Starting phenix.real_space_refine on Sat Aug 23 21:45:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0a_36758/08_2025/8k0a_36758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0a_36758/08_2025/8k0a_36758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k0a_36758/08_2025/8k0a_36758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0a_36758/08_2025/8k0a_36758.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0a_36758/08_2025/8k0a_36758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0a_36758/08_2025/8k0a_36758.cif" } resolution = 3.12 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= 0.003 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 63 5.16 5 C 9435 2.51 5 N 2655 2.21 5 O 2799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 177 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14952 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3531 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 423} Chain breaks: 1 Chain: "B" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1453 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 166} Restraints were copied for chains: C, E, D, F Time building chain proxies: 3.12, per 1000 atoms: 0.21 Number of scatterers: 14952 At special positions: 0 Unit cell: (118.575, 112.625, 93.925, 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 63 16.00 O 2799 8.00 N 2655 7.00 C 9435 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 745.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 21 sheets defined 37.2% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 8 through 11 removed outlier: 3.617A pdb=" N GLN A 11 " --> pdb=" O ASN A 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 8 through 11' Processing helix chain 'A' and resid 22 through 26 Processing helix chain 'A' and resid 27 through 38 Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 169 through 179 removed outlier: 4.011A pdb=" N TYR A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A 176 " --> pdb=" O TRP A 172 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N MET A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 210 removed outlier: 3.635A pdb=" N ALA A 204 " --> pdb=" O TRP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.211A pdb=" N THR A 248 " --> pdb=" O PRO A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 295 removed outlier: 4.861A pdb=" N ALA A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 346 through 362 removed outlier: 3.632A pdb=" N GLY A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 removed outlier: 3.917A pdb=" N ASP A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 433 Processing helix chain 'A' and resid 436 through 452 removed outlier: 3.814A pdb=" N MET A 452 " --> pdb=" O GLN A 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 28 through 36 removed outlier: 3.597A pdb=" N LEU B 36 " --> pdb=" O TRP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 58 Processing helix chain 'B' and resid 70 through 83 Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.707A pdb=" N GLU B 90 " --> pdb=" O TRP B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 11 removed outlier: 3.617A pdb=" N GLN C 11 " --> pdb=" O ASN C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 8 through 11' Processing helix chain 'C' and resid 22 through 26 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 169 through 179 removed outlier: 4.010A pdb=" N TYR C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY C 176 " --> pdb=" O TRP C 172 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET C 177 " --> pdb=" O TYR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 210 removed outlier: 3.635A pdb=" N ALA C 204 " --> pdb=" O TRP C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 Processing helix chain 'C' and resid 218 through 226 Processing helix chain 'C' and resid 244 through 249 removed outlier: 4.211A pdb=" N THR C 248 " --> pdb=" O PRO C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 295 removed outlier: 4.861A pdb=" N ALA C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 346 through 362 removed outlier: 3.632A pdb=" N GLY C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 382 removed outlier: 3.918A pdb=" N ASP C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 433 Processing helix chain 'C' and resid 436 through 452 removed outlier: 3.813A pdb=" N MET C 452 " --> pdb=" O GLN C 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 26 Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.597A pdb=" N LEU D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 58 Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.707A pdb=" N GLU D 90 " --> pdb=" O TRP D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 11 removed outlier: 3.617A pdb=" N GLN E 11 " --> pdb=" O ASN E 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 8 through 11' Processing helix chain 'E' and resid 22 through 26 Processing helix chain 'E' and resid 27 through 38 Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 162 through 168 Processing helix chain 'E' and resid 169 through 179 removed outlier: 4.010A pdb=" N TYR E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY E 176 " --> pdb=" O TRP E 172 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N MET E 177 " --> pdb=" O TYR E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 210 