Starting phenix.real_space_refine on Thu Mar 5 10:16:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6val_21142/03_2026/6val_21142.cif Found real_map, /net/cci-nas-00/data/ceres_data/6val_21142/03_2026/6val_21142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6val_21142/03_2026/6val_21142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6val_21142/03_2026/6val_21142.map" model { file = "/net/cci-nas-00/data/ceres_data/6val_21142/03_2026/6val_21142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6val_21142/03_2026/6val_21142.cif" } resolution = 3.87 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= 0.072 sd= 0.561 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 165 5.16 5 C 14047 2.51 5 N 3663 2.21 5 O 3740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21615 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1965 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 1, 'ARG:plan': 6, 'GLU:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 75 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K Time building chain proxies: 2.61, per 1000 atoms: 0.12 Number of scatterers: 21615 At special positions: 0 Unit cell: (145.22, 147.34, 99.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 165 16.00 O 3740 8.00 N 3663 7.00 C 14047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 126 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 126 " distance=2.03 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5390 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 0 sheets defined 75.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 48 through 70 removed outlier: 3.946A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 72 through 83 removed outlier: 4.024A pdb=" N MET A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 107 Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.671A pdb=" N VAL A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 128 Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 265 Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.536A pdb=" N LEU A 304 " --> pdb=" O TRP A 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 70 removed outlier: 3.945A pdb=" N LEU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 72 through 83 removed outlier: 4.024A pdb=" N MET B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 107 Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 170 through 208 removed outlier: 4.060A pdb=" N ALA B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 265 Processing helix chain 'B' and resid 272 through 280 removed outlier: 3.636A pdb=" N THR B 280 " --> pdb=" O TRP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 removed outlier: 3.535A pdb=" N LEU B 304 " --> pdb=" O TRP B 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 70 removed outlier: 3.945A pdb=" N LEU C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 72 through 83 removed outlier: 4.024A pdb=" N MET C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 107 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE C 248 " --> pdb=" O ASN C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR C 280 " --> pdb=" O TRP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 304 removed outlier: 3.535A pdb=" N LEU C 304 " --> pdb=" O TRP C 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 70 removed outlier: 3.945A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 72 through 83 removed outlier: 4.024A pdb=" N MET D 76 " --> pdb=" O ASN D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 107 Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE D 248 " --> pdb=" O ASN D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 Processing helix chain 'D' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR D 280 " --> pdb=" O TRP D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 304 removed outlier: 3.535A pdb=" N LEU D 304 " --> pdb=" O TRP D 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 70 removed outlier: 3.946A pdb=" N LEU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 72 through 83 removed outlier: 4.024A pdb=" N MET E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 107 Processing helix chain 'E' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 147 through 157 Processing helix chain 'E' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 249 removed outlier: 3.519A pdb=" N PHE E 248 " --> pdb=" O ASN E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 265 Processing helix chain 'E' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR E 280 " --> pdb=" O TRP E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 304 removed outlier: 3.535A pdb=" N LEU E 304 " --> pdb=" O TRP E 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 70 removed outlier: 3.944A pdb=" N LEU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 72 through 83 removed outlier: 4.024A pdb=" N MET F 76 " --> pdb=" O ASN F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 107 Processing helix chain 'F' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL F 112 " --> pdb=" O ILE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 147 through 157 Processing helix chain 'F' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA F 174 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 249 removed outlier: 3.519A pdb=" N PHE F 248 " --> pdb=" O ASN F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 265 Processing helix chain 'F' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR F 280 " --> pdb=" O TRP F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 304 removed outlier: 3.536A pdb=" N LEU F 304 " --> pdb=" O TRP F 300 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 70 removed outlier: 3.945A pdb=" N LEU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 72 through 83 removed outlier: 4.023A pdb=" N MET G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 107 Processing helix chain 'G' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL G 112 " --> pdb=" O ILE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 128 Processing helix chain 'G' and resid 147 through 157 Processing helix chain 'G' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE G 248 " --> pdb=" O ASN G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 265 Processing helix chain 'G' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR G 280 " --> pdb=" O TRP G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 304 removed outlier: 3.535A pdb=" N LEU G 304 " --> pdb=" O TRP G 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 70 removed outlier: 3.945A pdb=" N LEU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY H 54 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 72 through 83 removed outlier: 4.023A pdb=" N MET H 76 " --> pdb=" O ASN H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 107 Processing helix chain 'H' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL H 112 " --> pdb=" O ILE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 147 through 157 Processing helix chain 'H' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA H 174 " --> pdb=" O ALA H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE H 248 " --> pdb=" O ASN H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 Processing helix chain 'H' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR H 280 " --> pdb=" O TRP H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 304 removed outlier: 3.535A pdb=" N LEU H 304 " --> pdb=" O TRP H 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 70 removed outlier: 3.945A pdb=" N LEU I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Proline residue: I 59 - end of helix Processing helix chain 'I' and resid 72 through 83 removed outlier: 4.023A pdb=" N MET I 76 " --> pdb=" O ASN I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 107 Processing helix chain 'I' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 147 through 157 Processing helix chain 'I' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA I 174 " --> pdb=" O ALA I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 249 removed outlier: 3.519A pdb=" N PHE I 248 " --> pdb=" O ASN I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 265 Processing helix chain 'I' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR I 280 " --> pdb=" O TRP I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 304 removed outlier: 3.536A pdb=" N LEU I 304 " --> pdb=" O TRP I 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 70 removed outlier: 3.946A pdb=" N LEU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) Proline residue: J 59 - end of helix Processing helix chain 'J' and resid 72 through 83 removed outlier: 