Starting phenix.real_space_refine on Wed Mar 4 15:04:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n23_9321/03_2026/6n23_9321.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n23_9321/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6n23_9321/03_2026/6n23_9321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n23_9321/03_2026/6n23_9321.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n23_9321/03_2026/6n23_9321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n23_9321/03_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-dev-5986/lib/python3.9/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: 2.56, per 1000 atoms: 0.17 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: 1.16 Conformation dependent library (CDL) restraints added in 642.7 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: 0.39 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: 2.59 Time building geometry restraints manager: 1.58 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: 0.04 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: 0.300 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.710 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 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 covalent geometry : bond 0.00789 (15365) covalent geometry : angle 0.78465 (20925) SS BOND : bond 0.00965 ( 5) SS BOND : angle 2.69627 ( 10) hydrogen bonds : bond 0.31894 ( 805) hydrogen bonds : angle 9.84580 ( 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 : 0.483 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: 0.1814 time to fit residues: 35.7721 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 : 0.602 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3057 r_free = 0.3057 target = 0.073048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.055251 restraints weight = 30797.464| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.02 r_work: 0.2530 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15370 Z= 0.193 Angle : 0.618 7.771 20935 Z= 0.328 Chirality : 0.044 0.422 2290 Planarity : 0.005 0.043 2630 Dihedral : 4.338 16.087 2020 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.47 % Allowed : 3.12 % Favored : 95.41 % 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: -1.72 (0.17), residues: 1805 helix: -0.85 (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 A 159 TYR 0.022 0.001 TYR A 97 PHE 0.017 0.002 PHE D 80 TRP 0.027 0.002 TRP E 287 HIS 0.003 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00441 (15365) covalent geometry : angle 0.61707 (20925) SS BOND : bond 0.00518 ( 5) SS BOND : angle 1.73030 ( 10) hydrogen bonds : bond 0.06113 ( 805) hydrogen bonds : angle 4.52452 ( 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 : 0.607 Fit side-chains REVERT: A 61 MET cc_start: 0.9153 (tpp) cc_final: 0.8753 (ttp) REVERT: A 75 LEU cc_start: 0.7944 (mp) cc_final: 0.7605 (mp) REVERT: A 320 MET cc_start: 0.8785 (ttm) cc_final: 0.8375 (ttm) REVERT: B 61 MET cc_start: 0.9062 (tpp) cc_final: 0.8614 (ttp) REVERT: C 129 MET cc_start: 0.9219 (mmt) cc_final: 0.8894 (mmm) REVERT: E 163 MET cc_start: 0.8646 (ttm) cc_final: 0.8252 (ttp) REVERT: E 320 MET cc_start: 0.8320 (ttt) cc_final: 0.8118 (ttp) outliers start: 24 outliers final: 13 residues processed: 90 average time/residue: 0.0863 time to fit residues: 13.8973 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 : 0.655 ------------------------------------------------------------------------------- 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: 10.0000 chunk 89 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 158 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3088 r_free = 0.3088 target = 0.075273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.057664 restraints weight = 30653.789| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.07 r_work: 0.2580 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15370 Z= 0.109 Angle : 0.485 7.487 20935 Z= 0.252 Chirality : 0.039 0.388 2290 Planarity : 0.004 0.039 2630 Dihedral : 3.934 21.252 2020 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.86 % Allowed : 5.08 % Favored : 94.07 % 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: -0.13 (0.19), residues: 1805 helix: 0.59 (0.15), residues: 1160 sheet: None (None), residues: 0 loop : -1.27 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 159 TYR 0.012 0.001 TYR C 97 PHE 0.015 0.001 PHE D 80 TRP 0.019 0.001 TRP E 287 HIS 0.002 0.000 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00230 (15365) covalent geometry : angle 0.48443 (20925) SS BOND : bond 0.00286 ( 5) SS BOND : angle 0.83050 ( 10) hydrogen bonds : bond 0.04881 ( 805) hydrogen bonds : angle 3.97011 ( 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 91 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.609 Fit side-chains REVERT: A 80 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7976 (m-80) REVERT: A 320 MET cc_start: 0.8795 (ttm) cc_final: 0.8558 (ttp) REVERT: C 61 MET cc_start: 0.9083 (tpp) cc_final: 0.8842 (ttp) REVERT: C 129 MET cc_start: 0.9118 (mmt) cc_final: 0.8847 (mmm) REVERT: E 80 PHE cc_start: 0.8409 (m-80) cc_final: 0.7981 (m-80) REVERT: E 320 MET cc_start: 0.8400 (ttt) cc_final: 0.8189 (ttp) outliers start: 14 outliers final: 