Starting phenix.real_space_refine on Fri Jun 13 07:45:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kc9_62246/06_2025/9kc9_62246.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kc9_62246/06_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_62246/06_2025/9kc9_62246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kc9_62246/06_2025/9kc9_62246.map" model { file = "/net/cci-nas-00/data/ceres_data/9kc9_62246/06_2025/9kc9_62246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kc9_62246/06_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-5710/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: 7.04, per 1000 atoms: 0.47 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: 3.17 Conformation dependent library (CDL) restraints added in 1.7 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: 1.39 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: 4.03 Time building geometry restraints manager: 3.78 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 31.020 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- 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 : 2.900 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: 0.4001 time to fit residues: 131.6068 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 : 2.038 ------------------------------------------------------------------------------- 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 : 1.848 Fit side-chains REVERT: A 25 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7383 (mtp85) REVERT: A 51 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.6397 (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: 0.6871 (OUTLIER) cc_final: 0.6506 (mtt180) REVERT: E 208 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: E 236 TYR cc_start: 0.8608 (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: 0.7019 (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: 0.8782 (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: 0.8865 (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: 0.7971 (t0) cc_final: 0.7296 (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: 0.7269 (mtp85) REVERT: D 30 LYS cc_start: 0.8836 (tttt) cc_final: 0.8622 (ttpt) REVERT: D 51 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.6412 (mtt180) REVERT: D 208 GLN cc_start: 0.8761 (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: 0.3820 time to fit residues: 141.8263 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 : 1.638 ------------------------------------------------------------------------------- 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: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.133447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.096937 restraints weight = 16233.037| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.16 r_work: 0.2719 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.0852 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= 0.211 Angle : 0.557 6.407 21010 Z= 0.300 Chirality : 0.040 0.163 2310 Planarity : 0.005 0.058 2615 Dihedral : 6.166 77.564 2047 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.85 % Allowed : 25.93 % 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: -0.14 (0.20), residues: 1815 helix: 0.84 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -1.56 (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 0.025 0.002 TYR E 236 ARG 0.005 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.07067 ( 710) hydrogen bonds : angle 3.89161 ( 2100) covalent geometry : bond 0.00522 (15430) covalent geometry : angle 0.55655 (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 274 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 211 time to evaluate : 1.790 Fit side-chains REVERT: A 25 ARG cc_start: 0.7886 (mtp85) cc_final: 0.7473 (mtp85) REVERT: A 51 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6662 (mtt180) REVERT: A 208 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: A 310 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7944 (pt) REVERT: E 208 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: E 236 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.8389 (t80) REVERT: E 310 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7912 (pt) REVERT: B 25 ARG cc_start: 0.8062 (mtp85) cc_final: 0.7526 (mtp85) REVERT: B 51 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6772 (mtt180) REVERT: B 159 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7761 (mp) REVERT: B 173 LYS cc_start: 0.7104 (mtpt) cc_final: 0.6853 (pttt) REVERT: B 208 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8098 (tm-30) REVERT: B 310 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7946 (pt) REVERT: C 44 TYR cc_start: 0.7821 (m-80) cc_final: 0.7562 (m-80) REVERT: C 208 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8409 (tm-30) REVERT: C 310 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7889 (pt) REVERT: C 328 ASN cc_start: 0.8054 (t0) cc_final: 0.7762 (t0) REVERT: C 363 THR cc_start: 0.9333 (t) cc_final: 0.9028 (t) REVERT: D 25 ARG cc_start: 0.7903 (mtp85) cc_final: 0.7373 (mtp85) REVERT: D 51 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6588 (mtt180) REVERT: D 208 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: D 310 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7826 (pt) outliers start: 63 outliers final: 38 residues processed: 265 average time/residue: 0.3215 time to fit residues: 119.1245 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 : 1.532 ------------------------------------------------------------------------------- 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 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 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 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: 0.9990 chunk 166 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 176 optimal weight: 0.0870 chunk 152 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.132945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.096004 