4.024A pdb=" N MET J 76 " --> pdb=" O ASN J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 107 Processing helix chain 'J' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL J 112 " --> pdb=" O ILE J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 128 Processing helix chain 'J' and resid 147 through 157 Processing helix chain 'J' and resid 170 through 208 removed outlier: 4.060A pdb=" N ALA J 174 " --> pdb=" O ALA J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE J 248 " --> pdb=" O ASN J 244 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 265 Processing helix chain 'J' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR J 280 " --> pdb=" O TRP J 276 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 304 removed outlier: 3.535A pdb=" N LEU J 304 " --> pdb=" O TRP J 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 70 removed outlier: 3.945A pdb=" N LEU K 53 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY K 54 " --> pdb=" O ALA K 50 " (cutoff:3.500A) Proline residue: K 59 - end of helix Processing helix chain 'K' and resid 72 through 83 removed outlier: 4.023A pdb=" N MET K 76 " --> pdb=" O ASN K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 107 Processing helix chain 'K' and resid 107 through 121 removed outlier: 3.669A pdb=" N VAL K 112 " --> pdb=" O ILE K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 128 Processing helix chain 'K' and resid 147 through 157 Processing helix chain 'K' and resid 170 through 208 removed outlier: 4.060A pdb=" N ALA K 174 " --> pdb=" O ALA K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE K 248 " --> pdb=" O ASN K 244 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 265 Processing helix chain 'K' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR K 280 " --> pdb=" O TRP K 276 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 304 removed outlier: 3.536A pdb=" N LEU K 304 " --> pdb=" O TRP K 300 " (cutoff:3.500A) 1529 hydrogen bonds defined for protein. 4587 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: 3.78 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6952 1.34 - 1.46: 5054 1.46 - 1.58: 9917 1.58 - 1.69: 0 1.69 - 1.81: 220 Bond restraints: 22143 Sorted by residual: bond pdb=" N ILE K 162 " pdb=" CA ILE K 162 " ideal model delta sigma weight residual 1.462 1.449 0.013 1.06e-02 8.90e+03 1.50e+00 bond pdb=" N ILE C 162 " pdb=" CA ILE C 162 " ideal model delta sigma weight residual 1.462 1.449 0.013 1.06e-02 8.90e+03 1.49e+00 bond pdb=" N ILE H 162 " pdb=" CA ILE H 162 " ideal model delta sigma weight residual 1.462 1.449 0.013 1.06e-02 8.90e+03 1.48e+00 bond pdb=" N ILE G 162 " pdb=" CA ILE G 162 " ideal model delta sigma weight residual 1.462 1.450 0.013 1.06e-02 8.90e+03 1.46e+00 bond pdb=" N ILE F 162 " pdb=" CA ILE F 162 " ideal model delta sigma weight residual 1.462 1.450 0.013 1.06e-02 8.90e+03 1.45e+00 ... (remaining 22138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 28481 1.40 - 2.80: 1469 2.80 - 4.20: 223 4.20 - 5.59: 66 5.59 - 6.99: 22 Bond angle restraints: 30261 Sorted by residual: angle pdb=" N ARG G 46 " pdb=" CA ARG G 46 " pdb=" C ARG G 46 " ideal model delta sigma weight residual 114.56 111.24 3.32 1.27e+00 6.20e-01 6.84e+00 angle pdb=" N ARG D 46 " pdb=" CA ARG D 46 " pdb=" C ARG D 46 " ideal model delta sigma weight residual 114.56 111.24 3.32 1.27e+00 6.20e-01 6.84e+00 angle pdb=" N ARG B 46 " pdb=" CA ARG B 46 " pdb=" C ARG B 46 " ideal model delta sigma weight residual 114.56 111.25 3.31 1.27e+00 6.20e-01 6.80e+00 angle pdb=" N ARG K 46 " pdb=" CA ARG K 46 " pdb=" C ARG K 46 " ideal model delta sigma weight residual 114.56 111.26 3.30 1.27e+00 6.20e-01 6.76e+00 angle pdb=" N ARG I 46 " pdb=" CA ARG I 46 " pdb=" C ARG I 46 " ideal model delta sigma weight residual 114.56 111.27 3.29 1.27e+00 6.20e-01 6.72e+00 ... (remaining 30256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 11253 15.65 - 31.30: 1245 31.30 - 46.95: 449 46.95 - 62.60: 22 62.60 - 78.26: 22 Dihedral angle restraints: 12991 sinusoidal: 4686 harmonic: 8305 Sorted by residual: dihedral pdb=" CB CYS J 41 " pdb=" SG CYS J 41 " pdb=" SG CYS J 126 " pdb=" CB CYS J 126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.26 78.26 1 1.00e+01 1.00e-02 7.65e+01 dihedral pdb=" CB CYS F 41 " pdb=" SG CYS F 41 " pdb=" SG CYS F 126 " pdb=" CB CYS F 126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.24 78.24 1 1.00e+01 1.00e-02 7.64e+01 dihedral pdb=" CB CYS G 41 " pdb=" SG CYS G 41 " pdb=" SG CYS G 126 " pdb=" CB CYS G 126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.24 78.24 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 12988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2360 0.036 - 0.071: 932 0.071 - 0.107: 153 0.107 - 0.143: 31 0.143 - 0.178: 11 Chirality restraints: 3487 Sorted by residual: chirality pdb=" CA ILE F 169 " pdb=" N ILE F 169 " pdb=" C ILE F 169 " pdb=" CB ILE F 169 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA ILE G 169 " pdb=" N ILE G 169 " pdb=" C ILE G 169 " pdb=" CB ILE G 169 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE C 169 " pdb=" N ILE C 169 " pdb=" C ILE C 169 " pdb=" CB ILE C 169 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 3484 not shown) Planarity restraints: 3850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 59 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO E 60 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 59 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO C 60 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 59 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO F 60 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO F 60 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 60 " -0.028 5.00e-02 4.00e+02 ... (remaining 3847 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 137 2.62 - 3.19: 21082 3.19 - 3.76: 32928 3.76 - 4.33: 40664 4.33 - 4.90: 66759 Nonbonded interactions: 161570 Sorted by model distance: nonbonded pdb=" OH TYR K 97 " pdb=" OE2 GLU K 215 " model vdw 2.052 3.040 nonbonded pdb=" OH TYR E 97 " pdb=" OE2 GLU E 215 " model vdw 2.052 3.040 nonbonded pdb=" OH TYR F 97 " pdb=" OE2 GLU F 215 " model vdw 2.052 3.040 nonbonded pdb=" OH TYR I 97 " pdb=" OE2 GLU I 215 " model vdw 2.052 3.040 nonbonded pdb=" OH TYR H 97 " pdb=" OE2 GLU H 215 " model vdw 2.052 3.040 ... (remaining 161565 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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 group one per residue 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.520 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 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 : 0.005 0.044 22154 Z= 0.242 Angle : 0.740 6.992 30283 Z= 0.426 Chirality : 0.038 0.178 3487 Planarity : 0.005 0.050 3850 Dihedral : 14.395 63.578 7568 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.02 % Allowed : 4.96 % Favored : 94.02 % 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: -3.34 (0.13), residues: 2761 helix: -1.41 (0.09), residues: 1969 sheet: None (None), residues: 0 loop : -4.11 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 246 TYR 0.017 0.001 TYR J 97 PHE 0.011 0.001 PHE B 198 TRP 0.008 0.001 TRP I 300 HIS 0.005 0.001 HIS K 236 Details of bonding type rmsd covalent geometry : bond 0.00508 (22143) covalent geometry : angle 0.73850 (30261) SS BOND : bond 0.00159 ( 11) SS BOND : angle 1.78419 ( 22) hydrogen bonds : bond 0.13280 ( 1529) hydrogen bonds : angle 6.08064 ( 4587) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 477 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7889 (tp40) cc_final: 0.7322 (tm-30) REVERT: A 234 GLU cc_start: 0.8524 (tt0) cc_final: 0.8240 (tp30) REVERT: B 102 MET cc_start: 0.8879 (mmp) cc_final: 0.8595 (tpp) REVERT: B 104 GLN cc_start: 0.8008 (tp40) cc_final: 0.7424 (tm-30) REVERT: B 234 GLU cc_start: 0.8665 (tt0) cc_final: 0.8379 (tp30) REVERT: C 102 MET cc_start: 0.8904 (mmp) cc_final: 0.8424 (tpp) REVERT: C 104 GLN cc_start: 0.8075 (tp40) cc_final: 0.7323 (tm-30) REVERT: C 259 GLU cc_start: 0.6735 (tm-30) cc_final: 0.6358 (tp30) REVERT: D 104 GLN cc_start: 0.7823 (tp40) cc_final: 0.7429 (tm-30) REVERT: D 287 GLU cc_start: 0.8118 (tt0) cc_final: 0.7669 (tt0) REVERT: E 102 MET cc_start: 0.8954 (mmp) cc_final: 0.8484 (tpp) REVERT: E 104 GLN cc_start: 0.7892 (tp40) cc_final: 0.7231 (tm-30) REVERT: E 210 LEU cc_start: 0.8672 (mt) cc_final: 0.8336 (mp) REVERT: F 104 GLN cc_start: 0.7993 (tp40) cc_final: 0.7457 (tm-30) REVERT: F 234 GLU cc_start: 0.8481 (tt0) cc_final: 0.8269 (tp30) REVERT: G 102 MET cc_start: 0.8774 (mmp) cc_final: 0.8359 (tpp) REVERT: G 104 GLN cc_start: 0.8162 (tp40) cc_final: 0.7599 (tm-30) REVERT: H 41 