removed outlier: 3.635A pdb=" N ALA E 204 " --> pdb=" O TRP E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 216 Processing helix chain 'E' and resid 218 through 226 Processing helix chain 'E' and resid 244 through 249 removed outlier: 4.211A pdb=" N THR E 248 " --> pdb=" O PRO E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 295 removed outlier: 4.861A pdb=" N ALA E 289 " --> pdb=" O ARG E 285 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 302 Processing helix chain 'E' and resid 346 through 362 removed outlier: 3.631A pdb=" N GLY E 362 " --> pdb=" O THR E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 382 removed outlier: 3.918A pdb=" N ASP E 371 " --> pdb=" O LEU E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 433 Processing helix chain 'E' and resid 436 through 452 removed outlier: 3.814A pdb=" N MET E 452 " --> pdb=" O GLN E 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 26 Processing helix chain 'F' and resid 28 through 36 removed outlier: 3.597A pdb=" N LEU F 36 " --> pdb=" O TRP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 58 Processing helix chain 'F' and resid 70 through 83 Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.707A pdb=" N GLU F 90 " --> pdb=" O TRP F 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.695A pdb=" N VAL A 20 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 48 removed outlier: 6.780A pdb=" N ILE A 152 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS A 144 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 82 removed outlier: 3.590A pdb=" N ASP A 66 " --> pdb=" O MET A 63 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP A 57 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 98 " --> pdb=" O PHE A 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 104 removed outlier: 3.532A pdb=" N ASP A 120 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY A 113 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 118 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 187 Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 187 removed outlier: 3.693A pdb=" N THR A 321 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 69 removed outlier: 6.454A pdb=" N MET B 44 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN B 68 " --> pdb=" O TYR B 42 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR B 42 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR B 43 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU B 158 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ARG B 45 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS B 140 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG B 154 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE B 138 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE B 156 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR B 136 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU B 158 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL B 134 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA B 114 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE B 104 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG B 116 " --> pdb=" O CYS B 102 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N CYS B 102 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 removed outlier: 3.695A pdb=" N VAL C 20 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 44 through 48 removed outlier: 6.779A pdb=" N ILE C 152 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS C 144 " --> pdb=" O ASN C 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 78 through 82 removed outlier: 3.591A pdb=" N ASP C 66 " --> pdb=" O MET C 63 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP C 57 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 98 " --> pdb=" O PHE C 58 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 102 through 104 removed outlier: 3.534A pdb=" N ASP C 120 " --> pdb=" O SER C 111 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY C 113 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU C 118 " --> pdb=" O GLY C 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 185 through 187 Processing sheet with id=AB4, first strand: chain 'C' and resid 185 through 187 removed outlier: 3.693A pdb=" N THR C 321 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 65 through 69 removed outlier: 6.455A pdb=" N MET D 44 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN D 68 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR D 42 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR D 43 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU D 158 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ARG D 45 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS D 140 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG D 154 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE D 138 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE D 156 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR D 136 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU D 158 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL D 134 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA D 114 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE D 104 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG D 116 " --> pdb=" O CYS D 102 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N