restraints weight = 16254.108| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.20 r_work: 0.2784 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0773 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= 0.109 Angle : 0.462 7.382 21010 Z= 0.251 Chirality : 0.037 0.159 2310 Planarity : 0.004 0.055 2615 Dihedral : 5.857 72.830 2047 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.75 % Allowed : 26.67 % 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: 0.05 (0.20), residues: 1815 helix: 0.98 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -1.47 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 93 HIS 0.001 0.000 HIS A 165 PHE 0.008 0.001 PHE A 276 TYR 0.015 0.001 TYR E 236 ARG 0.006 0.000 ARG D 13 Details of bonding type rmsd hydrogen bonds : bond 0.04993 ( 710) hydrogen bonds : angle 3.80894 ( 2100) covalent geometry : bond 0.00248 (15430) covalent geometry : angle 0.46234 (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 269 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 1.890 Fit side-chains REVERT: A 51 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6573 (mtt180) REVERT: A 208 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: A 282 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7682 (mp) REVERT: A 310 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7865 (pt) REVERT: E 25 ARG cc_start: 0.7765 (mtm110) cc_final: 0.7252 (mtp85) REVERT: E 208 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: E 236 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8254 (t80) REVERT: E 310 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7889 (pt) REVERT: B 25 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7441 (mtp85) REVERT: B 51 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6745 (mtt180) REVERT: B 159 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7705 (mp) REVERT: B 208 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: B 310 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7838 (pt) REVERT: C 25 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7425 (mtp85) REVERT: C 30 LYS cc_start: 0.8891 (tttt) cc_final: 0.8620 (ttpt) REVERT: C 208 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8401 (tm-30) REVERT: C 310 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7845 (pt) REVERT: C 328 ASN cc_start: 0.7898 (t0) cc_final: 0.7263 (t0) REVERT: C 363 THR cc_start: 0.9281 (t) cc_final: 0.8984 (t) REVERT: D 25 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7325 (mtp85) REVERT: D 51 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6476 (mtt180) REVERT: D 208 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8233 (tm-30) outliers start: 45 outliers final: 27 residues processed: 265 average time/residue: 0.3554 time to fit residues: 132.3299 Evaluate side-chains 263 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 282 LEU 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 B residue 28 ILE Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 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 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 208 GLN 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: 0.9980 chunk 155 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.132766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.096450 restraints weight = 16533.616| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.17 r_work: 0.2735 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15430 Z= 0.171 Angle : 0.512 6.983 21010 Z= 0.275 Chirality : 0.039 0.165 2310 Planarity : 0.005 0.058 2615 Dihedral : 5.789 72.413 2045 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.91 % Allowed : 26.06 % 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: -0.07 (0.20), residues: 1815 helix: 0.91 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -1.54 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 93 HIS 0.002 0.001 HIS C 178 PHE 0.010 0.001 PHE A 283 TYR 0.021 0.002 TYR E 236 ARG 0.006 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.06277 ( 710) hydrogen bonds : angle 3.84229 ( 2100) covalent geometry : bond 0.00416 (15430) covalent geometry : angle 0.51166 (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 280 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 216 time to evaluate : 1.584 Fit side-chains REVERT: A 25 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7467 (mtp85) REVERT: A 51 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6629 (mtt180) REVERT: A 208 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: A 282 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7794 (mp) REVERT: A 310 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.8030 (pt) REVERT: E 25 ARG cc_start: 0.7818 (mtm110) cc_final: 0.7319 (mtp85) REVERT: E 208 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8246 (tm-30) REVERT: E 236 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8355 (t80) REVERT: E 310 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7947 (pt) REVERT: B 25 ARG cc_start: 0.8026 (mtp85) cc_final: 0.7500 (mtp85) REVERT: B 51 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6782 (mtt180) REVERT: B 159 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7773 (mp) REVERT: B 310 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7916 (pt) REVERT: C 25 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7457 (mtp85) REVERT: C 30 LYS cc_start: 0.8957 (tttt) cc_final: 0.8645 (ttpt) REVERT: C 44 TYR cc_start: 0.7732 (m-80) cc_final: 0.7465 (m-80) REVERT: C 310 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7968 (pt) REVERT: C 328 ASN cc_start: 0.8026 (t0) cc_final: 0.7772 (t0) REVERT: C 363 THR cc_start: 0.9300 (t) cc_final: 0.9000 (t) REVERT: D 13 ARG cc_start: 0.7631 (mmt90) cc_final: 0.7419 (mmt90) REVERT: D 25 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7340 (mtp85) REVERT: D 269 MET cc_start: 0.8347 (ttt) cc_final: 0.7899 (ttt) REVERT: D 282 