Starting phenix.real_space_refine on Wed Mar 4 14:01:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sio_54929/03_2026/9sio_54929.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sio_54929/03_2026/9sio_54929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sio_54929/03_2026/9sio_54929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sio_54929/03_2026/9sio_54929.map" model { file = "/net/cci-nas-00/data/ceres_data/9sio_54929/03_2026/9sio_54929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sio_54929/03_2026/9sio_54929.cif" } resolution = 2.9 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= 0.019 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 8880 2.51 5 N 2205 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s 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: 13645 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2715 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, E, C, D Time building chain proxies: 2.16, per 1000 atoms: 0.16 Number of scatterers: 13645 At special positions: 0 Unit cell: (96.18, 98.47, 119.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2470 8.00 N 2205 7.00 C 8880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 170 " - pdb=" SG CYS A 184 " distance=2.58 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 184 " distance=2.58 Simple disulfide: pdb=" SG CYS E 170 " - pdb=" SG CYS E 184 " distance=2.58 Simple disulfide: pdb=" SG CYS C 170 " - pdb=" SG CYS C 184 " distance=2.58 Simple disulfide: pdb=" SG CYS D 170 " - pdb=" SG CYS D 184 " distance=2.58 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 238 " " NAG B 901 " - " ASN B 238 " " NAG C 901 " - " ASN C 238 " " NAG D 901 " - " ASN D 238 " " NAG E 901 " - " ASN E 238 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 582.7 milliseconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 39.1% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 102 through 105 Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 259 through 276 removed outlier: 3.787A pdb=" N VAL A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TRP A 275 " --> pdb=" O TRP A 271 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 305 removed outlier: 3.980A pdb=" N ALA A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 340 removed outlier: 4.042A pdb=" N GLY A 337 " --> pdb=" O TYR A 333 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 462 removed outlier: 3.978A pdb=" N ILE A 441 " --> pdb=" O LYS A 437 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 442 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 45 through 51 Processing helix chain 'B' and resid 102 through 105 Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 204 through 207 Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 259 through 276 removed outlier: 3.787A pdb=" N VAL B 272 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER B 273 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TRP B 275 " --> pdb=" O TRP B 271 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 305 removed outlier: 3.980A pdb=" N ALA B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 340 removed outlier: 4.042A pdb=" N GLY B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B 338 " --> pdb=" O ALA B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 462 removed outlier: 3.978A pdb=" N ILE B 441 " --> pdb=" O LYS B 437 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 442 " --> pdb=" O TYR B 438 " (cutoff:3.500A) Proline residue: B 444 - end of helix Processing helix chain 'E' and resid 45 through 51 Processing helix chain 'E' and resid 102 through 105 Processing helix chain 'E' and resid 118 through 125 Processing helix chain 'E' and resid 204 through 207 Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 259 through 276 removed outlier: 3.787A pdb=" N VAL E 272 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER E 273 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE E 274 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TRP E 275 " --> pdb=" O TRP E 271 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 305 removed outlier: 3.979A pdb=" N ALA E 305 " --> pdb=" O SER E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 340 removed outlier: 4.042A pdb=" N GLY E 337 " --> pdb=" O TYR E 333 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR E 338 " --> pdb=" O ALA E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 462 removed outlier: 3.978A pdb=" N ILE E 441 " --> pdb=" O LYS E 437 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E 442 " --> pdb=" O TYR E 438 " (cutoff:3.500A) Proline residue: E 444 - end of helix Processing helix chain 'C' and resid 45 through 51 Processing helix chain 'C' and resid 102 through 105 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 204 through 207 Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 259 through 276 removed outlier: 3.787A pdb=" N VAL C 272 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER C 273 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE C 274 " --> pdb=" O SER C 270 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TRP C 275 " --> pdb=" O TRP C 271 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 305 removed outlier: 3.979A pdb=" N ALA C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 340 removed outlier: 4.041A pdb=" N GLY C 337 " --> pdb=" O TYR C 333 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR C 338 " --> pdb=" O ALA C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 462 removed outlier: 3.978A pdb=" N ILE C 441 " --> pdb=" O LYS C 437 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 442 " --> pdb=" O TYR C 438 " (cutoff:3.500A) Proline residue: C 444 - end of helix Processing helix chain 