Starting phenix.real_space_refine on Thu Oct 29 16:30:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/37ix_78219/10_2026/37ix_78219.cif Found real_map, /net/cci-nas-00/data/ceres_data/37ix_78219/10_2026/37ix_78219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/37ix_78219/10_2026/37ix_78219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/37ix_78219/10_2026/37ix_78219.map" model { file = "/net/cci-nas-00/data/ceres_data/37ix_78219/10_2026/37ix_78219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/37ix_78219/10_2026/37ix_78219.cif" } resolution = 2.4 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= 0.154 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 10386 2.51 5 N 2676 2.21 5 O 3126 1.98 5 H 16038 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32292 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5382 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 328} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 6.65, per 1000 atoms: 0.21 Number of scatterers: 32292 At special positions: 0 Unit cell: (115.867, 115.867, 126.497, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 O 3126 8.00 N 2676 7.00 C 10386 6.00 H 16038 1.00 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: 2.95 Conformation dependent library (CDL) restraints added in 814.8 milliseconds 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3792 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 42 sheets defined 30.0% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 239 through 249 Processing helix chain 'A' and resid 287 through 303 Processing helix chain 'B' and resid 1 through 12 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 75 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'B' and resid 287 through 303 Processing helix chain 'C' and resid 1 through 12 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 197 through 206 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 239 through 249 Processing helix chain 'C' and resid 287 through 303 Processing helix chain 'D' and resid 1 through 12 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 197 through 206 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 239 through 249 Processing helix chain 'D' and resid 287 through 303 Processing helix chain 'E' and resid 1 through 12 Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 75 Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 149 through 151 No H-bonds generated for 'chain 'E' and resid 149 through 151' Processing helix chain 'E' and resid 197 through 206 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 217 through 219 No H-bonds generated for 'chain 'E' and resid 217 through 219' Processing helix chain 'E' and resid 220 through 225 Processing helix chain 'E' and resid 239 through 249 Processing helix chain 'E' and resid 287 through 303 Processing helix chain 'F' and resid 1 through 12 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 119 through 121 No H-bonds generated for 'chain 'F' and resid 119 through 121' Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'F' and resid 197 through 206 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 217 through 219 No H-bonds generated for 'chain 'F' and resid 217 through 219' Processing helix chain 'F' and resid 220 through 225 Processing helix chain 'F' and resid 239 through 249 Processing helix chain 'F' and resid 287 through 303 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.743A pdb=" N VAL A 31 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.560A pdb=" N THR A 80 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL A 79 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N ASP A 117 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ASN A 81 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.560A pdb=" N THR A 80 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL A 79 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N ASP A 117 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ASN A 81 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 258 removed outlier: 7.759A pdb=" N ASN A 267 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL A 270 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN A 279 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA A 272 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR A 277 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 314 removed outlier: 5.846A pdb=" N GLU A 326 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.743A pdb=" N VAL B 31 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.560A pdb=" N THR B 80 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL B 79 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N ASP B 117 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ASN B 81 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.560A pdb=" N THR B 80 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL B 79 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N ASP B 117 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ASN B 81 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 258 removed outlier: 7.759A pdb=" N ASN B 267 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL B 270 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLN B 279 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA B 272 " --> pdb=" O TYR B 277 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR B 277 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 307 through 314 removed outlier: 5.847A pdb=" N GLU B 326 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 24 through 27 removed outlier: 6.743A pdb=" N VAL C 31 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AB8, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.560A pdb=" N THR C 80 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL C 79 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ASP C 117 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ASN C 81 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.560A pdb=" N THR C 80 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL C 79 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ASP C 117 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ASN C 81 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AC2, first strand: chain 'C' and resid 252 through 258 removed outlier: 7.759A pdb=" N ASN C 267 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL C 270 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN C 279 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA C 272 " --> pdb=" O TYR C 277 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR C 277 " --> pdb=" O ALA C 272 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 307 through 314 removed outlier: 5.848A pdb=" N GLU C 326 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.743A pdb=" N VAL D 31 " --> pdb=" O VAL D 42 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AC6, first strand: chain 'D' and resid 98 through 99 removed outlier: 6.560A pdb=" N THR D 80 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL D 79 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ASP D 117 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ASN