Starting phenix.real_space_refine on Fri Jul 3 15:26:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kc9_62246/07_2026/9kc9_62246.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kc9_62246/07_2026/9kc9_62246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kc9_62246/07_2026/9kc9_62246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kc9_62246/07_2026/9kc9_62246.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kc9_62246/07_2026/9kc9_62246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kc9_62246/07_2026/9kc9_62246.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.246 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 80 5.16 5 Cl 10 4.86 5 C 9840 2.51 5 N 2480 2.21 5 O 2590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15005 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2998 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 348} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 1, ' CL': 2} Chain breaks: 3 Restraints were copied for chains: E, B, C, D Time building chain proxies: 2.49, per 1000 atoms: 0.17 Number of scatterers: 15005 At special positions: 0 Unit cell: (97.44, 95.7, 113.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 Cl 10 17.00 S 80 16.00 O 2590 8.00 N 2480 7.00 C 9840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 593.6 milliseconds 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3450 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 67.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.681A pdb=" N LEU A 21 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 22 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 18 through 23' Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.135A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 71 Processing helix chain 'A' and resid 77 through 85 removed outlier: 5.037A pdb=" N GLY A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 99 removed outlier: 3.590A pdb=" N ASN A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.624A pdb=" N ILE A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 144 removed outlier: 3.742A pdb=" N ALA A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A 135 " --> pdb=" O TYR A 131 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.837A pdb=" N LEU A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 173 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.684A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.963A pdb=" N GLU A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 253 removed outlier: 3.746A pdb=" N PHE A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 4.045A pdb=" N LYS A 262 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP A 263 " --> pdb=" O PRO A 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 263' Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.781A pdb=" N ILE A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.562A pdb=" N SER A 354 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 355 " --> pdb=" O ALA A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 355' Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 18 through 23 removed outlier: 3.680A pdb=" N LEU E 21 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU E 22 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 18 through 23' Processing helix chain 'E' and resid 27 through 53 removed outlier: 5.135A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU E 37 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 Processing helix chain 'E' and resid 77 through 85 removed outlier: 5.038A pdb=" N GLY E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 99 removed outlier: 3.590A pdb=" N ASN E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.623A pdb=" N ILE E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 144 removed outlier: 3.742A pdb=" N ALA E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE E 133 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY E 135 " --> pdb=" O TYR E 131 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 removed outlier: 3.837A pdb=" N LEU E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL E 158 " --> pdb=" O LEU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 173 Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.684A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 230 removed outlier: 3.963A pdb=" N GLU E 213 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL E 214 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS E 215 " --> pdb=" O MET E 211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR E 216 " --> pdb=" O ASN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 253 removed outlier: 3.746A pdb=" N PHE E 247 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE E 248 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 4.045A pdb=" N LYS E 262 " --> pdb=" O ASN E 259 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP E 263 " --> pdb=" O PRO E 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 259 through 263' Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.782A pdb=" N ILE E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU E 279 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN E 280 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 324 Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.563A pdb=" N SER E 354 " --> pdb=" O SER E 351 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG E 355 " --> pdb=" O ALA E 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 355' Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 