CYS D 102 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.694A pdb=" N VAL E 20 " --> pdb=" O LEU E 392 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 44 through 48 removed outlier: 6.779A pdb=" N ILE E 152 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS E 144 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 78 through 82 removed outlier: 3.590A pdb=" N ASP E 66 " --> pdb=" O MET E 63 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP E 57 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY E 98 " --> pdb=" O PHE E 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 102 through 104 removed outlier: 3.534A pdb=" N ASP E 120 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY E 113 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU E 118 " --> pdb=" O GLY E 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AC2, first strand: chain 'E' and resid 185 through 187 removed outlier: 3.693A pdb=" N THR E 321 " --> pdb=" O LEU E 316 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 65 through 69 removed outlier: 6.455A pdb=" N MET F 44 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN F 68 " --> pdb=" O TYR F 42 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR F 42 " --> pdb=" O ASN F 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR F 43 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU F 158 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ARG F 45 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS F 140 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG F 154 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE F 138 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE F 156 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR F 136 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU F 158 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL F 134 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP F 129 " --> pdb=" O GLN F 125 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA F 114 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE F 104 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG F 116 " --> pdb=" O CYS F 102 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N CYS F 102 " --> pdb=" O ARG F 116 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1818 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: 2.23 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5052 1.34 - 1.46: 3483 1.46 - 1.58: 6702 1.58 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 15330 Sorted by residual: bond pdb=" C THR C 3 " pdb=" O THR C 3 " ideal model delta sigma weight residual 1.246 1.233 0.013 9.20e-03 1.18e+04 1.96e+00 bond pdb=" C THR E 3 " pdb=" O THR E 3 " ideal model delta sigma weight residual 1.246 1.234 0.012 9.20e-03 1.18e+04 1.81e+00 bond pdb=" C THR A 3 " pdb=" O THR A 3 " ideal model delta sigma weight residual 1.246 1.234 0.012 9.20e-03 1.18e+04 1.65e+00 bond pdb=" N GLY A 64 " pdb=" CA GLY A 64 " ideal model delta sigma weight residual 1.460 1.448 0.012 1.26e-02 6.30e+03 9.66e-01 bond pdb=" N GLY E 64 " pdb=" CA GLY E 64 " ideal model delta sigma weight residual 1.460 1.448 0.012 1.26e-02 6.30e+03 9.49e-01 ... (remaining 15325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 19280 1.05 - 2.11: 1221 2.11 - 3.16: 218 3.16 - 4.22: 59 4.22 - 5.27: 21 Bond angle restraints: 20799 Sorted by residual: angle pdb=" N ILE D 66 " pdb=" CA ILE D 66 " pdb=" C ILE D 66 " ideal model delta sigma weight residual 112.12 109.88 2.24 8.40e-01 1.42e+00 7.12e+00 angle pdb=" N ILE B 66 " pdb=" CA ILE B 66 " pdb=" C ILE B 66 " ideal model delta sigma weight residual 112.12 109.88 2.24 8.40e-01 1.42e+00 7.10e+00 angle pdb=" N ILE F 66 " pdb=" CA ILE F 66 " pdb=" C ILE F 66 " ideal model delta sigma weight residual 112.12 109.89 2.23 8.40e-01 1.42e+00 7.02e+00 angle pdb=" N THR E 312 " pdb=" CA THR E 312 " pdb=" C THR E 312 " ideal model delta sigma weight residual 111.56 114.92 -3.36 1.38e+00 5.25e-01 5.92e+00 angle pdb=" N THR C 312 " pdb=" CA THR C 312 " pdb=" C THR C 312 " ideal model delta sigma weight residual 111.56 114.90 -3.34 1.38e+00 5.25e-01 5.87e+00 ... (remaining 20794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 8106 17.53 - 35.07: 688 35.07 - 52.60: 149 52.60 - 70.13: 36 70.13 - 87.67: 42 Dihedral angle restraints: 9021 sinusoidal: 3687 harmonic: 5334 Sorted by residual: dihedral pdb=" CA ASP E 210 " pdb=" C ASP E 210 " pdb=" N GLN E 211 " pdb=" CA GLN E 211 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASP C 210 " pdb=" C ASP C 210 " pdb=" N GLN C 211 " pdb=" CA GLN C 211 " ideal model delta harmonic sigma weight residual 180.00 155.96 24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASP A 210 " pdb=" C ASP A 210 " pdb=" N GLN A 211 " pdb=" CA GLN A 211 " ideal model delta harmonic sigma weight residual 180.00 155.97 24.03 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 9018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1234 0.030 - 0.059: 565 0.059 - 0.089: 222 0.089 - 0.118: 107 0.118 - 0.148: 41 Chirality restraints: 2169 Sorted by residual: chirality pdb=" CA VAL C 191 " pdb=" N VAL C 191 " pdb=" C VAL C 191 " pdb=" CB VAL C 191 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA VAL E 191 " pdb=" N VAL E 191 " pdb=" C VAL E 191 " pdb=" CB VAL E 191 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA VAL A 191 " pdb=" N VAL A 191 " pdb=" C VAL A 191 " pdb=" CB VAL A 191 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2166 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 310 " -0.034 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO E 311 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 311 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 311 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 310 " -0.034 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO A 311 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 310 " -0.034 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO C 311 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 311 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 311 " -0.028 5.00e-02 4.00e+02 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 823 2.73 - 3.27: 13982 3.27 - 3.82: 23450 3.82 - 4.36: 29490 4.36 - 4.90: 52743 Nonbonded interactions: 120488 Sorted by model distance: nonbonded pdb=" OD2 ASP A 238 " pdb=" OG SER A 282 " model vdw 2.189 3.040 nonbonded pdb=" OD2 ASP C 238 " pdb=" OG SER C 282 " model vdw 2.190 3.040 nonbonded pdb=" OD2 ASP E 238 " pdb=" OG SER E 282 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR E 241 " pdb=" O ALA E 272 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR A 241 " pdb=" O ALA A 272 " model vdw 2.192 3.040 ... (remaining 120483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 21.590 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: 0.550 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.990 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15330 Z= 0.144 Angle : 0.609 5.273 20799 Z= 0.365 Chirality : 0.045 0.148 2169 Planarity : 0.004 0.053 2736 Dihedral : 15.541 87.666 5589 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: -0.50 (0.20), residues: 1827 helix: 0.64 (0.23), residues: 597 sheet: 0.62 (0.27), residues: 366 loop : -1.49 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 76 TYR 0.028 0.001 TYR E 107 PHE 0.012 0.001 PHE C 310 TRP 0.026 0.002 TRP E 428 HIS 0.005 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00298 (15330) covalent geometry : angle 0.60870 (20799) hydrogen bonds : bond 0.14118 ( 648) hydrogen bonds : angle 5.86345 ( 1818) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.451 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1461 time to fit residues: 42.7982 Evaluate side-chains 121 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 211 GLN A 213 HIS B 73 GLN C 73 GLN C 211 GLN D 73 GLN E 73 GLN E 211 GLN F 73 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.066981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.052696 restraints weight = 41758.984| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.81 r_work: 0.2546 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 15330 Z= 0.197 Angle : 0.546 5.196 20799 Z= 0.296 Chirality : 0.043 0.136 2169 Planarity : 0.004 0.039 2736 Dihedral : 5.089 47.779 2049 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.08 % Allowed : 6.17 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.10 (0.20), residues: 1827 helix: 1.38 (0.23), residues: 606 sheet: 0.34 (0.27), residues: 381 loop : -1.06 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 164 TYR 0.022 0.001 TYR E 107 PHE 0.019 0.001 PHE A 216 TRP 0.019 0.001 TRP E 428 HIS 0.005 0.001 HIS C 108 Details of bonding type rmsd covalent geometry : bond 0.00457 (15330) covalent geometry : angle 0.54628 (20799) hydrogen bonds : bond 0.04528 ( 648) hydrogen bonds : angle 4.85342 ( 1818) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 210 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.7703 (t0) outliers start: 17 outliers final: 10 residues processed: 145 average time/residue: 0.1306 time to fit residues: 27.5499 Evaluate side-chains 122 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 169 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 75 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN C 213 HIS D 73 GLN E 213 HIS F 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.067171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.052799 restraints weight = 41982.462| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.84 r_work: 0.2558 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15330 Z= 0.162 Angle : 0.502 5.001 20799 Z= 0.270 Chirality : 0.043 0.134 2169 Planarity : 0.003 0.040 2736 Dihedral : 4.940 50.476 2049 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.34 % Allowed : 7.70 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.38 (0.21), residues: 1827 helix: 1.74 (0.23), residues: 606 sheet: 0.39 (0.27), residues: 363 loop : -0.90 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 164 TYR 0.017 0.001 TYR C 107 PHE 0.010 0.001 PHE D 138 TRP 0.018 0.001 TRP E 428 HIS 0.004 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00376 (15330) covalent geometry : angle 0.50159 (20799) hydrogen bonds : bond 0.04038 ( 648) hydrogen bonds : angle 4.59875 ( 1818) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.662 Fit side-chains REVERT: A 243 ARG cc_start: 0.7378 (mmt180) cc_final: 0.6925 (mmp-170) REVERT: C 65 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8154 (mt-10) REVERT: C 210 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.7553 (t0) REVERT: C 243 ARG cc_start: 0.7377 (mmt180) cc_final: 