D 81 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 98 through 99 removed outlier: 6.560A pdb=" N THR D 80 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL D 79 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ASP D 117 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ASN D 81 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AC9, first strand: chain 'D' and resid 252 through 258 removed outlier: 7.759A pdb=" N ASN D 267 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL D 270 " --> pdb=" O GLN D 279 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN D 279 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA D 272 " --> pdb=" O TYR D 277 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR D 277 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 307 through 314 removed outlier: 5.846A pdb=" N GLU D 326 " --> pdb=" O ILE D 330 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE D 330 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 24 through 27 removed outlier: 6.744A pdb=" N VAL E 31 " --> pdb=" O VAL E 42 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 66 through 67 Processing sheet with id=AD4, first strand: chain 'E' and resid 98 through 99 removed outlier: 6.560A pdb=" N THR E 80 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL E 79 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ASP E 117 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ASN E 81 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 98 through 99 removed outlier: 6.560A pdb=" N THR E 80 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL E 79 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ASP E 117 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ASN E 81 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AD7, first strand: chain 'E' and resid 252 through 258 removed outlier: 7.759A pdb=" N ASN E 267 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VAL E 270 " --> pdb=" O GLN E 279 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLN E 279 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA E 272 " --> pdb=" O TYR E 277 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR E 277 " --> pdb=" O ALA E 272 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 307 through 314 removed outlier: 5.847A pdb=" N GLU E 326 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE E 330 " --> pdb=" O GLU E 326 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.743A pdb=" N VAL F 31 " --> pdb=" O VAL F 42 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 66 through 67 Processing sheet with id=AE2, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.560A pdb=" N THR F 80 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL F 79 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ASP F 117 " --> pdb=" O VAL F 79 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ASN F 81 " --> pdb=" O ASP F 117 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.560A pdb=" N THR F 80 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL F 79 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ASP F 117 " --> pdb=" O VAL F 79 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ASN F 81 " --> pdb=" O ASP F 117 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AE5, first strand: chain 'F' and resid 252 through 258 removed outlier: 7.760A pdb=" N ASN F 267 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL F 270 " --> pdb=" O GLN F 279 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN F 279 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA F 272 " --> pdb=" O TYR F 277 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR F 277 " --> pdb=" O ALA F 272 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 307 through 314 removed outlier: 5.846A pdb=" N GLU F 326 " --> pdb=" O ILE F 330 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE F 330 " --> pdb=" O GLU F 326 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 1926 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: 7.23 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.04: 4016 1.04 - 1.23: 14149 1.23 - 1.43: 5055 1.43 - 1.62: 9300 1.62 - 1.82: 102 Bond restraints: 32622 Sorted by residual: bond pdb=" N LEU B 134 " pdb=" H LEU B 134 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" CE1 TYR C 226 " pdb=" HE1 TYR C 226 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" CE2 PHE D 321 " pdb=" HE2 PHE D 321 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N LEU F 134 " pdb=" H LEU F 134 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" CE2 TYR F 334 " pdb=" HE2 TYR F 334 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.74e+01 ... (remaining 32617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 49804 2.64 - 5.28: 7057 5.28 - 7.92: 1868 7.92 - 10.56: 59 10.56 - 13.20: 30 Bond angle restraints: 58818 Sorted by residual: angle pdb=" CA GLY D 12 " pdb=" C GLY D 12 " pdb=" N GLY D 13 " ideal model delta sigma weight residual 114.65 119.70 -5.05 9.20e-01 1.18e+00 3.01e+01 angle pdb=" CA GLY B 12 " pdb=" C GLY B 12 " pdb=" N GLY B 13 " ideal model delta sigma weight residual 114.65 119.70 -5.05 9.20e-01 1.18e+00 3.01e+01 angle pdb=" CA GLY A 12 " pdb=" C GLY A 12 " pdb=" N GLY A 13 " ideal model delta sigma weight residual 114.65 119.68 -5.03 9.20e-01 1.18e+00 2.99e+01 angle pdb=" CA GLY C 12 " pdb=" C GLY C 12 " pdb=" N GLY C 13 " ideal model delta sigma weight residual 114.65 119.67 -5.02 9.20e-01 1.18e+00 2.98e+01 angle pdb=" CA GLY E 12 " pdb=" C GLY E 12 " pdb=" N GLY E 13 " ideal model delta sigma weight residual 114.65 119.66 -5.01 9.20e-01 1.18e+00 2.97e+01 ... (remaining 58813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 13846 16.70 - 33.40: 920 33.40 - 50.10: 223 50.10 - 66.80: 395 66.80 - 83.50: 24 Dihedral angle restraints: 15408 sinusoidal: 8322 harmonic: 7086 Sorted by residual: dihedral pdb=" CA TYR B 268 " pdb=" C TYR B 268 " pdb=" N PHE B 269 " pdb=" CA PHE B 269 " ideal model delta harmonic sigma weight residual 180.00 152.55 27.45 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA TYR C 268 " pdb=" C TYR C 268 " pdb=" N PHE C 269 " pdb=" CA PHE C 269 " ideal model delta harmonic sigma weight residual 180.00 152.58 27.42 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA TYR A 268 " pdb=" C TYR A 268 " pdb=" N PHE A 269 " pdb=" CA PHE A 269 " ideal model delta harmonic sigma weight residual 180.00 152.59 27.41 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 15405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1300 0.062 - 0.124: 818 0.124 - 0.186: 326 0.186 - 0.248: 58 0.248 - 0.310: 42 Chirality restraints: 2544 Sorted by residual: chirality pdb=" CB THR F 27 " pdb=" CA THR F 27 " pdb=" OG1 THR F 27 " pdb=" CG2 THR F 27 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB THR B 27 " pdb=" CA THR B 27 " pdb=" OG1 THR B 27 " pdb=" CG2 THR B 27 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB THR C 27 " pdb=" CA THR C 27 " pdb=" OG1 THR C 27 " pdb=" CG2 THR C 27 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 2541 not shown) Planarity restraints: 4878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 196 " 0.409 