Starting phenix.real_space_refine on Fri May 16 19:58:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kc9_62246/05_2025/9kc9_62246.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kc9_62246/05_2025/9kc9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9kc9_62246/05_2025/9kc9_62246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kc9_62246/05_2025/9kc9_62246.map" model { file = "/net/cci-nas-00/data/ceres_data/9kc9_62246/05_2025/9kc9_62246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kc9_62246/05_2025/9kc9_62246.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: C, B, E, D Time building chain proxies: 6.83, per 1000 atoms: 0.46 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: 3.37 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.18 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: 3.66 Time building geometry restraints manager: 3.98 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' 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: 1.350 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 29.670 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP B 93 HIS 0.002 0.000 HIS B 165 PHE 0.009 0.001 PHE D 276 TYR 0.019 0.001 TYR B 236 ARG 0.007 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.08382 ( 710) hydrogen bonds : angle 3.95743 ( 2100) covalent geometry : bond 0.00332 (15430) covalent geometry : angle 0.58695 (21010) *********************** 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 : 1.619 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: 0.3222 time to fit residues: 105.8615 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 : 1.768 ------------------------------------------------------------------------------- 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 151 optimal weight: 0.4980 chunk 136 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.133831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.096913 restraints weight = 16251.539| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.21 r_work: 0.2790 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0476 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= 0.128 Angle : 0.479 6.420 21010 Z= 0.259 Chirality : 0.037 0.161 2310 Planarity : 0.004 0.052 2615 Dihedral : 6.106 77.947 2047 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.51 % Allowed : 26.85 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1815 helix: 1.05 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -1.42 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 93 HIS 0.001 0.000 HIS C 178 PHE 0.010 0.001 PHE C 283 TYR 0.018 0.001 TYR A 236 ARG 0.006 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.05387 ( 710) hydrogen bonds : angle 3.72791 ( 2100) covalent geometry : bond 0.00299 (15430) covalent geometry : angle 0.47868 (21010) *********************** 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 267 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 1.527 Fit side-chains REVERT: A 25 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7383 (mtp85) REVERT: A 51 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.6394 (mtt180) REVERT: A 208 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: A 310 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7824 (pt) REVERT: E 51 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6505 (mtt180) REVERT: E 208 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: E 236 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8277 (t80) REVERT: B 25 ARG cc_start: 0.7936 (mtp85) cc_final: 0.7462 (mtp85) REVERT: B 51 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6669 (mtt180) REVERT: B 173 LYS cc_start: 0.7073 (mtpt) cc_final: 0.6778 (pttt) REVERT: B 208 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: B 310 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7799 (pt) REVERT: C 30 LYS cc_start: 0.8864 (tttt) cc_final: 0.8578 (tttt) REVERT: C 208 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: C 328 ASN cc_start: 0.7970 (t0) cc_final: 0.7295 (t0) REVERT: C 363 THR cc_start: 0.9317 (t) cc_final: 0.9020 (t) REVERT: D 25 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7270 (mtp85) REVERT: D 30 LYS cc_start: 0.8836 (tttt) cc_final: 0.8622 (ttpt) REVERT: D 51 ARG cc_start: 0.6747 (OUTLIER) cc_final: 0.6411 (mtt180) REVERT: D 208 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: D 310 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7705 (pt) outliers start: 41 outliers final: 11 residues processed: 266 average time/residue: 0.3212 time to fit residues: 118.1680 Evaluate side-chains 244 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 310 ILE 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 B residue 51 ARG Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 310 ILE 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 90 VAL Chi-restraints excluded: chain D residue 208 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 354 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 117 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.130760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.093557 restraints weight = 16385.408| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.20 r_work: 0.2720 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15430 Z= 0.195 Angle : 0.547 6.793 21010 Z= 0.295 Chirality : 0.040 0.160 2310 Planarity : 0.005 0.058 2615 Dihedral : 6.137 77.425 2047 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.85 % Allowed : 26.