18 through 23 removed outlier: 3.681A pdb=" N LEU B 21 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 18 through 23' Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.136A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 71 Processing helix chain 'B' and resid 77 through 85 removed outlier: 5.037A pdb=" N GLY B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.591A pdb=" N ASN B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.624A pdb=" N ILE B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 144 removed outlier: 3.742A pdb=" N ALA B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY B 135 " --> pdb=" O TYR B 131 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.837A pdb=" N LEU B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 173 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.684A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 230 removed outlier: 3.963A pdb=" N GLU B 213 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS B 215 " --> pdb=" O MET B 211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 253 removed outlier: 3.747A pdb=" N PHE B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B 248 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 4.045A pdb=" N LYS B 262 " --> pdb=" O ASN B 259 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP B 263 " --> pdb=" O PRO B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 259 through 263' Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.781A pdb=" N ILE B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.563A pdb=" N SER B 354 " --> pdb=" O SER B 351 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 355 " --> pdb=" O ALA B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 355' Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.681A pdb=" N LEU C 21 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU C 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 18 through 23' Processing helix chain 'C' and resid 27 through 53 removed outlier: 5.135A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 71 Processing helix chain 'C' and resid 77 through 85 removed outlier: 5.037A pdb=" N GLY C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 99 removed outlier: 3.591A pdb=" N ASN C 99 " --> pdb=" O SER C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.624A pdb=" N ILE C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 144 removed outlier: 3.742A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE C 133 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.837A pdb=" N LEU C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 173 Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.684A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 230 removed outlier: 3.963A pdb=" N GLU C 213 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS C 215 " --> pdb=" O MET C 211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 253 removed outlier: 3.746A pdb=" N PHE C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE C 248 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 4.045A pdb=" N LYS C 262 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP C 263 " --> pdb=" O PRO C 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 263' Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.782A pdb=" N ILE C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.563A pdb=" N SER C 354 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG C 355 " --> pdb=" O ALA C 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 355' Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 18 through 23 removed outlier: 3.681A pdb=" N LEU D 21 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 22 " --> pdb=" O SER D 19 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS D 23 " --> pdb=" O LEU D 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 18 through 23' Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.135A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU D 37 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL D 38 " --> pdb=" O GLY D 34 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 71 Processing helix chain 'D' and resid 77 through 85 removed outlier: 5.037A pdb=" N GLY D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.590A pdb=" N ASN D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.624A pdb=" N ILE D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 144 removed outlier: 3.742A pdb=" N ALA D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE D 133 " --> pdb=" O ILE D 129 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY D 135 " --> pdb=" O TYR D 131 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.837A pdb=" N LEU D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 173 Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.685A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 230 removed outlier: 3.964A pdb=" N GLU D 213 " --> pdb=" O SER D 209 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS D 215 " --> pdb=" O MET D 211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 216 " --> pdb=" O ASN D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 253 removed outlier: 3.746A pdb=" N PHE D 247 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE D 248 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 4.045A pdb=" N LYS D 262 " --> pdb=" O ASN D 259 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP D 263 " --> pdb=" O PRO D 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 259 through 263' Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.781A pdb=" N ILE D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 279 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN D 280 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.562A pdb=" N SER D 354 " --> pdb=" O SER D 351 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG D 355 " --> pdb=" O ALA D 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 355' 710 hydrogen bonds defined for protein. 