'D' and resid 45 through 51 Processing helix chain 'D' and resid 102 through 105 Processing helix chain 'D' and resid 118 through 125 Processing helix chain 'D' and resid 204 through 207 Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 259 through 276 removed outlier: 3.787A pdb=" N VAL D 272 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER D 273 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TRP D 275 " --> pdb=" O TRP D 271 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 305 removed outlier: 3.980A pdb=" N ALA D 305 " --> pdb=" O SER D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 340 removed outlier: 4.041A pdb=" N GLY D 337 " --> pdb=" O TYR D 333 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR D 338 " --> pdb=" O ALA D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 462 removed outlier: 3.978A pdb=" N ILE D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL D 442 " --> pdb=" O TYR D 438 " (cutoff:3.500A) Proline residue: D 444 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 117 removed outlier: 4.270A pdb=" N SER A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASP A 88 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER A 81 " --> pdb=" O ASP A 88 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 90 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE A 79 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP A 92 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR A 100 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU A 69 " --> pdb=" O THR A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 140 removed outlier: 6.667A pdb=" N THR A 167 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER A 138 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR A 165 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N PHE A 140 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N ARG A 163 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASP A 88 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER A 81 " --> pdb=" O ASP A 88 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 90 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE A 79 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP A 92 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR A 100 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU A 69 " --> pdb=" O THR A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 132 removed outlier: 4.353A pdb=" N SER A 190 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER A 240 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 224 " --> pdb=" O GLN A 247 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 249 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL A 222 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 117 removed outlier: 4.270A pdb=" N SER B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP B 88 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N SER B 81 " --> pdb=" O ASP B 88 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR B 90 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE B 79 " --> pdb=" O THR B 90 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP B 92 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR B 100 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU B 69 " --> pdb=" O THR B 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 135 through 140 removed outlier: 6.667A pdb=" N THR B 167 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER B 138 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR B 165 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE B 140 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N ARG B 163 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP B 88 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N SER B 81 " --> pdb=" O ASP B 88 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR B 90 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE B 79 " --> pdb=" O THR B 90 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP B 92 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR B 100 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU B 69 " --> pdb=" O THR B 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 132 removed outlier: 4.353A pdb=" N SER B 190 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER B 240 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 224 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 249 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL B 222 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 114 through 117 removed outlier: 4.271A pdb=" N SER E 157 " --> pdb=" O HIS E 153 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP E 88 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER E 81 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 90 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE E 79 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP E 92 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR E 100 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU E 69 " --> pdb=" O THR E 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 135 through 140 removed outlier: 6.667A pdb=" N THR E 167 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER E 138 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR E 165 " --> pdb=" O SER E 138 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N PHE E 140 " --> pdb=" O ARG E 163 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N ARG E 163 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP E 88 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER E 81 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 90 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE E 79 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP E 92 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR E 100 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU E 69 " --> pdb=" O THR E 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 130 through 132 removed outlier: 4.353A pdb=" N SER E 190 " --> pdb=" O SER E 240 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SER E 240 " --> pdb=" O SER E 190 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY E 224 " --> pdb=" O GLN E 247 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL E 249 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL E 222 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 114 through 117 removed outlier: 4.271A pdb=" N SER C 157 " --> pdb=" O HIS C 153 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASP C 88 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER C 81 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C 90 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE C 79 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP C 92 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR C 100 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU C 69 " --> pdb=" O THR C 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 135 through 140 removed outlier: 6.666A pdb=" N THR C 167 " --> pdb=" O LYS C 136 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER C 138 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR C 165 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N PHE C 140 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ARG C 163 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASP C 88 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER C 81 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C 90 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE C 79 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP C 92 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR C 100 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU C 69 " --> pdb=" O THR C 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 130 through 132 removed outlier: 4.353A pdb=" N SER C 190 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SER C 240 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY C 224 " --> pdb=" O GLN C 247 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C 249 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL C 222 " --> pdb=" O VAL C 249 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 114 through 117 removed outlier: 4.270A pdb=" N SER D 157 " --> pdb=" O HIS D 153 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASP D 88 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER D 81 " --> pdb=" O ASP D 88 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR D 90 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE D 79 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP D 92 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR D 100 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU D 69 " --> pdb=" O THR D 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 135 through 140 removed outlier: 6.667A pdb=" N THR D 167 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER D 138 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR D 165 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE D 140 " --> pdb=" O ARG D 163 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N ARG D 163 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASP D 88 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER D 81 " --> pdb=" O ASP D 88 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR D 90 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE D 79 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP D 92 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR D 100 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU D 69 " --> pdb=" O THR D 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 130 through 132 removed outlier: 4.353A pdb=" N SER D 190 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SER D 240 " --> pdb=" O SER D 190 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY D 224 " --> pdb=" O GLN D 247 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL D 249 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL D 222 " --> pdb=" O VAL D 249 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2313 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: 2.31 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: 4165 1.34 - 1.46: 3691 1.46 - 1.58: 5984 1.58 - 1.70: 0 1.70 - 1.83: 150 Bond restraints: 13990 Sorted by residual: bond pdb=" CB GLU B 214 " pdb=" CG GLU B 214 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" CB GLU D 214 " pdb=" CG GLU D 214 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CB GLU C 214 " pdb=" CG GLU C 214 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CB GLU A 214 " pdb=" CG GLU A 214 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" CB GLU E 214 " pdb=" CG GLU E 214 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 ... (remaining 13985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 18767 2.39 - 4.79: 198 4.79 - 7.18: 45 7.18 - 9.57: 0 9.57 - 11.96: 5 Bond angle restraints: 19015 Sorted by residual: angle pdb=" N THR E 144 " pdb=" CA THR E 144 " pdb=" C THR E 144 " ideal model delta sigma weight residual 114.75 108.85 5.90 1.26e+00 6.30e-01 2.20e+01 angle pdb=" N THR B 144 " pdb=" CA THR B 144 " pdb=" C THR B 144 " ideal model delta sigma weight residual 114.75 108.86 5.89 1.26e+00 6.30e-01 2.19e+01 angle pdb=" N THR D 144 " pdb=" CA THR D 144 " pdb=" C THR D 144 " ideal model delta sigma weight residual 114.75 108.86 5.89 1.26e+00 6.30e-01 2.18e+01 angle