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1815 helix: 0.86 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -1.55 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 93 HIS 0.002 0.001 HIS C 178 PHE 0.013 0.002 PHE A 283 TYR 0.024 0.002 TYR E 236 ARG 0.004 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.06937 ( 710) hydrogen bonds : angle 3.88690 ( 2100) covalent geometry : bond 0.00478 (15430) covalent geometry : angle 0.54663 (21010) *********************** 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 278 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 1.559 Fit side-chains REVERT: A 25 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7477 (mtp85) REVERT: A 51 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6652 (mtt180) REVERT: A 208 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: A 310 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7939 (pt) REVERT: E 208 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: E 236 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.8382 (t80) REVERT: E 310 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7911 (pt) REVERT: B 25 ARG cc_start: 0.8052 (mtp85) cc_final: 0.7516 (mtp85) REVERT: B 51 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6762 (mtt180) REVERT: B 159 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7753 (mp) REVERT: B 173 LYS cc_start: 0.7103 (mtpt) cc_final: 0.6858 (pttt) REVERT: B 208 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8102 (tm-30) REVERT: B 310 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7946 (pt) REVERT: C 44 TYR cc_start: 0.7789 (m-80) cc_final: 0.7530 (m-80) REVERT: C 208 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8414 (tm-30) REVERT: C 310 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7892 (pt) REVERT: C 328 ASN cc_start: 0.8045 (t0) cc_final: 0.7753 (t0) REVERT: C 363 THR cc_start: 0.9331 (t) cc_final: 0.9026 (t) REVERT: D 25 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7375 (mtp85) REVERT: D 51 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6525 (mtt180) REVERT: D 208 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8259 (tm-30) REVERT: D 310 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7836 (pt) outliers start: 63 outliers final: 38 residues processed: 269 average time/residue: 0.3140 time to fit residues: 117.9911 Evaluate side-chains 261 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 208 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 310 ILE 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 90 VAL 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 16 SER 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 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 90 VAL 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 C residue 332 MET Chi-restraints excluded: chain D residue 28 ILE 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 136 GLN Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 208 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 76 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 176 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.132008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.095131 restraints weight = 16284.942| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.19 r_work: 0.2762 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.0825 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= 0.132 Angle : 0.482 8.254 21010 Z= 0.261 Chirality : 0.037 0.151 2310 Planarity : 0.005 0.056 2615 Dihedral : 5.885 73.010 2047 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.12 % Allowed : 26.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1815 helix: 0.92 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -1.50 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 93 HIS 0.001 0.000 HIS C 178 PHE 0.008 0.001 PHE A 283 TYR 0.017 0.001 TYR E 236 ARG 0.005 0.000 ARG D 13 Details of bonding type rmsd hydrogen bonds : bond 0.05533 ( 710) hydrogen bonds : angle 3.82182 ( 2100) covalent geometry : bond 0.00312 (15430) covalent geometry : angle 0.48167 (21010) *********************** 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 275 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 224 time to evaluate : 1.886 Fit side-chains REVERT: A 51 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6627 (mtt180) REVERT: A 208 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: A 310 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7894 (pt) REVERT: E 25 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7278 (mtp85) REVERT: E 208 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: E 236 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8306 (t80) REVERT: E 310 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7878 (pt) REVERT: B 25 ARG cc_start: 0.7995 (mtp85) cc_final: 0.7459 (mtp85) REVERT: B 51 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6709 (mtt180) REVERT: B 159 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7714 (mp) REVERT: B 208 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: B 310 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7870 (pt) REVERT: C 25 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7434 (mtp85) REVERT: C 30 LYS cc_start: 0.8907 (tttt) cc_final: 0.8631 (ttpt) REVERT: C 44 TYR cc_start: 0.7754 (m-80) cc_final: 0.7485 (m-80) REVERT: C 208 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8397 (tm-30) REVERT: C 310 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7881 (pt) REVERT: C 328 ASN cc_start: 0.7932 (t0) cc_final: 0.7293 (t0) REVERT: C 363 THR cc_start: 0.9297 (t) cc_final: 0.8999 (t) REVERT: D 25 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7338 (mtp85) REVERT: D 51 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6486 (mtt180) REVERT: D 208 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8228 (tm-30) outliers start: 51 outliers final: 34 residues processed: 267 average time/residue: 0.3267 time to fit residues: 123.0728 Evaluate side-chains 266 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 236 TYR Chi-restraints excluded: chain A residue 310 ILE 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 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 E residue 354 SER 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 159 LEU 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 90 VAL 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 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 51 ARG Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 208 GLN Chi-restraints excluded: chain D residue 236 TYR 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 140 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 35 optimal weight: 0.3980 chunk 110 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.099876 restraints weight = 16444.294| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.16 r_work: 0.2758 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.0887 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= 0.135 Angle : 0.480 7.952 21010 Z= 0.259 Chirality : 0.037 0.163 2310 Planarity : 0.005 0.057 2615 Dihedral : 5.682 70.813 2045 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.04 % Allowed : 26.12 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.20), residues: 1815 helix: 0.96 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -1.52 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.002 0.000 HIS D 178 PHE 0.010 0.001 PHE E 283 TYR 0.018 0.001 TYR E 236 ARG 0.006 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.05586 ( 710) hydrogen bonds : angle 3.81082 ( 2100) covalent geometry : bond 0.00322 (15430) covalent geometry : angle 0.48032 (21010) *********************** 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 290 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 224 time to evaluate : 1.608 Fit side-chains REVERT: A 25 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7480 (mtp85) REVERT: A 51 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6614 (mtt180) REVERT: A 208 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: A 310 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7991 (pt) REVERT: E 25 ARG cc_start: 0.7797 (mtm110) cc_final: 0.7318 (mtp85) REVERT: E 236 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.8297 (t80) REVERT: E 310 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7933 (pt) REVERT: B 25 ARG cc_start: 0.7997 (mtp85) cc_final: 0.7479 (mtp85) REVERT: B 51 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6767 (mtt180) REVERT: B 159 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7760 (mp) REVERT: B 208 GLN cc_start: 0.8811 (tm130) cc_final: 0.8140 (tm-30) REVERT: B 310 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7897 (pt) REVERT: C 25 ARG cc_start: 0.7952 (mtp85) cc_final: 0.7457 (mtp85) REVERT: C 30 LYS cc_start: 0.8949 (tttt) cc_final: 0.8656 (tttt) REVERT: C 282 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7558 (mp) REVERT: C 310 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7958 (pt) REVERT: C 328 ASN cc_start: 0.7977 (t0) cc_final: 0.7729 (t0) REVERT: C 363 THR cc_start: 0.9293 (t) cc_final: 0.8995 (t) REVERT: D 13 ARG cc_start: 0.7642 (mmt90) cc_final: 0.7438 (mmt90) REVERT: D 25 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7332 (mtp85) REVERT: D 269 MET cc_start: 0.8320 (ttt) cc_final: 0.7860 (ttt) REVERT: D 282 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7746 (mp) REVERT: D 310 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7869 (pt) outliers start: 66 outliers final: 49 residues processed: 283 average time/residue: 0.3010 time to fit residues: 120.0281 Evaluate side-chains 277 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 216 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 159 LEU 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 310 ILE 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 90 VAL 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 E residue 354 SER 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 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 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 136 GLN 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 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 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 310 ILE 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 62 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.097340 restraints weight = 16306.973| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.17 r_work: 0.2791 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.0904 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= 0.108 Angle : 0.451 8.494 21010 Z= 0.242 Chirality : 0.036 0.146 2310 Planarity : 0.004 0.055 2615 Dihedral : 4.278 66.074 2033 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.98 % Allowed : 26.06 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1815 helix: 0.99 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -1.46 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 93 HIS 0.001 0.000 HIS C 357 PHE 0.008 0.001 PHE E 276 TYR 0.014 0.001 TYR E 236 ARG 0.006 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 710) hydrogen bonds : angle 3.76710 ( 2100) covalent geometry : bond 0.00250 (15430) covalent geometry : angle 0.45093 (21010) *********************** 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 279 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 214 time to evaluate : 1.522 Fit side-chains REVERT: A 25 ARG cc_start: 0.7805 (mtp85) cc_final: 0.7449 (mtp85) REVERT: A 51 ARG cc_start: 0.6872 (OUTLIER) cc_final: 0.6559 (mtt180) REVERT: A 208 GLN cc_start: 0.8755 (tm130) cc_final: 0.8092 (tm-30) REVERT: E 25 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7302 (mtp85) REVERT: E 236 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.8243 (t80) REVERT: E 310 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7965 (pt) REVERT: B 25 ARG cc_start: 0.7990 (mtp85) cc_final: 0.7486 (mtp85) REVERT: B 51 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6720 (mtt180) REVERT: B 310 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7879 (pt) REVERT: C 25 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7440 (mtp85) REVERT: C 30 LYS cc_start: 0.8925 (tttt) cc_final: 0.8630 (tttt) REVERT: C 328 ASN cc_start: 0.7930 (t0) cc_final: 0.7299 (t0) REVERT: D 25 ARG cc_start: 0.7823 (mtp85) cc_final: 0.7325 (mtp85) REVERT: D 269 MET cc_start: 0.8273 (ttt) cc_final: 0.7788 (ttt) REVERT: D 310 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7896 (pt) outliers start: 65 outliers final: 49 residues processed: 276 average time/residue: 0.3128 time to fit residues: 121.3218 Evaluate side-chains 269 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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 90 VAL 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 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 E residue 354 SER 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 153 THR 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 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 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 71 SER Chi-restraints excluded: chain D residue 90 VAL 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 310 ILE 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 136 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.136495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.100480 restraints weight = 16396.021| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.14 r_work: 0.2789 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0968 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= 0.115 Angle : 0.463 8.598 21010 Z= 0.246 Chirality : 0.036 0.152 2310 Planarity : 0.004 0.056 2615 Dihedral : 3.839 15.301 2030 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.73 % Allowed : 25.99 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1815 helix: 1.02 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.44 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 93 HIS 0.001 0.000 HIS C 178 PHE 0.008 0.001 PHE E 283 TYR 0.016 0.001 TYR E 236 ARG 0.006 0.000 ARG D 13 Details of bonding type rmsd hydrogen bonds : bond 0.04982 ( 710) hydrogen bonds : angle 3.74177 ( 2100) covalent geometry : bond 0.00270 (15430) covalent geometry : angle 0.46300 (21010) *********************** 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 277 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 216 time to evaluate : 1.716 Fit side-chains REVERT: A 25 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7474 (mtp85) REVERT: A 51 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6655 (mtt180) REVERT: A 208 GLN cc_start: 0.8739 (tm130) cc_final: 0.8071 (tm-30) REVERT: E 25 ARG cc_start: 0.7776 (mtm110) cc_final: 0.7330 (mtp85) REVERT: E 208 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8223 (tm-30) REVERT: E 236 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.8247 (t80) REVERT: B 25 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7510 (mtp85) REVERT: B 51 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6733 (mtt180) REVERT: C 25 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7430 (mtp85) REVERT: C 282 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7499 (mp) REVERT: C 328 ASN cc_start: 0.7943 (t0) cc_final: 0.7315 (t0) REVERT: D 25 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7363 (mtp85) REVERT: D 269 MET cc_start: 0.8218 (ttt) cc_final: 0.7756 (ttt) REVERT: D 282 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7666 (mp) outliers start: 61 outliers final: 47 residues processed: 272 average time/residue: 0.3084 time to fit residues: 117.8018 Evaluate side-chains 267 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 214 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 67 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 90 VAL 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 354 SER 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 231 SER Chi-restraints excluded: chain B residue 236 TYR 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 129 ILE Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 211 MET 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 71 SER Chi-restraints excluded: chain D residue 90 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 83 optimal weight: 2.9990 chunk 144 optimal weight: 0.0470 chunk 161 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 177 optimal weight: 0.0000 chunk 87 optimal weight: 0.6980 chunk 134 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 101 optimal weight: 0.0980 overall best weight: 0.