Starting phenix.real_space_refine on Sat Sep 12 07:12:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6n23_9321/09_2026/6n23_9321.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n23_9321/09_2026/6n23_9321.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6n23_9321/09_2026/6n23_9321.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6n23_9321/09_2026/6n23_9321.cif" model { file = "/net/cci-nas-00/data/ceres_data/6n23_9321/09_2026/6n23_9321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n23_9321/09_2026/6n23_9321.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n23_9321/09_2026/6n23_9321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n23_9321/09_2026/6n23_9321.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 65 5.16 5 C 9790 2.51 5 N 2430 2.21 5 O 2645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14935 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2986 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 344} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.88, per 1000 atoms: 0.19 Number of scatterers: 14935 At special positions: 0 Unit cell: (96.832, 97.92, 113.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 65 16.00 O 2645 8.00 N 2430 7.00 C 9790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 185 " distance=2.04 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 185 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 185 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 185 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 185 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 527.0 milliseconds 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3480 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 68.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.597A pdb=" N GLN A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.649A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 53 removed outlier: 3.701A pdb=" N LEU A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 removed outlier: 3.512A pdb=" N LEU A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 98 removed outlier: 3.653A pdb=" N VAL A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.847A pdb=" N LEU A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.699A pdb=" N SER A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.783A pdb=" N VAL A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 removed outlier: 3.531A pdb=" N SER A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 198 removed outlier: 4.298A pdb=" N SER A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 3.577A pdb=" N GLU A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.939A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.546A pdb=" N PHE A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.644A pdb=" N LEU A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.815A pdb=" N LYS A 355 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 removed outlier: 3.595A pdb=" N GLN B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.649A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 53 removed outlier: 3.701A pdb=" N LEU B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 73 removed outlier: 3.512A pdb=" N LEU B 65 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 98 removed outlier: 3.653A pdb=" N VAL B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.847A pdb=" N LEU B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.700A pdb=" N SER B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.784A pdb=" N VAL B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 174 removed outlier: 3.532A pdb=" N SER B 173 " --> pdb=" O LYS B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 198 removed outlier: 4.298A pdb=" N SER B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.577A pdb=" N GLU B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.938A pdb=" N VAL B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.545A pdb=" N PHE B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.643A pdb=" N LEU B 310 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP B 312 " --> pdb=" O ASN B 308 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.815A pdb=" N LYS B 355 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.595A pdb=" N GLN C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.649A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 53 removed outlier: 3.701A pdb=" N LEU C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 73 removed outlier: 3.512A pdb=" N LEU C 65 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 98 removed outlier: 3.652A pdb=" N VAL C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.847A pdb=" N LEU