9.50e-02 1.11e+02 4.09e-01 3.37e+03 pdb=" NE ARG D 196 " 0.231 2.00e-02 2.50e+03 pdb=" CZ ARG D 196 " 0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG D 196 " -0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG D 196 " -0.015 2.00e-02 2.50e+03 pdb="HH11 ARG D 196 " 0.662 2.00e-02 2.50e+03 pdb="HH12 ARG D 196 " -0.832 2.00e-02 2.50e+03 pdb="HH21 ARG D 196 " 0.230 2.00e-02 2.50e+03 pdb="HH22 ARG D 196 " -0.311 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 196 " -0.408 9.50e-02 1.11e+02 4.09e-01 3.37e+03 pdb=" NE ARG C 196 " -0.231 2.00e-02 2.50e+03 pdb=" CZ ARG C 196 " -0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG C 196 " 0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG C 196 " 0.014 2.00e-02 2.50e+03 pdb="HH11 ARG C 196 " -0.662 2.00e-02 2.50e+03 pdb="HH12 ARG C 196 " 0.832 2.00e-02 2.50e+03 pdb="HH21 ARG C 196 " -0.229 2.00e-02 2.50e+03 pdb="HH22 ARG C 196 " 0.311 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 196 " -0.409 9.50e-02 1.11e+02 4.09e-01 3.37e+03 pdb=" NE ARG B 196 " -0.231 2.00e-02 2.50e+03 pdb=" CZ ARG B 196 " -0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG B 196 " 0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG B 196 " 0.015 2.00e-02 2.50e+03 pdb="HH11 ARG B 196 " -0.662 2.00e-02 2.50e+03 pdb="HH12 ARG B 196 " 0.832 2.00e-02 2.50e+03 pdb="HH21 ARG B 196 " -0.230 2.00e-02 2.50e+03 pdb="HH22 ARG B 196 " 0.311 2.00e-02 2.50e+03 ... (remaining 4875 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 2487 2.24 - 2.83: 61232 2.83 - 3.42: 87513 3.42 - 4.01: 120613 4.01 - 4.60: 173691 Nonbonded interactions: 445536 Sorted by model distance: nonbonded pdb=" HH TYR F 10 " pdb=" OD2 ASP F 35 " model vdw 1.649 2.450 nonbonded pdb=" HH TYR B 10 " pdb=" OD2 ASP B 35 " model vdw 1.649 2.450 nonbonded pdb=" HH TYR E 10 " pdb=" OD2 ASP E 35 " model vdw 1.649 2.450 nonbonded pdb=" HH TYR A 10 " pdb=" OD2 ASP A 35 " model vdw 1.649 2.450 nonbonded pdb=" HH TYR D 10 " pdb=" OD2 ASP D 35 " model vdw 1.649 2.450 ... (remaining 445531 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.820 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.014 0.049 16584 Z= 0.836 Angle : 1.875 7.804 22530 Z= 1.271 Chirality : 0.092 0.310 2544 Planarity : 0.016 0.197 2910 Dihedral : 13.069 83.501 6060 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.16), residues: 2028 helix: -1.57 (0.17), residues: 558 sheet: 0.80 (0.29), residues: 270 loop : -0.35 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 119 TYR 0.119 0.018 TYR E 190 PHE 0.062 0.013 PHE F 269 TRP 0.099 0.032 TRP E 324 HIS 0.009 0.003 HIS B 14 Details of bonding type rmsd/Z covalent geometry : bond 0.01351 / 0.84 (16584) covalent geometry : angle 1.87527 / 1.27 (22530) hydrogen bonds : bond 0.17626 / 11.60 ( 660) hydrogen bonds : angle 7.33050 / 5.20 ( 1926) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.707 Fit side-chains REVERT: A 100 LYS cc_start: 0.8319 (mttt) cc_final: 0.8019 (mttp) REVERT: A 108 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6636 (mm-30) REVERT: A 191 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7224 (mt-10) REVERT: A 233 GLN cc_start: 0.7540 (tt0) cc_final: 0.6611 (mm110) REVERT: A 263 ASP cc_start: 0.7496 (m-30) cc_final: 0.7250 (m-30) REVERT: A 293 GLU cc_start: 0.5693 (tt0) cc_final: 0.5323 (tp30) REVERT: A 308 LYS cc_start: 0.5162 (tttt) cc_final: 0.4073 (tptt) REVERT: A 324 TRP cc_start: 0.6165 (m100) cc_final: 0.5358 (m100) REVERT: B 21 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7927 (mt-10) REVERT: B 100 LYS cc_start: 0.8118 (mttt) cc_final: 0.7068 (ttpt) REVERT: B 142 ARG cc_start: 0.7138 (ttt180) cc_final: 0.6505 (mpp80) REVERT: B 191 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7506 (mt-10) REVERT: B 233 GLN cc_start: 0.7332 (tt0) cc_final: 0.6345 (mm110) REVERT: B 234 LEU cc_start: 0.7942 (tt) cc_final: 0.7741 (tt) REVERT: B 251 LYS cc_start: 0.7816 (mttt) cc_final: 0.7341 (mtpt) REVERT: B 293 GLU cc_start: 0.6133 (tt0) cc_final: 0.5791 (tp30) REVERT: B 301 GLU cc_start: 0.5636 (tt0) cc_final: 0.5340 (tp30) REVERT: B 315 ASP cc_start: 0.6908 (m-30) cc_final: 0.6700 (m-30) REVERT: C 21 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7756 (mp0) REVERT: C 96 ARG cc_start: 0.6860 (ttm170) cc_final: 0.6422 (ptm160) REVERT: C 100 LYS cc_start: 0.8280 (mttt) cc_final: 0.8029 (mttp) REVERT: C 181 ASN cc_start: 0.8166 (m-40) cc_final: 0.7739 (m110) REVERT: C 191 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 233 GLN cc_start: 0.7461 (tt0) cc_final: 0.6634 (mm110) REVERT: C 251 LYS cc_start: 0.7794 (mttt) cc_final: 0.7271 (mttt) REVERT: C 253 ASN cc_start: 0.8858 (m-40) cc_final: 0.8641 (m-40) REVERT: C 273 ASP cc_start: 0.7360 (t0) cc_final: 0.6701 (t0) REVERT: C 301 GLU cc_start: 0.5738 (tt0) cc_final: 0.5292 (tp30) REVERT: C 308 LYS cc_start: 0.5065 (tttt) cc_final: 0.3999 (tptp) REVERT: D 21 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7761 (mp0) REVERT: D 96 ARG cc_start: 0.6866 (ttm170) cc_final: 0.6484 (ptm160) REVERT: D 100 LYS cc_start: 0.8287 (mttt) cc_final: 0.8043 (mttp) REVERT: D 181 ASN cc_start: 0.8189 (m-40) cc_final: 0.7762 (m110) REVERT: D 191 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7508 (mt-10) REVERT: D 233 GLN cc_start: 0.7413 (tt0) cc_final: 0.6595 (mm110) REVERT: D 251 LYS cc_start: 0.7780 (mttt) cc_final: 0.7316 (mttt) REVERT: D 253 ASN cc_start: 0.8895 (m-40) cc_final: 0.8681 (m-40) REVERT: D 301 GLU cc_start: 0.5710 (tt0) cc_final: 0.5275 (tp30) REVERT: D 308 LYS cc_start: 0.5014 (tttt) cc_final: 0.3963 (tptp) REVERT: E 21 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7930 (mt-10) REVERT: E 100 LYS cc_start: 0.8104 (mttt) cc_final: 0.7057 (ttpt) REVERT: E 142 ARG cc_start: 0.7159 (ttt180) cc_final: 0.6562 (mpp80) REVERT: E 191 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7508 (mt-10) REVERT: E 233 GLN cc_start: 0.7336 (tt0) cc_final: 0.6348 (mm110) REVERT: E 234 LEU cc_start: 0.7938 (tt) cc_final: 0.7726 (tt) REVERT: E 251 LYS cc_start: 0.7776 (mttt) cc_final: 0.7316 (mtpt) REVERT: E 293 GLU cc_start: 0.6131 (tt0) cc_final: 0.5788 (tp30) REVERT: E 301 GLU cc_start: 0.5710 (tt0) cc_final: 0.5352 (tp30) REVERT: E 315 ASP cc_start: 0.6892 (m-30) cc_final: 0.6678 (m-30) REVERT: F 100 LYS cc_start: 0.8331 (mttt) cc_final: 0.8034 (mttp) REVERT: F 108 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6628 (mm-30) REVERT: F 191 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7234 (mt-10) REVERT: F 233 GLN cc_start: 0.7454 (tt0) cc_final: 0.6529 (mm110) REVERT: F 263 ASP cc_start: 0.7513 (m-30) cc_final: 0.7273 (m-30) REVERT: F 293 GLU cc_start: 0.5706 (tt0) cc_final: 0.5323 (tp30) REVERT: F 308 LYS cc_start: 0.5156 (tttt) cc_final: 0.4056 (tptt) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 1.1905 time to fit residues: 396.7623 Evaluate side-chains 202 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN B 90 ASN C 36 GLN C 336 GLN D 36 GLN D 90 ASN E 90 ASN F 181 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.166836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.122901 restraints weight = 37028.513| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.47 r_work: 0.3236 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16584 Z= 0.136 Angle : 0.574 3.861 22530 Z= 0.325 Chirality : 0.044 0.139 2544 Planarity : 0.005 0.043 2910 Dihedral : 6.142 24.406 2256 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 0.