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7818 (mp) outliers start: 64 outliers final: 46 residues processed: 272 average time/residue: 0.3617 time to fit residues: 138.9021 Evaluate side-chains 277 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 1.877 ------------------------------------------------------------------------------- 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 282 LEU 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 208 GLN Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain 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 159 LEU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 273 VAL 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 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 236 TYR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 322 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 62 optimal weight: 0.0070 chunk 172 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 51 optimal weight: 0.0000 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.5404 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.138700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.102963 restraints weight = 16175.547| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.13 r_work: 0.2830 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.0900 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= 0.094 Angle : 0.433 6.589 21010 Z= 0.233 Chirality : 0.036 0.141 2310 Planarity : 0.004 0.054 2615 Dihedral : 4.581 66.796 2036 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.18 % Allowed : 26.97 % 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: 0.13 (0.20), residues: 1815 helix: 0.97 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.41 (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 326 PHE 0.008 0.001 PHE A 276 TYR 0.011 0.001 TYR C 97 ARG 0.006 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 710) hydrogen bonds : angle 3.76591 ( 2100) covalent geometry : bond 0.00211 (15430) covalent geometry : angle 0.43343 (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 278 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 226 time to evaluate : 2.476 Fit side-chains REVERT: A 25 ARG cc_start: 0.7782 (mtp85) cc_final: 0.7472 (mtp85) REVERT: A 51 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6633 (mtt180) REVERT: A 208 GLN cc_start: 0.8742 (tm130) cc_final: 0.8060 (tm-30) REVERT: A 282 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7670 (mp) REVERT: A 310 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7988 (pt) REVERT: E 25 ARG cc_start: 0.7759 (mtm110) cc_final: 0.7302 (mtp85) REVERT: E 208 GLN cc_start: 0.8734 (tm130) cc_final: 0.8196 (tm-30) REVERT: E 236 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.8206 (t80) REVERT: E 310 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7980 (pt) REVERT: B 25 ARG cc_start: 0.7971 (mtp85) cc_final: 0.7490 (mtp85) REVERT: B 51 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6757 (mtt180) REVERT: B 310 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7865 (pt) REVERT: C 25 ARG cc_start: 0.7930 (mtp85) cc_final: 0.7472 (mtp85) REVERT: C 30 LYS cc_start: 0.8890 (tttt) cc_final: 0.8588 (ttpt) REVERT: C 282 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7462 (mp) REVERT: C 328 ASN cc_start: 0.7832 (t0) cc_final: 0.7229 (t0) REVERT: D 25 ARG cc_start: 0.7781 (mtp85) cc_final: 0.7310 (mtp85) REVERT: D 269 MET cc_start: 0.8247 (ttt) cc_final: 0.7767 (ttt) REVERT: D 282 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7632 (mp) REVERT: D 310 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7891 (pt) outliers start: 52 outliers final: 31 residues processed: 277 average time/residue: 0.3831 time to fit residues: 151.2406 Evaluate side-chains 262 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 236 TYR Chi-restraints excluded: chain A residue 282 LEU 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 78 ILE 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 153 THR 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 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 322 VAL 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 136 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 108 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.135225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.099057 restraints weight = 16432.120| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.14 r_work: 0.2770 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.0960 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= 0.139 Angle : 0.485 9.290 21010 Z= 0.258 Chirality : 0.037 0.155 2310 Planarity : 0.005 0.057 2615 Dihedral : 3.898 16.229 2030 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.24 % Allowed : 26.73 % 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: 0.13 (0.20), residues: 1815 helix: 1.07 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -1.49 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 93 HIS 0.002 0.000 HIS A 178 PHE 0.009 0.001 PHE A 283 TYR 0.019 0.001 TYR E 236 ARG 0.006 0.000 ARG D 13 Details of bonding type rmsd hydrogen bonds : bond 0.05478 ( 710) hydrogen bonds : angle 3.76365 ( 2100) covalent geometry : bond 0.00333 (15430) covalent geometry : angle 0.48477 (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 278 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 225 time to evaluate : 2.374 Fit side-chains REVERT: A 25 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7496 (mtp85) REVERT: A 51 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6582 (mtt180) REVERT: A 208 GLN cc_start: 0.8753 (tm130) cc_final: 0.8070 (tm-30) REVERT: E 25 ARG cc_start: 0.7787 (mtm110) cc_final: 0.7323 (mtp85) REVERT: E 236 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8303 (t80) REVERT: B 25 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7522 (mtp85) REVERT: B 159 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7786 (mp) REVERT: B 208 