2100 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2270 1.29 - 1.42: 4510 1.42 - 1.56: 8515 1.56 - 1.69: 0 1.69 - 1.82: 135 Bond restraints: 15430 Sorted by residual: bond pdb=" C GLN B 208 " pdb=" O GLN B 208 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.32e-02 5.74e+03 3.27e+01 bond pdb=" C GLN A 208 " pdb=" O GLN A 208 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.32e-02 5.74e+03 3.26e+01 bond pdb=" C GLN D 208 " pdb=" O GLN D 208 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.32e-02 5.74e+03 3.24e+01 bond pdb=" C GLN C 208 " pdb=" O GLN C 208 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.32e-02 5.74e+03 3.22e+01 bond pdb=" C GLN E 208 " pdb=" O GLN E 208 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.32e-02 5.74e+03 3.22e+01 ... (remaining 15425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 20676 1.99 - 3.98: 289 3.98 - 5.97: 30 5.97 - 7.97: 5 7.97 - 9.96: 10 Bond angle restraints: 21010 Sorted by residual: angle pdb=" N ILE B 311 " pdb=" CA ILE B 311 " pdb=" C ILE B 311 " ideal model delta sigma weight residual 113.39 103.43 9.96 1.47e+00 4.63e-01 4.59e+01 angle pdb=" N ILE A 311 " pdb=" CA ILE A 311 " pdb=" C ILE A 311 " ideal model delta sigma weight residual 113.39 103.43 9.96 1.47e+00 4.63e-01 4.59e+01 angle pdb=" N ILE D 311 " pdb=" CA ILE D 311 " pdb=" C ILE D 311 " ideal model delta sigma weight residual 113.39 103.43 9.96 1.47e+00 4.63e-01 4.59e+01 angle pdb=" N ILE C 311 " pdb=" CA ILE C 311 " pdb=" C ILE C 311 " ideal model delta sigma weight residual 113.39 103.45 9.94 1.47e+00 4.63e-01 4.57e+01 angle pdb=" N ILE E 311 " pdb=" CA ILE E 311 " pdb=" C ILE E 311 " ideal model delta sigma weight residual 113.39 103.48 9.91 1.47e+00 4.63e-01 4.54e+01 ... (remaining 21005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 7490 17.23 - 34.47: 1085 34.47 - 51.70: 285 51.70 - 68.94: 70 68.94 - 86.17: 30 Dihedral angle restraints: 8960 sinusoidal: 3585 harmonic: 5375 Sorted by residual: dihedral pdb=" C GLN E 208 " pdb=" N GLN E 208 " pdb=" CA GLN E 208 " pdb=" CB GLN E 208 " ideal model delta harmonic sigma weight residual -122.60 -112.14 -10.46 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" C GLN B 208 " pdb=" N GLN B 208 " pdb=" CA GLN B 208 " pdb=" CB GLN B 208 " ideal model delta harmonic sigma weight residual -122.60 -112.20 -10.40 0 2.50e+00 1.60e-01 1.73e+01 dihedral pdb=" C GLN C 208 " pdb=" N GLN C 208 " pdb=" CA GLN C 208 " pdb=" CB GLN C 208 " ideal model delta harmonic sigma weight residual -122.60 -112.21 -10.39 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 8957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1702 0.039 - 0.079: 489 0.079 - 0.118: 89 0.118 - 0.157: 25 0.157 - 0.197: 5 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CA GLN E 208 " pdb=" N GLN E 208 " pdb=" C GLN E 208 " pdb=" CB GLN E 208 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA GLN C 208 " pdb=" N GLN C 208 " pdb=" C GLN C 208 " pdb=" CB GLN C 208 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" CA GLN B 208 " pdb=" N GLN B 208 " pdb=" C GLN B 208 " pdb=" CB GLN B 208 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 2307 not shown) Planarity restraints: 2615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 208 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C GLN A 208 " -0.061 2.00e-02 2.50e+03 pdb=" O GLN A 208 " 0.023 2.00e-02 2.50e+03 pdb=" N SER A 209 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 208 " -0.017 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C GLN C 208 " 0.061 2.00e-02 2.50e+03 pdb=" O GLN C 208 " -0.022 2.00e-02 2.50e+03 pdb=" N SER C 209 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 208 " -0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C GLN E 208 " 0.060 2.00e-02 2.50e+03 pdb=" O GLN E 208 " -0.022 2.00e-02 2.50e+03 pdb=" N SER E 209 " -0.021 2.00e-02 2.50e+03 ... (remaining 2612 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2799 2.77 - 3.30: 13058 3.30 - 3.84: 23694 3.84 - 4.37: 26957 4.37 - 4.90: 50387 Nonbonded interactions: 116895 Sorted by model distance: nonbonded pdb=" O ILE B 76 " pdb=" N ILE B 78 " model vdw 2.239 3.120 nonbonded pdb=" O ILE A 76 " pdb=" N ILE A 78 " model vdw 2.239 3.120 nonbonded pdb=" O ILE D 76 " pdb=" N ILE D 78 " model vdw 2.239 3.120 nonbonded pdb=" O ILE E 76 " pdb=" N ILE E 78 " model vdw 2.239 3.120 nonbonded pdb=" O ILE C 76 " pdb=" N ILE C 78 " model vdw 2.239 3.120 ... (remaining 116890 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.410 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 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 0.075 15430 Z= 0.194 Angle : 0.587 9.957 21010 Z= 0.353 Chirality : 0.039 0.197 2310 Planarity : 0.005 0.050 2615 Dihedral : 18.099 86.174 5510 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.61 % Allowed : 28.44 % Favored : 70.95 % 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: 0.26 (0.20), residues: 1815 helix: 1.17 (0.16), residues: 1085 sheet: None (None), residues: 0 loop : -1.37 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 13 TYR 0.019 