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.72 % Allowed : 5.83 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 2028 helix: 0.30 (0.22), residues: 558 sheet: 0.08 (0.28), residues: 342 loop : -0.61 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 188 TYR 0.015 0.002 TYR B 316 PHE 0.009 0.002 PHE F 325 TRP 0.005 0.001 TRP F 86 HIS 0.003 0.001 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (16584) covalent geometry : angle 0.57378 / 0.32 (22530) hydrogen bonds : bond 0.04647 / 3.11 ( 660) hydrogen bonds : angle 5.44357 / 3.82 ( 1926) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 230 time to evaluate : 0.846 Fit side-chains REVERT: A 100 LYS cc_start: 0.8422 (mttt) cc_final: 0.7261 (tmtt) REVERT: A 108 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6524 (mm-30) REVERT: A 142 ARG cc_start: 0.6406 (ttt-90) cc_final: 0.5680 (mpp-170) REVERT: A 191 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7269 (mt-10) REVERT: A 209 GLU cc_start: 0.4833 (mp0) cc_final: 0.4512 (OUTLIER) REVERT: A 233 GLN cc_start: 0.7319 (tt0) cc_final: 0.6434 (mm110) REVERT: A 261 ASP cc_start: 0.6487 (p0) cc_final: 0.5945 (p0) REVERT: A 293 GLU cc_start: 0.5027 (tt0) cc_final: 0.4606 (tp30) REVERT: B 21 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7564 (mp0) REVERT: B 100 LYS cc_start: 0.8099 (mttt) cc_final: 0.7024 (tmtt) REVERT: B 142 ARG cc_start: 0.6928 (ttt180) cc_final: 0.6193 (mpp80) REVERT: B 191 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7496 (mt-10) REVERT: B 218 GLU cc_start: 0.5378 (OUTLIER) cc_final: 0.5101 (tt0) REVERT: B 233 GLN cc_start: 0.6947 (tt0) cc_final: 0.6146 (mm110) REVERT: B 251 LYS cc_start: 0.7553 (mttt) cc_final: 0.7046 (mtpt) REVERT: B 273 ASP cc_start: 0.6841 (t0) cc_final: 0.6457 (t70) REVERT: B 293 GLU cc_start: 0.6054 (tt0) cc_final: 0.5453 (tp30) REVERT: B 323 THR cc_start: 0.6368 (OUTLIER) cc_final: 0.6112 (t) REVERT: C 21 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7652 (mp0) REVERT: C 22 MET cc_start: 0.8391 (ptm) cc_final: 0.8106 (ptm) REVERT: C 96 ARG cc_start: 0.7028 (ttm170) cc_final: 0.6583 (ptm160) REVERT: C 100 LYS cc_start: 0.8347 (mttt) cc_final: 0.7369 (tmtt) REVERT: C 181 ASN cc_start: 0.8070 (m-40) cc_final: 0.7589 (m110) REVERT: C 191 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7397 (mt-10) REVERT: C 233 GLN cc_start: 0.7195 (tt0) cc_final: 0.6122 (mm110) REVERT: C 251 LYS cc_start: 0.7583 (mttt) cc_final: 0.6987 (mttt) REVERT: C 308 LYS cc_start: 0.4807 (tttt) cc_final: 0.3741 (tptp) REVERT: C 322 MET cc_start: 0.6485 (OUTLIER) cc_final: 0.5490 (mmt) REVERT: D 21 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7635 (mp0) REVERT: D 22 MET cc_start: 0.8379 (ptm) cc_final: 0.8078 (ptm) REVERT: D 96 ARG cc_start: 0.6817 (ttm170) cc_final: 0.6319 (ptm160) REVERT: D 100 LYS cc_start: 0.8357 (mttt) cc_final: 0.7438 (tmtt) REVERT: D 181 ASN cc_start: 0.8050 (m-40) cc_final: 0.7570 (m110) REVERT: D 191 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7375 (mt-10) REVERT: D 233 GLN cc_start: 0.7208 (tt0) cc_final: 0.6278 (mm110) REVERT: D 251 LYS cc_start: 0.7600 (mttt) cc_final: 0.6991 (mttt) REVERT: D 308 LYS cc_start: 0.4767 (tttt) cc_final: 0.3720 (tptp) REVERT: D 322 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.5498 (mmt) REVERT: E 21 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7556 (mp0) REVERT: E 100 LYS cc_start: 0.8091 (mttt) cc_final: 0.7014 (tmtt) REVERT: E 142 ARG cc_start: 0.6936 (ttt180) cc_final: 0.6197 (mpp80) REVERT: E 191 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7501 (mt-10) REVERT: E 218 GLU cc_start: 0.5486 (OUTLIER) cc_final: 0.5157 (tt0) REVERT: E 233 GLN cc_start: 0.6942 (tt0) cc_final: 0.6132 (mm110) REVERT: E 251 LYS cc_start: 0.7548 (mttt) cc_final: 0.7039 (mtpt) REVERT: E 273 ASP cc_start: 0.6834 (t0) cc_final: 0.6456 (t70) REVERT: E 293 GLU cc_start: 0.6062 (tt0) cc_final: 0.5450 (tp30) REVERT: E 323 THR cc_start: 0.6331 (OUTLIER) cc_final: 0.6057 (t) REVERT: F 100 LYS cc_start: 0.8374 (mttt) cc_final: 0.7369 (tmtt) REVERT: F 108 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6538 (mm-30) REVERT: F 142 ARG cc_start: 0.6374 (ttt-90) cc_final: 0.5645 (mpp-170) REVERT: F 191 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7285 (mt-10) REVERT: F 209 GLU cc_start: 0.4836 (mp0) cc_final: 0.4348 (tp30) REVERT: F 233 GLN cc_start: 0.7342 (tt0) cc_final: 0.6426 (mm110) REVERT: F 261 ASP cc_start: 0.6483 (p0) cc_final: 0.5931 (p0) REVERT: F 293 GLU cc_start: 0.5149 (tt0) cc_final: 0.4691 (tp30) outliers start: 13 outliers final: 3 residues processed: 234 average time/residue: 1.2439 time to fit residues: 322.9951 Evaluate side-chains 216 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 323 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [100, 21, 123, 98, 13, 175, 187, 161, 3, 151, 156] chunk 100 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN B 267 ASN C 36 GLN D 36 GLN E 267 ASN F 181 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.164080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120688 restraints weight = 36871.168| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.46 r_work: 0.3208 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16584 Z= 0.185 Angle : 0.597 4.677 22530 Z= 0.338 Chirality : 0.045 0.138 2544 Planarity : 0.005 0.048 2910 Dihedral : 5.857 23.747 2256 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.44 % Allowed : 7.44 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.17), residues: 2028 helix: 0.52 (0.22), residues: 558 sheet: -0.08 (0.27), residues: 342 loop : -0.73 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 70 TYR 0.020 0.002 TYR E 316 PHE 0.013 0.002 PHE B 43 TRP 0.007 0.002 TRP B 86 HIS 0.005 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (16584) covalent geometry : angle 0.59701 / 0.34 (22530) hydrogen bonds : bond 0.05102 / 3.36 ( 660) hydrogen bonds : angle 5.18000 / 3.64 ( 1926) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.866 Fit side-chains REVERT: A 108 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6686 (mm-30) REVERT: A 209 GLU cc_start: 0.5204 (mp0) cc_final: 0.4685 (tp30) REVERT: A 233 GLN cc_start: 0.7348 (tt0) cc_final: 0.6416 (mm110) REVERT: A 273 ASP cc_start: 0.6854 (t0) cc_final: 0.6427 (t70) REVERT: A 293 GLU cc_start: 0.5274 (tt0) cc_final: 0.4773 (tp30) REVERT: B 21 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7836 (mp0) REVERT: B 39 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: B 142 ARG cc_start: 0.7055 (ttt180) cc_final: 0.6292 (mpp80) REVERT: B 191 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7531 (mt-10) REVERT: B 233 GLN cc_start: 0.7119 (tt0) cc_final: 0.6188 (mm110) REVERT: B 273 ASP cc_start: 0.7273 (t0) cc_final: 0.5944 (p0) REVERT: B 293 GLU cc_start: 0.5983 (tt0) cc_final: 0.5400 (tp30) REVERT: C 21 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7757 (mp0) REVERT: C 96 ARG cc_start: 0.7226 (ttm170) cc_final: 0.6609 (ptm160) REVERT: C 100 LYS cc_start: 0.8308 (mttt) cc_final: 0.7308 (ttpt) REVERT: C 191 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7332 (mt-10) REVERT: C 194 GLU cc_start: 0.4679 (pm20) cc_final: 0.4054 (tm-30) REVERT: C 233 GLN cc_start: 0.7228 (tt0) cc_final: 0.6125 (mm110) REVERT: C 251 LYS cc_start: 0.7660 (mttt) cc_final: 0.7076 (mttt) REVERT: C 273 ASP cc_start: 0.6958 (t0) cc_final: 0.6124 (p0) REVERT: D 21 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7755 (mp0) REVERT: D 96 ARG cc_start: 0.7244 (ttm170) cc_final: 0.6608 (ptm160) REVERT: D 100 LYS cc_start: 0.8308 (mttt) cc_final: 0.7319 (ttpt) REVERT: D 191 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7293 (mt-10) REVERT: D 233 GLN cc_start: 0.7192 (tt0) cc_final: 0.6283 (mm110) REVERT: D 251 LYS cc_start: 0.7764 (mttt) cc_final: 0.7161 (mttt) REVERT: D 273 ASP cc_start: 0.6757 (t70) cc_final: 0.6003 (p0) REVERT: E 21 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7842 (mp0) REVERT: E 39 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: E 142 ARG cc_start: 0.7054 (ttt180) cc_final: 0.6249 (mpp80) REVERT: E 191 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7521 (mt-10) REVERT: E 233 GLN cc_start: 0.7108 (tt0) cc_final: 0.6176 (mm110) REVERT: E 273 ASP cc_start: 0.7244 (t0) cc_final: 0.5930 (p0) REVERT: E 293 GLU cc_start: 0.6019 (tt0) cc_final: 0.5408 (tp30) REVERT: F 108 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6684 (mm-30) REVERT: F 209 GLU cc_start: 0.5201 (mp0) cc_final: 0.4714 (tp30) REVERT: F 233 GLN cc_start: 0.7325 (tt0) cc_final: 0.6394 (mm110) REVERT: F 273 ASP cc_start: 0.6932 (t0) cc_final: 0.6445 (t70) REVERT: F 293 GLU cc_start: 0.5265 (tt0) cc_final: 0.4761 (tp30) outliers start: 26 outliers final: 17 residues processed: 211 average time/residue: 1.2833 time to fit residues: 300.5324 Evaluate side-chains 209 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain F residue 234 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [86, 91, 121, 110, 129, 115, 172, 9, 80, 156, 118] chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN C 36 GLN D 36 GLN F 181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.164964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121887 restraints weight = 36770.644| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.46 r_work: 0.3225 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16584 Z= 0.146 Angle : 0.529 4.323 22530 Z= 0.298 Chirality : 0.044 0.135 2544 Planarity : 0.004 0.052 2910 Dihedral : 5.486 23.381 2256 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.33 % Allowed : 7.89 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.18), residues: 2028 helix: 0.70 (0.22), residues: 558 sheet: -0.10 (0.28), residues: 342 loop : -0.73 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 70 TYR 0.015 0.002 TYR E 316 PHE 0.011 0.002 PHE E 32 TRP 0.005 0.002 TRP E 86 HIS 0.004 0.001 HIS F 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (16584) covalent geometry : angle 0.52944 / 0.30 (22530) hydrogen bonds : bond 0.04367 / 2.89 ( 660) hydrogen bonds : angle 4.86195 / 3.42 ( 1926) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.749 Fit side-chains REVERT: A 108 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6717 (mm-30) REVERT: A 209 GLU cc_start: 0.5257 (mp0) cc_final: 0.4946 (tp30) REVERT: A 233 GLN cc_start: 0.7124 (tt0) cc_final: 0.6269 (mm110) REVERT: A 273 ASP cc_start: 0.6843 (t0) cc_final: 0.5817 (p0) REVERT: A 293 GLU cc_start: 0.5410 (tt0) cc_final: 0.4894 (tp30) REVERT: B 21 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7704 (mp0) REVERT: B 142 ARG cc_start: 0.7049 (ttt180) cc_final: 0.6237 (mpp80) REVERT: B 233 GLN cc_start: 0.7087 (tt0) cc_final: 0.6167 (mm110) REVERT: B 273 ASP cc_start: 0.6962 (t0) cc_final: 0.6247 (p0) REVERT: B 293 GLU cc_start: 0.5923 (tt0) cc_final: 0.5338 (tp30) REVERT: C 21 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7745 (mp0) REVERT: C 96 ARG cc_start: 0.6959 (ttm170) cc_final: 0.6361 (ptm160) REVERT: C 100 LYS cc_start: 0.8329 (mttt) cc_final: 0.7335 (ttpt) REVERT: C 191 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7315 (mt-10) REVERT: C 194 GLU cc_start: 0.4911 (OUTLIER) cc_final: 0.4243 (tm-30) REVERT: C 233 GLN cc_start: 0.6935 (tt0) cc_final: 0.5948 (mm110) REVERT: C 251 LYS cc_start: 0.7725 (mttt) cc_final: 0.7112 (mttt) REVERT: C 262 SER cc_start: 0.7733 (t) cc_final: 0.7395 (p) REVERT: C 273 ASP cc_start: 0.7052 (t70) cc_final: 0.6371 (p0) REVERT: C 322 MET cc_start: 0.6363 (OUTLIER) cc_final: 0.5469 (mmt) REVERT: D 21 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7765 (mp0) REVERT: D 96 ARG cc_start: 0.6836 (ttm170) cc_final: 0.6090 (ptm160) REVERT: D 100 LYS cc_start: 0.8325 (mttt) cc_final: 0.7335 (ttpt) REVERT: D 191 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7289 (mt-10) REVERT: D 194 GLU cc_start: 0.4889 (OUTLIER) cc_final: 0.4234 (tm-30) REVERT: D 233 GLN cc_start: 0.7201 (tt0) cc_final: 0.6294 (mm110) REVERT: D 251 LYS cc_start: 0.7737 (mttt) cc_final: 0.7126 (mttt) REVERT: D 262 SER cc_start: 0.7642 (t) cc_final: 0.7313 (p) REVERT: D 273 ASP cc_start: 0.6950 (t70) cc_final: 0.6269 (p0) REVERT: E 21 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7708 (mp0) REVERT: E 142 ARG cc_start: 0.7056 (ttt180) cc_final: 0.6236 (mpp80) REVERT: E 233 GLN cc_start: 0.7092 (tt0) cc_final: 0.6160 (mm110) REVERT: E 273 ASP cc_start: 0.6932 (t0) cc_final: 0.6254 (p0) REVERT: E 293 GLU cc_start: 0.5810 (tt0) cc_final: 0.5348 (tp30) REVERT: F 108 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6751 (mm-30) REVERT: F 209 GLU cc_start: 0.5207 (mp0) cc_final: 0.4912 (tp30) REVERT: F 233 GLN cc_start: 0.7124 (tt0) cc_final: 0.6274 (mm110) REVERT: F 273 ASP cc_start: 0.6956 (t0) cc_final: 0.5889 (p0) REVERT: F 293 GLU cc_start: 0.5410 (tt0) cc_final: 0.4891 (tp30) outliers start: 24 outliers final: 14 residues processed: 211 average time/residue: 1.2265 time to fit residues: 288.6676 Evaluate side-chains 209 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain F residue 234 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [77, 147, 128, 0, 85, 203, 140, 19, 4, 32, 51] chunk 77 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN B 36 GLN B 90 ASN C 181 ASN D 36 GLN D 181 ASN E 36 GLN E 90 ASN F 181 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.164034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.121081 restraints weight = 36798.870| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.46 r_work: 0.3213 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16584 Z= 0.162 Angle : 0.551 4.444 22530 Z= 0.310 Chirality : 0.045 0.134 2544 Planarity : 0.005 0.051 2910 Dihedral : 5.519 23.555 2256 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.28 % Allowed : 8.06 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.18), residues: 2028 helix: 0.75 (0.22), residues: 558 sheet: -0.02 (0.28), residues: 342 loop : -0.75 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 70 TYR 0.016 0.002 TYR B 316 PHE 0.012 0.002 PHE F 32 TRP 0.006 0.002 TRP B 86 HIS 0.005 0.001 HIS F 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (16584) covalent