7 residues processed: 88 average time/residue: 0.0901 time to fit residues: 14.1298 Evaluate side-chains 60 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 351 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 80 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 149 optimal weight: 0.0040 chunk 137 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.8000 ------------------------------------------------------------------------------- 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 = 0.3011 r_free = 0.3011 target = 0.070892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.053227 restraints weight = 31248.195| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 2.98 r_work: 0.2496 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15370 Z= 0.175 Angle : 0.519 10.222 20935 Z= 0.265 Chirality : 0.040 0.259 2290 Planarity : 0.004 0.044 2630 Dihedral : 3.862 22.088 2020 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.47 % Allowed : 5.99 % Favored : 92.54 % 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: 0.76 (0.20), residues: 1805 helix: 1.33 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -0.87 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 150 TYR 0.018 0.001 TYR A 97 PHE 0.013 0.001 PHE C 283 TRP 0.018 0.002 TRP D 287 HIS 0.002 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00405 (15365) covalent geometry : angle 0.51881 (20925) SS BOND : bond 0.00345 ( 5) SS BOND : angle 1.08264 ( 10) hydrogen bonds : bond 0.04833 ( 805) hydrogen bonds : angle 3.91590 ( 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 78 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.677 Fit side-chains REVERT: A 80 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: A 320 MET cc_start: 0.8862 (ttm) cc_final: 0.8637 (ttp) REVERT: B 75 LEU cc_start: 0.7850 (mt) cc_final: 0.7614 (mt) REVERT: C 129 MET cc_start: 0.9188 (mmt) cc_final: 0.8938 (mmm) REVERT: E 80 PHE cc_start: 0.8583 (m-80) cc_final: 0.8148 (m-80) REVERT: E 320 MET cc_start: 0.8600 (ttt) cc_final: 0.8397 (ttp) outliers start: 24 outliers final: 15 residues processed: 71 average time/residue: 0.0907 time to fit residues: 11.4251 Evaluate side-chains 70 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 351 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 136 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 136 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 72 optimal weight: 0.0370 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- 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 = 0.3028 r_free = 0.3028 target = 0.071503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.054773 restraints weight = 31548.644| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.87 r_work: 0.2546 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15370 Z= 0.101 Angle : 0.454 8.860 20935 Z= 0.233 Chirality : 0.037 0.150 2290 Planarity : 0.003 0.038 2630 Dihedral : 3.742 24.838 2020 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: 0.96 (0.20), residues: 1805 helix: 1.56 (0.15), residues: 1160 sheet: None (None), residues: 0 loop : -1.08 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 159 TYR 0.013 0.001 TYR D 284 PHE 0.016 0.001 PHE D 80 TRP 0.013 0.001 TRP A 287 HIS 0.002 0.000 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00224 (15365) covalent geometry : angle 0.45404 (20925) SS BOND : bond 0.00228 ( 5) SS BOND : angle 0.85874 ( 10) hydrogen bonds : bond 0.04142 ( 805) hydrogen bonds : angle 3.66586 ( 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 98 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.596 Fit side-chains REVERT: A 80 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: A 320 MET cc_start: 0.9030 (ttm) cc_final: 0.8554 (ttm) REVERT: B 75 LEU cc_start: 0.8188 (mt) cc_final: 0.7867 (mt) REVERT: B 80 PHE cc_start: 0.8421 (m-80) cc_final: 0.7885 (m-80) REVERT: C 75 LEU cc_start: 0.7973 (mp) cc_final: 0.7518 (mp) REVERT: C 80 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: D 75 LEU cc_start: 0.7928 (mt) cc_final: 0.7717 (mt) REVERT: E 320 MET cc_start: 0.8798 (ttt) cc_final: 0.8583 (ttp) outliers start: 22 outliers final: 14 residues processed: 92 average time/residue: 0.1118 time to fit residues: 17.0138 Evaluate side-chains 75 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 273 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 18 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 115 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 chunk 26 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 = 0.2974 r_free = 0.2974 target = 0.068478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.051687 restraints weight = 32159.222| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 2.84 r_work: 0.2462 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15370 Z= 0.175 Angle : 0.513 9.364 20935 Z= 0.260 Chirality : 0.040 0.150 2290 Planarity : 0.004 0.045 2630 Dihedral : 3.732 20.939 2020 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.71 % Allowed : 6.54 % Favored : 91.74 % 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: 1.48 (0.20), residues: 1805 helix: 2.00 (0.16), residues: 1105 sheet: None (None), residues: 0 loop : -0.70 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 