C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.700A pdb=" N SER C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.785A pdb=" N VAL C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 174 removed outlier: 3.531A pdb=" N SER C 173 " --> pdb=" O LYS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 198 removed outlier: 4.298A pdb=" N SER C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.577A pdb=" N GLU C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 252 removed outlier: 3.938A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.546A pdb=" N PHE C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 322 removed outlier: 3.644A pdb=" N LEU C 310 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP C 312 " --> pdb=" O ASN C 308 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.815A pdb=" N LYS C 355 " --> pdb=" O ALA C 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 removed outlier: 3.595A pdb=" N GLN D 23 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.649A pdb=" N LEU D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 53 removed outlier: 3.700A pdb=" N LEU D 37 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.512A pdb=" N LEU D 65 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 98 removed outlier: 3.653A pdb=" N VAL D 81 " --> pdb=" O PRO D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.848A pdb=" N LEU D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.701A pdb=" N SER D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.784A pdb=" N VAL D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 174 removed outlier: 3.531A pdb=" N SER D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 198 removed outlier: 4.298A pdb=" N SER D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 198 " --> pdb=" O LYS D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 removed outlier: 3.577A pdb=" N GLU D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.939A pdb=" N VAL D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.546A pdb=" N PHE D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 322 removed outlier: 3.644A pdb=" N LEU D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP D 312 " --> pdb=" O ASN D 308 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 322 " --> pdb=" O SER D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.815A pdb=" N LYS D 355 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 removed outlier: 3.596A pdb=" N GLN E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 32 removed outlier: 3.648A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 53 removed outlier: 3.700A pdb=" N LEU E 37 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 removed outlier: 3.513A pdb=" N LEU E 65 " --> pdb=" O MET E 61 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 98 removed outlier: 3.652A pdb=" N VAL E 81 " --> pdb=" O PRO E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.847A pdb=" N LEU E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.700A pdb=" N SER E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE E 139 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 149 Processing helix chain 'E' and resid 153 through 160 removed outlier: 3.785A pdb=" N VAL E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 174 removed outlier: 3.531A pdb=" N SER E 173 " --> pdb=" O LYS E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 198 removed outlier: 4.298A pdb=" N SER E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.577A pdb=" N GLU E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 252 removed outlier: 3.938A pdb=" N VAL E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.545A pdb=" N PHE E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 322 removed outlier: 3.644A pdb=" N LEU E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP E 312 " --> pdb=" O ASN E 308 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 322 " --> pdb=" O SER E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.816A pdb=" N LYS E 355 " --> pdb=" O ALA E 352 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2370 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4624 1.34 - 1.47: 4141 1.47 - 1.59: 6500 1.59 - 1.71: 0 1.71 - 1.84: 100 Bond restraints: 15365 Sorted by residual: bond pdb=" CB TRP E 309 " pdb=" CG TRP E 309 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.41e+00 bond pdb=" CB TRP A 309 " pdb=" CG TRP A 309 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.40e+00 bond pdb=" CB TRP C 309 " pdb=" CG TRP C 309 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.37e+00 bond pdb=" CB TRP B 309 " pdb=" CG TRP B 309 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.36e+00 bond