0.001 TYR B 236 PHE 0.009 0.001 PHE D 276 TRP 0.011 0.001 TRP B 93 HIS 0.002 0.000 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.19 (15430) covalent geometry : angle 0.58695 / 0.35 (21010) hydrogen bonds : bond 0.08382 / 4.93 ( 710) hydrogen bonds : angle 3.95743 / 2.88 ( 2100) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 226 time to evaluate : 0.492 Fit side-chains REVERT: A 208 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8270 (tm-30) REVERT: E 13 ARG cc_start: 0.7713 (mmt90) cc_final: 0.7511 (mmt90) REVERT: E 208 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: B 25 ARG cc_start: 0.7707 (mtp85) cc_final: 0.7392 (mtp85) REVERT: B 208 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: C 208 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: C 328 ASN cc_start: 0.7874 (t0) cc_final: 0.7414 (t0) REVERT: C 363 THR cc_start: 0.9308 (t) cc_final: 0.9036 (t) REVERT: D 25 ARG cc_start: 0.7765 (mtp85) cc_final: 0.7359 (mtp85) REVERT: D 208 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: D 310 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7659 (pt) outliers start: 10 outliers final: 0 residues processed: 235 average time/residue: 0.1436 time to fit residues: 47.5229 Evaluate side-chains 229 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 223 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain D residue 208 GLN Chi-restraints excluded: chain D residue 310 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.095365 restraints weight = 16290.426| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.18 r_work: 0.2719 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 15430 Z= 0.222 Angle : 0.577 6.815 21010 Z= 0.312 Chirality : 0.041 0.175 2310 Planarity : 0.005 0.057 2615 Dihedral : 6.319 80.431 2047 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.06 % Allowed : 26.36 % Favored : 70.58 % 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: -0.14 (0.20), residues: 1815 helix: 0.81 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -1.50 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 13 TYR 0.028 0.002 TYR A 236 PHE 0.014 0.002 PHE A 283 TRP 0.015 0.002 TRP A 93 HIS 0.003 0.001 HIS D 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.22 (15430) covalent geometry : angle 0.57692 / 0.31 (21010) hydrogen bonds : bond 0.07284 / 4.70 ( 710) hydrogen bonds : angle 3.87631 / 2.80 ( 2100) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 0.539 Fit side-chains REVERT: A 51 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6566 (mtt180) REVERT: A 173 LYS cc_start: 0.7169 (mtpt) cc_final: 0.6919 (pttt) REVERT: A 208 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: E 51 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6642 (mtt180) REVERT: E 208 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: E 236 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.8405 (t80) REVERT: B 25 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7501 (mtp85) REVERT: B 51 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6736 (mtt180) REVERT: B 159 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7734 (mp) REVERT: B 173 LYS cc_start: 0.7173 (mtpt) cc_final: 0.6877 (pttt) REVERT: B 208 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8098 (tm-30) REVERT: B 310 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7899 (pt) REVERT: B 328 ASN cc_start: 0.8052 (t0) cc_final: 0.7583 (t0) REVERT: C 30 LYS cc_start: 0.8967 (tttt) cc_final: 0.8650 (tttt) REVERT: C 44 TYR cc_start: 0.7816 (m-80) cc_final: 0.7558 (m-80) REVERT: C 51 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6760 (mtt180) REVERT: C 208 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8282 (tm-30) REVERT: C 328 ASN cc_start: 0.8090 (t0) cc_final: 0.7794 (t0) REVERT: C 363 THR cc_start: 0.9350 (t) cc_final: 0.9037 (t) REVERT: D 25 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7335 (mtp85) REVERT: D 51 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6498 (mtt180) REVERT: D 208 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8244 (tm-30) REVERT: D 310 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7765 (pt) outliers start: 50 outliers final: 17 residues processed: 260 average time/residue: 0.1352 time to fit residues: 49.1818 Evaluate side-chains 246 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 208 GLN Chi-restraints excluded: chain D residue 310 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 171 optimal weight: 0.9990 chunk 161 optimal weight: 0.5980 chunk 167 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 68 optimal weight: 0.0050 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.134934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.098084 restraints weight = 16411.213| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.22 r_work: 0.2814 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15430 Z= 0.100 Angle : 0.448 6.842 21010 Z= 0.243 Chirality : 0.036 0.168 2310 Planarity : 0.004 0.052 2615 Dihedral : 5.925 74.836 2047 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.94 % Allowed : 25.69 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.20), residues: 1815 helix: 0.99 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -1.35 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 13 TYR 0.012 0.001 TYR C 97 PHE 0.008 0.001 PHE A 276 TRP 0.011 0.001 TRP D 93 HIS 0.001 0.000 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (15430) covalent geometry : angle 0.44789 / 0.24 (21010) hydrogen bonds : bond 0.04523 / 2.93 ( 