0.7076 (mmp-170) REVERT: E 243 ARG cc_start: 0.7398 (mmt180) cc_final: 0.7006 (mmp-170) outliers start: 21 outliers final: 13 residues processed: 142 average time/residue: 0.1273 time to fit residues: 26.2360 Evaluate side-chains 123 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 169 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 170 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN F 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.068549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.054390 restraints weight = 41436.348| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.80 r_work: 0.2600 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15330 Z= 0.097 Angle : 0.452 5.369 20799 Z= 0.241 Chirality : 0.041 0.131 2169 Planarity : 0.003 0.035 2736 Dihedral : 4.641 50.445 2049 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.27 % Allowed : 9.16 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.72 (0.21), residues: 1827 helix: 2.14 (0.23), residues: 588 sheet: 0.54 (0.28), residues: 363 loop : -0.71 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 164 TYR 0.010 0.001 TYR A 107 PHE 0.007 0.001 PHE E 216 TRP 0.015 0.001 TRP A 428 HIS 0.002 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00220 (15330) covalent geometry : angle 0.45164 (20799) hydrogen bonds : bond 0.03302 ( 648) hydrogen bonds : angle 4.41381 ( 1818) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7393 (mmt180) cc_final: 0.6910 (mmp-170) REVERT: A 312 THR cc_start: 0.9561 (p) cc_final: 0.9067 (t) REVERT: C 210 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.7547 (t70) REVERT: C 243 ARG cc_start: 0.7366 (mmt180) cc_final: 0.7060 (mmp-170) REVERT: C 312 THR cc_start: 0.9546 (p) cc_final: 0.9045 (t) REVERT: E 90 MET cc_start: 0.9181 (tpt) cc_final: 0.8928 (tpt) REVERT: E 243 ARG cc_start: 0.7385 (mmt180) cc_final: 0.6930 (mmp-170) REVERT: E 312 THR cc_start: 0.9546 (p) cc_final: 0.9062 (t) outliers start: 20 outliers final: 10 residues processed: 151 average time/residue: 0.1266 time to fit residues: 27.6715 Evaluate side-chains 123 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 381 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 32 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 135 optimal weight: 0.2980 chunk 156 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 152 optimal weight: 0.3980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN F 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.066786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.052620 restraints weight = 42081.008| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 3.81 r_work: 0.2555 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 15330 Z= 0.154 Angle : 0.487 6.224 20799 Z= 0.259 Chirality : 0.042 0.136 2169 Planarity : 0.003 0.036 2736 Dihedral : 4.695 48.958 2049 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.72 % Allowed : 9.86 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.85 (0.21), residues: 1827 helix: 2.23 (0.23), residues: 591 sheet: 0.60 (0.28), residues: 363 loop : -0.63 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 164 TYR 0.022 0.001 TYR B 119 PHE 0.010 0.001 PHE B 138 TRP 0.014 0.001 TRP A 428 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00359 (15330) covalent geometry : angle 0.48651 (20799) hydrogen bonds : bond 0.03862 ( 648) hydrogen bonds : angle 4.49014 ( 1818) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.509 Fit side-chains REVERT: A 243 ARG cc_start: 0.7425 (mmt180) cc_final: 0.6895 (mmp-170) REVERT: A 312 THR cc_start: 0.9571 (p) cc_final: 0.9050 (t) REVERT: C 210 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.7669 (t70) REVERT: C 243 ARG cc_start: 0.7394 (mmt180) cc_final: 0.7081 (mmp-170) REVERT: C 312 THR cc_start: 0.9557 (p) cc_final: 0.9031 (t) REVERT: E 243 ARG cc_start: 0.7439 (mmt180) cc_final: 0.6953 (mmp-170) REVERT: E 312 THR cc_start: 0.9559 (p) cc_final: 0.9028 (t) outliers start: 27 outliers final: 17 residues processed: 145 average time/residue: 0.1286 time to fit residues: 26.9091 Evaluate side-chains 131 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain D residue 73 GLN Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 169 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 134 optimal weight: 0.0470 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 49 optimal weight: 0.0770 chunk 138 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 overall best weight: 0.8038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN C 254 GLN D 73 GLN E 254 GLN ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.068388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.054289 restraints weight = 41235.244| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 3.74 r_work: 0.2601 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15330 Z= 0.092 Angle : 0.454 7.461 20799 Z= 0.238 Chirality : 0.041 0.140 2169 Planarity : 0.003 0.035 2736 Dihedral : 4.488 48.780 2049 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.46 % Allowed : 10.62 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.95 (0.21), residues: 1827 helix: 2.31 (0.23), residues: 588 sheet: 0.68 (0.28), residues: 363 loop : -0.55 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 76 TYR 0.008 0.001 TYR C 107 PHE 0.006 0.001 PHE F 138 TRP 0.015 0.001 TRP A 