geometry : angle 0.55089 / 0.31 (22530) hydrogen bonds : bond 0.04712 / 3.11 ( 660) hydrogen bonds : angle 4.85989 / 3.41 ( 1926) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.837 Fit side-chains REVERT: A 108 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6800 (mm-30) REVERT: A 142 ARG cc_start: 0.6898 (ttt-90) cc_final: 0.5908 (ptt90) REVERT: A 209 GLU cc_start: 0.5265 (mp0) cc_final: 0.4942 (tp30) REVERT: A 218 GLU cc_start: 0.5880 (tt0) cc_final: 0.5597 (pm20) REVERT: A 233 GLN cc_start: 0.6994 (tt0) cc_final: 0.6179 (mm110) REVERT: A 273 ASP cc_start: 0.6988 (t0) cc_final: 0.6106 (p0) REVERT: A 293 GLU cc_start: 0.5430 (tt0) cc_final: 0.4938 (tp30) REVERT: B 21 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7718 (mp0) REVERT: B 142 ARG cc_start: 0.7033 (ttt180) cc_final: 0.6328 (mpp80) REVERT: B 233 GLN cc_start: 0.7037 (tt0) cc_final: 0.6099 (mm110) REVERT: B 273 ASP cc_start: 0.6992 (t0) cc_final: 0.6276 (p0) REVERT: B 293 GLU cc_start: 0.5782 (tt0) cc_final: 0.5443 (tp30) REVERT: C 21 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7735 (mp0) REVERT: C 96 ARG cc_start: 0.6917 (ttm170) cc_final: 0.6318 (ptm160) REVERT: C 100 LYS cc_start: 0.8344 (mttt) cc_final: 0.7364 (ttpt) REVERT: C 191 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7308 (mt-10) REVERT: C 194 GLU cc_start: 0.4828 (OUTLIER) cc_final: 0.4097 (tm-30) REVERT: C 233 GLN cc_start: 0.6951 (tt0) cc_final: 0.6122 (mm110) REVERT: C 251 LYS cc_start: 0.7707 (mttt) cc_final: 0.7092 (mttt) REVERT: C 262 SER cc_start: 0.7673 (t) cc_final: 0.7328 (p) REVERT: C 273 ASP cc_start: 0.7278 (t70) cc_final: 0.6552 (p0) REVERT: D 21 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7763 (mp0) REVERT: D 96 ARG cc_start: 0.6915 (ttm170) cc_final: 0.6311 (ptm160) REVERT: D 100 LYS cc_start: 0.8346 (mttt) cc_final: 0.7373 (ttpt) REVERT: D 191 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7325 (mt-10) REVERT: D 194 GLU cc_start: 0.4819 (OUTLIER) cc_final: 0.4098 (tm-30) REVERT: D 233 GLN cc_start: 0.6951 (tt0) cc_final: 0.6113 (mm110) REVERT: D 251 LYS cc_start: 0.7731 (mttt) cc_final: 0.7113 (mttt) REVERT: D 262 SER cc_start: 0.7536 (t) cc_final: 0.7215 (p) REVERT: D 273 ASP cc_start: 0.6986 (t70) cc_final: 0.6401 (p0) REVERT: E 21 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7725 (mp0) REVERT: E 142 ARG cc_start: 0.7039 (ttt180) cc_final: 0.6330 (mpp80) REVERT: E 233 GLN cc_start: 0.7039 (tt0) cc_final: 0.6091 (mm110) REVERT: E 273 ASP cc_start: 0.6958 (t0) cc_final: 0.6279 (p0) REVERT: E 293 GLU cc_start: 0.5772 (tt0) cc_final: 0.5439 (tp30) REVERT: F 108 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6807 (mm-30) REVERT: F 142 ARG cc_start: 0.6899 (ttt-90) cc_final: 0.5907 (ptt90) REVERT: F 209 GLU cc_start: 0.5263 (mp0) cc_final: 0.4945 (tp30) REVERT: F 233 GLN cc_start: 0.6973 (tt0) cc_final: 0.6161 (mm110) REVERT: F 273 ASP cc_start: 0.6970 (t0) cc_final: 0.6144 (p0) REVERT: F 293 GLU cc_start: 0.5429 (tt0) cc_final: 0.4931 (tp30) outliers start: 23 outliers final: 17 residues processed: 212 average time/residue: 1.1943 time to fit residues: 282.8824 Evaluate side-chains 213 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain F residue 234 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [17, 164, 135, 168, 10, 14, 92, 186, 107, 9, 147] chunk 17 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 147 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN B 90 ASN C 36 GLN C 173 ASN C 181 ASN D 36 GLN D 173 ASN D 181 ASN E 90 ASN F 181 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.195308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.166201 restraints weight = 39837.924| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.35 r_work: 0.3782 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16584 Z= 0.085 Angle : 0.441 3.633 22530 Z= 0.246 Chirality : 0.042 0.133 2544 Planarity : 0.004 0.052 2910 Dihedral : 4.888 22.431 2256 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 0.89 % Allowed : 8.56 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.18), residues: 2028 helix: 1.14 (0.23), residues: 564 sheet: 0.07 (0.29), residues: 342 loop : -0.55 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 61 TYR 0.010 0.001 TYR C 10 PHE 0.006 0.001 PHE D 32 TRP 0.003 0.001 TRP B 324 HIS 0.003 0.001 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.09 (16584) covalent geometry : angle 0.44107 / 0.25 (22530) hydrogen bonds : bond 0.03352 / 2.23 ( 660) hydrogen bonds : angle 4.48651 / 3.17 ( 1926) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.839 Fit side-chains REVERT: A 233 GLN cc_start: 0.7506 (tt0) cc_final: 0.6986 (mm110) REVERT: A 273 ASP cc_start: 0.7095 (t0) cc_final: 0.6792 (p0) REVERT: A 293 GLU cc_start: 0.5963 (tt0) cc_final: 0.5647 (tp30) REVERT: B 21 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7752 (mp0) REVERT: B 233 GLN cc_start: 0.7542 (tt0) cc_final: 0.6914 (mm110) REVERT: B 273 ASP cc_start: 0.7154 (t0) cc_final: 0.6927 (p0) REVERT: B 323 THR cc_start: 0.7084 (OUTLIER) cc_final: 0.6849 (t) REVERT: C 21 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7750 (mp0) REVERT: C 100 LYS cc_start: 0.8354 (mttt) cc_final: 0.7830 (ttpt) REVERT: C 191 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7582 (mt-10) REVERT: C 194 GLU cc_start: 0.5539 (pm20) cc_final: 0.5185 (tm-30) REVERT: C 233 GLN cc_start: 0.7644 (tt0) cc_final: 0.7021 (mm110) REVERT: C 251 LYS cc_start: 0.8041 (mttt) cc_final: 0.7606 (mttt) REVERT: C 273 ASP cc_start: 0.7532 (t70) cc_final: 0.7250 (p0) REVERT: D 21 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7791 (mp0) REVERT: D 100 LYS cc_start: 0.8344 (mttt) cc_final: 0.7825 (ttpt) REVERT: D 191 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7578 (mt-10) REVERT: D 194 GLU cc_start: 0.5535 (pm20) cc_final: 0.5195 (tm-30) REVERT: D 233 GLN cc_start: 0.7648 (tt0) cc_final: 0.6995 (mm110) REVERT: D 251 LYS cc_start: 0.8040 (mttt) cc_final: 0.7606 (mttt) REVERT: E 21 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7765 (mp0) REVERT: E 233 GLN cc_start: 0.7525 (tt0) cc_final: 0.6896 (mm110) REVERT: E 234 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7710 (mt) REVERT: E 323 THR cc_start: 0.7096 (OUTLIER) cc_final: 0.6865 (t) REVERT: F 233 GLN cc_start: 0.7480 (tt0) cc_final: 0.6953 (mm110) REVERT: F 273 ASP cc_start: 0.7200 (t0) cc_final: 0.6808 (p0) REVERT: F 293 GLU cc_start: 0.5995 (tt0) cc_final: 0.5660 (tp30) outliers start: 16 outliers final: 9 residues processed: 215 average time/residue: 1.1453 time to fit residues: 275.7518 Evaluate side-chains 207 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 313 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [36, 198, 47, 16, 124, 87, 46, 151, 117, 20, 58] chunk 36 optimal weight: 0.5980 chunk 198 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN C 173 ASN D 173 ASN E 36 GLN F 181 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.183843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.163051 restraints weight = 37331.523| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 0.81 r_work: 0.3586 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16584 Z= 0.153 Angle : 0.526 4.294 22530 Z= 0.295 Chirality : 0.044 0.134 2544 Planarity : 0.005 0.051 2910 Dihedral : 5.259 23.334 2256 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 0.