pdb=" N THR A 144 " pdb=" CA THR A 144 " pdb=" C THR A 144 " ideal model delta sigma weight residual 114.75 108.89 5.86 1.26e+00 6.30e-01 2.17e+01 angle pdb=" N THR C 144 " pdb=" CA THR C 144 " pdb=" C THR C 144 " ideal model delta sigma weight residual 114.75 108.91 5.84 1.26e+00 6.30e-01 2.15e+01 ... (remaining 19010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 7300 16.47 - 32.95: 744 32.95 - 49.42: 202 49.42 - 65.89: 44 65.89 - 82.37: 15 Dihedral angle restraints: 8305 sinusoidal: 3310 harmonic: 4995 Sorted by residual: dihedral pdb=" CA ALA B 143 " pdb=" C ALA B 143 " pdb=" N THR B 144 " pdb=" CA THR B 144 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ALA A 143 " pdb=" C ALA A 143 " pdb=" N THR A 144 " pdb=" CA THR A 144 " ideal model delta harmonic sigma weight residual 180.00 163.05 16.95 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ALA D 143 " pdb=" C ALA D 143 " pdb=" N THR D 144 " pdb=" CA THR D 144 " ideal model delta harmonic sigma weight residual 180.00 163.05 16.95 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 8302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1149 0.029 - 0.058: 656 0.058 - 0.087: 233 0.087 - 0.117: 123 0.117 - 0.146: 34 Chirality restraints: 2195 Sorted by residual: chirality pdb=" CA ILE A 188 " pdb=" N ILE A 188 " pdb=" C ILE A 188 " pdb=" CB ILE A 188 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE B 188 " pdb=" N ILE B 188 " pdb=" C ILE B 188 " pdb=" CB ILE B 188 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE E 188 " pdb=" N ILE E 188 " pdb=" C ILE E 188 " pdb=" CB ILE E 188 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 2192 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 255 " 0.013 2.00e-02 2.50e+03 1.32e-02 3.49e+00 pdb=" CG TYR E 255 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR E 255 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR E 255 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR E 255 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 255 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 255 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 255 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 255 " 0.012 2.00e-02 2.50e+03 1.32e-02 3.49e+00 pdb=" CG TYR B 255 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 255 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 255 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 255 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 255 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 255 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 255 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 255 " -0.012 2.00e-02 2.50e+03 1.32e-02 3.47e+00 pdb=" CG TYR D 255 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR D 255 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR D 255 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR D 255 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 255 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 255 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 255 " -0.001 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 7107 2.98 - 3.46: 13773 3.46 - 3.94: 22410 3.94 - 4.42: 26144 4.42 - 4.90: 43036 Nonbonded interactions: 112470 Sorted by model distance: nonbonded pdb=" N GLU D 214 " pdb=" OE1 GLU D 214 " model vdw 2.502 3.120 nonbonded pdb=" N GLU A 214 " pdb=" OE1 GLU A 214 " model vdw 2.502 3.120 nonbonded pdb=" N GLU E 214 " pdb=" OE1 GLU E 214 " model vdw 2.502 3.120 nonbonded pdb=" N GLU B 214 " pdb=" OE1 GLU B 214 " model vdw 2.503 3.120 nonbonded pdb=" N GLU C 214 " pdb=" OE1 GLU C 214 " model vdw 2.503 3.120 ... (remaining 112465 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 'E' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 11.930 Find NCS groups from input model: 0.100 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:8.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.011 0.546 14000 Z= 0.544 Angle : 0.660 11.964 19040 Z= 0.363 Chirality : 0.045 0.146 2195 Planarity : 0.004 0.039 2335 Dihedral : 14.902 82.365 5070 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.85 % Allowed : 17.12 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.88 (0.21), residues: 1670 helix: 1.07 (0.23), residues: 560 sheet: 0.44 (0.25), residues: 405 loop : 0.45 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 241 TYR 0.033 0.002 TYR E 255 PHE 0.019 0.002 PHE E 149 TRP 0.011 0.001 TRP A 271 HIS 0.002 0.001 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00399 (13990) covalent geometry : angle 0.65966 (19015) SS BOND : bond 0.54508 ( 5) SS BOND : angle 0.84751 ( 10) hydrogen bonds : bond 0.10434 ( 721) hydrogen bonds : angle 5.78123 ( 2313) link_NAG-ASN : bond 0.00125 ( 5) link_NAG-ASN : angle 1.05831 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.537 Fit side-chains REVERT: A 182 GLN cc_start: 0.8335 (mm-40) cc_final: 0.8120 (mm-40) REVERT: A 293 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8692 (mm) REVERT: B 177 PHE cc_start: 0.8712 (t80) cc_final: 0.8508 (t80) REVERT: B 179 MET cc_start: 0.9185 (mtp) cc_final: 0.8802 (mtp) REVERT: B 457 ILE cc_start: 0.8791 (tp) cc_final: 0.8375 (pt) REVERT: E 87 MET cc_start: 0.9296 (mmt) cc_final: 0.8938 (mmm) REVERT: E 123 LYS cc_start: 0.9118 (mtmm) cc_final: 0.8828 (mtmm) REVERT: E 293 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8730 (mm) REVERT: C 457 ILE cc_start: 0.8815 (tp) cc_final: 0.8383 (pt) outliers start: 13 outliers final: 2 residues processed: 166 average time/residue: 0.5108 time to fit residues: 94.0580 Evaluate side-chains 145 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain D residue 331 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.0470 