start: 0.9011 (t70) cc_final: 0.8119 (t0) REVERT: F 145 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8667 (mt-10) REVERT: F 170 LEU cc_start: 0.9666 (mt) cc_final: 0.9239 (mt) REVERT: F 175 ARG cc_start: 0.8611 (tpt170) cc_final: 0.8298 (tpm170) REVERT: F 183 ASP cc_start: 0.8857 (t0) cc_final: 0.8646 (t0) REVERT: F 185 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8202 (tm-30) REVERT: F 190 PHE cc_start: 0.9475 (m-80) cc_final: 0.8884 (m-10) REVERT: F 199 LEU cc_start: 0.8084 (tp) cc_final: 0.7675 (tp) REVERT: F 210 MET cc_start: 0.9514 (mtm) cc_final: 0.9227 (mtp) REVERT: F 229 MET cc_start: 0.9416 (mtp) cc_final: 0.9183 (mtp) REVERT: G 36 LEU cc_start: 0.9195 (tp) cc_final: 0.8980 (mm) REVERT: G 75 TYR cc_start: 0.8571 (m-10) cc_final: 0.8119 (m-10) REVERT: G 93 TYR cc_start: 0.5549 (m-10) cc_final: 0.5216 (m-10) REVERT: G 140 MET cc_start: 0.9028 (ttm) cc_final: 0.8564 (mtm) REVERT: G 154 PHE cc_start: 0.9084 (m-80) cc_final: 0.8826 (m-80) REVERT: G 174 ASP cc_start: 0.8635 (p0) cc_final: 0.8291 (p0) REVERT: G 210 MET cc_start: 0.8721 (ttt) cc_final: 0.8443 (mmp) REVERT: G 250 GLU cc_start: 0.9328 (tp30) cc_final: 0.8703 (tp30) REVERT: G 271 VAL cc_start: 0.9144 (m) cc_final: 0.8942 (m) REVERT: H 103 LYS cc_start: 0.9381 (tttt) cc_final: 0.9059 (pttt) REVERT: H 116 ARG cc_start: 0.8598 (mmm160) cc_final: 0.8087 (tpp80) REVERT: H 127 ASP cc_start: 0.8930 (m-30) cc_final: 0.8726 (m-30) REVERT: H 144 ASP cc_start: 0.8915 (t70) cc_final: 0.8537 (t0) REVERT: H 176 LEU cc_start: 0.9545 (tp) cc_final: 0.9294 (tt) REVERT: H 183 ASP cc_start: 0.8756 (m-30) cc_final: 0.7915 (t70) REVERT: H 185 GLN cc_start: 0.8989 (mm110) cc_final: 0.8775 (mm110) REVERT: H 189 ARG cc_start: 0.9224 (tpt170) cc_final: 0.8944 (mmm160) REVERT: H 210 MET cc_start: 0.9404 (ptp) cc_final: 0.8965 (ptp) REVERT: H 223 ASN cc_start: 0.9299 (t0) cc_final: 0.8812 (t0) REVERT: I 93 TYR cc_start: 0.9247 (t80) cc_final: 0.8845 (t80) REVERT: I 158 ARG cc_start: 0.9172 (ptm-80) cc_final: 0.8965 (tmm-80) REVERT: I 185 GLN cc_start: 0.9162 (mt0) cc_final: 0.8429 (mp10) REVERT: I 210 MET cc_start: 0.9127 (tmm) cc_final: 0.8732 (tmm) REVERT: I 224 LEU cc_start: 0.9488 (mt) cc_final: 0.9129 (mt) REVERT: I 229 MET cc_start: 0.8894 (mmp) cc_final: 0.8665 (mmm) REVERT: J 99 LYS cc_start: 0.9618 (tppt) cc_final: 0.9369 (mmmm) REVERT: J 103 LYS cc_start: 0.9240 (tttt) cc_final: 0.9018 (tttp) REVERT: J 127 ASP cc_start: 0.9067 (m-30) cc_final: 0.8764 (m-30) REVERT: J 144 ASP cc_start: 0.8258 (t0) cc_final: 0.7932 (p0) REVERT: J 159 ASP cc_start: 0.9354 (t70) cc_final: 0.8931 (t70) REVERT: J 162 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8439 (mm-30) REVERT: J 177 ASP cc_start: 0.9382 (p0) cc_final: 0.9176 (p0) REVERT: J 187 LEU cc_start: 0.8953 (mt) cc_final: 0.8733 (mt) REVERT: J 210 MET cc_start: 0.9644 (mtm) cc_final: 0.9402 (mtp) REVERT: J 229 MET cc_start: 0.9248 (mmt) cc_final: 0.8997 (mmm) REVERT: J 246 GLU cc_start: 0.9011 (pp20) cc_final: 0.8776 (pp20) REVERT: K 54 LYS cc_start: 0.9441 (tppt) cc_final: 0.9049 (mmmt) REVERT: K 116 ARG cc_start: 0.8589 (mmp80) cc_final: 0.7941 (mmp80) REVERT: K 129 THR cc_start: 0.9777 (m) cc_final: 0.9486 (p) REVERT: K 145 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7858 (mm-30) REVERT: K 158 ARG cc_start: 0.8770 (ptt90) cc_final: 0.8491 (ttp80) REVERT: K 162 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8291 (mm-30) REVERT: K 223 ASN cc_start: 0.9521 (m110) cc_final: 0.9287 (m110) REVERT: K 248 LEU cc_start: 0.9784 (mt) cc_final: 0.9383 (mt) REVERT: L 38 GLN cc_start: 0.9003 (mm110) cc_final: 0.8500 (pm20) REVERT: L 93 TYR cc_start: 0.8911 (t80) cc_final: 0.8374 (t80) REVERT: L 100 CYS cc_start: 0.7080 (t) cc_final: 0.6069 (t) REVERT: L 104 ASP cc_start: 0.8607 (t0) cc_final: 0.8391 (t0) REVERT: L 124 ASP cc_start: 0.9398 (m-30) cc_final: 0.9121 (m-30) REVERT: L 131 GLU cc_start: 0.9261 (tt0) cc_final: 0.8957 (pt0) REVERT: L 141 LEU cc_start: 0.9715 (tp) cc_final: 0.9487 (tp) REVERT: L 184 GLU cc_start: 0.8738 (mp0) cc_final: 0.8502 (mp0) REVERT: L 213 GLN cc_start: 0.8490 (pp30) cc_final: 0.7977 (pp30) REVERT: L 215 VAL cc_start: 0.9525 (t) cc_final: 0.9137 (t) REVERT: L 240 TYR cc_start: 0.8818 (m-10) cc_final: 0.8370 (m-80) REVERT: L 269 GLN cc_start: 0.9330 (pp30) cc_final: 0.9091 (pp30) REVERT: O 106 PHE cc_start: 0.9482 (m-80) cc_final: 0.9161 (m-80) REVERT: O 127 ASP cc_start: 0.9637 (m-30) cc_final: 0.9417 (m-30) REVERT: O 134 LYS cc_start: 0.9415 (pttm) cc_final: 0.9098 (tptp) REVERT: O 147 ASP cc_start: 0.8898 (p0) cc_final: 0.8328 (t0) REVERT: O 158 ARG cc_start: 0.8884 (tpt-90) cc_final: 0.8369 (tpt90) REVERT: O 183 ASP cc_start: 0.9169 (t0) cc_final: 0.8568 (t0) REVERT: O 185 GLN cc_start: 0.9606 (tm-30) cc_final: 0.9099 (tm-30) REVERT: O 240 TYR cc_start: 0.9253 (m-80) cc_final: 0.8839 (m-80) REVERT: P 56 CYS cc_start: 0.9139 (p) cc_final: 0.8233 (p) REVERT: P 106 PHE cc_start: 0.9242 (m-80) cc_final: 0.8998 (m-80) REVERT: P 113 LEU cc_start: 0.9660 (tt) cc_final: 0.9075 (tt) REVERT: P 115 TYR cc_start: 0.8454 (m-10) cc_final: 0.8085 (m-10) REVERT: P 140 MET cc_start: 0.9052 (ptp) cc_final: 0.8718 (mtm) REVERT: P 144 ASP cc_start: 0.8716 (t0) cc_final: 0.8218 (t0) REVERT: P 154 PHE cc_start: 0.9619 (m-10) cc_final: 0.9387 (m-80) REVERT: P 168 VAL cc_start: 0.9498 (t) cc_final: 0.9127 (t) REVERT: P 189 ARG cc_start: 0.9306 (tpm170) cc_final: 0.8852 (mmm160) REVERT: P 214 MET cc_start: 0.8723 (mtm) cc_final: 0.8098 (ptm) REVERT: P 229 MET cc_start: 0.0878 (mtt) cc_final: 0.0218 (mtt) outliers start: 4 outliers final: 1 residues processed: 931 average time/residue: 0.1946 time to fit residues: 291.4016 Evaluate side-chains 737 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 736 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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: 0.2980 chunk 202 optimal weight: 0.7980 chunk 295 optimal weight: 0.4980 chunk 255 optimal weight: 0.8980 chunk 321 optimal weight: 1.9990 chunk 93 optimal weight: 0.0040 chunk 13 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 281 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN D 97 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN L 38 GLN P 97 HIS P 185 GLN ** P 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.089087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.063437 restraints weight = 122575.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.065563 restraints weight = 68171.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066974 restraints weight = 45843.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.067897 restraints weight = 34826.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.068490 restraints weight = 28878.686| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31134 Z= 0.138 Angle : 0.709 13.425 42181 Z= 0.362 Chirality : 0.044 0.263 4756 Planarity : 0.004 0.064 5084 Dihedral : 15.696 178.016 4907 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.32 % Favored : 97.62 % Rotamer: Outliers : 0.26 % Allowed : 1.66 % Favored : 98.08 % 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: 1.00 (0.14), residues: 3570 helix: 0.94 (0.12), residues: 2036 sheet: 1.20 (0.27), residues: 358 loop : 0.21 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 254 TYR 0.021 0.002 TYR G 93 PHE 0.032 0.002 PHE O 106 TRP 0.042 0.002 TRP G 211 HIS 0.013 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (31132) covalent geometry : angle 0.70864 / 0.36 (42181) hydrogen bonds : bond 0.04502 / 2.99 ( 1579) hydrogen bonds : angle 4.76113 / 3.47 ( 4611) Misc. bond : bond 0.00593 / 0.31 ( 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 972 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 964 time to evaluate : 1.298 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: A 36 LEU cc_start: 0.9436 (tp) cc_final: 0.8887 (tp) REVERT: A 38 GLN cc_start: 0.9479 (mp10) cc_final: 0.9046 (mp10) REVERT: A 43 HIS cc_start: 0.9297 (m90) cc_final: 0.8898 (m-70) REVERT: A 46 LEU cc_start: 0.9816 (mt) cc_final: 0.9584 (mt) REVERT: A 75 TYR cc_start: 0.8875 (m-80) cc_final: 0.8576 (m-80) REVERT: A 93 TYR cc_start: 0.8942 (t80) cc_final: 0.8545 (t80) REVERT: A 113 LEU cc_start: 0.9669 (mt) cc_final: 0.9393 (tt) REVERT: A 140 MET cc_start: 0.9180 (ttm) cc_final: 0.8763 (ttp) REVERT: A 154 PHE cc_start: 0.9501 (m-80) cc_final: 0.9128 (m-80) REVERT: A 162 GLU cc_start: 0.9007 (pp20) cc_final: 0.8405 (pp20) REVERT: A 183 ASP cc_start: 0.8561 (t0) cc_final: 0.8259 (t70) REVERT: A 246 GLU cc_start: 0.9467 (OUTLIER) cc_final: 0.9197 (pm20) REVERT: B 75 TYR cc_start: 0.8228 (m-80) cc_final: 0.7915 (m-80) REVERT: B 111 GLU cc_start: 0.9046 (tp30) cc_final: 0.8679 (tp30) REVERT: B 159 ASP cc_start: 0.8782 (m-30) cc_final: 0.8450 (m-30) REVERT: B 210 MET cc_start: 0.9612 (ttt) cc_final: 0.9118 (mtt) REVERT: B 214 MET cc_start: 0.9463 (mmp) cc_final: 0.8989 (mtt) REVERT: B 216 LEU cc_start: 0.8985 (mp) cc_final: 0.8615 (tp) REVERT: B 218 LEU cc_start: 0.8785 (mt) cc_final: 0.8426 (mt) REVERT: B 223 ASN cc_start: 0.9460 (t0) cc_final: 0.8796 (t0) REVERT: B 229 MET cc_start: 0.8981 (mpp) cc_final: 0.8773 (pmm) REVERT: C 98 GLN cc_start: 0.9251 (tp-100) cc_final: 0.8975 (tp-100) REVERT: C 173 THR cc_start: 0.8239 (p) cc_final: 0.8007 (p) REVERT: C 215 VAL cc_start: 0.9249 (t) cc_final: 0.8853 (t) REVERT: C 223 ASN cc_start: 0.9297 (t0) cc_final: 0.8970 (t0) REVERT: C 250 GLU cc_start: 0.9223 (tp30) cc_final: 0.8745 (tp30) REVERT: C 254 ARG cc_start: 0.8893 (ttp-170) cc_final: 0.8321 (ttp-170) REVERT: D 38 GLN cc_start: 0.9178 (mt0) cc_final: 0.8753 (mt0) REVERT: D 80 GLN cc_start: 0.8688 (mp-120) cc_final: 0.8294 (mp10) REVERT: D 159 ASP cc_start: 0.8861 (m-30) cc_final: 0.8601 (m-30) REVERT: D 163 ASP cc_start: 0.9136 (m-30) cc_final: 0.8813 (m-30) REVERT: D 176 LEU cc_start: 0.9438 (tp) cc_final: 0.9216 (tp) REVERT: D 180 ILE cc_start: 0.9391 (mt) cc_final: 0.9098 (mt) REVERT: D 184 GLU cc_start: 0.9340 (pm20) cc_final: 0.9127 (pm20) REVERT: D 211 TRP cc_start: 0.8578 (t-100) cc_final: 0.8137 (t60) REVERT: D 247 ILE cc_start: 0.9516 (mm) cc_final: 0.9176 (mm) REVERT: E 47 ASP cc_start: 0.8852 (m-30) cc_final: 0.8426 (m-30) REVERT: E 100 CYS cc_start: 0.8556 (t) cc_final: 0.8347 (t) REVERT: E 104 ASP cc_start: 0.8462 (t70) cc_final: 0.7821 (t0) REVERT: E 127 ASP cc_start: 0.8939 (t70) cc_final: 0.8735 (t0) REVERT: E 159 ASP cc_start: 0.8704 (t0) cc_final: 0.7967 (t0) REVERT: E 183 ASP cc_start: 0.9394 (t0) cc_final: 0.8938 (t70) REVERT: E 199 LEU cc_start: 0.8489 (tp) cc_final: 0.8122 (tp) REVERT: E 210 MET cc_start: 0.9688 (ttt) cc_final: 0.9301 (ttt) REVERT: E 253 ILE cc_start: 0.9668 (tt) cc_final: 0.9378 (pt) REVERT: F 114 LYS cc_start: 0.9679 (mmtt) cc_final: 0.9478 (mmmm) REVERT: F 144 ASP cc_start: 0.8955 (t70) cc_final: 0.8155 (t0) REVERT: F 145 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8685 (mt-10) REVERT: F 150 LYS cc_start: 0.8465 (mtmt) cc_final: 0.8048 (mtmm) REVERT: F 170 LEU cc_start: 0.9675 (mt) cc_final: 0.9290 (mt) REVERT: F 190 PHE cc_start: 0.9470 (m-80) cc_final: 0.8868 (m-10) REVERT: F 199 LEU cc_start: 0.8003 (tp) cc_final: 0.7622 (tp) REVERT: F 210 MET cc_start: 0.9508 (mtm) cc_final: 0.9188 (mtp) REVERT: F 229 MET cc_start: 0.9383 (mtp) cc_final: 0.9157 (mtp) REVERT: G 75 TYR cc_start: 0.8475 (m-10) cc_final: 0.7990 (m-10) REVERT: G 93 TYR cc_start: 0.5286 (m-10) cc_final: 0.4930 (m-10) REVERT: G 142 ILE cc_start: 0.9503 (pt) cc_final: 0.8944 (pt) REVERT: G 154 PHE cc_start: 0.9036 (m-80) cc_final: 0.8746 (m-80) REVERT: G 174 ASP cc_start: 0.8636 (p0) cc_final: 0.8177 (p0) REVERT: G 210 MET cc_start: 0.8809 (ttt) cc_final: 0.8355 (ttt) REVERT: G 250 GLU cc_start: 0.9366 (tp30) cc_final: 0.8626 (tp30) REVERT: G 271 VAL cc_start: 0.9092 (m) cc_final: 0.8859 (t) REVERT: H 93 TYR cc_start: 0.8760 (t80) cc_final: 0.8450 (t80) REVERT: H 103 LYS cc_start: 0.9299 (tttt) cc_final: 0.8994 (pttm) REVERT: H 116 ARG cc_start: 0.8562 (mmm160) cc_final: 0.8208 (tpp80) REVERT: H 139 GLU cc_start: 0.8774 (mp0) cc_final: 0.8190 (tt0) REVERT: H 176 LEU cc_start: 0.9556 (tp) cc_final: 0.9279 (tt) REVERT: H 183 ASP cc_start: 0.8636 (m-30) cc_final: 0.7865 (t70) REVERT: H 185 GLN cc_start: 0.9122 (mm110) cc_final: 0.8898 (mm110) REVERT: H 189 ARG cc_start: 0.9193 (tpt170) cc_final: 0.8639 (mmm-85) REVERT: H 210 MET cc_start: 0.9467 (ptp) cc_final: 0.9112 (ptp) REVERT: H 223 ASN cc_start: 0.9320 (t0) cc_final: 0.8920 (t0) REVERT: I 93 TYR cc_start: 0.9279 (t80) cc_final: 0.8920 (t80) REVERT: I 139 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8475 (mm-30) REVERT: I 158 ARG cc_start: 0.9114 (ptm-80) cc_final: 0.8842 (tmm-80) REVERT: I 185 GLN cc_start: 0.9164 (mt0) cc_final: 0.8454 (mp10) REVERT: I 210 MET cc_start: 0.9123 (tmm) cc_final: 0.8862 (tmm) REVERT: I 211 TRP cc_start: 0.9210 (t-100) cc_final: 0.8826 (t-100) REVERT: I 224 LEU cc_start: 0.9516 (mt) cc_final: 0.9089 (mt) REVERT: I 233 LEU cc_start: 0.9807 (tp) cc_final: 0.9557 (pp) REVERT: J 94 ILE cc_start: 0.9607 (pt) cc_final: 0.8843 (pt) REVERT: J 99 LYS cc_start: 0.9572 (tppt) cc_final: 0.9367 (mmmm) REVERT: J 100 CYS cc_start: 0.9154 (t) cc_final: 0.8813 (t) REVERT: J 103 LYS cc_start: 0.9299 (tttt) cc_final: 0.9040 (ttmp) REVERT: J 111 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8690 (tm-30) REVERT: J 112 TYR cc_start: 0.9508 (t80) cc_final: 0.9305 (t80) REVERT: J 127 ASP cc_start: 0.9068 (m-30) cc_final: 0.8850 (m-30) REVERT: J 159 ASP cc_start: 0.9315 (t70) cc_final: 0.9098 (t0) REVERT: J 162 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8348 (mm-30) REVERT: J 185 GLN cc_start: 0.9499 (mm110) cc_final: 0.9265 (mm110) REVERT: J 187 LEU cc_start: 0.8902 (mt) cc_final: 0.8632 (mt) REVERT: J 229 MET cc_start: 0.9223 (mmt) cc_final: 0.8981 (mmm) REVERT: J 246 GLU cc_start: 0.8955 (pp20) cc_final: 0.8734 (pp20) REVERT: K 46 LEU cc_start: 0.9674 (mt) cc_final: 0.9464 (mt) REVERT: K 54 LYS cc_start: 0.9450 (tppt) cc_final: 0.9041 (mmmt) REVERT: K 92 VAL cc_start: 0.9756 (t) cc_final: 0.9481 (m) REVERT: K 116 ARG cc_start: 0.8538 (mmp80) cc_final: 0.8009 (mmp80) REVERT: K 129 THR cc_start: 0.9740 (m) cc_final: 0.9449 (p) REVERT: K 140 MET cc_start: 0.8821 (ttp) cc_final: 0.8461 (ttp) REVERT: K 145 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7825 (mm-30) REVERT: K 158 ARG cc_start: 0.8665 (ptt90) cc_final: 0.8460 (ttp80) REVERT: K 162 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8259 (mm-30) REVERT: K 223 ASN cc_start: 0.9544 (m110) cc_final: 0.9299 (m110) REVERT: K 254 ARG cc_start: 0.9082 (ttp-170) cc_final: 0.8874 (ptm160) REVERT: L 38 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8287 (pm20) REVERT: L 93 TYR cc_start: 0.8891 (t80) cc_final: 0.8486 (t80) REVERT: L 100 CYS cc_start: 0.6680 (t) cc_final: 0.5420 (t) REVERT: L 104 ASP cc_start: 0.8607 (t0) cc_final: 0.8323 (t0) REVERT: L 124 ASP cc_start: 0.9390 (m-30) cc_final: 0.9097 (m-30) REVERT: L 131 GLU cc_start: 0.9258 (tt0) cc_final: 0.8896 (pt0) REVERT: L 141 LEU cc_start: 0.9769 (tp) cc_final: 0.9558 (tp) REVERT: L 213 GLN cc_start: 0.8597 (pp30) cc_final: 0.8167 (pp30) REVERT: L 215 VAL cc_start: 0.9580 (t) cc_final: 0.9184 (t) REVERT: L 240 TYR cc_start: 0.8841 (m-10) cc_final: 0.8379 (m-80) REVERT: L 269 GLN cc_start: 0.9337 (pp30) cc_final: 0.8869 (pp30) REVERT: O 42 LEU cc_start: 0.9620 (mm) cc_final: 0.9419 (mm) REVERT: O 71 ASP cc_start: 0.9125 (t0) cc_final: 0.8646 (p0) REVERT: O 124 ASP cc_start: 0.9572 (m-30) cc_final: 0.9370 (m-30) REVERT: O 131 GLU cc_start: 0.9241 (pp20) cc_final: 0.8940 (pp20) REVERT: O 134 LYS cc_start: 0.9460 (pttm) cc_final: 0.9146 (tptp) REVERT: O 158 ARG cc_start: 0.9119 (tpt-90) cc_final: 0.8312 (tpp80) REVERT: O 183 ASP cc_start: 0.8882 (t0) cc_final: 0.8377 (t0) REVERT: O 185 GLN cc_start: 0.9584 (tm-30) cc_final: 0.9193 (tm-30) REVERT: O 240 TYR cc_start: 0.9244 (m-80) cc_final: 