710) hydrogen bonds : angle 3.81628 / 2.76 ( 2100) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 0.536 Fit side-chains REVERT: A 25 ARG cc_start: 0.7722 (mtp85) cc_final: 0.7469 (mtp85) REVERT: A 51 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6524 (mtt180) REVERT: A 208 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: E 51 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6518 (mtt180) REVERT: E 208 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8041 (tm-30) REVERT: E 236 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.8161 (t80) REVERT: E 310 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7735 (pt) REVERT: B 25 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7464 (mtp85) REVERT: B 51 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6669 (mtt180) REVERT: B 173 LYS cc_start: 0.7003 (mtpt) cc_final: 0.6779 (pttt) REVERT: B 208 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: B 310 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7681 (pt) REVERT: C 25 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7444 (mtp85) REVERT: C 208 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8304 (tm-30) REVERT: C 310 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7675 (pt) REVERT: C 328 ASN cc_start: 0.7859 (t0) cc_final: 0.7417 (t0) REVERT: D 25 ARG cc_start: 0.7772 (mtp85) cc_final: 0.7365 (mtp85) REVERT: D 208 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: D 310 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7683 (pt) outliers start: 48 outliers final: 24 residues processed: 264 average time/residue: 0.1439 time to fit residues: 52.6378 Evaluate side-chains 250 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 208 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 322 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 175 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.097256 restraints weight = 16362.830| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.19 r_work: 0.2748 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15430 Z= 0.170 Angle : 0.509 6.866 21010 Z= 0.274 Chirality : 0.039 0.167 2310 Planarity : 0.005 0.057 2615 Dihedral : 5.893 74.280 2047 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.67 % Allowed : 25.93 % Favored : 70.40 % 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: 0.02 (0.20), residues: 1815 helix: 0.93 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -1.43 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 13 TYR 0.023 0.002 TYR A 236 PHE 0.011 0.001 PHE B 283 TRP 0.013 0.001 TRP C 93 HIS 0.002 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (15430) covalent geometry : angle 0.50902 / 0.27 (21010) hydrogen bonds : bond 0.06224 / 4.03 ( 710) hydrogen bonds : angle 3.81489 / 2.75 ( 2100) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 220 time to evaluate : 0.563 Fit side-chains REVERT: A 25 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7490 (mtp85) REVERT: A 51 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6633 (mtt180) REVERT: A 208 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: E 25 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7319 (mtp85) REVERT: E 208 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8238 (tm-30) REVERT: E 236 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.8369 (t80) REVERT: E 310 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7914 (pt) REVERT: B 25 ARG cc_start: 0.7980 (mtp85) cc_final: 0.7490 (mtp85) REVERT: B 51 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6760 (mtt180) REVERT: B 159 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7725 (mp) REVERT: B 208 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: B 310 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7891 (pt) REVERT: C 25 ARG cc_start: 0.7920 (mtp85) cc_final: 0.7434 (mtp85) REVERT: C 30 LYS cc_start: 0.8948 (tttt) cc_final: 0.8672 (ttpt) REVERT: C 44 TYR cc_start: 0.7766 (m-80) cc_final: 0.7489 (m-80) REVERT: C 208 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8412 (tm-30) REVERT: C 310 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7892 (pt) REVERT: C 328 ASN cc_start: 0.7983 (t0) cc_final: 0.7726 (t0) REVERT: C 363 THR cc_start: 0.9312 (t) cc_final: 0.9007 (t) REVERT: D 25 ARG cc_start: 0.7837 (mtp85) cc_final: 0.7333 (mtp85) REVERT: D 208 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8252 (tm-30) REVERT: D 310 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7804 (pt) outliers start: 60 outliers final: 39 residues processed: 272 average time/residue: 0.1414 time to fit residues: 54.2688 Evaluate side-chains 272 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 208 GLN Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 322 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 96 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 159 optimal weight: 0.1980 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.136068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.099401 restraints weight = 16221.722| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.18 r_work: 0.2780 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15430 Z= 0.123 Angle : 0.465 6.977 21010 Z= 0.251 Chirality : 0.037 0.160 2310 Planarity : 0.004 0.056 2615 Dihedral : 5.682 71.492 2047 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.30 % Allowed : 26.12 % Favored : 70.58 % 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: 0.06 (0.20), residues: 1815 helix: 0.95 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -1.41 