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN B 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.137804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.101649 restraints weight = 16324.490| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.18 r_work: 0.2854 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15430 Z= 0.087 Angle : 0.428 9.477 21010 Z= 0.227 Chirality : 0.035 0.140 2310 Planarity : 0.004 0.053 2615 Dihedral : 3.674 14.415 2030 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.87 % Allowed : 27.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.20), residues: 1815 helix: 1.17 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.32 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 93 HIS 0.001 0.000 HIS A 326 PHE 0.008 0.001 PHE A 276 TYR 0.010 0.001 TYR C 196 ARG 0.006 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 710) hydrogen bonds : angle 3.68898 ( 2100) covalent geometry : bond 0.00196 (15430) covalent geometry : angle 0.42849 (21010) *********************** 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 256 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 1.734 Fit side-chains REVERT: A 25 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7463 (mtp85) REVERT: A 49 LEU cc_start: 0.6535 (OUTLIER) cc_final: 0.6289 (tt) REVERT: A 51 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6616 (mtt180) REVERT: A 208 GLN cc_start: 0.8705 (tm130) cc_final: 0.8284 (tm-30) REVERT: E 25 ARG cc_start: 0.7718 (mtm110) cc_final: 0.7295 (mtp85) REVERT: E 51 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6514 (mtt180) REVERT: E 211 MET cc_start: 0.8439 (mtp) cc_final: 0.8138 (mmm) REVERT: B 25 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7506 (mtp85) REVERT: B 49 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6343 (tt) REVERT: B 51 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6683 (mtt180) REVERT: C 25 ARG cc_start: 0.7874 (mtp85) cc_final: 0.7448 (mtp85) REVERT: C 30 LYS cc_start: 0.8884 (tttt) cc_final: 0.8672 (ttpt) REVERT: C 49 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6347 (tt) REVERT: C 328 ASN cc_start: 0.7827 (t0) cc_final: 0.7238 (t0) REVERT: D 25 ARG cc_start: 0.7718 (mtp85) cc_final: 0.7299 (mtp85) REVERT: D 49 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6344 (tt) REVERT: D 269 MET cc_start: 0.8192 (ttt) cc_final: 0.7670 (ttt) REVERT: D 282 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7490 (mp) outliers start: 47 outliers final: 32 residues processed: 255 average time/residue: 0.3287 time to fit residues: 116.0518 Evaluate side-chains 248 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 67 LEU 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 51 ARG Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 78 ILE 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 236 TYR Chi-restraints excluded: chain C residue 322 VAL 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 78 ILE Chi-restraints excluded: chain D residue 153 THR 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 71 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 0.0980 chunk 91 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.135981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099551 restraints weight = 16294.173| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.17 r_work: 0.2836 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15430 Z= 0.095 Angle : 0.442 11.545 21010 Z= 0.231 Chirality : 0.035 0.140 2310 Planarity : 0.004 0.055 2615 Dihedral : 3.593 13.720 2030 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.45 % Allowed : 27.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1815 helix: 1.24 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.28 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 93 HIS 0.001 0.000 HIS B 357 PHE 0.008 0.001 PHE A 276 TYR 0.010 0.001 TYR C 196 ARG 0.006 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 710) hydrogen bonds : angle 3.63548 ( 2100) covalent geometry : bond 0.00219 (15430) covalent geometry : angle 0.44172 (21010) *********************** 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 248 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 1.787 Fit side-chains REVERT: A 25 ARG cc_start: 0.7718 (mtp85) cc_final: 0.7447 (mtp85) REVERT: A 51 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6657 (mtt180) REVERT: A 208 GLN cc_start: 0.8746 (tm130) cc_final: 0.8324 (tm-30) REVERT: E 25 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7282 (mtp85) REVERT: E 208 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: E 211 MET cc_start: 0.8443 (mtp) cc_final: 0.8160 (mmm) REVERT: B 14 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8531 (tt) REVERT: B 25 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7504 (mtp85) REVERT: B 51 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6711 (mtt180) REVERT: C 13 ARG cc_start: 0.7672 (mmt90) cc_final: 0.7367 (mmt90) REVERT: C 25 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7404 (mtp85) REVERT: C 30 LYS cc_start: 0.8889 (tttt) cc_final: 