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 219 GLN A 277 ASN A 279 ASN A 303 ASN B 185 HIS ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN E 182 GLN E 185 HIS E 219 GLN ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN C 185 HIS ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN D 185 HIS D 219 GLN D 277 ASN D 279 ASN D 303 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.117992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.084078 restraints weight = 23174.097| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.95 r_work: 0.2923 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14000 Z= 0.172 Angle : 0.562 7.352 19040 Z= 0.303 Chirality : 0.046 0.146 2195 Planarity : 0.003 0.026 2335 Dihedral : 5.994 53.440 1973 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.49 % Allowed : 13.79 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.05 (0.21), residues: 1670 helix: 1.26 (0.22), residues: 565 sheet: 0.64 (0.26), residues: 405 loop : 0.44 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 241 TYR 0.025 0.002 TYR A 255 PHE 0.022 0.002 PHE C 177 TRP 0.007 0.001 TRP C 271 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00395 (13990) covalent geometry : angle 0.56214 (19015) SS BOND : bond 0.00059 ( 5) SS BOND : angle 0.11640 ( 10) hydrogen bonds : bond 0.04479 ( 721) hydrogen bonds : angle 4.94793 ( 2313) link_NAG-ASN : bond 0.00196 ( 5) link_NAG-ASN : angle 0.88480 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 152 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 293 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8421 (mm) REVERT: B 108 LYS cc_start: 0.9410 (ttpp) cc_final: 0.9165 (ptmm) REVERT: B 252 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.6178 (ttp) REVERT: B 293 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8391 (mm) REVERT: B 457 ILE cc_start: 0.8359 (tp) cc_final: 0.8066 (pt) REVERT: B 468 ASP cc_start: 0.8620 (m-30) cc_final: 0.8182 (p0) REVERT: E 87 MET cc_start: 0.9036 (mmt) cc_final: 0.8660 (mmm) REVERT: E 172 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8127 (mtm) REVERT: E 182 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7585 (mm-40) REVERT: E 468 ASP cc_start: 0.8468 (m-30) cc_final: 0.8004 (p0) REVERT: C 172 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8223 (mmm) REVERT: C 457 ILE cc_start: 0.8312 (tp) cc_final: 0.8001 (pt) REVERT: C 468 ASP cc_start: 0.8575 (m-30) cc_final: 0.8164 (p0) REVERT: D 142 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8452 (pt) REVERT: D 179 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8737 (mtm) REVERT: D 295 MET cc_start: 0.8485 (tpp) cc_final: 0.8228 (mmm) REVERT: D 457 ILE cc_start: 0.8442 (tp) cc_final: 0.8176 (pt) REVERT: D 468 ASP cc_start: 0.8428 (m-30) cc_final: 0.8021 (p0) outliers start: 84 outliers final: 26 residues processed: 203 average time/residue: 0.4895 time to fit residues: 110.2469 Evaluate side-chains 171 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 329 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 HIS E 185 HIS ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.114330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.080598 restraints weight = 23260.440| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.92 r_work: 0.2860 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14000 Z= 0.248 Angle : 0.591 7.034 19040 Z= 0.318 Chirality : 0.046 0.151 2195 Planarity : 0.003 0.025 2335 Dihedral : 5.879 53.968 1967 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.31 % Allowed : 16.93 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.92 (0.21), residues: 1670 helix: 1.25 (0.22), residues: 570 sheet: 0.46 (0.25), residues: 405 loop : 0.33 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 241 TYR 0.025 0.002 TYR B 254 PHE 0.016 0.002 PHE C 177 TRP 0.007 0.001 TRP B 99 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00584 (13990) covalent geometry : angle 0.59023 (19015) SS BOND : bond 0.00121 ( 5) SS BOND : angle 0.55271 ( 10) hydrogen bonds : bond 0.04366 ( 721) hydrogen bonds : angle 4.94860 ( 2313) link_NAG-ASN : bond 0.00118 ( 5) link_NAG-ASN : angle 1.03437 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 153 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8098 (mm-40) REVERT: A 293 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8423 (mm) REVERT: A 457 ILE cc_start: 0.8331 (tp) cc_final: 0.8026 (pt) REVERT: B 87 MET cc_start: 0.9338 (mmp) cc_final: 0.8911 (mmt) REVERT: B 293 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8339 (mm) REVERT: B 308 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7613 (tppt) REVERT: B 457 ILE cc_start: 0.8381 (tp) cc_final: 0.8175 (pt) REVERT: B 468 ASP cc_start: 0.8571 (m-30) cc_final: 0.8024 (p0) REVERT: E 87 MET cc_start: 0.9064 (mmt) cc_final: 0.8706 (mmm) REVERT: E 108 LYS cc_start: 0.9423 (ttpp) cc_final: 0.9128 (ptmm) REVERT: E 123 LYS cc_start: 0.9396 (mmmm) cc_final: 0.9121 (mppt) REVERT: E 172 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8112 (mtm) REVERT: E 182 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7635 (mm-40) REVERT: E 468 ASP cc_start: 0.8476 (m-30) cc_final: 0.7958 (p0) REVERT: C 123 LYS cc_start: 0.9232 (mppt) cc_final: 0.8964 (mppt) REVERT: C 457 ILE cc_start: 0.8240 (tp) cc_final: 0.7914 (pt) REVERT: C 468 ASP cc_start: 0.8584 (m-30) cc_final: 0.8077 (p0) REVERT: D 142 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8484 (pt) REVERT: D 457 ILE cc_start: 0.8409 (tp) cc_final: 0.8126 (pt) REVERT: D 468 ASP cc_start: 0.8437 (m-30) cc_final: 0.7964 (p0) outliers start: 66 outliers final: 26 residues processed: 190 average time/residue: 0.5120 time to fit residues: 107.3480 Evaluate side-chains 168 