0.8849 (m-80) REVERT: P 113 LEU cc_start: 0.9658 (tt) cc_final: 0.9187 (tt) REVERT: P 115 TYR cc_start: 0.8440 (m-10) cc_final: 0.8063 (m-10) REVERT: P 144 ASP cc_start: 0.8758 (t0) cc_final: 0.8270 (t0) REVERT: P 154 PHE cc_start: 0.9585 (m-10) cc_final: 0.9335 (m-80) REVERT: P 168 VAL cc_start: 0.9423 (t) cc_final: 0.9162 (t) REVERT: P 190 PHE cc_start: 0.9219 (m-80) cc_final: 0.8813 (m-80) REVERT: P 210 MET cc_start: 0.7996 (mtm) cc_final: 0.7694 (mtp) REVERT: P 214 MET cc_start: 0.8738 (mtm) cc_final: 0.8262 (ptp) REVERT: P 229 MET cc_start: 0.0930 (mtt) cc_final: 0.0303 (mtt) outliers start: 8 outliers final: 2 residues processed: 969 average time/residue: 0.2021 time to fit residues: 312.9617 Evaluate side-chains 748 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 745 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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: 9.9990 chunk 139 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 297 optimal weight: 8.9990 chunk 318 optimal weight: 6.9990 chunk 234 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 336 optimal weight: 20.0000 chunk 232 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS 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 = 0.3609 r_free = 0.3609 target = 0.087680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.062214 restraints weight = 125004.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.064294 restraints weight = 69707.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.065660 restraints weight = 46989.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.066567 restraints weight = 35799.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.067176 restraints weight = 29692.521| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.6897 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 : 0.706 11.207 42181 Z= 0.367 Chirality : 0.043 0.262 4756 Planarity : 0.004 0.054 5084 Dihedral : 15.623 177.236 4907 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.70 % Rotamer: Outliers : 0.03 % Allowed : 1.34 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.14), residues: 3570 helix: 0.90 (0.12), residues: 2050 sheet: 1.16 (0.27), residues: 358 loop : 0.24 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 74 TYR 0.020 0.001 TYR G 93 PHE 0.034 0.002 PHE L 154 TRP 0.042 0.002 TRP G 211 HIS 0.013 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (31132) covalent geometry : angle 0.70623 / 0.37 (42181) hydrogen bonds : bond 0.04518 / 2.99 ( 1579) hydrogen bonds : angle 4.93589 / 3.60 ( 4611) Misc. bond : bond 0.00242 / 0.13 ( 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 918 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 917 time to evaluate : 1.243 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: A 38 GLN cc_start: 0.9496 (mp10) cc_final: 0.9276 (mp10) REVERT: A 43 HIS cc_start: 0.9309 (m90) cc_final: 0.8933 (m-70) REVERT: A 46 LEU cc_start: 0.9817 (mt) cc_final: 0.9580 (mt) REVERT: A 75 TYR cc_start: 0.8871 (m-80) cc_final: 0.8621 (m-80) REVERT: A 113 LEU cc_start: 0.9668 (mt) cc_final: 0.9346 (tt) REVERT: A 140 MET cc_start: 0.9146 (ttm) cc_final: 0.8723 (ttp) REVERT: A 154 PHE cc_start: 0.9489 (m-80) cc_final: 0.9136 (m-80) REVERT: A 162 GLU cc_start: 0.9058 (pp20) cc_final: 0.8458 (pp20) REVERT: A 183 ASP cc_start: 0.8728 (t0) cc_final: 0.8272 (t0) REVERT: A 190 PHE cc_start: 0.9029 (m-80) cc_final: 0.8316 (m-80) REVERT: A 210 MET cc_start: 0.9347 (ptp) cc_final: 0.8911 (ptp) REVERT: B 75 TYR cc_start: 0.8259 (m-80) cc_final: 0.7929 (m-80) REVERT: B 111 GLU cc_start: 0.9032 (tp30) cc_final: 0.8675 (tp30) REVERT: B 159 ASP cc_start: 0.8714 (m-30) cc_final: 0.8402 (m-30) REVERT: B 210 MET cc_start: 0.9605 (ttt) cc_final: 0.9107 (mtt) REVERT: B 214 MET cc_start: 0.9457 (mmp) cc_final: 0.8954 (mtt) REVERT: B 216 LEU cc_start: 0.9022 (mp) cc_final: 0.8644 (tp) REVERT: B 218 LEU cc_start: 0.8818 (mt) cc_final: 0.8468 (mt) REVERT: B 223 ASN cc_start: 0.9472 (t0) cc_final: 0.9070 (t0) REVERT: C 46 LEU cc_start: 0.9879 (mt) cc_final: 0.9628 (mt) REVERT: C 173 THR cc_start: 0.8326 (p) cc_final: 0.8085 (p) REVERT: C 213 GLN cc_start: 0.9326 (tm-30) cc_final: 0.9110 (tm-30) REVERT: C 214 MET cc_start: 0.9393 (tpp) cc_final: 0.8982 (tpp) REVERT: C 215 VAL cc_start: 0.9227 (t) cc_final: 0.8784 (t) REVERT: C 223 ASN cc_start: 0.9368 (t0) cc_final: 0.9067 (t0) REVERT: C 246 GLU cc_start: 0.8300 (pp20) cc_final: 0.7874 (pp20) REVERT: C 247 ILE cc_start: 0.9138 (mt) cc_final: 0.8622 (mt) REVERT: C 250 GLU cc_start: 0.9282 (tp30) cc_final: 0.8703 (tp30) REVERT: D 80 GLN cc_start: 0.8575 (mp-120) cc_final: 0.8263 (mp-120) REVERT: D 159 ASP cc_start: 0.8862 (m-30) cc_final: 0.8632 (m-30) REVERT: D 163 ASP cc_start: 0.9131 (m-30) cc_final: 0.8821 (m-30) REVERT: D 176 LEU cc_start: 0.9460 (tp) cc_final: 0.9187 (tp) REVERT: D 180 ILE cc_start: 0.9424 (mt) cc_final: 0.9091 (mt) REVERT: D 211 TRP cc_start: 0.8776 (t-100) cc_final: 0.8329 (t60) REVERT: D 213 GLN cc_start: 0.9426 (mp10) cc_final: 0.9124 (mp10) REVERT: D 247 ILE cc_start: 0.9707 (mm) cc_final: 0.9279 (mm) REVERT: D 275 TYR cc_start: 0.7270 (m-10) cc_final: 0.6731 (m-10) REVERT: E 47 ASP cc_start: 0.8756 (m-30) cc_final: 0.8360 (m-30) REVERT: E 100 CYS cc_start: 0.8523 (t) cc_final: 0.8217 (t) REVERT: E 104 ASP cc_start: 0.8484 (t70) cc_final: 0.7847 (t0) REVERT: E 127 ASP cc_start: 0.8931 (t70) cc_final: 0.8689 (t0) REVERT: E 159 ASP cc_start: 0.8657 (t0) cc_final: 0.8307 (t0) REVERT: E 183 ASP cc_start: 0.9398 (t0) cc_final: 0.8954 (t70) REVERT: E 199 LEU cc_start: 0.8570 (tp) cc_final: 0.8251 (tp) REVERT: E 210 MET cc_start: 0.9691 (ttt) cc_final: 0.8450 (tpt) REVERT: E 213 GLN cc_start: 0.8938 (pp30) cc_final: 0.8206 (pp30) REVERT: E 214 MET cc_start: 0.8737 (mmp) cc_final: 0.8513 (mmm) REVERT: E 253 ILE cc_start: 0.9683 (tt) cc_final: 0.9385 (pt) REVERT: F 114 LYS cc_start: 0.9690 (mmtt) cc_final: 0.9479 (mmmm) REVERT: F 144 ASP cc_start: 0.9032 (t70) cc_final: 0.8094 (t0) REVERT: F 145 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8639 (mt-10) REVERT: F 170 LEU cc_start: 0.9720 (mt) cc_final: 0.9392 (mt) REVERT: F 190 PHE cc_start: 0.9485 (m-80) cc_final: 0.8985 (m-10) REVERT: F 199 LEU cc_start: 0.8068 (tp) cc_final: 0.7632 (tp) REVERT: F 210 MET cc_start: 0.9502 (mtm) cc_final: 0.9168 (mtp) REVERT: F 229 MET cc_start: 0.9396 (mtp) cc_final: 0.9173 (mtp) REVERT: G 75 TYR cc_start: 0.8534 (m-10) cc_final: 0.8042 (m-10) REVERT: G 93 TYR cc_start: 0.5528 (m-10) cc_final: 0.5251 (m-10) REVERT: G 140 MET cc_start: 0.8988 (ttm) cc_final: 0.8611 (mtm) REVERT: G 174 ASP cc_start: 0.8723 (p0) cc_final: 0.8269 (p0) REVERT: G 210 MET cc_start: 0.8707 (ttt) cc_final: 0.8422 (mmp) REVERT: G 250 GLU cc_start: 0.9352 (tp30) cc_final: 0.8636 (tp30) REVERT: H 93 TYR cc_start: 0.8809 (t80) cc_final: 0.8594 (t80) REVERT: H 103 LYS cc_start: 0.9361 (tttt) cc_final: 0.9024 (pttm) REVERT: H 116 ARG cc_start: 0.8579 (mmm160) cc_final: 0.8286 (tpp80) REVERT: H 176 LEU cc_start: 0.9572 (tp) cc_final: 0.9299 (tt) REVERT: H 183 ASP cc_start: 0.8677 (m-30) cc_final: 0.7856 (t70) REVERT: H 185 GLN cc_start: 0.9163 (mm110) cc_final: 0.8917 (mm110) REVERT: H 189 ARG cc_start: 0.9195 (tpt170) cc_final: 0.8887 (mmm-85) REVERT: H 210 MET cc_start: 0.9432 (ptp) cc_final: 0.9089 (ptp) REVERT: H 223 ASN cc_start: 0.9327 (t0) cc_final: 0.9020 (t0) REVERT: I 93 TYR cc_start: 0.9275 (t80) cc_final: 0.8905 (t80) REVERT: I 139 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8473 (mm-30) REVERT: I 158 ARG cc_start: 0.9135 (ptm-80) cc_final: 0.8837 (tmm-80) REVERT: I 185 GLN cc_start: 0.9127 (mt0) cc_final: 0.8431 (mp10) REVERT: I 210 MET cc_start: 0.9130 (tmm) cc_final: 0.8759 (tmm) REVERT: I 211 TRP cc_start: 0.9221 (t-100) cc_final: 0.8823 (t-100) REVERT: I 224 LEU cc_start: 0.9474 (mt) cc_final: 0.9106 (mt) REVERT: I 229 MET cc_start: 0.8984 (mmp) cc_final: 0.8776 (mmm) REVERT: I 233 LEU cc_start: 0.9806 (tp) cc_final: 0.9572 (pp) REVERT: J 99 LYS cc_start: 0.9595 (tppt) cc_final: 0.9364 (mmmm) REVERT: J 100 CYS cc_start: 0.9132 (t) cc_final: 0.8923 (t) REVERT: J 103 LYS cc_start: 0.9235 (tttt) cc_final: 0.9015 (tttp) REVERT: J 109 ILE cc_start: 0.9611 (pt) cc_final: 0.9397 (pt) REVERT: J 111 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8698 (tm-30) REVERT: J 112 TYR cc_start: 0.9538 (t80) cc_final: 0.9302 (t80) REVERT: J 127 ASP cc_start: 0.9059 (m-30) cc_final: 0.8736 (m-30) REVERT: J 129 THR cc_start: 0.9716 (p) cc_final: 0.9452 (t) REVERT: J 144 ASP cc_start: 0.8162 (p0) cc_final: 0.7695 (p0) REVERT: J 159 ASP cc_start: 0.9400 (t70) cc_final: 0.8975 (t0) REVERT: J 162 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8307 (mm-30) REVERT: J 180 ILE cc_start: 0.9517 (mt) cc_final: 0.9312 (mt) REVERT: J 185 GLN cc_start: 0.9543 (mm110) cc_final: 0.9271 (mm110) REVERT: J 187 LEU cc_start: 0.8933 (mt) cc_final: 0.8641 (mt) REVERT: J 210 MET cc_start: 0.9620 (mtp) cc_final: 0.9232 (mtp) REVERT: J 229 MET cc_start: 0.9328 (mmt) cc_final: 0.9072 (mmm) REVERT: J 248 LEU cc_start: 0.9831 (mm) cc_final: 0.9602 (mm) REVERT: K 36 LEU cc_start: 0.9420 (mt) cc_final: 0.9101 (mt) REVERT: K 54 LYS cc_start: 0.9377 (tppt) cc_final: 0.8983 (mmmt) REVERT: K 92 VAL cc_start: 0.9724 (t) cc_final: 0.9458 (m) REVERT: K 116 ARG cc_start: 0.8544 (mmp80) cc_final: 0.8016 (mmp80) REVERT: K 129 THR cc_start: 0.9744 (m) cc_final: 0.9457 (p) REVERT: K 140 MET cc_start: 0.8839 (ttp) cc_final: 0.8543 (ttp) REVERT: K 145 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7809 (mm-30) REVERT: K 162 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8390 (mm-30) REVERT: K 223 ASN cc_start: 0.9539 (m110) cc_final: 0.9299 (m110) REVERT: L 38 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8364 (pm20) REVERT: L 70 CYS cc_start: 0.9693 (t) cc_final: 0.9487 (p) REVERT: L 93 TYR cc_start: 0.8920 (t80) cc_final: 0.8701 (t80) REVERT: L 100 CYS cc_start: 0.6744 (t) cc_final: 0.5436 (t) REVERT: L 104 ASP cc_start: 0.8713 (t0) cc_final: 0.8477 (t0) REVERT: L 124 ASP cc_start: 0.9380 (m-30) cc_final: 0.9065 (m-30) REVERT: L 131 GLU cc_start: 0.9270 (tt0) cc_final: 0.8883 (pt0) REVERT: L 185 GLN cc_start: 0.7583 (tm-30) cc_final: 0.7367 (tm-30) REVERT: L 215 VAL cc_start: 0.9626 (t) cc_final: 0.9129 (t) REVERT: L 240 TYR cc_start: 0.8879 (m-10) cc_final: 0.8404 (m-80) REVERT: O 71 ASP cc_start: 0.9435 (t0) cc_final: 0.8582 (p0) REVERT: O 104 ASP cc_start: 0.9464 (m-30) cc_final: 0.9237 (m-30) REVERT: O 106 PHE cc_start: 0.9460 (m-80) cc_final: 0.8909 (m-80) REVERT: O 131 GLU cc_start: 0.9314 (pp20) cc_final: 0.8986 (pp20) REVERT: O 134 LYS cc_start: 0.9449 (pttm) cc_final: 0.9124 (tptp) REVERT: O 158 ARG cc_start: 0.9149 (tpt-90) cc_final: 0.8586 (tpt-90) REVERT: O 183 ASP cc_start: 0.9015 (t0) cc_final: 0.8468 (t0) REVERT: O 185 GLN cc_start: 0.9565 (tm-30) cc_final: 0.9175 (tm-30) REVERT: O 191 ARG cc_start: 0.8923 (mtt-85) cc_final: 0.8364 (ptm160) REVERT: O 240 TYR cc_start: 0.9245 (m-80) cc_final: 0.8837 (m-80) REVERT: P 56 CYS cc_start: 0.9047 (p) cc_final: 0.8354 (p) REVERT: P 113 LEU cc_start: 0.9659 (tt) cc_final: 0.9141 (tt) REVERT: P 115 TYR cc_start: 0.8575 (m-10) cc_final: 0.8317 (m-10) REVERT: P 140 MET cc_start: 0.9064 (ptp) cc_final: 0.8706 (mpp) REVERT: P 144 ASP cc_start: 0.8736 (t0) cc_final: 0.8233 (t0) REVERT: P 154 PHE cc_start: 0.9595 (m-10) cc_final: 0.9385 (m-80) REVERT: P 166 ILE cc_start: 0.9325 (mm) cc_final: 0.8741 (tp) REVERT: P 190 PHE cc_start: 0.9246 (m-80) cc_final: 0.8834 (m-80) REVERT: P 210 MET cc_start: 0.8010 (mtm) cc_final: 0.7703 (mtp) REVERT: P 214 MET cc_start: 0.8701 (mtm) cc_final: 0.8249 (ptp) REVERT: P 229 MET cc_start: 0.0926 (mtt) cc_final: 0.0295 (mtt) outliers start: 1 outliers final: 0 residues processed: 918 average time/residue: 0.1994 time to fit residues: 292.5238 Evaluate side-chains 723 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 723 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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: 0.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 293 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 283 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 228 optimal weight: 0.8980 chunk 285 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN C 185 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3612 r_free = 0.3612 target = 0.087941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.062336 restraints weight = 124695.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.064427 restraints weight = 69544.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.065816 restraints weight = 46925.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.066750 restraints weight = 35631.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.067360 restraints weight = 29543.770| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.7043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31134 Z= 0.141 Angle : 0.707 10.058 42181 Z= 0.365 Chirality : 0.044 0.277 4756 Planarity : 0.004 0.050 5084 Dihedral : 15.531 178.280 4907 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.32 % Favored : 97.59 % Rotamer: Outliers : 0.03 % Allowed : 1.21 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.14), residues: 3570 helix: 0.87 (0.11), residues: 2110 sheet: 1.13 (0.27), residues: 358 loop : 0.13 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 158 TYR 0.021 0.001 TYR G 93 PHE 0.035 0.002 PHE O 106 TRP 0.047 0.002 TRP I 45 HIS 0.007 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (31132) covalent geometry : angle 0.70689 / 0.37 (42181) hydrogen bonds : bond 0.04396 / 2.91 ( 1579) hydrogen bonds : angle 4.86599 / 3.54 ( 4611) Misc. bond : bond 0.00298 / 0.16 ( 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 914 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 913 time to evaluate : 1.281 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 38 GLN cc_start: 0.9523 (mp10) cc_final: 0.9302 (mp10) REVERT: A 43 HIS cc_start: 0.9223 (m90) cc_final: 0.8889 (m-70) REVERT: A 46 LEU cc_start: 0.9817 (mt) cc_final: 0.9577 (mt) REVERT: A 75 TYR cc_start: 0.8845 (m-80) cc_final: 0.8601 (m-80) REVERT: A 95 ARG cc_start: 0.8363 (ptm160) cc_final: 0.7720 (tmt170) REVERT: A 113 LEU cc_start: 0.9668 (mt) cc_final: 0.9362 (tt) REVERT: A 140 MET cc_start: 0.9128 (ttm) cc_final: 0.8773 (ttp) REVERT: A 154 PHE cc_start: 0.9449 (m-80) cc_final: 0.9078 (m-80) REVERT: A 162 GLU cc_start: 0.9002 (pp20) cc_final: 0.8407 (pp20) REVERT: A 182 ARG cc_start: 0.8905 (ttm110) cc_final: 0.8563 (mtm-85) REVERT: A 183 ASP cc_start: 0.8550 (t0) cc_final: 0.8092 (t0) REVERT: A 185 GLN cc_start: 0.9490 (tp40) cc_final: 0.9049 (tp40) REVERT: A 190 PHE cc_start: 0.9016 (m-80) cc_final: 0.8248 (m-80) REVERT: A 214 MET cc_start: 0.9441 (mmp) cc_final: 0.9135 (mmm) REVERT: B 61 GLU cc_start: 0.8656 (mp0) cc_final: 0.8253 (pm20) REVERT: B 75 TYR cc_start: 0.8260 (m-80) cc_final: 0.7911 (m-80) REVERT: B 111 GLU cc_start: 0.9052 (tp30) cc_final: 0.8700 (tp30) REVERT: B 159 ASP cc_start: 0.8735 (m-30) cc_final: 0.8440 (m-30) REVERT: B 210 MET cc_start: 0.9592 (ttt) cc_final: 0.9086 (mtt) REVERT: B 214 MET cc_start: 0.9456 (mmp) cc_final: 0.8981 (mtt) REVERT: B 216 LEU cc_start: 0.9037 (mp) cc_final: 0.8635 (tp) REVERT: B 218 LEU cc_start: 0.8822 (mt) cc_final: 0.8468 (mt) REVERT: B 223 ASN cc_start: 0.9519 (t0) cc_final: 0.8959 (t0) REVERT: B 229 MET cc_start: 0.9053 (mpp) cc_final: 0.8670 (pmm) REVERT: C 46 LEU cc_start: 0.9856 (mt) cc_final: 0.9640 (mt) REVERT: C 214 MET cc_start: 0.9381 (tpp) cc_final: 0.9026 (tpp) REVERT: C 223 ASN cc_start: 0.9379 (t0) cc_final: 0.9103 (t0) REVERT: C 246 GLU cc_start: 0.8457 (pp20) cc_final: 0.7825 (pp20) REVERT: C 247 ILE cc_start: 0.9329 (mt) cc_final: 0.8718 (mt) REVERT: C 250 GLU cc_start: 0.9281 (tp30) cc_final: 0.8821 (tp30) REVERT: C 254 ARG cc_start: 0.9050 (ttp-170) cc_final: 