CYS cc_start: 0.6574 (m) cc_final: 0.6361 (m) REVERT: H 104 GLN cc_start: 0.7956 (tp40) cc_final: 0.7470 (tm-30) REVERT: I 102 MET cc_start: 0.8832 (mmp) cc_final: 0.8517 (tpp) REVERT: I 104 GLN cc_start: 0.7934 (tp40) cc_final: 0.7302 (tm-30) REVERT: I 163 TYR cc_start: 0.6920 (t80) cc_final: 0.6549 (t80) REVERT: I 259 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6265 (tp30) REVERT: J 41 CYS cc_start: 0.6529 (m) cc_final: 0.6294 (m) REVERT: J 102 MET cc_start: 0.8917 (mmp) cc_final: 0.8645 (tpp) REVERT: J 104 GLN cc_start: 0.8036 (tp40) cc_final: 0.7647 (tm-30) REVERT: J 234 GLU cc_start: 0.8582 (tt0) cc_final: 0.8347 (tp30) REVERT: K 102 MET cc_start: 0.8937 (mmp) cc_final: 0.8572 (tpp) REVERT: K 104 GLN cc_start: 0.7637 (tp40) cc_final: 0.6983 (tm-30) outliers start: 22 outliers final: 3 residues processed: 499 average time/residue: 0.1107 time to fit residues: 94.4485 Evaluate side-chains 318 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 315 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain K residue 116 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 227 GLN A 230 GLN A 298 HIS B 227 GLN B 230 GLN B 298 HIS C 205 HIS C 227 GLN C 230 GLN C 298 HIS D 205 HIS D 227 GLN D 230 GLN D 298 HIS E 214 GLN E 227 GLN E 230 GLN E 298 HIS F 214 GLN F 227 GLN F 230 GLN F 298 HIS G 230 GLN G 298 HIS H 205 HIS H 227 GLN H 230 GLN H 298 HIS I 205 HIS I 214 GLN I 230 GLN I 298 HIS J 214 GLN J 227 GLN J 230 GLN J 298 HIS K 205 HIS K 214 GLN K 227 GLN K 230 GLN K 298 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.115638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.093477 restraints weight = 47868.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096584 restraints weight = 27808.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.098774 restraints weight = 19300.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100329 restraints weight = 14983.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.101423 restraints weight = 12478.494| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22154 Z= 0.154 Angle : 0.647 6.424 30283 Z= 0.333 Chirality : 0.038 0.171 3487 Planarity : 0.005 0.052 3850 Dihedral : 4.783 21.764 3061 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.13 % Allowed : 13.27 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.15), residues: 2761 helix: 0.29 (0.11), residues: 1947 sheet: None (None), residues: 0 loop : -3.22 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 238 TYR 0.022 0.001 TYR C 285 PHE 0.008 0.001 PHE E 198 TRP 0.008 0.001 TRP E 300 HIS 0.006 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00323 (22143) covalent geometry : angle 0.64647 (30261) SS BOND : bond 0.00203 ( 11) SS BOND : angle 1.11219 ( 22) hydrogen bonds : bond 0.05346 ( 1529) hydrogen bonds : angle 4.46269 ( 4587) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 374 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7995 (tp40) cc_final: 0.7305 (tm-30) REVERT: A 259 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8226 (tp30) REVERT: B 104 GLN cc_start: 0.8055 (tp40) cc_final: 0.7448 (tm-30) REVERT: B 193 MET cc_start: 0.7219 (tpp) cc_final: 0.6603 (tpt) REVERT: B 215 GLU cc_start: 0.8771 (tp30) cc_final: 0.8552 (tp30) REVERT: B 259 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8050 (tp30) REVERT: C 104 GLN cc_start: 0.7948 (tp40) cc_final: 0.7218 (tm-30) REVERT: C 259 GLU cc_start: 0.8638 (tm-30) cc_final: 0.7915 (tp30) REVERT: D 104 GLN cc_start: 0.8125 (tp40) cc_final: 0.7684 (tm-30) REVERT: D 259 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8368 (tp30) REVERT: D 287 GLU cc_start: 0.8773 (tt0) cc_final: 0.8252 (tt0) REVERT: E 104 GLN cc_start: 0.7959 (tp40) cc_final: 0.7598 (tm-30) REVERT: E 193 MET cc_start: 0.7208 (tpp) cc_final: 0.6656 (tpt) REVERT: E 259 GLU cc_start: 0.8560 (tp30) cc_final: 0.8340 (tp30) REVERT: E 275 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7980 (mm-40) REVERT: F 104 GLN cc_start: 0.8130 (tp40) cc_final: 0.7682 (tm-30) REVERT: F 193 MET cc_start: 0.7345 (tpp) cc_final: 0.6645 (tmm) REVERT: F 259 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8247 (tp30) REVERT: G 104 GLN cc_start: 0.8280 (tp40) cc_final: 0.7628 (tm-30) REVERT: G 119 LEU cc_start: 0.8492 (mt) cc_final: 0.8286 (mm) REVERT: G 193 MET cc_start: 0.7220 (tpp) cc_final: 0.6728 (tmm) REVERT: G 215 GLU cc_start: 0.8751 (tp30) cc_final: 0.8505 (tp30) REVERT: G 259 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8106 (tp30) REVERT: G 275 GLN cc_start: 0.8335 (mm-40) cc_final: 0.8080 (mm-40) REVERT: H 104 GLN cc_start: 0.8113 (tp40) cc_final: 0.7632 (tm-30) REVERT: H 259 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8261 (tp30) REVERT: H 287 GLU cc_start: 0.8412 (tt0) cc_final: 0.8026 (tt0) REVERT: I 196 LEU cc_start: 0.8886 (tp) cc_final: 0.8604 (tt) REVERT: I 259 GLU cc_start: 0.8782 (tm-30) cc_final: 0.7976 (tp30) REVERT: J 104 GLN cc_start: 0.8152 (tp40) cc_final: 0.7730 (tm-30) REVERT: J 196 LEU cc_start: 0.8809 (tp) cc_final: 0.8503 (tp) REVERT: J 259 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8218 (tp30) REVERT: K 104 GLN cc_start: 0.7926 (tp40) cc_final: 0.7187 (tm-30) REVERT: K 259 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8185 (tp30) REVERT: K 287 GLU cc_start: 0.8591 (tt0) cc_final: 0.8301 (tt0) outliers start: 89 outliers final: 54 residues processed: 409 average time/residue: 0.1104 time to fit residues: 78.5009 Evaluate side-chains 384 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 330 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 206 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 156 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS B 205 HIS C 205 HIS D 205 HIS E 205 HIS F 205 HIS G 205 HIS H 205 HIS I 205 HIS J 205 HIS K 205 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.115459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.093059 restraints weight = 47559.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.096139 restraints weight = 27643.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.098314 restraints weight = 19258.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099831 restraints weight = 14976.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.100939 restraints weight = 12532.295| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22154 Z= 0.156 Angle : 0.619 5.829 30283 Z= 0.316 Chirality : 0.038 0.165 3487 Planarity : 0.005 0.051 3850 Dihedral : 4.499 20.006 3058 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.68 % Allowed : 15.45 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.15), residues: 2761 helix: 0.73 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -3.64 (0.16), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 238 TYR 0.013 0.001 TYR A 97 PHE 0.009 0.001 PHE H 198 TRP 0.007 0.001 TRP E 300 HIS 0.006 0.002 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00343 (22143) covalent geometry : angle 0.61838 (30261) SS BOND : bond 0.00383 ( 11) SS BOND : angle 0.82604 ( 22) hydrogen bonds : bond 0.04969 ( 1529) hydrogen bonds : angle 4.15396 ( 4587) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 357 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.8032 (tp40) cc_final: 0.7407 (tm-30) REVERT: A 234 GLU cc_start: 0.8511 (tp30) cc_final: 0.8308 (tp30) REVERT: A 259 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8161 (tp30) REVERT: B 104 GLN cc_start: 0.8053 (tp40) cc_final: 0.7489 (tm-30) REVERT: B 215 GLU cc_start: 0.8712 (tp30) cc_final: 0.8376 (tp30) REVERT: B 234 GLU cc_start: 0.8596 (tp30) cc_final: 0.8160 (tp30) REVERT: B 259 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8159 (tp30) REVERT: B 287 GLU cc_start: 0.8586 (tt0) cc_final: 0.8225 (tt0) REVERT: C 104 GLN cc_start: 0.7917 (tp40) cc_final: 0.7184 (tm-30) REVERT: C 196 LEU cc_start: 0.8636 (tp) cc_final: 0.8100 (tp) REVERT: C 234 GLU cc_start: 0.8675 (tp30) cc_final: 0.8420 (tp30) REVERT: C 259 GLU cc_start: 0.8555 (tm-30) cc_final: 0.7959 (tp30) REVERT: D 104 GLN cc_start: 0.8036 (tp40) cc_final: 0.7653 (tm-30) REVERT: D 259 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8128 (tp30) REVERT: D 287 GLU cc_start: 0.8822 (tt0) cc_final: 0.8312 (tt0) REVERT: E 98 MET cc_start: 0.8315 (mtt) cc_final: 0.7954 (mtp) REVERT: E 104 GLN cc_start: 0.7977 (tp40) cc_final: 0.7590 (tm-30) REVERT: E 259 GLU cc_start: 0.8586 (tp30) cc_final: 0.8173 (tp30) REVERT: E 275 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7976 (mm-40) REVERT: F 104 GLN cc_start: 0.8120 (tp40) cc_final: 0.7278 (tm-30) REVERT: F 193 MET cc_start: 0.7426 (tpp) cc_final: 0.6598 (tmm) REVERT: F 259 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8267 (tp30) REVERT: G 104 GLN cc_start: 0.8261 (tp40) cc_final: 0.7720 (tm-30) REVERT: G 149 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7268 (mm-30) REVERT: G 259 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8192 (tp30) REVERT: G 275 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8171 (mm-40) REVERT: H 104 GLN cc_start: 0.8114 (tp40) cc_final: 0.7683 (tm-30) REVERT: H 259 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8177 (tp30) REVERT: H 287 GLU cc_start: 0.8419 (tt0) cc_final: 0.8032 (tt0) REVERT: I 196 LEU cc_start: 0.8805 (tp) cc_final: 0.8504 (tt) REVERT: I 259 GLU cc_start: 0.8706 (tm-30) cc_final: 0.7924 (tp30) REVERT: J 104 GLN cc_start: 0.8102 (tp40) cc_final: 0.7709 (tm-30) REVERT: J 196 LEU cc_start: 0.8783 (tp) cc_final: 0.8538 (tp) REVERT: J 259 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8253 (tp30) REVERT: K 104 GLN cc_start: 0.7929 (tp40) cc_final: 0.7290 (tm-30) REVERT: K 193 MET cc_start: 0.6215 (tpt) cc_final: 0.5754 (tpp) REVERT: K 259 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8207 (tp30) REVERT: K 275 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7872 (mm-40) REVERT: K 287 GLU cc_start: 0.8492 (tt0) cc_final: 0.7997 (tt0) outliers start: 101 outliers final: 69 residues processed: 399 average time/residue: 0.1094 time to fit residues: 75.8970 Evaluate side-chains 409 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 340 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 270 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 196 optimal weight: 7.9990 chunk 263 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 237 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS B 205 HIS C 205 HIS D 205 HIS E 205 HIS F 205 HIS G 205 HIS H 205 HIS I 205 HIS J 205 HIS K 205 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.115478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.092993 restraints weight = 47659.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.096063 restraints weight = 27868.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.098238 restraints weight = 19473.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099786 restraints weight = 15149.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100811 restraints weight = 12633.588| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22154 Z= 0.163 Angle : 0.613 6.358 30283 Z= 0.314 Chirality : 0.038 0.160 3487 Planarity : 0.005 0.051 3850 Dihedral : 4.416 19.397 3058 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.41 % Allowed : 18.78 % Favored : 76.81 % 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 (0.15), residues: 2761 helix: 1.00 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -3.29 (0.17), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 105 TYR 0.011 0.001 TYR A 97 PHE 0.010 0.001 PHE G 198 TRP 0.008 0.001 TRP H 300 HIS 0.006 0.001 HIS F 236 Details of bonding type rmsd covalent geometry : bond 0.00361 (22143) covalent geometry : angle 0.61252 (30261) SS BOND : bond 0.00302 ( 11) SS BOND : angle 0.77549 ( 22) hydrogen bonds : bond 0.04896 ( 1529) hydrogen bonds : angle 4.04475 ( 4587) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 363 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.8018 (tp40) cc_final: 0.7446 (tm-30) REVERT: A 234 GLU cc_start: 0.8553 (tp30) cc_final: 0.8292 (tp30) REVERT: A 259 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8303 (tp30) REVERT: B 104 GLN cc_start: 0.8011 (tp40) cc_final: 0.7481 (tm-30) REVERT: B 234 GLU cc_start: 0.8626 (tp30) cc_final: 0.8185 (tp30) REVERT: B 259 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8174 (tp30) REVERT: C 104 GLN cc_start: 0.7962 (tp40) cc_final: 0.7170 (tm-30) REVERT: C 196 LEU cc_start: 0.8595 (tp) cc_final: 0.8039 (tp) REVERT: C 259 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7956 (tp30) REVERT: D 104 GLN cc_start: 0.8120 (tp40) cc_final: 0.7697 (tm-30) REVERT: D 193 MET cc_start: 0.7506 (tpp) cc_final: 0.6907 (tmm) REVERT: D 234 GLU cc_start: 0.8536 (tp30) cc_final: 0.8273 (tp30) REVERT: D 259 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8286 (tp30) REVERT: D 287 GLU cc_start: 0.8824 (tt0) cc_final: 0.8347 (tt0) REVERT: E 98 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7984 (mtp) REVERT: E 259 GLU cc_start: 0.8609 (tp30) cc_final: 0.8119 (tp30) REVERT: E 275 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7969 (mm-40) REVERT: F 104 GLN cc_start: 0.8078 (tp40) cc_final: 0.7214 (tm-30) REVERT: F 193 MET cc_start: 0.7535 (tpp) cc_final: 0.6652 (tmm) REVERT: F 259 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8250 (tp30) REVERT: G 76 MET cc_start: 0.8682 (mmt) cc_final: 0.8111 (mmm) REVERT: G 104 GLN cc_start: 0.8220 (tp40) cc_final: 0.7692 (tm-30) REVERT: G 149 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7304 (mm-30) REVERT: G 259 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8225 (tp30) REVERT: H 104 GLN cc_start: 0.8097 (tp40) cc_final: 0.7605 (tm-30) REVERT: H 234 GLU cc_start: 0.8652 (tp30) cc_final: 0.8279 (tp30) REVERT: H 259 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8291 (tp30) REVERT: H 287 GLU cc_start: 0.8417 (tt0) cc_final: 0.8030 (tt0) REVERT: I 196 LEU cc_start: 0.8848 (tp) cc_final: 0.8561 (tt) REVERT: I 259 GLU cc_start: 0.8632 (tm-30) cc_final: 0.7918 (tp30) REVERT: J 104 GLN cc_start: 0.8096 (tp40) cc_final: 0.7702 (tm-30) REVERT: J 196 LEU cc_start: 0.8786 (tp) cc_final: 0.8513 (tp) REVERT: J 259 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8272 (tp30) REVERT: J 287 GLU cc_start: 0.8670 (tt0) cc_final: 0.8268 (tt0) REVERT: K 104 GLN cc_start: 0.7847 (tp40) cc_final: 0.7227 (tm-30) REVERT: K 193 MET cc_start: 0.6197 (tpt) cc_final: 0.5767 (tpp) REVERT: K 234 GLU cc_start: 0.8683 (tp30) cc_final: 0.8465 (tp30) REVERT: K 259 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8269 (tp30) REVERT: K 275 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7906 (mm-40) REVERT: K 287 GLU cc_start: 0.8507 (tt0) cc_final: 0.7967 (tt0) outliers start: 95 outliers final: 80 residues processed: 403 average time/residue: 0.1060 time to fit residues: 74.3422 Evaluate side-chains 418 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 337 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 206 TYR Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain H residue 279 ILE Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 159 CYS Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 206 TYR Chi-restraints excluded: chain K residue 270 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 227 GLN B 205 HIS C 205 HIS D 205 HIS E 205 HIS F 205 HIS G 205 HIS H 205 HIS I 205 HIS J 205 HIS K 205 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.114430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.092101 restraints weight = 47925.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.095172 restraints weight = 27962.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.097321 restraints weight = 19459.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098854 restraints weight = 15142.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099940 restraints weight = 12624.755| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22154 Z= 0.178 Angle : 0.626 6.235 30283 Z= 0.321 Chirality : 0.039 0.159 3487 Planarity : 0.005 0.050 3850 Dihedral : 4.403 19.215 3058 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.01 % Allowed : 20.78 % Favored : 74.21 % 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 (0.15), residues: 2761 helix: 1.07 (0.11), residues: 2024 sheet: None (None), residues: 0 loop : -3.07 (0.18), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 105 TYR 0.024 0.001 TYR A 163 PHE 0.011 0.001 PHE F 198 TRP 0.008 0.001 TRP H 300 HIS 0.006 0.002 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00399 (22143) covalent geometry : angle 0.62617 (30261) SS BOND : bond 0.00162 ( 11) SS BOND : angle 0.66747 ( 22) hydrogen bonds : bond 0.04962 ( 1529) hydrogen bonds : angle 4.04976 ( 4587) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 342 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.8005 (tp40) cc_final: 0.7467 (tm-30) REVERT: A 234 GLU cc_start: 0.8519 (tp30) cc_final: 0.8247 (tp30) REVERT: A 259 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8266 (tp30) REVERT: B 104 GLN cc_start: 0.8135 (tp40) cc_final: 0.7578 (tm-30) REVERT: B 234 GLU cc_start: 0.8672 (tp30) cc_final: 0.8208 (tp30) REVERT: B 259 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8314 (tp30) REVERT: B 287 GLU cc_start: 0.8734 (tt0) cc_final: 0.7611 (tt0) REVERT: C 104 GLN cc_start: 0.8073 (tp40) cc_final: 0.7289 (tm-30) REVERT: C 196 LEU