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 172 MET Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 329 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 160 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS B 185 HIS E 185 HIS C 185 HIS D 185 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.115918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.082322 restraints weight = 23114.298| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.92 r_work: 0.2903 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14000 Z= 0.146 Angle : 0.538 7.849 19040 Z= 0.289 Chirality : 0.045 0.151 2195 Planarity : 0.003 0.027 2335 Dihedral : 5.737 53.655 1967 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.73 % Allowed : 18.04 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.04 (0.21), residues: 1670 helix: 1.40 (0.22), residues: 570 sheet: 0.48 (0.25), residues: 405 loop : 0.38 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 241 TYR 0.025 0.001 TYR C 254 PHE 0.015 0.002 PHE A 149 TRP 0.030 0.001 TRP A 271 HIS 0.003 0.001 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00331 (13990) covalent geometry : angle 0.53809 (19015) SS BOND : bond 0.00187 ( 5) SS BOND : angle 0.24117 ( 10) hydrogen bonds : bond 0.04086 ( 721) hydrogen bonds : angle 4.80159 ( 2313) link_NAG-ASN : bond 0.00213 ( 5) link_NAG-ASN : angle 0.85759 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 141 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 123 LYS cc_start: 0.9174 (mppt) cc_final: 0.8920 (mppt) REVERT: B 468 ASP cc_start: 0.8554 (m-30) cc_final: 0.7958 (p0) REVERT: E 87 MET cc_start: 0.9130 (mmt) cc_final: 0.8735 (mmm) REVERT: E 123 LYS cc_start: 0.9399 (mmmm) cc_final: 0.9009 (mtmm) REVERT: E 182 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7635 (mm-40) REVERT: C 457 ILE cc_start: 0.8214 (tp) cc_final: 0.7947 (pt) REVERT: C 468 ASP cc_start: 0.8522 (m-30) cc_final: 0.7974 (p0) REVERT: D 142 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8564 (pt) REVERT: D 457 ILE cc_start: 0.8218 (tp) cc_final: 0.7970 (pt) REVERT: D 468 ASP cc_start: 0.8451 (m-30) cc_final: 0.7950 (p0) outliers start: 57 outliers final: 32 residues processed: 183 average time/residue: 0.4874 time to fit residues: 99.0836 Evaluate side-chains 170 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN B 147 ASN B 185 HIS E 185 HIS C 185 HIS D 147 ASN D 185 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.078598 restraints weight = 23366.265| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.92 r_work: 0.2824 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 14000 Z= 0.296 Angle : 0.607 8.682 19040 Z= 0.325 Chirality : 0.047 0.179 2195 Planarity : 0.003 0.030 2335 Dihedral : 5.834 54.170 1965 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.90 % Allowed : 17.58 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.83 (0.21), residues: 1670 helix: 1.51 (0.22), residues: 540 sheet: 0.35 (0.24), residues: 430 loop : 0.05 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 103 TYR 0.020 0.002 TYR C 254 PHE 0.014 0.002 PHE D 323 TRP 0.045 0.002 TRP A 271 HIS 0.015 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00696 (13990) covalent geometry : angle 0.60643 (19015) SS BOND : bond 0.00084 ( 5) SS BOND : angle 0.47140 ( 10) hydrogen bonds : bond 0.04310 ( 721) hydrogen bonds : angle 4.97357 ( 2313) link_NAG-ASN : bond 0.00095 ( 5) link_NAG-ASN : angle 1.11251 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 147 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 457 ILE cc_start: 0.8298 (tp) cc_final: 0.8045 (pt) REVERT: B 135 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.8959 (tt0) REVERT: B 308 LYS cc_start: 0.7615 (ttmt) cc_final: 0.7197 (tppt) REVERT: B 468 ASP cc_start: 0.8610 (m-30) cc_final: 0.8044 (p0) REVERT: E 108 LYS cc_start: 0.9335 (ttpp) cc_final: 0.9089 (ptmm) REVERT: E 123 LYS cc_start: 0.9426 (mmmm) cc_final: 0.9039 (mtmm) REVERT: E 182 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8072 (mm-40) REVERT: E 468 ASP cc_start: 0.8621 (m-30) cc_final: 0.8400 (m-30) REVERT: C 123 LYS cc_start: 0.9276 (mppt) cc_final: 0.8986 (mppt) REVERT: C 457 ILE cc_start: 0.8194 (tp) cc_final: 0.7938 (pt) REVERT: D 142 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8594 (pt) REVERT: D 468 ASP cc_start: 0.8493 (m-30) cc_final: 0.7944 (p0) outliers start: 75 outliers final: 46 residues processed: 199 average time/residue: 0.4887 time to fit residues: 108.1317 Evaluate side-chains 191 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 453 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 109 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS B 147 ASN B 185 HIS E 185 HIS C 185 HIS D 147 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.114903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.080962 restraints weight = 23128.390| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.91 r_work: 0.2871 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14000 Z= 0.150 Angle : 0.554 9.722 19040 Z= 0.296 Chirality : 0.045 0.232 2195 Planarity : 0.003 0.032 2335 Dihedral : 5.708 53.815 1965 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.38 % Allowed : 17.71 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.87 (0.21), residues: 1670 helix: 1.51 (0.23), residues: 545 sheet: 0.33 (0.24), residues: 430 loop : 0.13 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 241 TYR 0.019 0.001 TYR E 254 PHE 0.015 0.002 PHE A 149 TRP 0.053 0.002 TRP D 271 HIS 0.014 0.001 HIS D 185 Details of bonding type rmsd covalent geometry : bond 0.00341 (13990) covalent geometry : angle 0.55321 (19015) SS BOND : bond 0.00156 ( 5) SS BOND : angle 0.48715 ( 10) hydrogen bonds : bond 0.04025 ( 721) hydrogen bonds : angle 4.82918 ( 2313) link_NAG-ASN : bond 0.00205 ( 5) link_NAG-ASN : angle 0.91325 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 147 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 PHE cc_start: 0.7436 (t80) cc_final: 0.7090 (t80) REVERT: B 135 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8870 (tt0) REVERT: B 468 ASP cc_start: 0.8549 (m-30) cc_final: 0.7915 (p0) REVERT: E 87 MET cc_start: 0.9076 (mmt) cc_final: 0.8739 (mmm) REVERT: E 108 LYS cc_start: 0.9287 (ttpp) cc_final: 0.9085 (ptmm) REVERT: E 123 LYS cc_start: 0.9425 (mmmm) cc_final: 0.9037 (mtmm) REVERT: E 182 GLN cc_start: 0.8324 (mm-40) cc_final: 0.7910 (mm-40) REVERT: C 123 LYS cc_start: 0.9242 (mppt) cc_final: 0.9029 (mppt) REVERT: C 457 ILE cc_start: 0.8158 (tp) cc_final: 0.7926 (pt) REVERT: D 142 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8523 (pt) REVERT: D 468 ASP cc_start: 0.8504 (m-30) cc_final: 0.8027 (p0) outliers start: 67 outliers final: 38 residues processed: 188 average time/residue: 0.4739 time to fit residues: 99.1217 Evaluate side-chains 183 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 185 HIS Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 15 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 157 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS B 147 ASN C 185 HIS D 147 ASN D 185 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.115342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.081238 restraints weight = 22937.935| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.90 r_work: 0.2881 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14000 Z= 0.150 Angle : 0.552 10.121 19040 Z= 0.294 Chirality : 0.045 0.183 2195 Planarity : 0.003 0.032 2335 Dihedral : 5.648 53.629 1965 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.99 % Allowed : 17.91 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.85 (0.21), residues: 1670 helix: 1.47 (0.23), residues: 545 sheet: 0.37 (0.24), residues: 430 loop : 0.10 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 241 TYR 0.014 0.001 TYR B 254 PHE 0.015 0.002 PHE A 149 TRP 0.063 0.003 TRP D 271 HIS 0.014 0.001 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00343 (13990) covalent geometry : angle 0.55127 (19015) SS BOND : bond 0.00139 ( 5) SS BOND : angle 0.56266 ( 10) hydrogen bonds : bond 0.03930 ( 721) hydrogen bonds : angle 4.77546 ( 2313) link_NAG-ASN : bond 0.00208 ( 5) link_NAG-ASN : angle 0.86136 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 149 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.9182 (mppt) cc_final: 0.8931 (mppt) REVERT: A 447 PHE cc_start: 0.7497 (t80) cc_final: 0.7228 (t80) REVERT: B 135 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8863 (tt0) REVERT: B 468 ASP cc_start: 0.8499 (m-30) cc_final: 0.7839 (p0) REVERT: E 87 MET cc_start: 0.9147 (mmt) cc_final: 0.8807 (mmm) REVERT: E 123 LYS cc_start: 0.9429 (mmmm) cc_final: 0.9044 (mtmm) REVERT: E 182 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8135 (mm-40) REVERT: C 123 LYS cc_start: 0.9267 (mppt) cc_final: 0.8950 (mtmm) REVERT: D 142 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8525 (pt) REVERT: D 468 ASP cc_start: 0.8505 (m-30) cc_final: 0.8027 (p0) outliers start: 61 outliers final: 37 residues processed: 187 average time/residue: 0.4874 time to fit residues: 101.2256 Evaluate side-chains 181 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 118 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 chunk 94 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS B 147 ASN B 185 HIS C 185 HIS D 147 ASN D 185 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.115782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.081793 restraints weight = 22976.346| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.90 r_work: 0.2885 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14000 Z= 0.148 Angle : 0.552 10.414 19040 Z= 0.295 Chirality : 0.045 0.229 2195 Planarity : 0.003 0.033 2335 Dihedral : 5.600 53.658 1965 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.92 % Allowed : 18.17 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.84 (0.21), residues: 1670 helix: 1.42 (0.23), residues: 545 sheet: 0.35 (0.24), residues: 440 loop : 0.16 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 241 TYR 0.013 0.001 TYR C 254 PHE 0.014 0.002 PHE C 149 TRP 0.070 0.003 TRP C 271 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00338 (13990) covalent geometry : angle 0.55148 (19015) SS BOND : bond 0.00148 ( 5) SS BOND : angle 0.26423 ( 10) hydrogen bonds : bond 0.03800 ( 721) hydrogen bonds : angle 4.72837 ( 2313) link_NAG-ASN : bond 0.00197 ( 5) link_NAG-ASN : angle 0.85088 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 154 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 ILE cc_start: 0.8718 (mt) cc_final: 0.8425 (pt) REVERT: B 135 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8862 (tt0) REVERT: E 87 MET cc_start: 0.9174 (mmt) cc_final: 0.8820 (mmm) REVERT: E 123 LYS cc_start: 0.9429 (mmmm) cc_final: 0.9042 (mtmm) REVERT: E 182 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8208 (mm-40) REVERT: C 123 LYS cc_start: 0.9255 (mppt) cc_final: 0.8951 (mtmm) REVERT: C 257 ILE cc_start: 0.8593 (mt) cc_final: 0.8354 (pt) REVERT: D 137 GLN cc_start: 0.8839 (mt0) cc_final: 0.8451 (mm-40) REVERT: D 142 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8538 (pt) REVERT: D 468 ASP cc_start: 0.8492 (m-30) cc_final: 0.8022 (p0) outliers start: 60 outliers final: 34 residues processed: 188 average time/residue: 0.4988 time to fit residues: 103.8795 Evaluate side-chains 180 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 107 optimal weight: 0.0770 chunk 132 