0.8508 (ttp-170) REVERT: C 263 ILE cc_start: 0.8837 (mm) cc_final: 0.8025 (mm) REVERT: D 80 GLN cc_start: 0.8502 (mp-120) cc_final: 0.8224 (mp10) REVERT: D 159 ASP cc_start: 0.8780 (m-30) cc_final: 0.8550 (m-30) REVERT: D 163 ASP cc_start: 0.9105 (m-30) cc_final: 0.8802 (m-30) REVERT: D 176 LEU cc_start: 0.9427 (tp) cc_final: 0.9166 (tp) REVERT: D 180 ILE cc_start: 0.9388 (mt) cc_final: 0.9108 (mt) REVERT: D 211 TRP cc_start: 0.8725 (t-100) cc_final: 0.8254 (t60) REVERT: D 247 ILE cc_start: 0.9528 (mm) cc_final: 0.9241 (mm) REVERT: E 47 ASP cc_start: 0.8875 (m-30) cc_final: 0.8452 (m-30) REVERT: E 97 HIS cc_start: 0.8210 (m-70) cc_final: 0.7992 (m170) REVERT: E 100 CYS cc_start: 0.8612 (t) cc_final: 0.8348 (t) REVERT: E 104 ASP cc_start: 0.8462 (t70) cc_final: 0.7854 (t0) REVERT: E 127 ASP cc_start: 0.8944 (t70) cc_final: 0.8698 (t0) REVERT: E 183 ASP cc_start: 0.9395 (t0) cc_final: 0.8943 (t70) REVERT: E 185 GLN cc_start: 0.8947 (mp10) cc_final: 0.8727 (mp10) REVERT: E 199 LEU cc_start: 0.8642 (tp) cc_final: 0.8290 (tp) REVERT: E 210 MET cc_start: 0.9661 (ttt) cc_final: 0.8607 (tpt) REVERT: E 253 ILE cc_start: 0.9675 (tt) cc_final: 0.9379 (pt) REVERT: F 42 LEU cc_start: 0.9153 (mt) cc_final: 0.8902 (mt) REVERT: F 114 LYS cc_start: 0.9670 (mmtt) cc_final: 0.9464 (mmmm) REVERT: F 144 ASP cc_start: 0.9026 (t70) cc_final: 0.8183 (t0) REVERT: F 145 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8726 (mt-10) REVERT: F 152 GLU cc_start: 0.9462 (pm20) cc_final: 0.9235 (pm20) REVERT: F 170 LEU cc_start: 0.9745 (mt) cc_final: 0.9438 (mt) REVERT: F 190 PHE cc_start: 0.9457 (m-80) cc_final: 0.8960 (m-10) REVERT: F 199 LEU cc_start: 0.7928 (tp) cc_final: 0.7493 (tp) REVERT: F 210 MET cc_start: 0.9527 (mtm) cc_final: 0.9157 (mtp) REVERT: G 75 TYR cc_start: 0.8479 (m-10) cc_final: 0.7971 (m-10) REVERT: G 93 TYR cc_start: 0.5504 (m-80) cc_final: 0.5230 (m-10) REVERT: G 140 MET cc_start: 0.9073 (ttm) cc_final: 0.8588 (mtm) REVERT: G 154 PHE cc_start: 0.9110 (m-80) cc_final: 0.8861 (m-80) REVERT: G 174 ASP cc_start: 0.8707 (p0) cc_final: 0.8224 (p0) REVERT: G 175 ARG cc_start: 0.8535 (mmp80) cc_final: 0.8332 (mmm160) REVERT: G 210 MET cc_start: 0.8756 (ttt) cc_final: 0.8407 (mmp) REVERT: G 246 GLU cc_start: 0.9332 (pt0) cc_final: 0.8990 (pp20) REVERT: G 250 GLU cc_start: 0.9307 (tp30) cc_final: 0.8705 (tp30) REVERT: G 271 VAL cc_start: 0.9169 (t) cc_final: 0.8965 (m) REVERT: H 103 LYS cc_start: 0.9323 (tttt) cc_final: 0.9013 (pttm) REVERT: H 116 ARG cc_start: 0.8549 (mmm160) cc_final: 0.8288 (tpp80) REVERT: H 176 LEU cc_start: 0.9576 (tp) cc_final: 0.9305 (tt) REVERT: H 183 ASP cc_start: 0.8671 (m-30) cc_final: 0.7911 (t70) REVERT: H 185 GLN cc_start: 0.9166 (mm110) cc_final: 0.8947 (mm110) REVERT: H 189 ARG cc_start: 0.9253 (tpt170) cc_final: 0.8995 (mmm160) REVERT: H 210 MET cc_start: 0.9436 (ptp) cc_final: 0.9101 (ptp) REVERT: H 223 ASN cc_start: 0.9347 (t0) cc_final: 0.8998 (t0) REVERT: I 93 TYR cc_start: 0.9231 (t80) cc_final: 0.8872 (t80) REVERT: I 185 GLN cc_start: 0.9127 (mt0) cc_final: 0.8471 (mp10) REVERT: I 210 MET cc_start: 0.9126 (tmm) cc_final: 0.8894 (tmm) REVERT: I 211 TRP cc_start: 0.9211 (t-100) cc_final: 0.8915 (t-100) REVERT: I 224 LEU cc_start: 0.9502 (mt) cc_final: 0.9123 (mt) REVERT: I 233 LEU cc_start: 0.9807 (tp) cc_final: 0.9573 (pp) REVERT: J 100 CYS cc_start: 0.9075 (t) cc_final: 0.8714 (t) REVERT: J 103 LYS cc_start: 0.9220 (tttt) cc_final: 0.8998 (ttmp) REVERT: J 111 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8726 (tm-30) REVERT: J 112 TYR cc_start: 0.9556 (t80) cc_final: 0.9334 (t80) REVERT: J 127 ASP cc_start: 0.9016 (m-30) cc_final: 0.8761 (m-30) REVERT: J 149 LEU cc_start: 0.9726 (mt) cc_final: 0.9489 (mm) REVERT: J 159 ASP cc_start: 0.9336 (t70) cc_final: 0.8968 (t0) REVERT: J 162 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8300 (mm-30) REVERT: J 180 ILE cc_start: 0.9510 (mt) cc_final: 0.9292 (mt) REVERT: J 185 GLN cc_start: 0.9546 (mm110) cc_final: 0.9257 (mm110) REVERT: J 187 LEU cc_start: 0.8938 (mt) cc_final: 0.8628 (mt) REVERT: J 210 MET cc_start: 0.9600 (mtp) cc_final: 0.9289 (mtp) REVERT: J 229 MET cc_start: 0.9252 (mmt) cc_final: 0.8999 (mmm) REVERT: K 20 TRP cc_start: 0.8846 (p-90) cc_final: 0.8322 (p-90) REVERT: K 46 LEU cc_start: 0.9707 (mt) cc_final: 0.9503 (mt) REVERT: K 54 LYS cc_start: 0.9384 (tppt) cc_final: 0.8930 (mmmt) REVERT: K 92 VAL cc_start: 0.9701 (t) cc_final: 0.9474 (m) REVERT: K 116 ARG cc_start: 0.8555 (mmp80) cc_final: 0.8020 (mmp80) REVERT: K 129 THR cc_start: 0.9732 (m) cc_final: 0.9444 (p) REVERT: K 145 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7834 (mm-30) REVERT: K 159 ASP cc_start: 0.9363 (t70) cc_final: 0.9128 (t0) REVERT: K 162 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8615 (mm-30) REVERT: K 223 ASN cc_start: 0.9546 (m110) cc_final: 0.9334 (m110) REVERT: K 254 ARG cc_start: 0.9058 (ttp-170) cc_final: 0.8839 (ptm160) REVERT: L 38 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8271 (pm20) REVERT: L 93 TYR cc_start: 0.8855 (t80) cc_final: 0.8633 (t80) REVERT: L 100 CYS cc_start: 0.6585 (t) cc_final: 0.5267 (t) REVERT: L 104 ASP cc_start: 0.8660 (t0) cc_final: 0.8358 (t0) REVERT: L 124 ASP cc_start: 0.9324 (m-30) cc_final: 0.9065 (m-30) REVERT: L 131 GLU cc_start: 0.9275 (tt0) cc_final: 0.8867 (pt0) REVERT: L 215 VAL cc_start: 0.9631 (t) cc_final: 0.9088 (t) REVERT: L 240 TYR cc_start: 0.8880 (m-10) cc_final: 0.8351 (m-10) REVERT: O 71 ASP cc_start: 0.9414 (t0) cc_final: 0.8767 (p0) REVERT: O 103 LYS cc_start: 0.9237 (ptpp) cc_final: 0.8990 (ptpp) REVERT: O 106 PHE cc_start: 0.9449 (m-80) cc_final: 0.9155 (m-80) REVERT: O 131 GLU cc_start: 0.9364 (pp20) cc_final: 0.9037 (pp20) REVERT: O 134 LYS cc_start: 0.9416 (pttm) cc_final: 0.9141 (tptp) REVERT: O 158 ARG cc_start: 0.9100 (tpt-90) cc_final: 0.8607 (tpt-90) REVERT: O 183 ASP cc_start: 0.9029 (t0) cc_final: 0.8466 (t0) REVERT: O 185 GLN cc_start: 0.9558 (tm-30) cc_final: 0.9178 (tm-30) REVERT: O 191 ARG cc_start: 0.8970 (mtt-85) cc_final: 0.8371 (ptm160) REVERT: O 240 TYR cc_start: 0.9241 (m-80) cc_final: 0.8823 (m-80) REVERT: P 113 LEU cc_start: 0.9666 (tt) cc_final: 0.9131 (tt) REVERT: P 144 ASP cc_start: 0.8774 (t0) cc_final: 0.8266 (t0) REVERT: P 168 VAL cc_start: 0.9378 (t) cc_final: 0.9065 (t) REVERT: P 190 PHE cc_start: 0.9221 (m-80) cc_final: 0.8634 (m-80) REVERT: P 214 MET cc_start: 0.8738 (mtm) cc_final: 0.8148 (ptm) REVERT: P 229 MET cc_start: 0.1034 (mtt) cc_final: 0.0411 (mtt) outliers start: 1 outliers final: 0 residues processed: 914 average time/residue: 0.1962 time to fit residues: 287.2035 Evaluate side-chains 723 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 723 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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: 4.9990 chunk 304 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 288 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 344 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 262 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN D 38 GLN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN L 38 GLN P 97 HIS P 185 GLN ** 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 = 0.3621 r_free = 0.3621 target = 0.088310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.062840 restraints weight = 125078.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.064930 restraints weight = 69788.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.066315 restraints weight = 47013.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.067235 restraints weight = 35764.