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.17 % Allowed : 9.00 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.18), residues: 2028 helix: 1.00 (0.23), residues: 564 sheet: 0.10 (0.28), residues: 342 loop : -0.61 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 70 TYR 0.015 0.002 TYR E 316 PHE 0.013 0.002 PHE F 32 TRP 0.006 0.002 TRP B 86 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (16584) covalent geometry : angle 0.52644 / 0.30 (22530) hydrogen bonds : bond 0.04427 / 2.92 ( 660) hydrogen bonds : angle 4.72527 / 3.32 ( 1926) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.755 Fit side-chains REVERT: A 142 ARG cc_start: 0.7241 (ttt-90) cc_final: 0.6650 (ptt90) REVERT: A 233 GLN cc_start: 0.7614 (tt0) cc_final: 0.7085 (mm110) REVERT: A 273 ASP cc_start: 0.7225 (t0) cc_final: 0.6964 (p0) REVERT: A 293 GLU cc_start: 0.6239 (tt0) cc_final: 0.5930 (tp30) REVERT: B 21 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7959 (mp0) REVERT: B 233 GLN cc_start: 0.7701 (tt0) cc_final: 0.7026 (mm110) REVERT: B 273 ASP cc_start: 0.7312 (t0) cc_final: 0.7095 (p0) REVERT: C 21 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7909 (mp0) REVERT: C 100 LYS cc_start: 0.8470 (mttt) cc_final: 0.7931 (ttpt) REVERT: C 191 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7519 (mt-10) REVERT: C 194 GLU cc_start: 0.5445 (OUTLIER) cc_final: 0.4908 (tm-30) REVERT: C 233 GLN cc_start: 0.7614 (tt0) cc_final: 0.7060 (mm110) REVERT: C 273 ASP cc_start: 0.7602 (t70) cc_final: 0.7341 (p0) REVERT: D 21 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7929 (mp0) REVERT: D 100 LYS cc_start: 0.8476 (mttt) cc_final: 0.7933 (ttpt) REVERT: D 191 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7537 (mt-10) REVERT: D 194 GLU cc_start: 0.5423 (OUTLIER) cc_final: 0.4887 (tm-30) REVERT: D 233 GLN cc_start: 0.7599 (tt0) cc_final: 0.7046 (mm110) REVERT: E 21 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7978 (mp0) REVERT: E 233 GLN cc_start: 0.7701 (tt0) cc_final: 0.7006 (mm110) REVERT: F 142 ARG cc_start: 0.7229 (ttt-90) cc_final: 0.6648 (ptt90) REVERT: F 233 GLN cc_start: 0.7610 (tt0) cc_final: 0.7079 (mm110) REVERT: F 273 ASP cc_start: 0.7236 (t0) cc_final: 0.6954 (p0) REVERT: F 293 GLU cc_start: 0.6250 (tt0) cc_final: 0.5932 (tp30) outliers start: 21 outliers final: 16 residues processed: 204 average time/residue: 1.1858 time to fit residues: 269.8350 Evaluate side-chains 205 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 313 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [42, 158, 118, 203, 179, 87, 163, 93, 98, 8, 56] chunk 42 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 chunk 163 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN B 36 GLN C 173 ASN C 181 ASN D 173 ASN D 181 ASN E 36 GLN F 181 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.182246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.158164 restraints weight = 37320.371| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 0.95 r_work: 0.3543 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16584 Z= 0.201 Angle : 0.598 5.621 22530 Z= 0.336 Chirality : 0.046 0.137 2544 Planarity : 0.005 0.051 2910 Dihedral : 5.584 23.746 2256 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.50 % Allowed : 8.78 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.18), residues: 2028 helix: 0.76 (0.22), residues: 564 sheet: 0.00 (0.27), residues: 342 loop : -0.69 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 70 TYR 0.018 0.003 TYR E 10 PHE 0.014 0.002 PHE F 32 TRP 0.008 0.003 TRP E 86 HIS 0.006 0.001 HIS F 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (16584) covalent geometry : angle 0.59818 / 0.34 (22530) hydrogen bonds : bond 0.05103 / 3.36 ( 660) hydrogen bonds : angle 4.95661 / 3.48 ( 1926) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.854 Fit side-chains REVERT: A 142 ARG cc_start: 0.7269 (ttt-90) cc_final: 0.6685 (ptt90) REVERT: A 233 GLN cc_start: 0.7521 (tt0) cc_final: 0.7012 (mm110) REVERT: A 273 ASP cc_start: 0.7290 (t0) cc_final: 0.7065 (p0) REVERT: A 293 GLU cc_start: 0.6253 (tt0) cc_final: 0.5890 (tp30) REVERT: B 21 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8069 (mp0) REVERT: B 141 LYS cc_start: 0.8080 (mttt) cc_final: 0.7774 (mmtp) REVERT: B 142 ARG cc_start: 0.7380 (ttt180) cc_final: 0.6865 (mpp80) REVERT: B 233 GLN cc_start: 0.7700 (tt0) cc_final: 0.6990 (mm110) REVERT: B 273 ASP cc_start: 0.7326 (t0) cc_final: 0.7059 (p0) REVERT: C 21 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7975 (mp0) REVERT: C 191 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7535 (mt-10) REVERT: C 194 GLU cc_start: 0.5505 (OUTLIER) cc_final: 0.4948 (tm-30) REVERT: C 231 LYS cc_start: 0.8122 (mttt) cc_final: 0.7608 (mttp) REVERT: C 233 GLN cc_start: 0.7613 (tt0) cc_final: 0.7018 (mm110) REVERT: D 21 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8012 (mp0) REVERT: D 191 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7588 (mt-10) REVERT: D 194 GLU cc_start: 0.5499 (OUTLIER) cc_final: 0.4935 (tm-30) REVERT: D 231 LYS cc_start: 0.8117 (mttt) cc_final: 0.7594 (mttp) REVERT: D 233 GLN cc_start: 0.7601 (tt0) cc_final: 0.7006 (mm110) REVERT: E 21 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8086 (mp0) REVERT: E 141 LYS cc_start: 0.8058 (mttt) cc_final: 0.7760 (mmtp) REVERT: E 142 ARG cc_start: 0.7343 (ttt180) cc_final: 0.6883 (mpp80) REVERT: E 233 GLN cc_start: 0.7703 (tt0) cc_final: 0.7014 (mm110) REVERT: E 273 ASP cc_start: 0.7074 (p0) cc_final: 0.6836 (p0) REVERT: F 142 ARG cc_start: 0.7253 (ttt-90) cc_final: 0.6676 (ptt90) REVERT: F 233 GLN cc_start: 0.7495 (tt0) cc_final: 0.6982 (mm110) REVERT: F 293 GLU cc_start: 0.6290 (tt0) cc_final: 0.5930 (tp30) outliers start: 27 outliers final: 17 residues processed: 207 average time/residue: 1.1833 time to fit residues: 273.6331 Evaluate side-chains 211 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 322 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [95, 125, 63, 69, 64, 193, 156, 200, 86, 53, 41] chunk 95 optimal weight: 3.9990 chunk 125 optimal weight: 0.0570 chunk 63 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN B 36 GLN C 181 ASN D 36 GLN D 181 ASN E 36 GLN F 181 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.184103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.160081 restraints weight = 37344.390| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 0.95 r_work: 0.3585 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16584 Z= 0.130 Angle : 0.498 4.532 22530 Z= 0.279 Chirality : 0.043 0.134 2544 Planarity : 0.004 0.051 2910 Dihedral : 5.228 23.286 2256 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.00 % Allowed : 9.67 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.18), residues: 2028 helix: 1.01 (0.23), residues: 564 sheet: 0.06 (0.28), residues: 342 loop : -0.62 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 70 TYR 0.014 0.002 TYR E 316 PHE 0.009 0.001 PHE C 32 TRP 0.004 0.001 TRP B 86 HIS 