pdb=" CB TRP D 309 " pdb=" CG TRP D 309 " ideal model delta sigma weight residual 1.498 1.451 0.047 3.10e-02 1.04e+03 2.29e+00 ... (remaining 15360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 19912 1.57 - 3.14: 839 3.14 - 4.72: 104 4.72 - 6.29: 40 6.29 - 7.86: 30 Bond angle restraints: 20925 Sorted by residual: angle pdb=" N VAL A 186 " pdb=" CA VAL A 186 " pdb=" C VAL A 186 " ideal model delta sigma weight residual 112.96 106.53 6.43 1.00e+00 1.00e+00 4.13e+01 angle pdb=" N VAL B 186 " pdb=" CA VAL B 186 " pdb=" C VAL B 186 " ideal model delta sigma weight residual 112.96 106.54 6.42 1.00e+00 1.00e+00 4.12e+01 angle pdb=" N VAL C 186 " pdb=" CA VAL C 186 " pdb=" C VAL C 186 " ideal model delta sigma weight residual 112.96 106.55 6.41 1.00e+00 1.00e+00 4.11e+01 angle pdb=" N VAL D 186 " pdb=" CA VAL D 186 " pdb=" C VAL D 186 " ideal model delta sigma weight residual 112.96 106.55 6.41 1.00e+00 1.00e+00 4.11e+01 angle pdb=" N VAL E 186 " pdb=" CA VAL E 186 " pdb=" C VAL E 186 " ideal model delta sigma weight residual 112.96 106.55 6.41 1.00e+00 1.00e+00 4.11e+01 ... (remaining 20920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 8600 14.94 - 29.87: 295 29.87 - 44.81: 105 44.81 - 59.74: 10 59.74 - 74.68: 10 Dihedral angle restraints: 9020 sinusoidal: 3625 harmonic: 5395 Sorted by residual: dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 185 " pdb=" CB CYS A 185 " ideal model delta sinusoidal sigma weight residual -86.00 -120.63 34.63 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" CB CYS C 135 " pdb=" SG CYS C 135 " pdb=" SG CYS C 185 " pdb=" CB CYS C 185 " ideal model delta sinusoidal sigma weight residual -86.00 -120.62 34.62 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 185 " pdb=" CB CYS D 185 " ideal model delta sinusoidal sigma weight residual -86.00 -120.62 34.62 1 1.00e+01 1.00e-02 1.70e+01 ... (remaining 9017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1065 0.033 - 0.065: 815 0.065 - 0.098: 298 0.098 - 0.131: 90 0.131 - 0.164: 22 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CA ILE E 232 " pdb=" N ILE E 232 " pdb=" C ILE E 232 " pdb=" CB ILE E 232 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA ILE C 232 " pdb=" N ILE C 232 " pdb=" C ILE C 232 " pdb=" CB ILE C 232 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 2287 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 287 " 0.030 2.00e-02 2.50e+03 2.41e-02 1.46e+01 pdb=" CG TRP D 287 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 287 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 287 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 287 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 287 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 287 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 287 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 287 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 287 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 287 " -0.030 2.00e-02 2.50e+03 2.41e-02 1.45e+01 pdb=" CG TRP A 287 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 287 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 287 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 287 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 287 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 287 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 287 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 287 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 287 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 287 " -0.030 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP B 287 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 287 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 287 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 287 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 287 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 287 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 287 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 287 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 287 " -0.005 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3462 2.76 - 3.30: 13161 3.30 - 3.83: 24541 3.83 - 4.37: 30586 4.37 - 4.90: 51416 Nonbonded interactions: 123166 Sorted by model distance: nonbonded pdb=" OD2 ASP C 203 " pdb=" OG SER D 204 " model vdw 2.231 3.040 nonbonded pdb=" OD2 ASP C 104 " pdb=" NH2 ARG D 218 " model vdw 2.278 3.120 nonbonded pdb=" OD2 ASP A 203 " pdb=" OG SER B 204 " model vdw 2.279 3.040 nonbonded pdb=" OD2 ASP B 203 " pdb=" OG SER C 204 " model vdw 2.328 3.040 nonbonded pdb=" OD2 ASP D 104 " pdb=" NH2 ARG E 218 " model vdw 2.329 3.120 ... (remaining 123161 