cc_start: 0.8601 (tp) cc_final: 0.8045 (tp) REVERT: C 259 GLU cc_start: 0.8499 (tm-30) cc_final: 0.7982 (tp30) REVERT: C 285 TYR cc_start: 0.7389 (t80) cc_final: 0.6600 (t80) REVERT: C 287 GLU cc_start: 0.8615 (tt0) cc_final: 0.8134 (tt0) REVERT: D 193 MET cc_start: 0.7486 (tpp) cc_final: 0.6896 (tmm) REVERT: D 234 GLU cc_start: 0.8522 (tp30) cc_final: 0.8231 (tp30) REVERT: D 259 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8290 (tp30) REVERT: D 287 GLU cc_start: 0.8838 (tt0) cc_final: 0.8413 (tt0) REVERT: E 98 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7986 (mtp) REVERT: E 259 GLU cc_start: 0.8575 (tp30) cc_final: 0.8014 (tp30) REVERT: F 104 GLN cc_start: 0.8033 (tp40) cc_final: 0.7229 (tm-30) REVERT: F 193 MET cc_start: 0.7627 (tpp) cc_final: 0.6651 (tmm) REVERT: F 215 GLU cc_start: 0.8792 (tp30) cc_final: 0.8266 (tp30) REVERT: F 259 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8238 (tp30) REVERT: G 76 MET cc_start: 0.8658 (mmt) cc_final: 0.8077 (mmm) REVERT: G 104 GLN cc_start: 0.8204 (tp40) cc_final: 0.7709 (tm-30) REVERT: G 149 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7318 (mm-30) REVERT: G 259 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8221 (tp30) REVERT: G 287 GLU cc_start: 0.8714 (tt0) cc_final: 0.7924 (tt0) REVERT: H 104 GLN cc_start: 0.8168 (tp40) cc_final: 0.7951 (tm-30) REVERT: H 193 MET cc_start: 0.7197 (tpp) cc_final: 0.6606 (tmm) REVERT: H 234 GLU cc_start: 0.8664 (tp30) cc_final: 0.8269 (tp30) REVERT: H 259 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8246 (tp30) REVERT: H 287 GLU cc_start: 0.8369 (tt0) cc_final: 0.7958 (tt0) REVERT: I 193 MET cc_start: 0.6817 (tmm) cc_final: 0.6486 (tmm) REVERT: I 196 LEU cc_start: 0.8839 (tp) cc_final: 0.8427 (tt) REVERT: I 259 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8041 (tp30) REVERT: J 104 GLN cc_start: 0.8125 (tp40) cc_final: 0.7706 (tm-30) REVERT: J 196 LEU cc_start: 0.8799 (tp) cc_final: 0.8528 (tp) REVERT: J 259 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8271 (tp30) REVERT: K 104 GLN cc_start: 0.7881 (tp40) cc_final: 0.7300 (tm-30) REVERT: K 149 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7157 (mm-30) REVERT: K 193 MET cc_start: 0.6195 (tpt) cc_final: 0.5763 (tpp) REVERT: K 234 GLU cc_start: 0.8703 (tp30) cc_final: 0.8494 (tp30) REVERT: K 259 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8235 (tp30) REVERT: K 275 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7960 (mm-40) REVERT: K 287 GLU cc_start: 0.8519 (tt0) cc_final: 0.7986 (tt0) outliers start: 108 outliers final: 92 residues processed: 402 average time/residue: 0.1113 time to fit residues: 77.6498 Evaluate side-chains 432 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 339 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 206 TYR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 206 TYR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 279 ILE Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 159 CYS Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 206 TYR Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 279 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 66 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 184 optimal weight: 0.0970 chunk 187 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS B 205 HIS C 205 HIS D 205 HIS E 205 HIS F 205 HIS G 205 HIS I 205 HIS J 205 HIS K 205 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.115622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.093205 restraints weight = 47698.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.096295 restraints weight = 27754.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.098453 restraints weight = 19323.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099993 restraints weight = 15009.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101098 restraints weight = 12517.034| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 22154 Z= 0.158 Angle : 0.607 7.390 30283 Z= 0.309 Chirality : 0.038 0.154 3487 Planarity : 0.005 0.050 3850 Dihedral : 4.235 18.643 3058 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 5.29 % Allowed : 21.75 % Favored : 72.96 % 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: 0.36 (0.15), residues: 2761 helix: 1.29 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -2.96 (0.19), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 105 TYR 0.014 0.001 TYR A 163 PHE 0.009 0.001 PHE E 198 TRP 0.008 0.001 TRP G 300 HIS 0.006 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00351 (22143) covalent geometry : angle 0.60738 (30261) SS BOND : bond 0.00386 ( 11) SS BOND : angle 0.52259 ( 22) hydrogen bonds : bond 0.04726 ( 1529) hydrogen bonds : angle 3.89850 ( 4587) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 358 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.8030 (tp40) cc_final: 0.7471 (tm-30) REVERT: A 234 GLU cc_start: 0.8552 (tp30) cc_final: 0.8301 (tp30) REVERT: A 259 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8241 (tp30) REVERT: B 104 GLN cc_start: 0.8195 (tp40) cc_final: 0.7612 (tm-30) REVERT: B 234 GLU cc_start: 0.8708 (tp30) cc_final: 0.8238 (tp30) REVERT: B 259 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8336 (tp30) REVERT: B 285 TYR cc_start: 0.7399 (t80) cc_final: 0.6065 (t80) REVERT: B 287 GLU cc_start: 0.8679 (tt0) cc_final: 0.7916 (tt0) REVERT: C 104 GLN cc_start: 0.8084 (tp40) cc_final: 0.7294 (tm-30) REVERT: C 196 LEU cc_start: 0.8579 (tp) cc_final: 0.8030 (tp) REVERT: C 259 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8021 (tp30) REVERT: D 193 MET cc_start: 0.7481 (tpp) cc_final: 0.6905 (tmm) REVERT: D 234 GLU cc_start: 0.8555 (tp30) cc_final: 0.8248 (tp30) REVERT: D 259 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8293 (tp30) REVERT: D 287 GLU cc_start: 0.8796 (tt0) cc_final: 0.8376 (tt0) REVERT: E 193 MET cc_start: 0.7329 (tpp) cc_final: 0.6772 (tpt) REVERT: E 259 GLU cc_start: 0.8532 (tp30) cc_final: 0.8238 (tp30) REVERT: E 285 TYR cc_start: 0.7620 (t80) cc_final: 0.6984 (t80) REVERT: E 287 GLU cc_start: 0.8644 (tt0) cc_final: 0.7878 (tt0) REVERT: F 104 GLN cc_start: 0.8006 (tp40) cc_final: 0.7221 (tm-30) REVERT: F 193 MET cc_start: 0.7657 (tpp) cc_final: 0.6706 (tmm) REVERT: F 215 GLU cc_start: 0.8750 (tp30) cc_final: 0.8150 (tp30) REVERT: F 259 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8237 (tp30) REVERT: G 104 GLN cc_start: 0.8213 (tp40) cc_final: 0.7716 (tm-30) REVERT: G 119 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8301 (mm) REVERT: G 149 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7320 (mm-30) REVERT: G 259 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8180 (tp30) REVERT: G 287 GLU cc_start: 0.8703 (tt0) cc_final: 0.7931 (tt0) REVERT: H 76 MET cc_start: 0.8590 (mmt) cc_final: 0.8299 (mmm) REVERT: H 104 GLN cc_start: 0.8177 (tp40) cc_final: 0.7940 (tm-30) REVERT: H 193 MET cc_start: 0.7282 (tpp) cc_final: 0.6712 (tmm) REVERT: H 234 GLU cc_start: 0.8633 (tp30) cc_final: 0.8244 (tp30) REVERT: H 259 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8236 (tp30) REVERT: H 287 GLU cc_start: 0.8413 (tt0) cc_final: 0.7970 (tt0) REVERT: I 193 MET cc_start: 0.6889 (tmm) cc_final: 0.6571 (tmm) REVERT: I 196 LEU cc_start: 0.8749 (tp) cc_final: 0.8306 (tt) REVERT: I 259 GLU cc_start: 0.8625 (tm-30) cc_final: 0.7983 (tp30) REVERT: J 104 GLN cc_start: 0.8128 (tp40) cc_final: 0.7685 (tm-30) REVERT: J 196 LEU cc_start: 0.8771 (tp) cc_final: 0.8418 (tp) REVERT: J 258 ASP cc_start: 0.8402 (m-30) cc_final: 0.8101 (m-30) REVERT: J 259 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8278 (tp30) REVERT: J 285 TYR cc_start: 0.7538 (t80) cc_final: 0.6338 (t80) REVERT: J 287 GLU cc_start: 0.8577 (tt0) cc_final: 0.7759 (tt0) REVERT: K 104 GLN cc_start: 0.7909 (tp40) cc_final: 0.7308 (tm-30) REVERT: K 149 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7190 (mm-30) REVERT: K 193 MET cc_start: 0.6176 (tpt) cc_final: 0.5740 (tpp) REVERT: K 259 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8236 (tp30) REVERT: K 275 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7890 (mm-40) REVERT: K 287 GLU cc_start: 0.8561 (tt0) cc_final: 0.8105 (tt0) outliers start: 114 outliers final: 96 residues processed: 420 average time/residue: 0.1126 time to fit residues: 81.2425 Evaluate side-chains 443 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 346 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 206 TYR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 279 ILE Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 159 CYS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 180 CYS Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 279 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 161 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 268 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 216 optimal weight: 0.0030 chunk 26 optimal weight: 0.0770 chunk 183 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 233 optimal weight: 0.9990 overall best weight: 0.5952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS B 205 HIS C 205 HIS D 205 HIS E 205 HIS F 205 HIS G 205 HIS I 205 HIS J 205 HIS K 205 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.120151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.097826 restraints weight = 46648.