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.067851 restraints weight = 29667.028| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.7170 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= 0.141 Angle : 0.714 8.854 42181 Z= 0.370 Chirality : 0.045 0.619 4756 Planarity : 0.004 0.050 5084 Dihedral : 15.459 174.916 4907 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.55 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 0.88 (0.14), residues: 3570 helix: 0.83 (0.11), residues: 2112 sheet: 1.15 (0.27), residues: 358 loop : 0.13 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 148 TYR 0.029 0.001 TYR F 75 PHE 0.032 0.002 PHE L 196 TRP 0.048 0.002 TRP G 211 HIS 0.009 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (31132) covalent geometry : angle 0.71419 / 0.37 (42181) hydrogen bonds : bond 0.04325 / 2.84 ( 1579) hydrogen bonds : angle 4.86111 / 3.54 ( 4611) Misc. bond : bond 0.00590 / 0.29 ( 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 923 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 923 time to evaluate : 1.240 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: A 38 GLN cc_start: 0.9532 (mp10) cc_final: 0.9317 (mp10) REVERT: A 43 HIS cc_start: 0.9197 (m90) cc_final: 0.8940 (m-70) REVERT: A 46 LEU cc_start: 0.9815 (mt) cc_final: 0.9572 (mt) REVERT: A 75 TYR cc_start: 0.8854 (m-80) cc_final: 0.8640 (m-80) REVERT: A 95 ARG cc_start: 0.8369 (ptm160) cc_final: 0.7738 (tmt170) REVERT: A 113 LEU cc_start: 0.9657 (mt) cc_final: 0.9343 (tt) REVERT: A 140 MET cc_start: 0.9093 (ttm) cc_final: 0.8781 (ttp) REVERT: A 154 PHE cc_start: 0.9430 (m-80) cc_final: 0.9084 (m-80) REVERT: A 162 GLU cc_start: 0.9028 (pp20) cc_final: 0.8468 (pp20) REVERT: A 183 ASP cc_start: 0.8566 (t0) cc_final: 0.8158 (t0) REVERT: A 185 GLN cc_start: 0.9513 (tp40) cc_final: 0.9071 (tp40) REVERT: A 214 MET cc_start: 0.9404 (mmp) cc_final: 0.9146 (mmm) REVERT: A 233 LEU cc_start: 0.9824 (tp) cc_final: 0.9621 (tp) REVERT: B 61 GLU cc_start: 0.8646 (mp0) cc_final: 0.8266 (pm20) REVERT: B 75 TYR cc_start: 0.8240 (m-80) cc_final: 0.7883 (m-80) REVERT: B 111 GLU cc_start: 0.9054 (tp30) cc_final: 0.8712 (tp30) REVERT: B 156 ASP cc_start: 0.9492 (m-30) cc_final: 0.9252 (m-30) REVERT: B 159 ASP cc_start: 0.8625 (m-30) cc_final: 0.8333 (m-30) REVERT: B 210 MET cc_start: 0.9581 (ttt) cc_final: 0.9088 (mtt) REVERT: B 214 MET cc_start: 0.9462 (mmp) cc_final: 0.8966 (mtt) REVERT: B 223 ASN cc_start: 0.9521 (t0) cc_final: 0.8975 (t0) REVERT: B 229 MET cc_start: 0.9061 (mpp) cc_final: 0.8750 (pmm) REVERT: C 46 LEU cc_start: 0.9861 (mt) cc_final: 0.9650 (mt) REVERT: C 173 THR cc_start: 0.8117 (p) cc_final: 0.7908 (p) REVERT: C 214 MET cc_start: 0.9359 (tpp) cc_final: 0.8985 (tpp) REVERT: C 223 ASN cc_start: 0.9380 (t0) cc_final: 0.9103 (t0) REVERT: C 247 ILE cc_start: 0.9056 (mt) cc_final: 0.8721 (mt) REVERT: C 250 GLU cc_start: 0.9341 (tp30) cc_final: 0.8857 (tp30) REVERT: D 80 GLN cc_start: 0.8498 (mp-120) cc_final: 0.8182 (mp-120) REVERT: D 98 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7729 (tm-30) REVERT: D 163 ASP cc_start: 0.9061 (m-30) cc_final: 0.8752 (m-30) REVERT: D 176 LEU cc_start: 0.9427 (tp) cc_final: 0.9132 (tp) REVERT: D 180 ILE cc_start: 0.9396 (mt) cc_final: 0.9082 (mt) REVERT: D 211 TRP cc_start: 0.8736 (t-100) cc_final: 0.8228 (t-100) REVERT: E 47 ASP cc_start: 0.8826 (m-30) cc_final: 0.8362 (m-30) REVERT: E 97 HIS cc_start: 0.8257 (m-70) cc_final: 0.8009 (m170) REVERT: E 99 LYS cc_start: 0.9179 (mmmt) cc_final: 0.8766 (tppt) REVERT: E 104 ASP cc_start: 0.8457 (t70) cc_final: 0.7852 (t0) REVERT: E 127 ASP cc_start: 0.8924 (t70) cc_final: 0.8653 (t0) REVERT: E 159 ASP cc_start: 0.8920 (t70) cc_final: 0.8494 (t0) REVERT: E 162 GLU cc_start: 0.9041 (pm20) cc_final: 0.8787 (pm20) REVERT: E 163 ASP cc_start: 0.8613 (m-30) cc_final: 0.8148 (m-30) REVERT: E 183 ASP cc_start: 0.9399 (t0) cc_final: 0.8950 (t70) REVERT: E 199 LEU cc_start: 0.8658 (tp) cc_final: 0.8353 (tp) REVERT: E 210 MET cc_start: 0.9640 (ttt) cc_final: 0.8193 (tpt) REVERT: E 213 GLN cc_start: 0.8831 (pp30) cc_final: 0.8014 (pp30) REVERT: E 214 MET cc_start: 0.8617 (mmp) cc_final: 0.8289 (mmm) REVERT: E 253 ILE cc_start: 0.9643 (tt) cc_final: 0.9360 (pt) REVERT: F 42 LEU cc_start: 0.9187 (mt) cc_final: 0.8928 (mt) REVERT: F 114 LYS cc_start: 0.9655 (mmtt) cc_final: 0.9443 (mmmm) REVERT: F 144 ASP cc_start: 0.9020 (t70) cc_final: 0.8168 (t0) REVERT: F 145 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8687 (mt-10) REVERT: F 170 LEU cc_start: 0.9750 (mt) cc_final: 0.9434 (mt) REVERT: F 190 PHE cc_start: 0.9447 (m-80) cc_final: 0.8958 (m-10) REVERT: F 199 LEU cc_start: 0.7850 (tp) cc_final: 0.7472 (tp) REVERT: F 210 MET cc_start: 0.9535 (mtm) cc_final: 0.9174 (mtp) REVERT: F 238 GLU cc_start: 0.8918 (pp20) cc_final: 0.8014 (pp20) REVERT: F 240 TYR cc_start: 0.8412 (m-10) cc_final: 0.7686 (m-10) REVERT: G 71 ASP cc_start: 0.9373 (m-30) cc_final: 0.8750 (m-30) REVERT: G 75 TYR cc_start: 0.8453 (m-10) cc_final: 0.7950 (m-10) REVERT: G 93 TYR cc_start: 0.5407 (m-80) cc_final: 0.4768 (m-10) REVERT: G 107 LYS cc_start: 0.9578 (mtpp) cc_final: 0.9230 (mtmm) REVERT: G 140 MET cc_start: 0.9079 (ttm) cc_final: 0.8569 (mtm) REVERT: G 142 ILE cc_start: 0.9363 (pt) cc_final: 0.8601 (pt) REVERT: G 154 PHE cc_start: 0.9079 (m-80) cc_final: 0.8844 (m-80) REVERT: G 174 ASP cc_start: 0.8764 (p0) cc_final: 0.8308 (p0) REVERT: G 210 MET cc_start: 0.8743 (ttt) cc_final: 0.8275 (ttt) REVERT: G 246 GLU cc_start: 0.9305 (pt0) cc_final: 0.8994 (pp20) REVERT: G 250 GLU cc_start: 0.9278 (tp30) cc_final: 0.8652 (tp30) REVERT: H 103 LYS cc_start: 0.9310 (tttt) cc_final: 0.8999 (pttm) REVERT: H 116 ARG cc_start: 0.8515 (mmm160) cc_final: 0.8297 (tpp80) REVERT: H 127 ASP cc_start: 0.8954 (m-30) cc_final: 0.8749 (m-30) REVERT: H 176 LEU cc_start: 0.9579 (tp) cc_final: 0.9302 (tt) REVERT: H 183 ASP cc_start: 0.8751 (m-30) cc_final: 0.7893 (t70) REVERT: H 189 ARG cc_start: 0.9189 (tpt170) cc_final: 0.8970 (mmm160) REVERT: H 210 MET cc_start: 0.9419 (ptp) cc_final: 0.9155 (ptp) REVERT: H 223 ASN cc_start: 0.9300 (t0) cc_final: 0.8928 (t0) REVERT: H 229 MET cc_start: 0.9211 (pmm) cc_final: 0.9003 (pmm) REVERT: I 63 ARG cc_start: 0.7908 (tpm170) cc_final: 0.7636 (mmm-85) REVERT: I 93 TYR cc_start: 0.9189 (t80) cc_final: 0.8964 (t80) REVERT: I 97 HIS cc_start: 0.7147 (p90) cc_final: 0.6927 (p90) REVERT: I 139 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8489 (mm-30) REVERT: I 185 GLN cc_start: 0.9125 (mt0) cc_final: 0.8470 (mp10) REVERT: I 210 MET cc_start: 0.9110 (tmm) cc_final: 0.8899 (tmm) REVERT: I 211 TRP cc_start: 0.9210 (t-100) cc_final: 0.8926 (t-100) REVERT: I 224 LEU cc_start: 0.9493 (mt) cc_final: 0.9147 (mt) REVERT: I 233 LEU cc_start: 0.9803 (tp) cc_final: 0.9571 (pp) REVERT: J 93 TYR cc_start: 0.8856 (t80) cc_final: 0.8492 (t80) REVERT: J 100 CYS cc_start: 0.8956 (t) cc_final: 0.8568 (t) REVERT: J 111 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8697 (tm-30) REVERT: J 127 ASP cc_start: 0.9033 (m-30) cc_final: 0.8822 (m-30) REVERT: J 149 LEU cc_start: 0.9700 (mt) cc_final: 0.9500 (mt) REVERT: J 159 ASP cc_start: 0.9275 (t70) cc_final: 0.8859 (t0) REVERT: J 162 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8302 (mm-30) REVERT: J 180 ILE cc_start: 0.9523 (mt) cc_final: 0.9321 (mt) REVERT: J 185 GLN cc_start: 0.9544 (mm110) cc_final: 0.9258 (mm110) REVERT: J 187 LEU cc_start: 0.8977 (mt) cc_final: 0.8667 (mt) REVERT: J 210 MET cc_start: 0.9567 (mtp) cc_final: 0.9216 (mtp) REVERT: J 224 LEU cc_start: 0.9387 (mm) cc_final: 0.9110 (pp) REVERT: J 229 MET cc_start: 0.9451 (mmt) cc_final: 0.9139 (mmm) REVERT: K 20 TRP cc_start: 0.8875 (p-90) cc_final: 0.8268 (p-90) REVERT: K 46 LEU cc_start: 0.9728 (mt) cc_final: 0.9508 (mt) REVERT: K 54 LYS cc_start: 0.9351 (tppt) cc_final: 0.8960 (mmmt) REVERT: K 63 ARG cc_start: 0.8915 (mmm160) cc_final: 0.8520 (mmm160) REVERT: K 92 VAL cc_start: 0.9693 (t) cc_final: 0.9470 (m) REVERT: K 116 ARG cc_start: 0.8534 (mmp80) cc_final: 0.7733 (mmp80) REVERT: K 129 THR cc_start: 0.9721 (m) cc_final: 0.9430 (p) REVERT: K 145 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7862 (mm-30) REVERT: K 162 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8619 (mm-30) REVERT: K 223 ASN cc_start: 0.9546 (m110) cc_final: 