Starting phenix.real_space_refine on Wed Mar 4 03:22:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l1u_0803/03_2026/6l1u_0803.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l1u_0803/03_2026/6l1u_0803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6l1u_0803/03_2026/6l1u_0803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l1u_0803/03_2026/6l1u_0803.map" model { file = "/net/cci-nas-00/data/ceres_data/6l1u_0803/03_2026/6l1u_0803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l1u_0803/03_2026/6l1u_0803.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 15 5.16 5 C 6540 2.51 5 N 1815 2.21 5 O 2130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10515 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O Time building chain proxies: 0.86, per 1000 atoms: 0.08 Number of scatterers: 10515 At special positions: 0 Unit cell: (197.357, 159.454, 56.201, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 15 15.00 O 2130 8.00 N 1815 7.00 C 6540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 499.8 milliseconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 30 sheets defined 0.0% alpha, 50.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.578A pdb=" N LYS A 6 " --> pdb=" O MET B 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 16 removed outlier: 7.549A pdb=" N ALA A 11 " --> pdb=" O LYS B 12 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N GLY B 14 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU A 13 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL B 16 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ALA B 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLU C 13 " --> pdb=" O LYS B 12 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY B 14 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL C 15 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL B 16 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA C 17 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA C 11 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N GLY D 14 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU C 13 " --> pdb=" O GLY D 14 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL D 16 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA D 18 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N ALA C 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA D 11 " --> pdb=" O LYS E 12 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N GLY E 14 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU D 13 " --> pdb=" O GLY E 14 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL E 16 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL D 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ALA E 18 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ALA D 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 22 through 23 Processing sheet with id=AA4, first strand: chain 'A' and resid 31 through 36 removed outlier: 9.229A pdb=" N GLY A 31 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 11.000A pdb=" N LYS B 34 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N THR A 33 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N GLY B 36 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLU A 35 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N GLY B 31 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 10.748A pdb=" N LYS C 34 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N THR B 33 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N GLY C 36 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLU B 35 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N GLY C 31 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 10.748A pdb=" N LYS D 34 " --> pdb=" O GLY C 31 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N THR C 33 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N GLY D 36 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLU C 35 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N GLY D 31 " --> pdb=" O LYS E 32 " (cutoff:3.500A) removed outlier: 10.716A pdb=" N LYS E 34 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N THR D 33 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N GLY E 36 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU D 35 " --> pdb=" O GLY E 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 39 through 45 removed outlier: 6.087A pdb=" N PTR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N SER B 42 " --> pdb=" O PTR A 39 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY A 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N THR B 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PTR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N SER C 42 " --> pdb=" O PTR B 39 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY B 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N THR C 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS B 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PTR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER D 42 " --> pdb=" O PTR C 39 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY C 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N THR D 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS C 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PTR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 39 through 45 removed outlier: 6.087A pdb=" N PTR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N SER B 42 " --> pdb=" O PTR A 39 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY A 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N THR B 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PTR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N SER C 42 " --> pdb=" O PTR B 39 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY B 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N THR C 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS B 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PTR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER D 42 " --> pdb=" O PTR C 39 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY C 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N THR D 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS C 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 48 through 54 removed outlier: 6.444A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ALA B 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N HIS C 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY B 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS D 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY C 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL D 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N HIS E 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY D 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 69 through 82 removed outlier: 7.221A pdb=" N VAL B 70 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL A 71 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR B 72 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY A 73 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 74 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 75 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 76 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 78 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS B 80 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 74 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR C 75 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA B 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL C 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 78 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN C 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS B 80 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR C 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 82 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 74 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR D 75 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA C 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL D 77 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA C 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLN D 79 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS C 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR D 81 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL C 82 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 69 through 82 removed outlier: 7.221A pdb=" N VAL B 70 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL A 71 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR B 72 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY A 73 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 74 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 75 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 76 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 78 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS B 80 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 