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8123 (tm-30) REVERT: C 25 ARG cc_start: 0.7936 (mtp85) cc_final: 0.7435 (mtp85) REVERT: C 30 LYS cc_start: 0.8958 (tttt) cc_final: 0.8641 (tttt) REVERT: C 208 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8343 (tm-30) REVERT: C 282 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7533 (mp) REVERT: C 328 ASN cc_start: 0.7971 (t0) cc_final: 0.7335 (t0) REVERT: C 363 THR cc_start: 0.9287 (t) cc_final: 0.8996 (t) REVERT: D 25 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7352 (mtp85) REVERT: D 269 MET cc_start: 0.8219 (ttt) cc_final: 0.7779 (ttt) REVERT: D 282 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7709 (mp) REVERT: D 310 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7922 (pt) outliers start: 53 outliers final: 41 residues processed: 274 average time/residue: 0.4323 time to fit residues: 168.5784 Evaluate side-chains 278 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 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 322 VAL Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 208 GLN 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 67 LEU Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 208 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 322 VAL Chi-restraints excluded: chain C residue 332 MET 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 83 optimal weight: 0.0370 chunk 144 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.1662 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.135991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.099911 restraints weight = 16297.195| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.13 r_work: 0.2782 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15430 Z= 0.123 Angle : 0.470 10.498 21010 Z= 0.250 Chirality : 0.037 0.145 2310 Planarity : 0.004 0.056 2615 Dihedral : 3.885 15.054 2030 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.43 % Allowed : 26.48 % 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: 0.16 (0.20), residues: 1815 helix: 1.08 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -1.47 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.001 0.000 HIS C 357 PHE 0.008 0.001 PHE D 276 TYR 0.016 0.001 TYR E 236 ARG 0.006 0.000 ARG D 13 Details of bonding type rmsd hydrogen bonds : bond 0.05100 ( 710) hydrogen bonds : angle 3.75856 ( 2100) covalent geometry : bond 0.00291 (15430) covalent geometry : angle 0.46980 (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 283 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 227 time to evaluate : 1.764 Fit side-chains REVERT: A 25 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7476 (mtp85) REVERT: A 51 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6621 (mtt180) REVERT: A 208 GLN cc_start: 0.8753 (tm130) cc_final: 0.8068 (tm-30) REVERT: E 25 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7324 (mtp85) REVERT: E 236 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8269 (t80) REVERT: B 25 ARG cc_start: 0.7983 (mtp85) cc_final: 0.7529 (mtp85) REVERT: B 51 ARG cc_start: 0.7053 (ttt180) cc_final: 0.6798 (mtt180) REVERT: B 208 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: C 25 ARG cc_start: 0.7939 (mtp85) cc_final: 0.7438 (mtp85) REVERT: C 208 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8299 (tm-30) REVERT: C 328 ASN cc_start: 0.7950 (t0) cc_final: 0.7327 (t0) REVERT: D 25 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7363 (mtp85) REVERT: D 208 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8560 (tm-30) REVERT: D 269 MET cc_start: 0.8283 (ttt) cc_final: 0.7818 (ttt) REVERT: D 282 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7695 (mp) REVERT: D 310 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7916 (pt) outliers start: 56 outliers final: 43 residues processed: 281 average time/residue: 0.3182 time to fit residues: 124.8747 Evaluate side-chains 276 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 226 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 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 67 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 208 GLN 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 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 208 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 332 MET 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 153 THR Chi-restraints excluded: chain D residue 208 GLN Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 322 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 137 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 8.9990 chunk 91 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.136172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.100114 restraints weight = 16255.670| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.13 r_work: 0.2786 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1029 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= 0.119 Angle : 0.475 11.255 21010 Z= 0.250 Chirality : 0.037 0.144 2310 Planarity : 0.004 0.056 2615 Dihedral : 3.849 14.318 2030 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.49 % Allowed : 26.54 % 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: 0.19 (0.20), residues: 1815 helix: 1.05 (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 0.002 0.000 HIS B 357 PHE 0.008 0.001 PHE A 276 TYR 0.016 0.001 TYR E 236 ARG 0.007 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.05040 ( 710) hydrogen bonds : angle 3.74114 ( 2100) covalent geometry : bond 0.00280 (15430) covalent geometry : angle 0.47510 (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 278 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 221 time to evaluate : 1.592 Fit side-chains REVERT: A 25 ARG cc_start: 0.7802 (mtp85) cc_final: 0.7479 (mtp85) REVERT: A 51 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6604 (mtt180) REVERT: A 208 GLN cc_start: 0.8734 (tm130) cc_final: 0.8305 (tm-30) REVERT: E 25 ARG cc_start: 