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.020 Process input model: 12.770 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 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 : 0.008 0.067 15370 Z= 0.338 Angle : 0.787 7.861 20935 Z= 0.437 Chirality : 0.050 0.164 2290 Planarity : 0.006 0.040 2630 Dihedral : 9.584 74.678 5525 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.52 (0.13), residues: 1805 helix: -4.33 (0.06), residues: 1120 sheet: None (None), residues: 0 loop : -2.05 (0.20), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 150 TYR 0.039 0.002 TYR C 236 PHE 0.022 0.003 PHE D 17 TRP 0.064 0.005 TRP D 287 HIS 0.005 0.002 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00789 / 0.34 (15365) covalent geometry : angle 0.78465 / 0.44 (20925) SS BOND : bond 0.00965 / 0.51 ( 5) SS BOND : angle 2.69627 / 1.63 ( 10) hydrogen bonds : bond 0.31894 / 20.35 ( 805) hydrogen bonds : angle 9.84580 / 6.87 ( 2370) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.577 Fit side-chains REVERT: E 320 MET cc_start: 0.8291 (ttt) cc_final: 0.7901 (ttm) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1698 time to fit residues: 33.8049 Evaluate side-chains 60 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 ASN B 7 ASN C 7 ASN C 293 GLN C 316 GLN D 7 ASN E 7 ASN E 293 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.073069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.055273 restraints weight = 30804.290| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 3.02 r_work: 0.2532 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15370 Z= 0.196 Angle : 0.621 7.825 20935 Z= 0.329 Chirality : 0.044 0.419 2290 Planarity : 0.005 0.042 2630 Dihedral : 4.334 16.147 2020 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.47 % Allowed : 3.06 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.17), residues: 1805 helix: -0.86 (0.13), residues: 1135 sheet: None (None), residues: 0 loop : -1.46 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 159 TYR 0.022 0.001 TYR A 97 PHE 0.018 0.002 PHE D 80 TRP 0.025 0.002 TRP E 287 HIS 0.003 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (15365) covalent geometry : angle 0.61953 / 0.33 (20925) SS BOND : bond 0.00488 / 0.27 ( 5) SS BOND : angle 1.72091 / 1.04 ( 10) hydrogen bonds : bond 0.06077 / 3.79 ( 805) hydrogen bonds : angle 4.53195 / 3.22 ( 2370) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.427 Fit side-chains REVERT: A 61 MET cc_start: 0.9156 (tpp) cc_final: 0.8755 (ttp) REVERT: A 75 LEU cc_start: 0.7955 (mp) cc_final: 0.7614 (mp) REVERT: A 320 MET cc_start: 0.8789 (ttm) cc_final: 0.8384 (ttm) REVERT: B 61 MET cc_start: 0.9063 (tpp) cc_final: 0.8610 (ttp) REVERT: C 129 MET cc_start: 0.9217 (mmt) cc_final: 0.8891 (mmm) REVERT: E 320 MET cc_start: 0.8320 (ttt) cc_final: 0.8117 (ttp) outliers start: 24 outliers final: 13 residues processed: 90 average time/residue: 0.0795 time to fit residues: 12.8123 Evaluate side-chains 63 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 109 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.071331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.053672 restraints weight = 31329.058| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.01 r_work: 0.2495 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15370 Z= 0.174 Angle : 0.540 6.394 20935 Z= 0.279 Chirality : 0.041 0.394 2290 Planarity : 0.004 0.041 2630 Dihedral : 3.997 21.415 2020 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.10 % Allowed : 4.95 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.19), residues: 1805 helix: 0.71 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.00 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.016 0.001 TYR C 97 PHE 0.018 0.001 PHE D 80 TRP 0.023 0.002 TRP E 287 HIS 0.002 0.001 HIS C 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (15365) covalent geometry : angle 0.53901 / 0.28 (20925) SS BOND : bond 0.00401 / 0.22 ( 5) SS BOND : angle 1.21592 / 0.73 ( 10) hydrogen bonds : bond 0.05445 / 3.40 ( 805) hydrogen bonds : angle 4.09564 / 2.90 ( 2370) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.500 Fit side-chains REVERT: A 80 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: A 320 MET cc_start: 0.8938 (ttm) cc_final: 0.8728 (ttp) REVERT: B 75 LEU cc_start: 0.7888 (mt) cc_final: 0.7667 (mt) REVERT: B 154 MET cc_start: 0.8618 (mmm) cc_final: 0.7842 (mmt) REVERT: C 61 MET cc_start: 0.9099 (tpp) cc_final: 0.8859 (ttp) REVERT: C 107 MET cc_start: 0.8846 (ttm) cc_final: 0.8624 (ttp) REVERT: C 129 MET cc_start: 0.9208 (mmt) cc_final: 0.8949 (mmm) REVERT: E 75 LEU cc_start: 0.7819 (mp) cc_final: 0.7503 (mp) REVERT: E 80 PHE cc_start: 0.8612 (m-80) cc_final: 