428 HIS 0.002 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00211 (15330) covalent geometry : angle 0.45371 (20799) hydrogen bonds : bond 0.03135 ( 648) hydrogen bonds : angle 4.36764 ( 1818) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7410 (mmt180) cc_final: 0.6890 (mmp-170) REVERT: A 312 THR cc_start: 0.9564 (p) cc_final: 0.9063 (t) REVERT: A 369 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6816 (mt0) REVERT: B 126 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7346 (pttm) REVERT: C 210 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.7941 (t70) REVERT: C 243 ARG cc_start: 0.7424 (mmt180) cc_final: 0.7118 (mmp-170) REVERT: C 312 THR cc_start: 0.9547 (p) cc_final: 0.9032 (t) REVERT: D 126 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7377 (pttm) REVERT: E 210 ASP cc_start: 0.8575 (m-30) cc_final: 0.7720 (t0) REVERT: E 243 ARG cc_start: 0.7412 (mmt180) cc_final: 0.6939 (mmp-170) REVERT: F 126 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7276 (pttm) outliers start: 23 outliers final: 17 residues processed: 153 average time/residue: 0.1264 time to fit residues: 28.0259 Evaluate side-chains 136 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain D residue 73 GLN Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 359 ARG Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 126 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 175 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.067595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.053406 restraints weight = 41320.020| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.81 r_work: 0.2584 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15330 Z= 0.133 Angle : 0.471 6.802 20799 Z= 0.248 Chirality : 0.042 0.137 2169 Planarity : 0.003 0.062 2736 Dihedral : 4.511 47.825 2049 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.65 % Allowed : 11.83 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.02 (0.21), residues: 1827 helix: 2.35 (0.23), residues: 591 sheet: 0.67 (0.28), residues: 363 loop : -0.49 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 323 TYR 0.011 0.001 TYR E 107 PHE 0.009 0.001 PHE B 138 TRP 0.015 0.001 TRP A 194 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00312 (15330) covalent geometry : angle 0.47080 (20799) hydrogen bonds : bond 0.03482 ( 648) hydrogen bonds : angle 4.37412 ( 1818) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7449 (mmt180) cc_final: 0.6921 (mmp-170) REVERT: A 369 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6820 (mt0) REVERT: B 126 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7541 (pttm) REVERT: C 210 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.7989 (t70) REVERT: C 243 ARG cc_start: 0.7463 (mmt180) cc_final: 0.7145 (mmp-170) REVERT: C 369 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6804 (mt0) REVERT: E 243 ARG cc_start: 0.7434 (mmt180) cc_final: 0.6944 (mmp-170) REVERT: F 126 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7599 (pttm) outliers start: 26 outliers final: 17 residues processed: 141 average time/residue: 0.1292 time to fit residues: 26.0750 Evaluate side-chains 131 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 369 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 359 ARG Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 169 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 114 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 171 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 98 optimal weight: 0.0170 chunk 33 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.068015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.053748 restraints weight = 41557.829| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.84 r_work: 0.2589 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15330 Z= 0.122 Angle : 0.473 8.778 20799 Z= 0.248 Chirality : 0.042 0.185 2169 Planarity : 0.003 0.039 2736 Dihedral : 4.487 47.153 2049 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.21 % Allowed : 12.60 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.05 (0.21), residues: 1827 helix: 2.36 (0.23), residues: 591 sheet: 0.70 (0.28), residues: 363 loop : -0.46 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 76 TYR 0.010 0.001 TYR A 107 PHE 0.008 0.001 PHE F 138 TRP 0.014 0.001 TRP E 194 HIS 0.002 0.001 HIS C 108 Details of bonding type rmsd covalent geometry : bond 0.00284 (15330) covalent geometry : angle 0.47331 (20799) hydrogen bonds : bond 0.03382 ( 648) hydrogen bonds : angle 4.37031 ( 1818) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7465 (mmt180) cc_final: 0.6937 (mmp-170) REVERT: A 369 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6761 (mt0) REVERT: C 210 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.7973 (t70) REVERT: C 243 ARG cc_start: 0.7489 (mmt180) cc_final: 0.7166 (mmp-170) REVERT: D 126 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7520 (pttm) REVERT: E 210 ASP cc_start: 0.8609 (m-30) cc_final: 0.7755 (t0) REVERT: E 243 ARG cc_start: 0.7436 (mmt180) cc_final: 0.6937 (mmp-170) outliers start: 19 outliers final: 13 residues processed: 130 average time/residue: 0.1296 time to fit residues: 24.6380 Evaluate side-chains 122 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 359 ARG Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 169 