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 13 TYR 0.016 0.001 TYR E 236 PHE 0.008 0.001 PHE D 276 TRP 0.013 0.001 TRP C 93 HIS 0.001 0.000 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (15430) covalent geometry : angle 0.46521 / 0.25 (21010) hydrogen bonds : bond 0.05214 / 3.38 ( 710) hydrogen bonds : angle 3.80209 / 2.73 ( 2100) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 221 time to evaluate : 0.491 Fit side-chains REVERT: A 25 ARG cc_start: 0.7805 (mtp85) cc_final: 0.7465 (mtp85) REVERT: A 51 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6615 (mtt180) REVERT: A 208 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8051 (tm-30) REVERT: E 25 ARG cc_start: 0.7754 (mtm110) cc_final: 0.7276 (mtp85) REVERT: E 236 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.8273 (t80) REVERT: E 310 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7885 (pt) REVERT: B 25 ARG cc_start: 0.7940 (mtp85) cc_final: 0.7452 (mtp85) REVERT: B 51 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6727 (mtt180) REVERT: B 159 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7721 (mp) REVERT: B 310 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7868 (pt) REVERT: C 25 ARG cc_start: 0.7928 (mtp85) cc_final: 0.7423 (mtp85) REVERT: C 30 LYS cc_start: 0.8901 (tttt) cc_final: 0.8617 (ttpt) REVERT: C 310 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7899 (pt) REVERT: C 328 ASN cc_start: 0.7946 (t0) cc_final: 0.7320 (t0) REVERT: C 363 THR cc_start: 0.9286 (t) cc_final: 0.8985 (t) REVERT: D 25 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7296 (mtp85) REVERT: D 282 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7718 (mp) outliers start: 54 outliers final: 41 residues processed: 269 average time/residue: 0.1323 time to fit residues: 50.5836 Evaluate side-chains 267 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 217 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 130 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 170 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 167 optimal weight: 0.0980 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 171 optimal weight: 0.0270 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.135131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.098634 restraints weight = 16283.499| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.18 r_work: 0.2809 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15430 Z= 0.102 Angle : 0.439 7.778 21010 Z= 0.236 Chirality : 0.036 0.143 2310 Planarity : 0.004 0.055 2615 Dihedral : 4.197 66.653 2033 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.91 % Allowed : 25.87 % Favored : 70.21 % 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: 0.18 (0.20), residues: 1815 helix: 0.99 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.34 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 13 TYR 0.013 0.001 TYR E 236 PHE 0.008 0.001 PHE E 276 TRP 0.012 0.001 TRP C 93 HIS 0.001 0.000 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (15430) covalent geometry : angle 0.43940 / 0.24 (21010) hydrogen bonds : bond 0.04504 / 2.93 ( 710) hydrogen bonds : angle 3.74294 / 2.68 ( 2100) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 219 time to evaluate : 0.546 Fit side-chains REVERT: A 25 ARG cc_start: 0.7739 (mtp85) cc_final: 0.7432 (mtp85) REVERT: A 51 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6627 (mtt180) REVERT: A 208 GLN cc_start: 0.8744 (tm130) cc_final: 0.8327 (tm-30) REVERT: E 25 ARG cc_start: 0.7722 (mtm110) cc_final: 0.7279 (mtp85) REVERT: E 208 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: E 236 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.8219 (t80) REVERT: E 310 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7986 (pt) REVERT: B 25 ARG cc_start: 0.7916 (mtp85) cc_final: 0.7466 (mtp85) REVERT: B 51 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6736 (mtt180) REVERT: B 208 GLN cc_start: 0.8829 (tm130) cc_final: 0.8137 (tm-30) REVERT: C 13 ARG cc_start: 0.7595 (mmt90) cc_final: 0.7378 (mmt90) REVERT: C 25 ARG cc_start: 0.7898 (mtp85) cc_final: 0.7438 (mtp85) REVERT: C 30 LYS cc_start: 0.8926 (tttt) cc_final: 0.8628 (ttpt) REVERT: C 282 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7429 (mp) REVERT: C 310 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7929 (pt) REVERT: C 328 ASN cc_start: 0.7901 (t0) cc_final: 0.7283 (t0) REVERT: D 25 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7346 (mtp85) REVERT: D 269 MET cc_start: 0.8165 (ttt) cc_final: 0.7714 (ttt) REVERT: D 282 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7592 (mp) outliers start: 64 outliers final: 46 residues processed: 279 average time/residue: 0.1319 time to fit residues: 52.0931 Evaluate side-chains 270 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 129 optimal weight: 3.9990 chunk 99 optimal weight: 0.0870 chunk 67 optimal weight: 5.9990 chunk 171 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.097926 restraints weight = 16204.134| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.14 r_work: 0.2754 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15430 Z= 0.155 Angle : 0.500 9.460 21010 Z= 0.267 Chirality : 0.038 0.154 2310 Planarity : 0.005 0.057 2615 Dihedral : 3.937 16.902 2030 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.55 % Allowed : 26.30 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.20), residues: 1815 helix: 0.94 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.41 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 