0.8154 (m-80) outliers start: 18 outliers final: 9 residues processed: 78 average time/residue: 0.0846 time to fit residues: 11.8964 Evaluate side-chains 62 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 246 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 80 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.069996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.053185 restraints weight = 31748.226| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 2.83 r_work: 0.2503 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15370 Z= 0.138 Angle : 0.489 7.874 20935 Z= 0.252 Chirality : 0.040 0.274 2290 Planarity : 0.003 0.038 2630 Dihedral : 3.870 24.433 2020 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.71 % Allowed : 5.44 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.20), residues: 1805 helix: 1.31 (0.15), residues: 1160 sheet: None (None), residues: 0 loop : -1.11 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.015 0.001 TYR A 97 PHE 0.012 0.001 PHE D 80 TRP 0.016 0.001 TRP B 287 HIS 0.002 0.000 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15365) covalent geometry : angle 0.48859 / 0.25 (20925) SS BOND : bond 0.00305 / 0.16 ( 5) SS BOND : angle 1.00566 / 0.57 ( 10) hydrogen bonds : bond 0.04535 / 2.83 ( 805) hydrogen bonds : angle 3.84741 / 2.72 ( 2370) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.604 Fit side-chains REVERT: A 75 LEU cc_start: 0.8192 (mt) cc_final: 0.7885 (mt) REVERT: A 80 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8072 (m-80) REVERT: A 320 MET cc_start: 0.9072 (ttm) cc_final: 0.8611 (ttm) REVERT: B 154 MET cc_start: 0.8822 (mmm) cc_final: 0.8036 (mmt) REVERT: C 129 MET cc_start: 0.9419 (mmt) cc_final: 0.9155 (mmm) REVERT: E 80 PHE cc_start: 0.8601 (m-80) cc_final: 0.8157 (m-80) outliers start: 28 outliers final: 21 residues processed: 91 average time/residue: 0.1035 time to fit residues: 15.7573 Evaluate side-chains 80 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 136 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 2 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.068751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.051944 restraints weight = 32082.666| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 2.83 r_work: 0.2473 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15370 Z= 0.155 Angle : 0.494 8.850 20935 Z= 0.253 Chirality : 0.039 0.227 2290 Planarity : 0.004 0.041 2630 Dihedral : 3.796 24.430 2020 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.83 % Allowed : 5.93 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.20), residues: 1805 helix: 1.77 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -0.82 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 150 TYR 0.015 0.001 TYR A 97 PHE 0.012 0.001 PHE D 80 TRP 0.013 0.001 TRP E 94 HIS 0.003 0.001 HIS C 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (15365) covalent geometry : angle 0.49403 / 0.25 (20925) SS BOND : bond 0.00333 / 0.18 ( 5) SS BOND : angle 1.04664 / 0.59 ( 10) hydrogen bonds : bond 0.04623 / 2.88 ( 805) hydrogen bonds : angle 3.80992 / 2.69 ( 2370) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.454 Fit side-chains REVERT: A 80 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: A 320 MET cc_start: 0.9074 (ttm) cc_final: 0.8611 (ttm) REVERT: B 75 LEU cc_start: 0.8220 (mt) cc_final: 0.7953 (mt) REVERT: C 80 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: C 129 MET cc_start: 0.9433 (mmt) cc_final: 0.9193 (mmm) REVERT: C 163 MET cc_start: 0.9395 (ttp) cc_final: 0.9086 (ttp) REVERT: D 75 LEU cc_start: 0.7939 (mt) cc_final: 0.7696 (mt) REVERT: E 80 PHE cc_start: 0.8713 (m-80) cc_final: 0.8124 (m-80) outliers start: 30 outliers final: 19 residues processed: 88 average time/residue: 0.0965 time to fit residues: 14.5955 Evaluate side-chains 77 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 282 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 115 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 26 optimal weight: 0.0980 chunk 9 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 35 optimal weight: 0.0770 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 overall best weight: 2.