0.8645 (ttpt) REVERT: C 49 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6357 (tt) REVERT: C 328 ASN cc_start: 0.7891 (t0) cc_final: 0.7261 (t0) REVERT: D 13 ARG cc_start: 0.7644 (mmt90) cc_final: 0.7421 (mmt90) REVERT: D 25 ARG cc_start: 0.7738 (mtp85) cc_final: 0.7305 (mtp85) REVERT: D 269 MET cc_start: 0.8204 (ttt) cc_final: 0.7675 (ttt) REVERT: D 282 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7478 (mp) outliers start: 40 outliers final: 31 residues processed: 247 average time/residue: 0.3354 time to fit residues: 116.3200 Evaluate side-chains 244 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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 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 67 LEU 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 322 VAL 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 78 ILE 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 236 TYR 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 78 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 12 optimal weight: 0.2980 chunk 100 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 82 optimal weight: 0.2980 chunk 70 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.137882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.101592 restraints weight = 16407.441| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.18 r_work: 0.2862 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 0.035 15430 Z= 0.088 Angle : 0.435 11.791 21010 Z= 0.225 Chirality : 0.035 0.140 2310 Planarity : 0.004 0.053 2615 Dihedral : 3.522 14.046 2030 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.45 % Allowed : 27.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.20), residues: 1815 helix: 1.14 (0.16), residues: 1160 sheet: None (None), residues: 0 loop : -1.37 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 93 HIS 0.002 0.000 HIS B 168 PHE 0.008 0.001 PHE E 276 TYR 0.010 0.001 TYR A 196 ARG 0.007 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 710) hydrogen bonds : angle 3.60683 ( 2100) covalent geometry : bond 0.00204 (15430) covalent geometry : angle 0.43491 (21010) ********************** 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 249 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 1.495 Fit side-chains REVERT: A 25 ARG cc_start: 0.7715 (mtp85) cc_final: 0.7442 (mtp85) REVERT: A 51 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6620 (mtt180) REVERT: A 208 GLN cc_start: 0.8721 (tm130) cc_final: 0.8308 (tm-30) REVERT: E 25 ARG cc_start: 0.7652 (mtm110) cc_final: 0.7262 (mtp85) REVERT: E 211 MET cc_start: 0.8353 (mtp) cc_final: 0.8092 (mmm) REVERT: B 14 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8501 (tt) REVERT: B 25 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7485 (mtp85) REVERT: B 51 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6684 (mtt180) REVERT: C 13 ARG cc_start: 0.7712 (mmt90) cc_final: 0.7338 (mmt90) REVERT: C 25 ARG cc_start: 0.7838 (mtp85) cc_final: 0.7391 (mtp85) REVERT: C 30 LYS cc_start: 0.8886 (tttt) cc_final: 0.8651 (ttpt) REVERT: C 49 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6366 (tt) REVERT: C 328 ASN cc_start: 0.7864 (t0) cc_final: 0.7243 (t0) REVERT: D 13 ARG cc_start: 0.7704 (mmt90) cc_final: 0.7481 (mmt90) REVERT: D 25 ARG cc_start: 0.7737 (mtp85) cc_final: 0.7343 (mtp85) REVERT: D 282 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7388 (mp) outliers start: 40 outliers final: 32 residues processed: 248 average time/residue: 0.3107 time to fit residues: 107.4750 Evaluate side-chains 247 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 1.515 ------------------------------------------------------------------------------- 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 231 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 322 VAL 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 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 71 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 236 TYR 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 78 ILE Chi-restraints excluded: chain D residue 153 THR 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 88 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.0980 chunk 10 optimal weight: 0.0070 chunk 129 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 54 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.134354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.097728 restraints weight = 16326.422| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.18 r_work: 0.2808 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1191 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= 0.114 Angle : 0.460 11.933 21010 Z= 0.240 Chirality : 0.036 0.137 2310 Planarity : 0.004 0.056 2615 Dihedral : 3.608 13.688 2030 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.69 % Allowed : 27.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1815 helix: 1.27 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.29 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 93 HIS 0.002 0.000 HIS C 178 PHE 0.007 0.001 PHE A 276 TYR 0.012 0.001 TYR C 97 ARG 0.007 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.04764 ( 710) hydrogen bonds : angle 3.63268 ( 2100) covalent geometry : bond 0.00270 (15430) covalent geometry : angle 0.46047 (21010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7256.67 seconds wall clock time: 126 minutes 25.88 seconds (7585.88 seconds total)