74 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR C 75 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA B 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL C 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 78 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN C 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS B 80 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR C 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 82 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 74 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR D 75 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA C 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL D 77 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA C 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLN D 79 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS C 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR D 81 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL C 82 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.814A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE D 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 95 through 96 removed outlier: 8.599A pdb=" N THR B 92 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL C 95 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N PHE B 94 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N THR C 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL D 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N PHE C 94 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N THR D 92 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL E 95 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N PHE D 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.608A pdb=" N LYS F 6 " --> pdb=" O MET G 5 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY G 7 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY H 7 " --> pdb=" O LYS G 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 11 through 16 removed outlier: 7.693A pdb=" N ALA F 11 " --> pdb=" O LYS G 12 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N GLY G 14 " --> pdb=" O ALA F 11 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU F 13 " --> pdb=" O GLY G 14 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL G 16 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL F 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ALA G 18 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA G 11 " --> pdb=" O LYS H 12 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N GLY H 14 " --> pdb=" O ALA G 11 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU G 13 " --> pdb=" O GLY H 14 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL H 16 " --> pdb=" O GLU G 13 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL G 15 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ALA H 18 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N ALA G 17 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU I 13 " --> pdb=" O LYS H 12 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY H 14 " --> pdb=" O GLU I 13 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL I 15 " --> pdb=" O GLY H 14 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL H 16 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA I 17 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA I 11 " --> pdb=" O LYS J 12 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N GLY J 14 " --> pdb=" O ALA I 11 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU I 13 " --> pdb=" O GLY J 14 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL J 16 " --> pdb=" O GLU I 13 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL I 15 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ALA J 18 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ALA I 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 22 through 23 Processing sheet with id=AB6, first strand: chain 'F' and resid 31 through 36 removed outlier: 9.160A pdb=" N GLY F 31 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N LYS G 34 " --> pdb=" O GLY F 31 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N THR F 33 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N GLY G 36 " --> pdb=" O THR F 33 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU F 35 " --> pdb=" O GLY G 36 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLY G 31 " --> pdb=" O LYS H 32 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N LYS H 34 " --> pdb=" O GLY G 31 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N THR G 33 " --> pdb=" O LYS H 34 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N GLY H 36 " --> pdb=" O THR G 33 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLU G 35 " --> pdb=" O GLY H 36 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N GLY H 31 " --> pdb=" O LYS I 32 " (cutoff:3.500A) removed outlier: 10.739A pdb=" N LYS I 34 " --> pdb=" O GLY H 31 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N THR H 33 " --> pdb=" O LYS I 34 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N GLY I 36 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU H 35 " --> pdb=" O GLY I 36 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N GLY I 31 " --> pdb=" O LYS J 32 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N LYS J 34 " --> pdb=" O GLY I 31 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N THR I 33 " --> pdb=" O LYS J 34 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N GLY J 36 " --> pdb=" O THR I 33 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU I 35 " --> pdb=" O GLY J 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 39 through 45 removed outlier: 5.979A pdb=" N PTR F 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N SER G 42 " --> pdb=" O PTR F 39 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY F 41 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR G 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS F 43 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PTR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N SER H 42 " --> pdb=" O PTR G 39 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY G 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N THR H 44 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS G 43 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PTR H 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N SER I 42 " --> pdb=" O PTR H 39 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY H 41 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N THR I 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS H 43 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PTR I 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N SER J 42 " --> pdb=" O PTR I 39 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY I 41 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N THR J 44 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS I 43 " --> pdb=" O THR J 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 48 through 54 removed outlier: 7.082A pdb=" N VAL F 49 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N HIS G 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY F 51 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL G 49 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N HIS H 50 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY G 51 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL H 48 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N GLY I 51 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N HIS H 50 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N ALA I 53 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N VAL H 52 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL I 49 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N HIS J 50 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY I 51 " --> pdb=" O HIS J 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 69 through 82 removed outlier: 6.867A pdb=" N VAL F 74 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR G 75 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA F 76 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL G 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA F 78 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN G 79 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS F 80 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR G 81 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL F 82 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL G 74 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR H 75 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA G 76 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL H 77 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA G 78 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLN H 79 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS G 80 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR H 81 