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.069968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.053056 restraints weight = 31762.918| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 2.84 r_work: 0.2499 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15370 Z= 0.118 Angle : 0.462 9.121 20935 Z= 0.238 Chirality : 0.038 0.229 2290 Planarity : 0.003 0.038 2630 Dihedral : 3.702 24.332 2020 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.47 % Allowed : 6.30 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.20), residues: 1805 helix: 2.02 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -0.79 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 196 TYR 0.019 0.001 TYR A 284 PHE 0.010 0.001 PHE A 80 TRP 0.012 0.001 TRP E 94 HIS 0.002 0.000 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15365) covalent geometry : angle 0.46169 / 0.24 (20925) SS BOND : bond 0.00260 / 0.14 ( 5) SS BOND : angle 0.92495 / 0.51 ( 10) hydrogen bonds : bond 0.04258 / 2.66 ( 805) hydrogen bonds : angle 3.69070 / 2.61 ( 2370) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.602 Fit side-chains REVERT: A 80 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: A 320 MET cc_start: 0.9027 (ttm) cc_final: 0.8535 (ttm) REVERT: B 75 LEU cc_start: 0.8166 (mt) cc_final: 0.7854 (mt) REVERT: B 80 PHE cc_start: 0.8489 (m-80) cc_final: 0.7982 (m-80) REVERT: C 80 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8439 (m-80) REVERT: C 129 MET cc_start: 0.9421 (mmt) cc_final: 0.9192 (mmm) REVERT: E 80 PHE cc_start: 0.8678 (m-80) cc_final: 0.8047 (m-80) outliers start: 24 outliers final: 17 residues processed: 83 average time/residue: 0.0941 time to fit residues: 13.6582 Evaluate side-chains 76 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 282 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 33 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.071195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.054346 restraints weight = 31272.000| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.83 r_work: 0.2523 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15370 Z= 0.101 Angle : 0.453 9.548 20935 Z= 0.232 Chirality : 0.037 0.225 2290 Planarity : 0.003 0.038 2630 Dihedral : 3.612 26.933 2020 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.28 % Allowed : 6.67 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.20), residues: 1805 helix: 2.02 (0.15), residues: 1160 sheet: None (None), residues: 0 loop : -0.93 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 196 TYR 0.018 0.001 TYR D 284 PHE 0.013 0.001 PHE D 80 TRP 0.012 0.001 TRP E 94 HIS 0.002 0.000 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (15365) covalent geometry : angle 0.45224 / 0.23 (20925) SS BOND : bond 0.00239 / 0.13 ( 5) SS BOND : angle 0.85976 / 0.47 ( 10) hydrogen bonds : bond 0.03997 / 2.50 ( 805) hydrogen bonds : angle 3.58695 / 2.53 ( 2370) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.615 Fit side-chains REVERT: A 80 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: A 320 MET cc_start: 0.9023 (ttm) cc_final: 0.8544 (ttm) REVERT: B 75 LEU cc_start: 0.8163 (mt) cc_final: 0.7807 (mt) REVERT: B 80 PHE cc_start: 0.8465 (m-80) cc_final: 0.8013 (m-80) REVERT: C 80 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8519 (m-80) REVERT: E 80 PHE cc_start: 0.8626 (m-80) cc_final: 0.8025 (m-80) outliers start: 21 outliers final: 16 residues processed: 80 average time/residue: 0.0957 time to fit residues: 13.3186 Evaluate side-chains 76 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 282 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 28 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 170 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.068494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.051582 restraints weight = 32206.763| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 2.85 r_work: 0.2459 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15370 Z= 0.187 Angle : 0.517 10.423 20935 Z= 0.262 Chirality : 0.040 0.220 2290 Planarity : 0.003 0.038 2630 Dihedral : 3.665 22.170 2020 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.41 % Allowed : 6.36 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.20), residues: 1805 helix: 2.32 (0.16), residues: 1105 sheet: None (None), residues: 0 loop : -0.52 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 150 TYR 0.022 0.001 TYR A 284 PHE 0.018 0.001 PHE D 283 TRP 0.011 0.001 TRP B 94 HIS 0.002 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (15365) covalent geometry : angle 0.51641 / 0.26 (20925) SS BOND : bond 0.00352 / 0.19 ( 5) SS BOND : angle 1.14412 / 0.64 ( 10) hydrogen bonds : bond 0.04581 / 2.87 ( 805) hydrogen bonds : angle 3.75486 / 2.65 ( 2370) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 80 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8242 (m-80) REVERT: A 320 MET cc_start: 0.9135 (ttm) cc_final: 0.8717 (ttm) REVERT: C 80 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8528 (m-80) REVERT: E 80 PHE cc_start: 0.8636 (m-80) cc_final: 0.7935 (m-80) outliers start: 23 outliers final: 19 residues processed: 79 average time/residue: 0.0919 time to fit residues: 12.7097 