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS B 147 ASN B 185 HIS C 185 HIS D 185 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.080907 restraints weight = 23042.361| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.94 r_work: 0.2876 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14000 Z= 0.165 Angle : 0.567 11.423 19040 Z= 0.301 Chirality : 0.046 0.219 2195 Planarity : 0.003 0.027 2335 Dihedral : 5.595 53.737 1965 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.40 % Allowed : 19.15 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.80 (0.21), residues: 1670 helix: 1.37 (0.23), residues: 545 sheet: 0.32 (0.24), residues: 440 loop : 0.13 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 241 TYR 0.013 0.001 TYR C 94 PHE 0.015 0.002 PHE D 323 TRP 0.071 0.003 TRP E 271 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00384 (13990) covalent geometry : angle 0.56637 (19015) SS BOND : bond 0.00118 ( 5) SS BOND : angle 0.23695 ( 10) hydrogen bonds : bond 0.03784 ( 721) hydrogen bonds : angle 4.74281 ( 2313) link_NAG-ASN : bond 0.00182 ( 5) link_NAG-ASN : angle 0.86918 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 123 LYS cc_start: 0.9189 (mppt) cc_final: 0.8915 (mppt) REVERT: B 135 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8873 (tt0) REVERT: B 295 MET cc_start: 0.8166 (mmm) cc_final: 0.7864 (tpt) REVERT: E 87 MET cc_start: 0.9186 (mmt) cc_final: 0.8807 (mmm) REVERT: E 123 LYS cc_start: 0.9442 (mmmm) cc_final: 0.9050 (mtmm) REVERT: E 182 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8275 (mm-40) REVERT: C 123 LYS cc_start: 0.9258 (mppt) cc_final: 0.8950 (mtmm) REVERT: D 74 MET cc_start: 0.9252 (ttm) cc_final: 0.8997 (ttp) REVERT: D 137 GLN cc_start: 0.8872 (mt0) cc_final: 0.8481 (mm-40) REVERT: D 142 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8574 (pt) REVERT: D 468 ASP cc_start: 0.8512 (m-30) cc_final: 0.7945 (p0) outliers start: 52 outliers final: 35 residues processed: 180 average time/residue: 0.5053 time to fit residues: 100.7457 Evaluate side-chains 180 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 6 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 145 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS B 147 ASN B 185 HIS C 185 HIS D 185 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.116270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.081717 restraints weight = 22962.753| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.93 r_work: 0.2896 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14000 Z= 0.141 Angle : 0.576 12.633 19040 Z= 0.303 Chirality : 0.046 0.206 2195 Planarity : 0.003 0.027 2335 Dihedral : 5.566 53.609 1965 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.01 % Allowed : 19.61 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.79 (0.21), residues: 1670 helix: 1.31 (0.23), residues: 545 sheet: 0.36 (0.24), residues: 440 loop : 0.14 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 241 TYR 0.014 0.001 TYR E 254 PHE 0.015 0.002 PHE D 323 TRP 0.069 0.003 TRP E 271 HIS 0.010 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00323 (13990) covalent geometry : angle 0.57596 (19015) SS BOND : bond 0.00165 ( 5) SS BOND : angle 0.28252 ( 10) hydrogen bonds : bond 0.03764 ( 721) hydrogen bonds : angle 4.68635 ( 2313) link_NAG-ASN : bond 0.00182 ( 5) link_NAG-ASN : angle 0.83149 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 144 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 LYS cc_start: 0.8972 (mtmm) cc_final: 0.8648 (mtmm) REVERT: B 295 MET cc_start: 0.8161 (mmm) cc_final: 0.7833 (tpt) REVERT: E 87 MET cc_start: 0.9138 (mmt) cc_final: 0.8787 (mmm) REVERT: E 123 LYS cc_start: 0.9431 (mmmm) cc_final: 0.9024 (mtmm) REVERT: E 182 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8193 (mm-40) REVERT: C 123 LYS cc_start: 0.9260 (mppt) cc_final: 0.9017 (mppt) REVERT: D 137 GLN cc_start: 0.8783 (mt0) cc_final: 0.8554 (mm-40) REVERT: D 142 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8485 (pt) REVERT: D 468 ASP cc_start: 0.8495 (m-30) cc_final: 0.7920 (p0) outliers start: 46 outliers final: 32 residues processed: 175 average time/residue: 0.5150 time to fit residues: 99.3843 Evaluate side-chains 175 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 114 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 145 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 138 optimal weight: 0.0980 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS B 147 ASN B 185 HIS C 185 HIS D 185 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.117025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.082629 restraints weight = 22882.056| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.94 r_work: 0.2908 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14000 Z= 0.134 Angle : 0.573 11.729 19040 Z= 0.299 Chirality : 0.046 0.192 2195 Planarity : 0.003 0.027 2335 Dihedral : 5.518 53.471 1965 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.42 % Allowed : 20.07 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.81 (0.21), residues: 1670 helix: 1.29 (0.23), residues: 545 sheet: 0.37 (0.24), residues: 440 loop : 0.18 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 241 TYR 0.014 0.001 TYR E 254 PHE 0.015 0.002 PHE D 323 TRP 0.067 0.003 TRP E 271 HIS 0.006 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00304 (13990) covalent geometry : angle 0.57243 (19015) SS BOND : bond 0.00122 ( 5) SS BOND : angle 0.20670 ( 10) hydrogen bonds : bond 0.03698 ( 721) hydrogen bonds : angle 4.68406 ( 2313) link_NAG-ASN : bond 0.00183 ( 5) link_NAG-ASN : angle 0.80484 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3592.75 seconds wall clock time: 62 minutes 14.83 seconds (3734.83 seconds total)