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101086 restraints weight = 26589.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.103390 restraints weight = 18202.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.105019 restraints weight = 13904.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.106160 restraints weight = 11451.779| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22154 Z= 0.123 Angle : 0.591 7.898 30283 Z= 0.294 Chirality : 0.036 0.146 3487 Planarity : 0.005 0.051 3850 Dihedral : 3.965 21.067 3058 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.39 % Allowed : 24.30 % Favored : 72.31 % 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: 0.87 (0.16), residues: 2761 helix: 1.63 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -2.68 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 247 TYR 0.011 0.001 TYR A 163 PHE 0.005 0.001 PHE B 189 TRP 0.010 0.001 TRP G 300 HIS 0.005 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00254 (22143) covalent geometry : angle 0.59131 (30261) SS BOND : bond 0.00122 ( 11) SS BOND : angle 0.40563 ( 22) hydrogen bonds : bond 0.04068 ( 1529) hydrogen bonds : angle 3.62672 ( 4587) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 413 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7877 (tp40) cc_final: 0.7332 (tm-30) REVERT: A 119 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8443 (mm) REVERT: A 215 GLU cc_start: 0.8651 (tp30) cc_final: 0.8364 (tp30) REVERT: A 234 GLU cc_start: 0.8617 (tp30) cc_final: 0.8329 (tp30) REVERT: A 259 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8044 (tp30) REVERT: B 104 GLN cc_start: 0.7998 (tp40) cc_final: 0.7428 (tm-30) REVERT: B 119 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8306 (mm) REVERT: B 234 GLU cc_start: 0.8744 (tp30) cc_final: 0.8252 (tp30) REVERT: B 259 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8299 (tp30) REVERT: B 285 TYR cc_start: 0.7244 (t80) cc_final: 0.5878 (t80) REVERT: B 287 GLU cc_start: 0.8612 (tt0) cc_final: 0.7718 (tt0) REVERT: C 104 GLN cc_start: 0.7989 (tp40) cc_final: 0.7193 (tm-30) REVERT: C 120 ASP cc_start: 0.7594 (m-30) cc_final: 0.7126 (t0) REVERT: C 196 LEU cc_start: 0.8399 (tp) cc_final: 0.7996 (tp) REVERT: C 234 GLU cc_start: 0.8685 (tp30) cc_final: 0.8289 (tp30) REVERT: C 259 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8019 (tp30) REVERT: C 287 GLU cc_start: 0.8427 (tt0) cc_final: 0.7724 (tt0) REVERT: D 193 MET cc_start: 0.7512 (tpp) cc_final: 0.6928 (tmm) REVERT: D 234 GLU cc_start: 0.8565 (tp30) cc_final: 0.8224 (tp30) REVERT: D 259 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8245 (tp30) REVERT: D 275 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8017 (mm-40) REVERT: D 287 GLU cc_start: 0.8774 (tt0) cc_final: 0.8363 (tt0) REVERT: E 120 ASP cc_start: 0.7558 (m-30) cc_final: 0.7172 (t0) REVERT: E 215 GLU cc_start: 0.8716 (tp30) cc_final: 0.8469 (tp30) REVERT: E 259 GLU cc_start: 0.8491 (tp30) cc_final: 0.8159 (tp30) REVERT: E 285 TYR cc_start: 0.7513 (t80) cc_final: 0.6464 (t80) REVERT: E 287 GLU cc_start: 0.8570 (tt0) cc_final: 0.7768 (tt0) REVERT: F 104 GLN cc_start: 0.7902 (tp40) cc_final: 0.7137 (tm-30) REVERT: F 193 MET cc_start: 0.7604 (tpp) cc_final: 0.6973 (tmm) REVERT: F 215 GLU cc_start: 0.8622 (tp30) cc_final: 0.8396 (tp30) REVERT: F 259 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8222 (tp30) REVERT: G 104 GLN cc_start: 0.8109 (tp40) cc_final: 0.7519 (tm-30) REVERT: G 149 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7153 (mm-30) REVERT: G 193 MET cc_start: 0.7274 (tpp) cc_final: 0.6842 (tpp) REVERT: G 234 GLU cc_start: 0.8652 (tp30) cc_final: 0.8195 (tp30) REVERT: G 258 ASP cc_start: 0.8374 (m-30) cc_final: 0.8095 (m-30) REVERT: G 287 GLU cc_start: 0.8692 (tt0) cc_final: 0.7936 (tt0) REVERT: H 104 GLN cc_start: 0.8003 (tp40) cc_final: 0.7501 (tm-30) REVERT: H 119 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8413 (mm) REVERT: H 120 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7200 (t0) REVERT: H 193 MET cc_start: 0.7482 (tpp) cc_final: 0.6857 (tmm) REVERT: H 210 LEU cc_start: 0.8912 (mt) cc_final: 0.8654 (mt) REVERT: H 215 GLU cc_start: 0.8641 (tp30) cc_final: 0.8398 (tp30) REVERT: H 234 GLU cc_start: 0.8600 (tp30) cc_final: 0.8215 (tp30) REVERT: H 259 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8256 (tp30) REVERT: H 287 GLU cc_start: 0.8462 (tt0) cc_final: 0.8086 (tt0) REVERT: I 193 MET cc_start: 0.6965 (tmm) cc_final: 0.6589 (tmm) REVERT: I 196 LEU cc_start: 0.8578 (tp) cc_final: 0.8156 (tt) REVERT: I 215 GLU cc_start: 0.8718 (tp30) cc_final: 0.8455 (tp30) REVERT: I 259 GLU cc_start: 0.8575 (tm-30) cc_final: 0.7917 (tp30) REVERT: I 287 GLU cc_start: 0.8559 (tt0) cc_final: 0.8306 (tt0) REVERT: J 104 GLN cc_start: 0.8016 (tp40) cc_final: 0.7596 (tm-30) REVERT: J 196 LEU cc_start: 0.8572 (tp) cc_final: 0.8218 (tp) REVERT: J 258 ASP cc_start: 0.8363 (m-30) cc_final: 0.8062 (m-30) REVERT: J 259 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8234 (tp30) REVERT: J 287 GLU cc_start: 0.8526 (tt0) cc_final: 0.7875 (tt0) REVERT: K 104 GLN cc_start: 0.7775 (tp40) cc_final: 0.7220 (tm-30) REVERT: K 149 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7131 (mm-30) REVERT: K 193 MET cc_start: 0.6422 (tpt) cc_final: 0.6012 (tpp) REVERT: K 215 GLU cc_start: 0.8633 (tp30) cc_final: 0.8395 (tp30) REVERT: K 259 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8209 (tp30) REVERT: K 287 GLU cc_start: 0.8527 (tt0) cc_final: 0.8068 (tt0) outliers start: 73 outliers final: 45 residues processed: 467 average time/residue: 0.1209 time to fit residues: 94.6420 Evaluate side-chains 413 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 364 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 159 CYS Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 206 TYR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 159 CYS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 180 CYS Chi-restraints excluded: chain K residue 206 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 47 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 255 optimal weight: 9.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS B 205 HIS C 205 HIS D 205 HIS E 205 HIS E 227 GLN F 205 HIS G 205 HIS I 205 HIS K 205 HIS K 227 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.118552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.096034 restraints weight = 46883.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.099300 restraints weight = 26480.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101562 restraints weight = 18027.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.103161 restraints weight = 13791.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.104304 restraints weight = 11385.391| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 22154 Z= 0.137 Angle : 0.606 7.514 30283 Z= 0.306 Chirality : 0.037 0.193 3487 Planarity : 0.005 0.049 3850 Dihedral : 3.928 18.905 3058 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.11 % Allowed : 25.79 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.16), residues: 2761 helix: 1.73 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -2.56 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 247 TYR 0.025 0.001 TYR G 163 PHE 0.008 0.001 PHE D 198 TRP 0.015 0.001 TRP G 276 HIS 0.006 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00307 (22143) covalent geometry : angle 0.60571 (30261) SS BOND : bond 0.00134 ( 11) SS BOND : angle 0.40270 ( 22) hydrogen bonds : bond 0.04266 ( 1529) hydrogen bonds : angle 3.67903 ( 4587) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 356 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8270 (mtt) cc_final: 0.7905 (ttm) REVERT: A 104 GLN cc_start: 0.7914 (tp40) cc_final: 0.7356 (tm-30) REVERT: A 234 GLU cc_start: 0.8589 (tp30) cc_final: 0.8301 (tp30) REVERT: A 259 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8328 (tp30) REVERT: B 104 GLN cc_start: 0.7970 (tp40) cc_final: 0.7412 (tm-30) REVERT: B 119 