0.9315 (m110) REVERT: K 254 ARG cc_start: 0.9043 (ttp-170) cc_final: 0.8835 (ttp-170) REVERT: L 28 LEU cc_start: 0.8963 (tt) cc_final: 0.8581 (mt) REVERT: L 38 GLN cc_start: 0.8999 (mm110) cc_final: 0.8518 (pm20) REVERT: L 100 CYS cc_start: 0.6551 (t) cc_final: 0.5129 (t) REVERT: L 104 ASP cc_start: 0.8735 (t0) cc_final: 0.8500 (t0) REVERT: L 124 ASP cc_start: 0.9318 (m-30) cc_final: 0.9091 (m-30) REVERT: L 131 GLU cc_start: 0.9195 (tt0) cc_final: 0.8813 (pt0) REVERT: L 215 VAL cc_start: 0.9654 (t) cc_final: 0.8791 (t) REVERT: L 240 TYR cc_start: 0.8869 (m-10) cc_final: 0.8398 (m-10) REVERT: O 71 ASP cc_start: 0.9341 (t0) cc_final: 0.8708 (p0) REVERT: O 103 LYS cc_start: 0.9230 (ptpp) cc_final: 0.8980 (ptpp) REVERT: O 104 ASP cc_start: 0.9368 (m-30) cc_final: 0.9168 (m-30) REVERT: O 106 PHE cc_start: 0.9429 (m-80) cc_final: 0.9101 (m-80) REVERT: O 111 GLU cc_start: 0.9502 (mt-10) cc_final: 0.9300 (mt-10) REVERT: O 131 GLU cc_start: 0.9346 (pp20) cc_final: 0.9014 (pp20) REVERT: O 134 LYS cc_start: 0.9387 (pttm) cc_final: 0.9112 (tptp) REVERT: O 158 ARG cc_start: 0.9103 (tpt-90) cc_final: 0.8289 (tpp80) REVERT: O 183 ASP cc_start: 0.8948 (t0) cc_final: 0.8361 (t0) REVERT: O 185 GLN cc_start: 0.9569 (tm-30) cc_final: 0.9269 (tm-30) REVERT: O 191 ARG cc_start: 0.8917 (mtt-85) cc_final: 0.8334 (ptm160) REVERT: O 240 TYR cc_start: 0.9257 (m-80) cc_final: 0.8823 (m-80) REVERT: P 37 GLN cc_start: 0.9778 (tp-100) cc_final: 0.9578 (tm-30) REVERT: P 113 LEU cc_start: 0.9615 (tt) cc_final: 0.9090 (tt) REVERT: P 115 TYR cc_start: 0.8245 (m-10) cc_final: 0.7976 (m-10) REVERT: P 144 ASP cc_start: 0.8784 (t0) cc_final: 0.8236 (t0) REVERT: P 154 PHE cc_start: 0.9699 (m-80) cc_final: 0.9244 (m-80) REVERT: P 168 VAL cc_start: 0.9230 (t) cc_final: 0.8712 (t) REVERT: P 180 ILE cc_start: 0.9451 (tp) cc_final: 0.9194 (tp) REVERT: P 187 LEU cc_start: 0.9678 (tt) cc_final: 0.9359 (tp) REVERT: P 189 ARG cc_start: 0.9334 (tpm170) cc_final: 0.8791 (mmm160) REVERT: P 190 PHE cc_start: 0.9177 (m-80) cc_final: 0.8471 (m-80) REVERT: P 214 MET cc_start: 0.8630 (mtm) cc_final: 0.8013 (ptm) REVERT: P 229 MET cc_start: 0.1035 (mtt) cc_final: 0.0425 (mtt) outliers start: 0 outliers final: 0 residues processed: 923 average time/residue: 0.1979 time to fit residues: 293.2903 Evaluate side-chains 725 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 725 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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: 8.9990 chunk 228 optimal weight: 0.0870 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 297 optimal weight: 6.9990 chunk 208 optimal weight: 0.0570 chunk 293 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 344 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 overall best weight: 1.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 HIS ** P 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.087791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.062401 restraints weight = 124866.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.064452 restraints weight = 69861.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.065819 restraints weight = 47208.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.066684 restraints weight = 35986.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.067302 restraints weight = 30055.922| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.7301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31134 Z= 0.153 Angle : 0.715 8.790 42181 Z= 0.372 Chirality : 0.044 0.485 4756 Planarity : 0.004 0.051 5084 Dihedral : 15.387 175.004 4907 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.58 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.14), residues: 3570 helix: 0.89 (0.11), residues: 2112 sheet: 1.05 (0.27), residues: 358 loop : 0.12 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG L 76 TYR 0.023 0.001 TYR G 93 PHE 0.030 0.002 PHE D 196 TRP 0.051 0.002 TRP G 211 HIS 0.007 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (31132) covalent geometry : angle 0.71542 / 0.37 (42181) hydrogen bonds : bond 0.04358 / 2.86 ( 1579) hydrogen bonds : angle 4.89484 / 3.57 ( 4611) Misc. bond : bond 0.00221 / 0.12 ( 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 903 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 903 time to evaluate : 1.279 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: A 43 HIS cc_start: 0.9213 (m90) cc_final: 0.8951 (m-70) REVERT: A 46 LEU cc_start: 0.9815 (mt) cc_final: 0.9575 (mt) REVERT: A 93 TYR cc_start: 0.8904 (t80) cc_final: 0.8521 (t80) REVERT: A 95 ARG cc_start: 0.8359 (ptm160) cc_final: 0.7732 (tmt170) REVERT: A 113 LEU cc_start: 0.9659 (mt) cc_final: 0.9391 (tt) REVERT: A 140 MET cc_start: 0.9123 (ttm) cc_final: 0.8823 (ttp) REVERT: A 154 PHE cc_start: 0.9435 (m-80) cc_final: 0.9053 (m-80) REVERT: A 162 GLU cc_start: 0.9019 (pp20) cc_final: 0.8535 (pp20) REVERT: A 183 ASP cc_start: 0.8598 (t0) cc_final: 0.8181 (t0) REVERT: A 185 GLN cc_start: 0.9515 (tp40) cc_final: 0.9080 (tp40) REVERT: A 214 MET cc_start: 0.9409 (mmp) cc_final: 0.9125 (mmm) REVERT: A 250 GLU cc_start: 0.9741 (tp30) cc_final: 0.9444 (tp30) REVERT: B 61 GLU cc_start: 0.8632 (mp0) cc_final: 0.8276 (pm20) REVERT: B 75 TYR cc_start: 0.8253 (m-80) cc_final: 0.7891 (m-80) REVERT: B 111 GLU cc_start: 0.9056 (tp30) cc_final: 0.8737 (tp30) REVERT: B 156 ASP cc_start: 0.9485 (m-30) cc_final: 0.9269 (m-30) REVERT: B 159 ASP cc_start: 0.8676 (m-30) cc_final: 0.8334 (m-30) REVERT: B 214 MET cc_start: 0.9477 (mmp) cc_final: 0.9212 (mmm) REVERT: B 223 ASN cc_start: 0.9531 (t0) cc_final: 0.8996 (t0) REVERT: B 229 MET cc_start: 0.9054 (mpp) cc_final: 0.8757 (pmm) REVERT: B 254 ARG cc_start: 0.9126 (tpm170) cc_final: 0.8859 (tpm170) REVERT: C 46 LEU cc_start: 0.9859 (mt) cc_final: 0.9638 (mt) REVERT: C 156 ASP cc_start: 0.9089 (m-30) cc_final: 0.8883 (m-30) REVERT: C 214 MET cc_start: 0.9367 (tpp) cc_final: 0.9040 (tpp) REVERT: C 223 ASN cc_start: 0.9358 (t0) cc_final: 0.9131 (t0) REVERT: C 250 GLU cc_start: 0.9349 (tp30) cc_final: 0.8876 (tp30) REVERT: C 263 ILE cc_start: 0.8876 (mm) cc_final: 0.8013 (mm) REVERT: D 144 ASP cc_start: 0.8707 (t0) cc_final: 0.8464 (t0) REVERT: D 159 ASP cc_start: 0.8867 (m-30) cc_final: 0.8561 (m-30) REVERT: D 163 ASP cc_start: 0.9041 (m-30) cc_final: 0.8755 (m-30) REVERT: D 176 LEU cc_start: 0.9440 (tp) cc_final: 0.9162 (tp) REVERT: D 180 ILE cc_start: 0.9364 (mt) cc_final: 0.9075 (mt) REVERT: D 211 TRP cc_start: 0.8762 (t-100) cc_final: 0.8196 (t-100) REVERT: D 213 GLN cc_start: 0.9539 (mp10) cc_final: 0.9334 (mp10) REVERT: D 246 GLU cc_start: 0.8594 (pp20) cc_final: 0.8248 (pp20) REVERT: D 247 ILE cc_start: 0.9511 (mm) cc_final: 0.9022 (mm) REVERT: E 99 LYS cc_start: 0.9172 (mmmt) cc_final: 0.8708 (tppt) REVERT: E 104 ASP cc_start: 0.8468 (t70) cc_final: 0.7860 (t0) REVERT: E 127 ASP cc_start: 0.8914 (t70) cc_final: 0.8670 (t0) REVERT: E 159 ASP cc_start: 0.8924 (t70) cc_final: 0.8669 (t70) REVERT: E 183 ASP cc_start: 0.9404 (t0) cc_final: 0.9057 (t0) REVERT: E 199 LEU cc_start: 0.8624 (tp) cc_final: 0.8356 (tp) REVERT: E 210 MET cc_start: 0.9656 (ttt) cc_final: 0.8383 (tpt) REVERT: E 213 GLN cc_start: 0.8829 (pp30) cc_final: 0.7993 (pp30) REVERT: E 253 ILE cc_start: 0.9657 (tt) cc_final: 0.9363 (pt) REVERT: F 47 ASP cc_start: 0.9434 (t70) cc_final: 0.9055 (t0) REVERT: F 114 LYS cc_start: 0.9680 (mmtt) cc_final: 0.9445 (mmmm) REVERT: F 144 ASP cc_start: 0.9014 (t70) cc_final: 0.8175 (t0) REVERT: F 145 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8629 (mt-10) REVERT: F 170 LEU cc_start: 0.9729 (mt) cc_final: 0.9409 (mt) REVERT: F 185 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8282 (tm-30) REVERT: F 190 PHE cc_start: 0.9430 (m-80) cc_final: 0.8991 (m-10) REVERT: F 199 LEU cc_start: 0.7918 (tp) cc_final: 0.7528 (tp) REVERT: F 210 MET cc_start: 0.9523 (mtm) cc_final: 0.9164 (mtp) REVERT: F 240 TYR cc_start: 0.8717 (m-10) cc_final: 0.8104 (m-10) REVERT: G 75 TYR cc_start: 0.8493 (m-10) cc_final: 0.7971 (m-10) REVERT: G 93 TYR cc_start: 0.5569 (m-80) cc_final: 0.5200 (m-10) REVERT: G 107 LYS cc_start: 0.9573 (mtpp) cc_final: 0.9239 (mtmm) REVERT: G 127 ASP cc_start: 0.9179 (m-30) cc_final: 0.8979 (m-30) REVERT: G 140 MET cc_start: 0.9071 (ttm) cc_final: 0.8451 (mtm) REVERT: G 154 PHE cc_start: 0.9160 (m-80) cc_final: 0.8899 (m-80) REVERT: G 170 LEU cc_start: 0.9688 (mm) cc_final: 0.9193 (mm) REVERT: G 174 ASP cc_start: 0.8772 (p0) cc_final: 0.8266 (p0) REVERT: G 175 ARG cc_start: 0.8571 (mmp80) cc_final: 0.8345 (mmm160) REVERT: G 210 MET cc_start: 0.8770 (ttt) cc_final: 0.8296 (ttt) REVERT: G 246 GLU cc_start: 0.9310 (pt0) cc_final: 0.8980 (pp20) REVERT: G 250 GLU cc_start: 0.9293 (tp30) cc_final: 0.8584 (tp30) REVERT: H 93 TYR cc_start: 0.8994 (t80) cc_final: 0.8772 (t80) REVERT: H 103 LYS cc_start: 0.9331 (tttt) cc_final: 0.9011 (pttm) REVERT: H 116 ARG cc_start: 0.8536 (mmm160) cc_final: 0.8317 (tpp80) REVERT: H 127 ASP cc_start: 0.8958 (m-30) cc_final: 0.8755 (m-30) REVERT: H 162 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8659 (mm-30) REVERT: H 176 LEU cc_start: 0.9605 (tp) cc_final: 0.9366 (tt) REVERT: H 183 ASP cc_start: 0.8674 (m-30) cc_final: 0.7838 (t70) REVERT: H 189 ARG cc_start: 0.9191 (tpt170) cc_final: 0.8901 (mmm-85) REVERT: H 210 MET cc_start: 0.9403 (ptp) cc_final: 0.9164 (ptp) REVERT: H 223 ASN cc_start: 0.9337 (t0) cc_final: 0.8977 (t0) REVERT: I 61 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8752 (tt0) REVERT: I 63 ARG cc_start: 0.8057 (tpm170) cc_final: 0.7545 (mmm-85) REVERT: I 93 TYR cc_start: 0.9197 (t80) cc_final: 0.8924 (t80) REVERT: I 97 HIS cc_start: 0.7367 (p90) cc_final: 0.7111 (p90) REVERT: I 185 GLN cc_start: 0.9146 (mt0) cc_final: 0.8461 (mp10) REVERT: I 210 MET cc_start: 0.9146 (tmm) cc_final: 0.8809 (tmm) REVERT: I 211 TRP cc_start: 0.9212 (t-100) cc_final: 0.8961 (t60) REVERT: I 224 LEU cc_start: 0.9457 (mt) cc_final: 0.9099 (mt) REVERT: I 233 LEU cc_start: 0.9801 (tp) cc_final: 0.9568 (pp) REVERT: J 100 CYS cc_start: 0.8976 (t) cc_final: 0.8698 (t) REVERT: J 103 LYS cc_start: 0.9182 (tttp) cc_final: 0.8810 (tppt) REVERT: J 111 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8779 (tm-30) REVERT: J 112 TYR cc_start: 0.9518 (t80) cc_final: 0.9311 (t80) REVERT: J 127 ASP cc_start: 0.9041 (m-30) cc_final: 0.8821 (m-30) REVERT: J 149 LEU cc_start: 0.9699 (mt) cc_final: 0.9497 (mm) REVERT: J 159 ASP cc_start: 0.9221 (t70) cc_final: 0.8840 (t0) REVERT: J 162 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8310 (mm-30) REVERT: J 180 ILE cc_start: 0.9534 (mt) cc_final: 0.9318 (mt) REVERT: J 185 GLN cc_start: 0.9554 (mm110) cc_final: 0.9262 (mm110) REVERT: J 187 LEU cc_start: 0.9026 (mt) cc_final: 0.8731 (mt) REVERT: J 210 MET cc_start: 0.9564 (mtp) cc_final: 0.9075 (mtt) REVERT: J 229 MET cc_start: 0.9558 (mmt) cc_final: 0.9214 (mmm) REVERT: J 248 LEU cc_start: 0.9825 (mm) cc_final: 0.9612 (mm) REVERT: K 20 TRP cc_start: 0.8909 (p-90) cc_final: 0.8253 (p-90) REVERT: K 54 LYS cc_start: 0.9179 (tppt) cc_final: 0.8932 (mmmt) REVERT: K 63 ARG cc_start: 0.8907 (mmm160) cc_final: 0.8477 (mmm160) REVERT: K 92 VAL cc_start: 0.9706 (t) cc_final: 0.9496 (m) REVERT: K 116 ARG cc_start: 0.8548 (mmp80) cc_final: 0.7770 (mmp80) REVERT: K 129 THR cc_start: 0.9724 (m) cc_final: 0.9432 (p) REVERT: K 145 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7845 (mm-30) REVERT: K 162 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8638 (mm-30) REVERT: K 223 ASN cc_start: 0.9521 (m110) cc_final: 0.9237 (m110) REVERT: K 254 ARG cc_start: 0.9028 (ttp-170) cc_final: 0.8532 (ptm160) REVERT: L 28 LEU cc_start: 0.8993 (tt) cc_final: 0.8594 (mt) REVERT: L 38 GLN cc_start: 0.9152 (mm110) cc_final: 0.8647 (pm20) REVERT: L 100 CYS cc_start: 0.6407 (t) cc_final: 0.4765 (t) REVERT: L 104 ASP cc_start: 0.8630 (t0) cc_final: 0.8323 (t0) REVERT: L 124 ASP cc_start: 0.9312 (m-30) cc_final: 0.9086 (m-30) REVERT: L 131 GLU cc_start: 0.9273 (tt0) cc_final: 0.8854 (pt0) REVERT: L 215 VAL cc_start: 0.9669 (t) cc_final: 0.8746 (t) REVERT: L 229 MET cc_start: 0.7486 (pmm) cc_final: 0.7244 (pmm) REVERT: O 71 ASP cc_start: 0.9246 (t0) cc_final: 0.8601 (p0) REVERT: O 103 LYS cc_start: 0.9228 (ptpp) cc_final: 0.8973 (ptpp) REVERT: O 106 PHE cc_start: 0.9464 (m-80) cc_final: 0.9228 (m-80) REVERT: O 111 GLU cc_start: 0.9481 (mt-10) cc_final: 0.9278 (mt-10) REVERT: O 130 ILE cc_start: 0.9848 (pt) cc_final: 0.9639 (pt) REVERT: O 131 GLU cc_start: 0.9372 (pp20) cc_final: 0.9025 (pp20) REVERT: O 134 LYS cc_start: 0.9379 (pttm) cc_final: 0.9133 (tptp) REVERT: O 158 ARG cc_start: 0.9130 (tpt-90) cc_final: 0.8316 (tpp80) REVERT: O 183 ASP cc_start: 0.9004 (t0) cc_final: 0.8439 (t0) REVERT: O 185 GLN cc_start: 0.9609 (tm-30) cc_final: 0.9219 (tm-30) REVERT: O 240 TYR cc_start: 0.9203 (m-80) cc_final: 0.8733 (m-80) REVERT: P 37 GLN cc_start: 0.9810 (tp-100) cc_final: 0.9425 (mm-40) REVERT: P 113 LEU cc_start: 0.9628 (tt) cc_final: 0.9014 (tt) REVERT: P 115 TYR cc_start: 0.8301 (m-10) cc_final: 0.8064 (m-10) REVERT: P 141 LEU cc_start: 0.9760 (mm) cc_final: 0.9526 (mm) REVERT: P 143 ILE cc_start: 0.9586 (mp) cc_final: 0.9277 (tp) REVERT: P 144 ASP cc_start: 0.8790 (t0) cc_final: 0.8367 (t0) REVERT: P 154 PHE cc_start: 0.9708 (m-80) cc_final: 0.9237 (m-80) REVERT: P 168 VAL cc_start: 0.9194 (t) cc_final: 0.8884 (t) REVERT: P 187 LEU cc_start: 0.9694 (tt) cc_final: 0.9474 (tp) REVERT: P 189 ARG cc_start: 0.9338 (tpm170) cc_final: 0.8725 (mmm160) REVERT: P 190 PHE cc_start: 0.9174 (m-80) cc_final: 0.8876 (m-80) REVERT: P 214 MET cc_start: 0.8627 (mtm) cc_final: 0.8018 (ptm) REVERT: P 229 MET cc_start: 0.1184 (mtt) cc_final: 0.0663 (mtt) outliers start: 0 outliers final: 0 residues processed: 903 average time/residue: 0.1956 time to fit residues: 284.2869 Evaluate side-chains 705 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 705 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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: 0.2980 chunk 203 optimal weight: 9.9990 chunk 113 optimal weight: 0.5980 chunk 242 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 201 optimal weight: 4.9990 chunk 317 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 324 optimal weight: 7.9990 chunk 265 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN C 98 GLN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 HIS ** 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 = 0.3603 r_free = 0.3603 target = 0.087535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.062007 restraints weight = 125177.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.064069 restraints weight = 70055.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.065443 restraints weight = 47262.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.066355 restraints weight = 36031.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066966 restraints weight = 29950.993| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.7412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 31134 Z= 0.148 Angle : 0.726 8.993 42181 Z= 0.377 Chirality : 0.045 0.404 4756 Planarity : 0.004 0.056 5084 Dihedral : 15.334 175.802 4907 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.58 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 0.92 (0.14), residues: 3570 helix: 0.90 (0.11), residues: 2110 sheet: 1.10 (0.28), residues: 358 loop : 0.09 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 254 TYR 0.023 0.001 TYR G 93 PHE 0.033 0.002 PHE O 106 TRP 0.050 0.002 TRP G 211 HIS 0.007 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (31132) covalent geometry : angle 0.72649 / 0.38 (42181) hydrogen bonds : bond 0.04355 / 2.85 ( 1579) hydrogen bonds : angle 4.91105 / 3.57 ( 4611) Misc. bond : bond 0.00198 / 0.10 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7818.82 seconds wall clock time: 135 minutes 9.43 seconds (8109.43 seconds total)