Evaluate side-chains 78 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 282 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 158 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 138 optimal weight: 0.0970 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.069640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.052681 restraints weight = 31898.379| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 2.86 r_work: 0.2486 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15370 Z= 0.127 Angle : 0.478 11.131 20935 Z= 0.244 Chirality : 0.039 0.217 2290 Planarity : 0.003 0.038 2630 Dihedral : 3.658 23.633 2020 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.47 % Allowed : 6.42 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.20), residues: 1805 helix: 2.32 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -0.58 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 150 TYR 0.025 0.001 TYR D 284 PHE 0.012 0.001 PHE D 283 TRP 0.012 0.001 TRP E 94 HIS 0.003 0.000 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15365) covalent geometry : angle 0.47757 / 0.24 (20925) SS BOND : bond 0.00266 / 0.14 ( 5) SS BOND : angle 0.99218 / 0.54 ( 10) hydrogen bonds : bond 0.04270 / 2.67 ( 805) hydrogen bonds : angle 3.66960 / 2.58 ( 2370) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 80 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8248 (m-80) REVERT: B 80 PHE cc_start: 0.8379 (m-80) cc_final: 0.7943 (m-80) REVERT: C 80 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8549 (m-80) REVERT: C 163 MET cc_start: 0.9212 (ttp) cc_final: 0.8463 (ttt) REVERT: E 80 PHE cc_start: 0.8549 (m-80) cc_final: 0.7908 (m-80) outliers start: 24 outliers final: 20 residues processed: 80 average time/residue: 0.0964 time to fit residues: 13.4671 Evaluate side-chains 80 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.070199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.053314 restraints weight = 31693.884| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 2.84 r_work: 0.2503 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15370 Z= 0.111 Angle : 0.466 11.829 20935 Z= 0.238 Chirality : 0.038 0.210 2290 Planarity : 0.003 0.038 2630 Dihedral : 3.625 22.534 2020 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.35 % Allowed : 6.73 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.20), residues: 1805 helix: 2.24 (0.15), residues: 1155 sheet: None (None), residues: 0 loop : -0.77 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.019 0.001 TYR A 284 PHE 0.010 0.001 PHE C 248 TRP 0.012 0.001 TRP B 94 HIS 0.003 0.001 HIS C 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (15365) covalent geometry : angle 0.46556 / 0.24 (20925) SS BOND : bond 0.00252 / 0.13 ( 5) SS BOND : angle 0.91462 / 0.49 ( 10) hydrogen bonds : bond 0.04098 / 2.57 ( 805) hydrogen bonds : angle 3.61514 / 2.54 ( 2370) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 80 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: A 320 MET cc_start: 0.9121 (ttm) cc_final: 0.8833 (ttp) REVERT: B 80 PHE cc_start: 0.8418 (m-80) cc_final: 0.7981 (m-80) REVERT: C 163 MET cc_start: 0.9209 (ttp) cc_final: 0.8604 (ttt) REVERT: E 80 PHE cc_start: 0.8612 (m-80) cc_final: 0.7835 (m-80) outliers start: 22 outliers final: 18 residues processed: 80 average time/residue: 0.0978 time to fit residues: 13.7170 Evaluate side-chains 78 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 19 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 137 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.069062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.052080 restraints weight = 31853.854| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 2.85 r_work: 0.2479 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15370 Z= 0.146 Angle : 0.491 12.262 20935 Z= 0.249 Chirality : 0.039 0.213 2290 Planarity : 0.003 0.038 2630 Dihedral : 3.627 20.736 2020 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.28 % Allowed : 6.85 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.20), residues: 1805 helix: 2.27 (0.15), residues: 1155 sheet: None (None), residues: 0 loop : -0.74 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 150 TYR 0.027 0.001 TYR D 284 PHE 0.015 0.001 PHE D 283 TRP 0.012 0.001 TRP B 94 HIS 0.003 0.000 HIS C 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (15365) covalent geometry : angle 0.49030 / 0.25 (20925) SS BOND : bond 0.00288 / 0.15 ( 5) SS BOND : angle 1.05128 / 0.58 ( 10) hydrogen bonds : bond 0.04293 / 2.69 ( 805) hydrogen bonds : angle 3.68710 / 2.59 ( 2370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.38 seconds wall clock time: 39 minutes 53.94 seconds (2393.94 seconds total)