150 TYR 0.017 0.001 TYR A 97 PHE 0.014 0.001 PHE A 80 TRP 0.013 0.001 TRP D 287 HIS 0.003 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00411 (15365) covalent geometry : angle 0.51219 (20925) SS BOND : bond 0.00381 ( 5) SS BOND : angle 1.13443 ( 10) hydrogen bonds : bond 0.04638 ( 805) hydrogen bonds : angle 3.79300 ( 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 85 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.492 Fit side-chains REVERT: A 80 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8205 (m-80) REVERT: A 320 MET cc_start: 0.9070 (ttm) cc_final: 0.8636 (ttm) REVERT: B 75 LEU cc_start: 0.8241 (mt) cc_final: 0.7878 (mt) REVERT: E 75 LEU cc_start: 0.8246 (mp) cc_final: 0.7910 (mt) REVERT: E 80 PHE cc_start: 0.8676 (m-80) cc_final: 0.8298 (m-80) outliers start: 28 outliers final: 19 residues processed: 81 average time/residue: 0.0974 time to fit residues: 13.3927 Evaluate side-chains 76 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 351 THR 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 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: 9.9990 chunk 111 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3012 r_free = 0.3012 target = 0.070494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.053541 restraints weight = 31361.069| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 2.84 r_work: 0.2508 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15370 Z= 0.103 Angle : 0.456 9.834 20935 Z= 0.234 Chirality : 0.037 0.148 2290 Planarity : 0.003 0.037 2630 Dihedral : 3.674 25.696 2020 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.35 % Allowed : 6.85 % Favored : 91.80 % 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: 1.46 (0.20), residues: 1805 helix: 2.02 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.94 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 105 TYR 0.019 0.001 TYR D 284 PHE 0.019 0.001 PHE D 80 TRP 0.012 0.001 TRP A 94 HIS 0.003 0.000 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00230 (15365) covalent geometry : angle 0.45539 (20925) SS BOND : bond 0.00219 ( 5) SS BOND : angle 0.87366 ( 10) hydrogen bonds : bond 0.04120 ( 805) hydrogen bonds : angle 3.62050 ( 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 86 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.593 Fit side-chains REVERT: A 80 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: A 320 MET cc_start: 0.9012 (ttm) cc_final: 0.8569 (ttm) REVERT: B 75 LEU cc_start: 0.8229 (mt) cc_final: 0.7850 (mt) REVERT: B 80 PHE cc_start: 0.8363 (m-80) cc_final: 0.7809 (m-80) REVERT: C 80 PHE cc_start: 0.8667 (m-80) cc_final: 0.8441 (m-80) REVERT: E 75 LEU cc_start: 0.8104 (mp) cc_final: 0.7740 (mt) REVERT: E 80 PHE cc_start: 0.8544 (m-80) cc_final: 0.8151 (m-80) outliers start: 22 outliers final: 17 residues processed: 81 average time/residue: 0.0901 time to fit residues: 12.8203 Evaluate side-chains 80 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 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 136 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 87 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: 10.0000 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 26 optimal weight: 0.4980 chunk 127 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.070564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.053618 restraints weight = 31747.814| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 2.86 r_work: 0.2507 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15370 Z= 0.113 Angle : 0.461 10.260 20935 Z= 0.235 Chirality : 0.038 0.149 2290 Planarity : 0.003 0.037 2630 Dihedral : 3.593 20.695 2020 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.35 % Allowed : 7.09 % Favored : 91.56 % 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: 1.61 (0.20), residues: 1805 helix: 2.15 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.90 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 150 TYR 0.019 0.001 TYR D 284 PHE 0.013 0.001 PHE D 283 TRP 0.011 0.001 TRP A 94 HIS 0.003 0.000 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00257 (15365) covalent geometry : angle 0.46077 (20925) SS BOND : bond 0.00270 ( 5) SS BOND : angle 0.92475 ( 10) hydrogen bonds : bond 0.04071 ( 805) hydrogen bonds : angle 3.60004 ( 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 92 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.623 Fit side-chains REVERT: A 80 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: A 320 MET cc_start: 0.8983 (ttm) cc_final: 0.8513 (ttm) REVERT: B 75 LEU cc_start: 0.8212 (mt) cc_final: 0.7802 (mt) REVERT: B 80 PHE cc_start: 0.8461 (m-80) cc_final: 0.7934 (m-80) REVERT: C 80 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: E 75 LEU cc_start: 0.8092 (mp) cc_final: 0.7738 (mt) REVERT: E 80 PHE cc_start: 0.8630 (m-80) cc_final: 0.8190 (m-80) outliers start: 22 outliers final: 18 residues processed: 87 average time/residue: 0.0800 time to fit residues: 12.2826 Evaluate side-chains 86 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 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 351 THR Chi-restraints excluded: chain D residue 61 MET 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 87 SER