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8264 (mm) REVERT: B 234 GLU cc_start: 0.8744 (tp30) cc_final: 0.8220 (tp30) REVERT: B 258 ASP cc_start: 0.8414 (m-30) cc_final: 0.8074 (m-30) REVERT: B 287 GLU cc_start: 0.8597 (tt0) cc_final: 0.7732 (tt0) REVERT: C 104 GLN cc_start: 0.8011 (tp40) cc_final: 0.7134 (tm-30) REVERT: C 196 LEU cc_start: 0.8395 (tp) cc_final: 0.7953 (tp) REVERT: C 234 GLU cc_start: 0.8859 (tp30) cc_final: 0.8494 (tp30) REVERT: C 259 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7964 (tp30) REVERT: C 287 GLU cc_start: 0.8452 (tt0) cc_final: 0.7669 (tt0) REVERT: D 193 MET cc_start: 0.7538 (tpp) cc_final: 0.6919 (tmm) REVERT: D 234 GLU cc_start: 0.8564 (tp30) cc_final: 0.8204 (tp30) REVERT: D 259 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8213 (tp30) REVERT: D 275 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7989 (mm-40) REVERT: D 287 GLU cc_start: 0.8736 (tt0) cc_final: 0.8310 (tt0) REVERT: E 215 GLU cc_start: 0.8717 (tp30) cc_final: 0.8481 (tp30) REVERT: E 259 GLU cc_start: 0.8457 (tp30) cc_final: 0.8095 (tp30) REVERT: E 287 GLU cc_start: 0.8537 (tt0) cc_final: 0.7787 (tt0) REVERT: F 104 GLN cc_start: 0.7912 (tp40) cc_final: 0.7137 (tm-30) REVERT: F 193 MET cc_start: 0.7576 (tpp) cc_final: 0.6970 (tmm) REVERT: F 215 GLU cc_start: 0.8675 (tp30) cc_final: 0.8027 (tp30) REVERT: F 259 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8211 (tp30) REVERT: G 104 GLN cc_start: 0.8120 (tp40) cc_final: 0.7541 (tm-30) REVERT: G 149 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7255 (mm-30) REVERT: G 259 GLU cc_start: 0.8212 (tp30) cc_final: 0.7946 (tp30) REVERT: G 287 GLU cc_start: 0.8636 (tt0) cc_final: 0.7840 (tt0) REVERT: H 104 GLN cc_start: 0.7970 (tp40) cc_final: 0.7444 (tm-30) REVERT: H 119 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8406 (mm) REVERT: H 193 MET cc_start: 0.7425 (tpp) cc_final: 0.6800 (tmm) REVERT: H 215 GLU cc_start: 0.8723 (tp30) cc_final: 0.8460 (tp30) REVERT: H 234 GLU cc_start: 0.8686 (tp30) cc_final: 0.8278 (tp30) REVERT: H 259 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8249 (tp30) REVERT: H 287 GLU cc_start: 0.8472 (tt0) cc_final: 0.8089 (tt0) REVERT: I 193 MET cc_start: 0.6989 (tmm) cc_final: 0.6615 (tmm) REVERT: I 196 LEU cc_start: 0.8583 (tp) cc_final: 0.8122 (tt) REVERT: I 259 GLU cc_start: 0.8600 (tm-30) cc_final: 0.7944 (tp30) REVERT: I 287 GLU cc_start: 0.8485 (tt0) cc_final: 0.8203 (tt0) REVERT: J 104 GLN cc_start: 0.8015 (tp40) cc_final: 0.7574 (tm-30) REVERT: J 196 LEU cc_start: 0.8571 (tp) cc_final: 0.8207 (tp) REVERT: J 258 ASP cc_start: 0.8423 (m-30) cc_final: 0.8101 (m-30) REVERT: J 259 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8297 (tp30) REVERT: J 287 GLU cc_start: 0.8492 (tt0) cc_final: 0.7849 (tt0) REVERT: K 104 GLN cc_start: 0.7832 (tp40) cc_final: 0.7265 (tm-30) REVERT: K 149 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7140 (mm-30) REVERT: K 193 MET cc_start: 0.6365 (tpt) cc_final: 0.5977 (tpp) REVERT: K 259 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8213 (tp30) REVERT: K 287 GLU cc_start: 0.8478 (tt0) cc_final: 0.7996 (tt0) outliers start: 67 outliers final: 53 residues processed: 409 average time/residue: 0.1134 time to fit residues: 80.8786 Evaluate side-chains 401 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 346 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 206 TYR Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 206 TYR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 159 CYS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 180 CYS Chi-restraints excluded: chain K residue 206 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 78 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 267 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 227 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 257 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS B 205 HIS C 205 HIS D 205 HIS E 205 HIS F 205 HIS I 205 HIS J 205 HIS K 205 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.120578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.097865 restraints weight = 46669.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101079 restraints weight = 26892.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.103329 restraints weight = 18566.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104919 restraints weight = 14313.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.105963 restraints weight = 11889.586| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22154 Z= 0.128 Angle : 0.613 9.964 30283 Z= 0.306 Chirality : 0.037 0.159 3487 Planarity : 0.005 0.050 3850 Dihedral : 3.883 18.249 3058 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.88 % Allowed : 26.62 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.16), residues: 2761 helix: 1.83 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -2.38 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 247 TYR 0.023 0.001 TYR G 163 PHE 0.006 0.001 PHE D 198 TRP 0.013 0.001 TRP F 276 HIS 0.006 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00280 (22143) covalent geometry : angle 0.61286 (30261) SS BOND : bond 0.00125 ( 11) SS BOND : angle 0.38264 ( 22) hydrogen bonds : bond 0.04116 ( 1529) hydrogen bonds : angle 3.63030 ( 4587) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 370 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8163 (mtt) cc_final: 0.7821 (ttm) REVERT: A 104 GLN cc_start: 0.7915 (tp40) cc_final: 0.7345 (tm-30) REVERT: A 193 MET cc_start: 0.7241 (tpp) cc_final: 0.6967 (tmm) REVERT: A 234 GLU cc_start: 0.8599 (tp30) cc_final: 0.8322 (tp30) REVERT: A 259 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8230 (tp30) REVERT: B 104 GLN cc_start: 0.7985 (tp40) cc_final: 0.7437 (tm-30) REVERT: B 193 MET cc_start: 0.7188 (tpp) cc_final: 0.6569 (tmm) REVERT: B 234 GLU cc_start: 0.8725 (tp30) cc_final: 0.8479 (tp30) REVERT: B 258 ASP cc_start: 0.8394 (m-30) cc_final: 0.8030 (m-30) REVERT: B 259 GLU cc_start: 0.8260 (tp30) cc_final: 0.7968 (tp30) REVERT: B 287 GLU cc_start: 0.8542 (tt0) cc_final: 0.7856 (tt0) REVERT: C 104 GLN cc_start: 0.8023 (tp40) cc_final: 0.7162 (tm-30) REVERT: C 196 LEU cc_start: 0.8354 (tp) cc_final: 0.7895 (tp) REVERT: C 234 GLU cc_start: 0.8817 (tp30) cc_final: 0.8449 (tp30) REVERT: C 259 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8042 (tp30) REVERT: C 287 GLU cc_start: 0.8418 (tt0) cc_final: 0.7678 (tt0) REVERT: D 193 MET cc_start: 0.7523 (tpp) cc_final: 0.6942 (tmm) REVERT: D 234 GLU cc_start: 0.8546 (tp30) cc_final: 0.8193 (tp30) REVERT: D 275 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7958 (mm-40) REVERT: D 287 GLU cc_start: 0.8694 (tt0) cc_final: 0.8289 (tt0) REVERT: E 193 MET cc_start: 0.7245 (tpp) cc_final: 0.6759 (tmm) REVERT: E 215 GLU cc_start: 0.8659 (tp30) cc_final: 0.8403 (tp30) REVERT: E 259 GLU cc_start: 0.8399 (tp30) cc_final: 0.8025 (tp30) REVERT: E 287 GLU cc_start: 0.8500 (tt0) cc_final: 0.7908 (tt0) REVERT: F 104 GLN cc_start: 0.7908 (tp40) cc_final: 0.7137 (tm-30) REVERT: F 193 MET cc_start: 0.7609 (tpp) cc_final: 0.7000 (tmm) REVERT: F 215 GLU cc_start: 0.8634 (tp30) cc_final: 0.7955 (tp30) REVERT: F 258 ASP cc_start: 0.8296 (m-30) cc_final: 0.8024 (m-30) REVERT: F 259 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8208 (tp30) REVERT: G 76 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8142 (mmm) REVERT: G 104 GLN cc_start: 0.8124 (tp40) cc_final: 0.7588 (tm-30) REVERT: G 149 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7073 (mm-30) REVERT: G 193 MET cc_start: 0.7121 (tpp) cc_final: 0.6902 (tmm) REVERT: G 259 GLU cc_start: 0.8187 (tp30) cc_final: 0.7960 (tp30) REVERT: G 276 TRP cc_start: 0.8090 (t-100) cc_final: 0.7834 (t-100) REVERT: H 104 GLN cc_start: 0.7962 (tp40) cc_final: 0.7442 (tm-30) REVERT: H 119 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8438 (mm) REVERT: H 193 MET cc_start: 0.7429 (tpp) cc_final: 0.6832 (tmm) REVERT: H 234 GLU cc_start: 0.8669 (tp30) cc_final: 0.8269 (tp30) REVERT: H 259 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8238 (tp30) REVERT: H 287 GLU cc_start: 0.8483 (tt0) cc_final: 0.8035 (tt0) REVERT: I 193 MET cc_start: 0.7084 (tmm) cc_final: 0.6728 (tmm) REVERT: I 215 GLU cc_start: 0.8754 (tp30) cc_final: 0.8466 (tp30) REVERT: I 259 GLU cc_start: 0.8568 (tm-30) cc_final: 0.7969 (tp30) REVERT: I 287 GLU cc_start: 0.8528 (tt0) cc_final: 0.8295 (tt0) REVERT: J 104 GLN cc_start: 0.8019 (tp40) cc_final: 0.7597 (tm-30) REVERT: J 196 LEU cc_start: 0.8496 (tp) cc_final: 0.8110 (tp) REVERT: J 258 ASP cc_start: 0.8360 (m-30) cc_final: 0.8067 (m-30) REVERT: J 259 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8250 (tp30) REVERT: J 287 GLU cc_start: 0.8467 (tt0) cc_final: 0.7851 (tt0) REVERT: K 104 GLN cc_start: 0.7835 (tp40) cc_final: 0.7260 (tm-30) REVERT: K 120 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7674 (t0) REVERT: K 259 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8199 (tp30) REVERT: K 275 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7777 (mm-40) REVERT: K 287 GLU cc_start: 0.8479 (tt0) cc_final: 0.7979 (tt0) outliers start: 62 outliers final: 55 residues processed: 417 average time/residue: 0.1131 time to fit residues: 81.8957 Evaluate side-chains 409 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 351 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 206 TYR Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 206 TYR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 159 CYS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 180 CYS Chi-restraints excluded: chain K residue 206 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 177 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 208 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 199 optimal weight: 0.0670 chunk 145 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS B 205 HIS C 205 HIS D 205 HIS E 205 HIS G 40 ASN I 205 HIS K 40 ASN K 205 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.121465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.098667 restraints weight = 46649.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.101866 restraints weight = 26967.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.104095 restraints weight = 18662.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.105704 restraints weight = 14417.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106852 restraints weight = 11958.761| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22154 Z= 0.128 Angle : 0.622 9.000 30283 Z= 0.309 Chirality : 0.037 0.215 3487 Planarity : 0.005 0.050 3850 Dihedral : 3.785 19.634 3058 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.88 % Allowed : 27.09 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.16), residues: 2761 helix: 1.92 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -2.24 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 247 TYR 0.020 0.001 TYR G 163 PHE 0.006 0.001 PHE D 198 TRP 0.011 0.001 TRP J 276 HIS 0.006 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00281 (22143) covalent geometry : angle 0.62247 (30261) SS BOND : bond 0.00129 ( 11) SS BOND : angle 0.51290 ( 22) hydrogen bonds : bond 0.03993 ( 1529) hydrogen bonds : angle 3.56756 ( 4587) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 372 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7935 (tp40) cc_final: 0.7371 (tm-30) REVERT: A 119 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8313 (mm) REVERT: A 193 MET cc_start: 0.7264 (tpp) cc_final: 0.6997 (tmm) REVERT: A 234 GLU cc_start: 0.8560 (tp30) cc_final: 0.8271 (tp30) REVERT: A 259 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8273 (tp30) REVERT: B 76 MET cc_start: 0.8443 (mmm) cc_final: 0.8188 (mmt) REVERT: B 104 GLN cc_start: 0.7896 (tp40) cc_final: 0.7302 (tm-30) REVERT: B 234 GLU cc_start: 0.8725 (tp30) cc_final: 0.8491 (tp30) REVERT: B 287 GLU cc_start: 0.8513 (tt0) cc_final: 0.7829 (tt0) REVERT: C 76 MET cc_start: 0.8275 (mmm) cc_final: 0.8065 (mmt) REVERT: C 104 GLN cc_start: 0.8082 (tp40) cc_final: 0.7220 (tm-30) REVERT: C 196 LEU cc_start: 0.8285 (tp) cc_final: 0.7809 (tp) REVERT: C 234 GLU cc_start: 0.8820 (tp30) cc_final: 0.8452 (tp30) REVERT: C 259 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8030 (tp30) REVERT: C 275 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8005 (mm-40) REVERT: C 287 GLU cc_start: 0.8413 (tt0) cc_final: 0.7657 (tt0) REVERT: D 149 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7057 (mm-30) REVERT: D 193 MET cc_start: 0.7470 (tpp) cc_final: 0.7019 (tmm) REVERT: D 234 GLU cc_start: 0.8546 (tp30) cc_final: 0.8188 (tp30) REVERT: D 259 GLU cc_start: 0.8305 (tp30) cc_final: 0.8105 (tp30) REVERT: D 275 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7967 (mm-40) REVERT: D 287 GLU cc_start: 0.8665 (tt0) cc_final: 0.8252 (tt0) REVERT: E 193 MET cc_start: 0.7350 (tpp) cc_final: 0.6771 (tmm) REVERT: E 215 GLU cc_start: 0.8626 (tp30) cc_final: 0.8361 (tp30) REVERT: E 259 GLU cc_start: 0.8381 (tp30) cc_final: 0.7896 (tp30) REVERT: E 287 GLU cc_start: 0.8455 (tt0) cc_final: 0.7858 (tt0) REVERT: F 104 GLN cc_start: 0.7873 (tp40) cc_final: 0.7112 (tm-30) REVERT: F 193 MET cc_start: 0.7612 (tpp) cc_final: 0.7034 (tmm) REVERT: F 215 GLU cc_start: 0.8628 (tp30) cc_final: 0.7949 (tp30) REVERT: F 258 ASP cc_start: 0.8290 (m-30) cc_final: 0.8009 (m-30) REVERT: F 259 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8088 (tp30) REVERT: G 104 GLN cc_start: 0.7956 (tp40) cc_final: 0.7408 (tm-30) REVERT: G 119 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8260 (mm) REVERT: G 193 MET cc_start: 0.7277 (tpp) cc_final: 0.6964 (tmm) REVERT: G 234 GLU cc_start: 0.8574 (tp30) cc_final: 0.8245 (tp30) REVERT: G 259 GLU cc_start: 0.8198 (tp30) cc_final: 0.7957 (tp30) REVERT: H 104 GLN cc_start: 0.7824 (tp40) cc_final: 0.7364 (tm-30) REVERT: H 119 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8409 (mm) REVERT: H 193 MET cc_start: 0.7425 (tpp) cc_final: 0.6883 (tmm) REVERT: H 215 GLU cc_start: 0.8711 (tp30) cc_final: 0.8479 (tp30) REVERT: H 234 GLU cc_start: 0.8636 (tp30) cc_final: 0.8230 (tp30) REVERT: H 259 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8249 (tp30) REVERT: H 285 TYR cc_start: 0.7370 (t80) cc_final: 0.6807 (t80) REVERT: H 287 GLU cc_start: 0.8507 (tt0) cc_final: 0.7937 (tt0) REVERT: I 215 GLU cc_start: 0.8716 (tp30) cc_final: 0.8415 (tp30) REVERT: I 259 GLU cc_start: 0.8557 (tm-30) cc_final: 0.7912 (tp30) REVERT: I 287 GLU cc_start: 0.8512 (tt0) cc_final: 0.7621 (tt0) REVERT: J 104 GLN cc_start: 0.7985 (tp40) cc_final: 0.7546 (tm-30) REVERT: J 196 LEU cc_start: 0.8495 (tp) cc_final: 0.8254 (tp) REVERT: J 287 GLU cc_start: 0.8421 (tt0) cc_final: 0.7787 (tt0) REVERT: K 104 GLN cc_start: 0.7850 (tp40) cc_final: 0.7230 (tm-30) REVERT: K 120 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7605 (t0) REVERT: K 149 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7104 (mm-30) REVERT: K 275 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7744 (mm-40) REVERT: K 287 GLU cc_start: 0.8520 (tt0) cc_final: 0.8007 (tt0) outliers start: 62 outliers final: 48 residues processed: 421 average time/residue: 0.1107 time to fit residues: 80.9452 Evaluate side-chains 409 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 357 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 206 TYR Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 206 TYR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 159 CYS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 180 CYS Chi-restraints excluded: chain K residue 206 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 250 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 122 optimal weight: 0.0000 chunk 273 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 overall best weight: 2.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 40 ASN E 205 HIS F 227 GLN H 227 GLN I 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.117051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.094547 restraints weight = 47081.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.097699 restraints weight = 26873.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099894 restraints weight = 18438.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.101450 restraints weight = 14175.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.102565 restraints weight = 11748.970| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22154 Z= 0.161 Angle : 0.650 8.634 30283 Z= 0.326 Chirality : 0.039 0.185 3487 Planarity : 0.005 0.048 3850 Dihedral : 3.877 16.997 3058 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.15 % Allowed : 27.27 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.16), residues: 2761 helix: 1.85 (0.11), residues: 2024 sheet: None (None), residues: 0 loop : -2.27 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 247 TYR 0.014 0.001 TYR I 163 PHE 0.011 0.001 PHE D 198 TRP 0.016 0.001 TRP G 276 HIS 0.006 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00367 (22143) covalent geometry : angle 0.64977 (30261) SS BOND : bond 0.00081 ( 11) SS BOND : angle 0.57894 ( 22) hydrogen bonds : bond 0.04487 ( 1529) hydrogen bonds : angle 3.69538 ( 4587) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2984.29 seconds wall clock time: 52 minutes 30.11 seconds (3150.11 seconds total)