13 TYR 0.020 0.001 TYR E 236 PHE 0.009 0.001 PHE A 283 TRP 0.013 0.001 TRP A 93 HIS 0.002 0.000 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (15430) covalent geometry : angle 0.50014 / 0.27 (21010) hydrogen bonds : bond 0.05827 / 3.78 ( 710) hydrogen bonds : angle 3.78598 / 2.72 ( 2100) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 217 time to evaluate : 0.538 Fit side-chains REVERT: A 25 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7486 (mtp85) REVERT: A 51 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6642 (mtt180) REVERT: A 208 GLN cc_start: 0.8753 (tm130) cc_final: 0.8088 (tm-30) REVERT: E 25 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7315 (mtp85) REVERT: E 208 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: E 236 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.8320 (t80) REVERT: B 25 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7515 (mtp85) REVERT: B 51 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6761 (mtt180) REVERT: B 159 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7773 (mp) REVERT: C 13 ARG cc_start: 0.7603 (mmt90) cc_final: 0.7249 (mmt90) REVERT: C 25 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7413 (mtp85) REVERT: C 282 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7509 (mp) REVERT: C 328 ASN cc_start: 0.7988 (t0) cc_final: 0.7350 (t0) REVERT: C 363 THR cc_start: 0.9286 (t) cc_final: 0.8992 (t) REVERT: D 25 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7372 (mtp85) REVERT: D 269 MET cc_start: 0.8282 (ttt) cc_final: 0.7859 (ttt) REVERT: D 282 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7706 (mp) outliers start: 58 outliers final: 47 residues processed: 268 average time/residue: 0.1393 time to fit residues: 53.1219 Evaluate side-chains 274 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 171 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.097995 restraints weight = 16277.051| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.15 r_work: 0.2754 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15430 Z= 0.145 Angle : 0.495 10.887 21010 Z= 0.263 Chirality : 0.038 0.151 2310 Planarity : 0.005 0.057 2615 Dihedral : 3.966 15.883 2030 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.91 % Allowed : 25.87 % Favored : 70.21 % 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: 0.10 (0.20), residues: 1815 helix: 1.01 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -1.44 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 13 TYR 0.018 0.001 TYR E 236 PHE 0.008 0.001 PHE A 283 TRP 0.013 0.001 TRP A 93 HIS 0.002 0.000 HIS D 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (15430) covalent geometry : angle 0.49500 / 0.26 (21010) hydrogen bonds : bond 0.05664 / 3.67 ( 710) hydrogen bonds : angle 3.79102 / 2.72 ( 2100) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 216 time to evaluate : 0.530 Fit side-chains REVERT: A 25 ARG cc_start: 0.7836 (mtp85) cc_final: 0.7481 (mtp85) REVERT: A 51 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6662 (mtt180) REVERT: A 208 GLN cc_start: 0.8746 (tm130) cc_final: 0.8076 (tm-30) REVERT: E 25 ARG cc_start: 0.7780 (mtm110) cc_final: 0.7324 (mtp85) REVERT: E 208 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8214 (tm-30) REVERT: E 236 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8304 (t80) REVERT: B 14 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8525 (tt) REVERT: B 25 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7504 (mtp85) REVERT: B 51 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6745 (mtt180) REVERT: B 159 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7774 (mp) REVERT: C 25 ARG cc_start: 0.7916 (mtp85) cc_final: 0.7415 (mtp85) REVERT: C 30 LYS cc_start: 0.8991 (tttt) cc_final: 0.8723 (ttpt) REVERT: C 49 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6374 (tt) REVERT: C 328 ASN cc_start: 0.7987 (t0) cc_final: 0.7359 (t0) REVERT: C 363 THR cc_start: 0.9280 (t) cc_final: 0.8983 (t) REVERT: D 25 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7356 (mtp85) REVERT: D 269 MET cc_start: 0.8281 (ttt) cc_final: 0.7874 (ttt) REVERT: D 282 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7723 (mp) outliers start: 64 outliers final: 54 residues processed: 271 average time/residue: 0.1353 time to fit residues: 52.0875 Evaluate side-chains 271 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 115 optimal weight: 0.3980 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 35 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.097548 restraints weight = 16233.572| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.14 r_work: 0.2748 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15430 Z= 0.149 Angle : 0.507 11.466 21010 Z= 0.267 Chirality : 0.038 0.150 2310 Planarity : 0.005 0.057 2615 Dihedral : 3.975 15.391 2030 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.10 % Allowed : 25.81 % Favored : 70.09 % 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: 0.10 (0.20), residues: 1815 helix: 1.02 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -1.45 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 13 TYR 0.019 0.001 TYR E 236 PHE 0.009 0.001 PHE A 283 TRP 0.013 0.001 TRP A 93 HIS 0.002 0.000 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (15430) covalent geometry : angle 0.50672 / 0.27 (21010) hydrogen bonds : bond 0.05801 / 3.76 ( 710) hydrogen bonds : angle 3.79843 / 2.72 ( 2100) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 216 time to evaluate : 0.565 