0.7779 (mtm110) cc_final: 0.7324 (mtp85) REVERT: E 236 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8267 (t80) REVERT: B 14 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8576 (tt) REVERT: B 25 ARG cc_start: 0.7995 (mtp85) cc_final: 0.7524 (mtp85) REVERT: B 208 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: C 25 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7437 (mtp85) REVERT: C 30 LYS cc_start: 0.8986 (tttt) cc_final: 0.8744 (ttpt) REVERT: C 49 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6365 (tt) REVERT: C 328 ASN cc_start: 0.7939 (t0) cc_final: 0.7316 (t0) REVERT: D 25 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7370 (mtp85) REVERT: D 208 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8558 (tm-30) REVERT: D 269 MET cc_start: 0.8254 (ttt) cc_final: 0.7775 (ttt) REVERT: D 282 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7703 (mp) outliers start: 57 outliers final: 48 residues processed: 274 average time/residue: 0.3213 time to fit residues: 124.5878 Evaluate side-chains 276 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 221 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 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 322 VAL Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 208 GLN 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 129 ILE Chi-restraints excluded: chain C residue 136 GLN 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 322 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 332 MET 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 78 ILE Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 208 GLN Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 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: 0.9990 chunk 100 optimal weight: 0.4980 chunk 123 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 chunk 82 optimal weight: 0.6980 chunk 70 optimal weight: 0.0370 chunk 16 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 126 optimal weight: 0.0470 chunk 103 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.138091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.101865 restraints weight = 16436.088| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.19 r_work: 0.2868 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15430 Z= 0.087 Angle : 0.439 11.857 21010 Z= 0.227 Chirality : 0.035 0.143 2310 Planarity : 0.004 0.052 2615 Dihedral : 3.644 14.485 2030 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.39 % Allowed : 27.71 % Favored : 69.91 % 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: 0.42 (0.20), residues: 1815 helix: 1.20 (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 0.013 0.001 TRP C 93 HIS 0.002 0.000 HIS A 326 PHE 0.008 0.001 PHE A 276 TYR 0.010 0.001 TYR C 196 ARG 0.007 0.000 ARG D 13 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 710) hydrogen bonds : angle 3.68214 ( 2100) covalent geometry : bond 0.00200 (15430) covalent geometry : angle 0.43870 (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 250 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 3.210 Fit side-chains REVERT: A 51 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6637 (mtt180) REVERT: A 208 GLN cc_start: 0.8727 (tm130) cc_final: 0.8301 (tm-30) REVERT: E 25 ARG cc_start: 0.7623 (mtm110) cc_final: 0.7288 (mtp85) REVERT: E 236 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7904 (t80) REVERT: B 14 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8530 (tt) REVERT: B 25 ARG cc_start: 0.7786 (mtp85) cc_final: 0.7494 (mtp85) REVERT: C 25 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7454 (mtp85) REVERT: C 30 LYS cc_start: 0.8879 (tttt) cc_final: 0.8630 (ttpt) REVERT: C 49 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6375 (tt) REVERT: C 328 ASN cc_start: 0.7799 (t0) cc_final: 0.7250 (t0) REVERT: D 13 ARG cc_start: 0.7564 (mmt90) cc_final: 0.7345 (mmt90) REVERT: D 25 ARG cc_start: 0.7683 (mtp85) cc_final: 0.7380 (mtp85) REVERT: D 269 MET cc_start: 0.8038 (ttt) cc_final: 0.7507 (ttt) outliers start: 39 outliers final: 32 residues processed: 248 average time/residue: 0.3971 time to fit residues: 140.8838 Evaluate side-chains 244 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 2.875 ------------------------------------------------------------------------------- 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 236 TYR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 136 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 153 THR 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 231 SER 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 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 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 88 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 54 optimal weight: 0.0370 chunk 22 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.132317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.095445 restraints weight = 16391.692| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.19 r_work: 0.2776 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1142 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= 0.134 Angle : 0.485 11.842 21010 Z= 0.253 Chirality : 0.037 0.139 2310 Planarity : 0.005 0.057 2615 Dihedral : 3.745 13.655 2030 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.32 % Allowed : 27.58 % 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: 0.36 (0.20), residues: 1815 helix: 1.17 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.35 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.002 0.001 HIS B 168 PHE 0.008 0.001 PHE D 188 TYR 0.018 0.001 TYR E 236 ARG 0.007 0.000 ARG D 13 Details of bonding type rmsd hydrogen bonds : bond 0.05322 ( 710) hydrogen bonds : angle 3.69835 ( 2100) covalent geometry : bond 0.00320 (15430) covalent geometry : angle 0.48519 (21010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8674.98 seconds wall clock time: 156 minutes 37.27 seconds (9397.27 seconds total)