0.005 0.001 HIS F 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (16584) covalent geometry : angle 0.49843 / 0.28 (22530) hydrogen bonds : bond 0.04089 / 2.71 ( 660) hydrogen bonds : angle 4.69552 / 3.31 ( 1926) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 0.753 Fit side-chains REVERT: A 142 ARG cc_start: 0.7158 (ttt-90) cc_final: 0.6623 (ptt90) REVERT: A 233 GLN cc_start: 0.7425 (tt0) cc_final: 0.6919 (mm110) REVERT: A 293 GLU cc_start: 0.6140 (tt0) cc_final: 0.5821 (tp30) REVERT: B 21 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7931 (mp0) REVERT: B 22 MET cc_start: 0.8547 (ptm) cc_final: 0.7789 (ptp) REVERT: B 141 LYS cc_start: 0.8005 (mttt) cc_final: 0.7742 (mmtm) REVERT: B 142 ARG cc_start: 0.7269 (ttt180) cc_final: 0.6778 (mpp80) REVERT: B 233 GLN cc_start: 0.7587 (tt0) cc_final: 0.6918 (mm110) REVERT: C 21 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7840 (mp0) REVERT: C 191 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7502 (mt-10) REVERT: C 194 GLU cc_start: 0.5386 (OUTLIER) cc_final: 0.4939 (tm-30) REVERT: C 233 GLN cc_start: 0.7524 (tt0) cc_final: 0.6937 (mm110) REVERT: D 21 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7902 (mp0) REVERT: D 191 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7532 (mt-10) REVERT: D 194 GLU cc_start: 0.5374 (OUTLIER) cc_final: 0.4918 (tm-30) REVERT: D 233 GLN cc_start: 0.7503 (tt0) cc_final: 0.6918 (mm110) REVERT: E 21 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7943 (mp0) REVERT: E 22 MET cc_start: 0.8538 (ptm) cc_final: 0.7776 (ptp) REVERT: E 141 LYS cc_start: 0.7992 (mttt) cc_final: 0.7738 (mmtm) REVERT: E 142 ARG cc_start: 0.7259 (ttt180) cc_final: 0.6770 (mpp80) REVERT: E 233 GLN cc_start: 0.7577 (tt0) cc_final: 0.6891 (mm110) REVERT: E 273 ASP cc_start: 0.7054 (p0) cc_final: 0.6828 (p0) REVERT: F 142 ARG cc_start: 0.7170 (ttt-90) cc_final: 0.6629 (ptt90) REVERT: F 233 GLN cc_start: 0.7383 (tt0) cc_final: 0.6883 (mm110) REVERT: F 273 ASP cc_start: 0.7155 (p0) cc_final: 0.6927 (p0) REVERT: F 293 GLU cc_start: 0.6154 (tt0) cc_final: 0.5828 (tp30) outliers start: 18 outliers final: 16 residues processed: 201 average time/residue: 1.2100 time to fit residues: 270.6851 Evaluate side-chains 211 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 322 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [84, 39, 188, 44, 76, 162, 168, 80, 68, 30, 157] chunk 84 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN B 36 GLN C 181 ASN D 181 ASN E 36 GLN F 181 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.185057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.159542 restraints weight = 37642.495| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.04 r_work: 0.3581 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16584 Z= 0.108 Angle : 0.466 4.408 22530 Z= 0.260 Chirality : 0.043 0.132 2544 Planarity : 0.004 0.051 2910 Dihedral : 4.954 22.887 2256 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.89 % Allowed : 9.78 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.18), residues: 2028 helix: 1.23 (0.23), residues: 564 sheet: 0.13 (0.29), residues: 342 loop : -0.54 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 70 TYR 0.013 0.001 TYR B 10 PHE 0.009 0.001 PHE C 32 TRP 0.003 0.001 TRP E 86 HIS 0.004 0.001 HIS F 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (16584) covalent geometry : angle 0.46621 / 0.26 (22530) hydrogen bonds : bond 0.03710 / 2.45 ( 660) hydrogen bonds : angle 4.55131 / 3.21 ( 1926) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.837 Fit side-chains REVERT: A 142 ARG cc_start: 0.7136 (ttt-90) cc_final: 0.6499 (ptt90) REVERT: A 233 GLN cc_start: 0.7441 (tt0) cc_final: 0.6916 (mm110) REVERT: A 293 GLU cc_start: 0.6141 (tt0) cc_final: 0.5807 (tp30) REVERT: B 21 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7918 (mp0) REVERT: B 22 MET cc_start: 0.8520 (ptm) cc_final: 0.7763 (ptp) REVERT: B 141 LYS cc_start: 0.7963 (mttt) cc_final: 0.7744 (mmtm) REVERT: B 142 ARG cc_start: 0.7282 (ttt180) cc_final: 0.6833 (mpp80) REVERT: B 233 GLN cc_start: 0.7642 (tt0) cc_final: 0.6948 (mm110) REVERT: C 21 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7873 (mp0) REVERT: C 181 ASN cc_start: 0.8249 (m-40) cc_final: 0.7866 (m110) REVERT: C 191 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7529 (mt-10) REVERT: C 194 GLU cc_start: 0.5479 (pm20) cc_final: 0.5022 (tm-30) REVERT: C 233 GLN cc_start: 0.7726 (tt0) cc_final: 0.7061 (mm110) REVERT: C 273 ASP cc_start: 0.7487 (p0) cc_final: 0.7216 (p0) REVERT: D 21 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7937 (mp0) REVERT: D 181 ASN cc_start: 0.8227 (m-40) cc_final: 0.7836 (m110) REVERT: D 191 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7541 (mt-10) REVERT: D 194 GLU cc_start: 0.5471 (pm20) cc_final: 0.5012 (tm-30) REVERT: D 233 GLN cc_start: 0.7506 (tt0) cc_final: 0.6925 (mm110) REVERT: E 21 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7931 (mp0) REVERT: E 22 MET cc_start: 0.8513 (ptm) cc_final: 0.7753 (ptp) REVERT: E 141 LYS cc_start: 0.7955 (mttt) cc_final: 0.7738 (mmtm) REVERT: E 142 ARG cc_start: 0.7273 (ttt180) cc_final: 0.6824 (mpp80) REVERT: E 233 GLN cc_start: 0.7628 (tt0) cc_final: 0.6926 (mm110) REVERT: F 142 ARG cc_start: 0.7128 (ttt-90) cc_final: 0.6624 (ptt90) REVERT: F 233 GLN cc_start: 0.7415 (tt0) cc_final: 0.6898 (mm110) REVERT: F 293 GLU cc_start: 0.6151 (tt0) cc_final: 0.5822 (tp30) outliers start: 16 outliers final: 16 residues processed: 197 average time/residue: 1.1506 time to fit residues: 253.7763 Evaluate side-chains 208 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 322 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [34, 46, 67, 43, 104, 95, 37, 155, 70, 109, 101] chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 0.0060 chunk 67 optimal weight: 8.9990 chunk 43 optimal weight: 0.0010 chunk 104 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 101 optimal weight: 0.0030 overall best weight: 0.3412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN C 186 GLN D 186 GLN E 36 GLN F 181 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.201388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.172758 restraints weight = 40030.558| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.32 r_work: 0.3791 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16584 Z= 0.074 Angle : 0.415 3.825 22530 Z= 0.229 Chirality : 0.042 0.131 2544 Planarity : 0.004 0.051 2910 Dihedral : 4.436 21.788 2256 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 0.72 % Allowed : 9.94 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 2028 helix: 1.59 (0.23), residues: 564 sheet: 0.13 (0.29), residues: 342 loop : -0.35 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 171 TYR 0.012 0.001 TYR D 10 PHE 0.004 0.001 PHE C 32 TRP 0.006 0.001 TRP D 324 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00160 / 0.07 (16584) covalent geometry : angle 0.41486 / 0.23 (22530) hydrogen bonds : bond 0.02913 / 1.95 ( 660) hydrogen bonds : angle 4.32678 / 3.06 ( 1926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10453.85 seconds wall clock time: 177 minutes 1.25 seconds (10621.25 seconds total)