Fit side-chains REVERT: A 25 ARG cc_start: 0.7836 (mtp85) cc_final: 0.7483 (mtp85) REVERT: A 51 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6665 (mtt180) REVERT: A 208 GLN cc_start: 0.8764 (tm130) cc_final: 0.8334 (tm-30) REVERT: E 25 ARG cc_start: 0.7787 (mtm110) cc_final: 0.7329 (mtp85) REVERT: E 208 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: E 236 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8320 (t80) REVERT: B 14 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8528 (tt) REVERT: B 25 ARG cc_start: 0.7997 (mtp85) cc_final: 0.7510 (mtp85) REVERT: B 51 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6778 (mtt180) REVERT: B 159 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7774 (mp) REVERT: B 328 ASN cc_start: 0.7987 (t0) cc_final: 0.7568 (t0) REVERT: C 25 ARG cc_start: 0.7934 (mtp85) cc_final: 0.7420 (mtp85) REVERT: C 30 LYS cc_start: 0.9006 (tttt) cc_final: 0.8712 (tttt) REVERT: C 328 ASN cc_start: 0.7991 (t0) cc_final: 0.7364 (t0) REVERT: C 363 THR cc_start: 0.9282 (t) cc_final: 0.8988 (t) REVERT: D 13 ARG cc_start: 0.7584 (mmt90) cc_final: 0.7379 (mmt90) REVERT: D 25 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7352 (mtp85) REVERT: D 49 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6424 (tt) REVERT: D 269 MET cc_start: 0.8271 (ttt) cc_final: 0.7846 (ttt) REVERT: D 282 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7740 (mp) outliers start: 67 outliers final: 58 residues processed: 273 average time/residue: 0.1316 time to fit residues: 51.4282 Evaluate side-chains 279 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 213 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 133 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.100876 restraints weight = 16316.248| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.13 r_work: 0.2797 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15430 Z= 0.109 Angle : 0.468 11.966 21010 Z= 0.245 Chirality : 0.036 0.140 2310 Planarity : 0.004 0.055 2615 Dihedral : 3.844 14.554 2030 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.55 % Allowed : 26.42 % Favored : 70.03 % 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: 0.22 (0.20), residues: 1815 helix: 1.05 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.39 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 13 TYR 0.014 0.001 TYR E 236 PHE 0.008 0.001 PHE A 276 TRP 0.013 0.001 TRP C 93 HIS 0.001 0.000 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (15430) covalent geometry : angle 0.46805 / 0.24 (21010) hydrogen bonds : bond 0.04726 / 3.07 ( 710) hydrogen bonds : angle 3.74957 / 2.68 ( 2100) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 0.421 Fit side-chains REVERT: A 25 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7494 (mtp85) REVERT: A 51 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6624 (mtt180) REVERT: A 208 GLN cc_start: 0.8795 (tm130) cc_final: 0.8360 (tm-30) REVERT: E 25 ARG cc_start: 0.7749 (mtm110) cc_final: 0.7320 (mtp85) REVERT: E 208 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: E 236 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8240 (t80) REVERT: B 14 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8556 (tt) REVERT: B 25 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7516 (mtp85) REVERT: B 51 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6753 (mtt180) REVERT: C 25 ARG cc_start: 0.7916 (mtp85) cc_final: 0.7422 (mtp85) REVERT: C 30 LYS cc_start: 0.9006 (tttt) cc_final: 0.8721 (tttt) REVERT: C 49 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6346 (tt) REVERT: C 328 ASN cc_start: 0.7879 (t0) cc_final: 0.7292 (t0) REVERT: D 13 ARG cc_start: 0.7643 (mmt90) cc_final: 0.7442 (mmt90) REVERT: D 25 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7351 (mtp85) REVERT: D 49 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6425 (tt) REVERT: D 269 MET cc_start: 0.8240 (ttt) cc_final: 0.7791 (ttt) REVERT: D 282 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7678 (mp) outliers start: 58 outliers final: 50 residues processed: 266 average time/residue: 0.1249 time to fit residues: 47.2182 Evaluate side-chains 265 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 207 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 102 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 99 optimal weight: 0.0970 chunk 84 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 89 optimal weight: 0.0270 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.139604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.103487 restraints weight = 16260.820| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.17 r_work: 0.2866 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15430 Z= 0.088 Angle : 0.438 11.803 21010 Z= 0.226 Chirality : 0.035 0.145 2310 Planarity : 0.004 0.053 2615 Dihedral : 3.613 14.840 2030 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.06 % Allowed : 26.79 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1815 helix: 1.21 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.24 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 13 TYR 0.011 0.001 TYR C 33 PHE 0.007 0.001 PHE E 276 TRP 0.012 0.001 TRP A 93 HIS 0.003 0.000 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (15430) covalent geometry : angle 0.43845 / 0.23 (21010) hydrogen bonds : bond 0.03674 / 2.39 ( 710) hydrogen bonds : angle 3.66960 / 2.61 ( 2100) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3245.53 seconds wall clock time: 56 minutes 25.20 seconds (3385.20 seconds total)