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 103 optimal weight: 0.0270 chunk 135 optimal weight: 0.0030 chunk 146 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 overall best weight: 0.4448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.070631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.056553 restraints weight = 40848.888| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.82 r_work: 0.2626 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15330 Z= 0.081 Angle : 0.450 7.928 20799 Z= 0.235 Chirality : 0.041 0.146 2169 Planarity : 0.003 0.034 2736 Dihedral : 4.242 44.605 2049 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.64 % Allowed : 13.49 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.20 (0.21), residues: 1827 helix: 2.74 (0.23), residues: 567 sheet: 0.81 (0.29), residues: 333 loop : -0.45 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 76 TYR 0.006 0.001 TYR E 107 PHE 0.007 0.001 PHE C 361 TRP 0.016 0.001 TRP A 194 HIS 0.002 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00181 (15330) covalent geometry : angle 0.45029 (20799) hydrogen bonds : bond 0.02828 ( 648) hydrogen bonds : angle 4.23164 ( 1818) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 210 ASP cc_start: 0.8308 (m-30) cc_final: 0.8004 (t70) REVERT: A 243 ARG cc_start: 0.7398 (mmt180) cc_final: 0.6885 (mmp-170) REVERT: A 369 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6593 (mt0) REVERT: B 126 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7273 (pttm) REVERT: C 243 ARG cc_start: 0.7486 (mmt180) cc_final: 0.7176 (mmp-170) REVERT: D 57 LYS cc_start: 0.9187 (ptpp) cc_final: 0.8986 (mtmm) REVERT: D 139 ASP cc_start: 0.7968 (m-30) cc_final: 0.7737 (m-30) REVERT: E 90 MET cc_start: 0.9107 (tpt) cc_final: 0.8906 (tpt) REVERT: E 210 ASP cc_start: 0.8396 (m-30) cc_final: 0.7937 (t70) REVERT: E 243 ARG cc_start: 0.7395 (mmt180) cc_final: 0.6912 (mmp-170) REVERT: F 75 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8641 (tm-30) outliers start: 10 outliers final: 8 residues processed: 146 average time/residue: 0.1385 time to fit residues: 28.1458 Evaluate side-chains 125 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 142 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.068477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.054427 restraints weight = 41373.661| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.76 r_work: 0.2601 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15330 Z= 0.130 Angle : 0.485 8.407 20799 Z= 0.253 Chirality : 0.042 0.152 2169 Planarity : 0.003 0.039 2736 Dihedral : 4.334 43.956 2049 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.89 % Allowed : 13.17 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.27 (0.21), residues: 1827 helix: 2.78 (0.23), residues: 570 sheet: 0.82 (0.29), residues: 333 loop : -0.40 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 76 TYR 0.010 0.001 TYR E 107 PHE 0.009 0.001 PHE E 338 TRP 0.012 0.001 TRP E 194 HIS 0.002 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00306 (15330) covalent geometry : angle 0.48478 (20799) hydrogen bonds : bond 0.03372 ( 648) hydrogen bonds : angle 4.30690 ( 1818) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 210 ASP cc_start: 0.8424 (m-30) cc_final: 0.7864 (t70) REVERT: A 243 ARG cc_start: 0.7455 (mmt180) cc_final: 0.6929 (mmp-170) REVERT: A 368 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8139 (mt-10) REVERT: A 369 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6729 (mt0) REVERT: B 126 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7400 (pttm) REVERT: C 243 ARG cc_start: 0.7516 (mmt180) cc_final: 0.7196 (mmp-170) REVERT: E 210 ASP cc_start: 0.8495 (m-30) cc_final: 0.7704 (t0) REVERT: E 243 ARG cc_start: 0.7448 (mmt180) cc_final: 0.6938 (mmp-170) outliers start: 14 outliers final: 11 residues processed: 134 average time/residue: 0.1350 time to fit residues: 25.8301 Evaluate side-chains 129 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 369 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain C residue 275 TRP Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 275 TRP Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 359 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 150 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.068659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.054484 restraints weight = 41045.800| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.79 r_work: 0.2584 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15330 Z= 0.122 Angle : 0.482 8.199 20799 Z= 0.250 Chirality : 0.042 0.142 2169 Planarity : 0.003 0.058 2736 Dihedral : 4.345 43.682 2049 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.89 % Allowed : 13.30 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.25 (0.21), residues: 1827 helix: 2.73 (0.23), residues: 570 sheet: 0.83 (0.28), residues: 333 loop : -0.39 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 323 TYR 0.010 0.001 TYR C 62 PHE 0.008 0.001 PHE A 338 TRP 0.013 0.001 TRP A 194 HIS 0.002 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00284 (15330) covalent geometry : angle 0.48168 (20799) hydrogen bonds : bond 0.03297 ( 648) hydrogen bonds : angle 4.29692 ( 1818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3007.56 seconds wall clock time: 52 minutes 33.33 seconds (3153.33 seconds total)