Chi-restraints excluded: chain E residue 136 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: 1.9990 chunk 59 optimal weight: 3.9990 chunk 119 optimal weight: 30.0000 chunk 92 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 63 optimal weight: 0.2980 chunk 138 optimal weight: 0.7980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.070994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.054010 restraints weight = 31641.961| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.86 r_work: 0.2526 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15370 Z= 0.101 Angle : 0.456 11.174 20935 Z= 0.232 Chirality : 0.037 0.148 2290 Planarity : 0.003 0.037 2630 Dihedral : 3.564 21.313 2020 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.28 % Allowed : 7.16 % Favored : 91.56 % 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: 1.75 (0.20), residues: 1805 helix: 2.23 (0.15), residues: 1160 sheet: None (None), residues: 0 loop : -0.90 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 196 TYR 0.026 0.001 TYR D 284 PHE 0.020 0.001 PHE D 80 TRP 0.011 0.001 TRP B 94 HIS 0.003 0.000 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00223 (15365) covalent geometry : angle 0.45539 (20925) SS BOND : bond 0.00236 ( 5) SS BOND : angle 0.87169 ( 10) hydrogen bonds : bond 0.03921 ( 805) hydrogen bonds : angle 3.55429 ( 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 90 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.414 Fit side-chains REVERT: A 80 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: B 75 LEU cc_start: 0.8212 (mt) cc_final: 0.7805 (mt) REVERT: B 80 PHE cc_start: 0.8427 (m-80) cc_final: 0.7907 (m-80) REVERT: C 80 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8546 (m-80) REVERT: E 80 PHE cc_start: 0.8631 (m-80) cc_final: 0.8199 (m-80) outliers start: 21 outliers final: 18 residues processed: 87 average time/residue: 0.0837 time to fit residues: 12.6507 Evaluate side-chains 82 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 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 351 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 18 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.070404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.053481 restraints weight = 31832.899| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.86 r_work: 0.2505 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15370 Z= 0.127 Angle : 0.476 12.162 20935 Z= 0.241 Chirality : 0.038 0.161 2290 Planarity : 0.003 0.037 2630 Dihedral : 3.567 19.942 2020 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.28 % Allowed : 7.58 % Favored : 91.13 % 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: 1.78 (0.20), residues: 1805 helix: 2.36 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : -0.93 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 150 TYR 0.036 0.001 TYR D 284 PHE 0.018 0.001 PHE D 283 TRP 0.011 0.001 TRP A 94 HIS 0.003 0.000 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00295 (15365) covalent geometry : angle 0.47528 (20925) SS BOND : bond 0.00279 ( 5) SS BOND : angle 1.00548 ( 10) hydrogen bonds : bond 0.04074 ( 805) hydrogen bonds : angle 3.58869 ( 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 85 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.613 Fit side-chains REVERT: A 80 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8209 (m-80) REVERT: B 75 LEU cc_start: 0.8201 (mt) cc_final: 0.7780 (mt) REVERT: E 75 LEU cc_start: 0.8123 (mp) cc_final: 0.7762 (mt) REVERT: E 80 PHE cc_start: 0.8683 (m-80) cc_final: 0.8246 (m-80) outliers start: 21 outliers final: 18 residues processed: 81 average time/residue: 0.0953 time to fit residues: 13.4855 Evaluate side-chains 81 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 C residue 37 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 18 SER 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=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: 6.9990 chunk 76 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 135 optimal weight: 0.0870 chunk 128 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 ASN D 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.054981 restraints weight = 31763.915| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.99 r_work: 0.2513 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15370 Z= 0.109 Angle : 0.460 11.956 20935 Z= 0.236 Chirality : 0.038 0.229 2290 Planarity : 0.003 0.037 2630 Dihedral : 3.543 19.844 2020 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.28 % Allowed : 7.71 % Favored : 91.01 % 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: 1.81 (0.20), residues: 1805 helix: 2.29 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -0.92 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 196 TYR 0.038 0.001 TYR D 284 PHE 0.026 0.001 PHE D 283 TRP 0.011 0.001 TRP E 94 HIS 0.003 0.000 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00246 (15365) covalent geometry : angle 0.45975 (20925) SS BOND : bond 0.00231 ( 5) SS BOND : angle 0.90678 ( 10) hydrogen bonds : bond 0.03931 ( 805) hydrogen bonds : angle 3.55476 ( 2370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.89 seconds wall clock time: 43 minutes 19.00 seconds (2599.00 seconds total)