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL G 82 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL H 74 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR I 75 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA H 76 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL I 77 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA H 78 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN I 79 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS H 80 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR I 81 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL H 82 " --> pdb=" O THR I 81 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL I 74 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR J 75 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA I 76 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL J 77 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA I 78 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN J 79 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS I 80 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR J 81 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL I 82 " --> pdb=" O THR J 81 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 88 through 89 removed outlier: 6.812A pdb=" N ILE F 88 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE G 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE H 88 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE I 88 " --> pdb=" O ALA J 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 95 through 96 removed outlier: 8.812A pdb=" N THR G 92 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL H 95 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N PHE G 94 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N THR H 92 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL I 95 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N PHE H 94 " --> pdb=" O VAL I 95 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N THR I 92 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL J 95 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N PHE I 94 " --> pdb=" O VAL J 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 22 through 23 Processing sheet with id=AC4, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.700A pdb=" N LYS K 6 " --> pdb=" O MET L 5 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY L 7 " --> pdb=" O LYS K 6 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 11 through 16 removed outlier: 7.748A pdb=" N ALA K 11 " --> pdb=" O LYS L 12 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N GLY L 14 " --> pdb=" O ALA K 11 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU K 13 " --> pdb=" O GLY L 14 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N VAL L 16 " --> pdb=" O GLU K 13 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL K 15 " --> pdb=" O VAL L 16 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ALA L 18 " --> pdb=" O VAL K 15 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA L 11 " --> pdb=" O LYS M 12 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N GLY M 14 " --> pdb=" O ALA L 11 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU L 13 " --> pdb=" O GLY M 14 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL M 16 " --> pdb=" O GLU L 13 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL L 15 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ALA M 18 " --> pdb=" O VAL L 15 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N ALA L 17 " --> pdb=" O ALA M 18 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU N 13 " --> pdb=" O LYS M 12 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY M 14 " --> pdb=" O GLU N 13 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL N 15 " --> pdb=" O GLY M 14 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL M 16 " --> pdb=" O VAL N 15 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA N 17 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ALA N 11 " --> pdb=" O LYS O 12 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY O 14 " --> pdb=" O ALA N 11 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU N 13 " --> pdb=" O GLY O 14 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL O 16 " --> pdb=" O GLU N 13 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL N 15 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ALA O 18 " --> pdb=" O VAL N 15 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N ALA N 17 " --> pdb=" O ALA O 18 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 22 through 23 Processing sheet with id=AC7, first strand: chain 'K' and resid 31 through 36 removed outlier: 9.271A pdb=" N GLY K 31 " --> pdb=" O LYS L 32 " (cutoff:3.500A) removed outlier: 11.024A pdb=" N LYS L 34 " --> pdb=" O GLY K 31 " (cutoff:3.500A) removed outlier: 9.441A pdb=" N THR K 33 " --> pdb=" O LYS L 34 " (cutoff:3.500A) removed outlier: 9.453A pdb=" N GLY L 36 " --> pdb=" O THR K 33 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLU K 35 " --> pdb=" O GLY L 36 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N GLY L 31 " --> pdb=" O LYS M 32 " (cutoff:3.500A) removed outlier: 10.848A pdb=" N LYS M 34 " --> pdb=" O GLY L 31 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N THR L 33 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N GLY M 36 " --> pdb=" O THR L 33 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU L 35 " --> pdb=" O GLY M 36 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N GLY M 31 " --> pdb=" O LYS N 32 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N LYS N 34 " --> pdb=" O GLY M 31 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N THR M 33 " --> pdb=" O LYS N 34 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N GLY N 36 " --> pdb=" O THR M 33 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU M 35 " --> pdb=" O GLY N 36 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N GLY N 31 " --> pdb=" O LYS O 32 " (cutoff:3.500A) removed outlier: 10.621A pdb=" N LYS O 34 " --> pdb=" O GLY N 31 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N THR N 33 " --> pdb=" O LYS O 34 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N GLY O 36 " --> pdb=" O THR N 33 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLU N 35 " --> pdb=" O GLY O 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'K' and resid 39 through 45 removed outlier: 6.160A pdb=" N PTR K 39 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N SER L 42 " --> pdb=" O PTR K 39 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY K 41 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR L 44 " --> pdb=" O GLY K 41 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS K 43 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PTR L 39 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N SER M 42 " --> pdb=" O PTR L 39 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY L 41 " --> pdb=" O SER M 42 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR M 44 " --> pdb=" O GLY L 41 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS L 43 " --> pdb=" O THR M 44 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PTR M 39 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N SER N 42 " --> pdb=" O PTR M 39 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY M 41 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR N 44 " --> pdb=" O GLY M 41 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS M 43 " --> pdb=" O THR N 44 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N PTR N 39 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N SER O 42 " --> pdb=" O PTR N 39 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY N 41 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N THR O 44 " --> pdb=" O GLY N 41 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS N 43 " --> pdb=" O THR O 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'K' and resid 48 through 54 removed outlier: 7.148A pdb=" N VAL K 49 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N HIS L 50 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLY K 51 " --> pdb=" O HIS L 50 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL L 49 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N HIS M 50 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY L 51 " --> pdb=" O HIS M 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL M 48 " --> pdb=" O VAL N 49 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLY N 51 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N HIS M 50 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ALA N 53 " --> pdb=" O HIS M 50 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N VAL M 52 " --> pdb=" O ALA N 53 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL N 49 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS O 50 " --> pdb=" O VAL N 49 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY N 51 " --> pdb=" O HIS O 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 69 through 82 removed outlier: 6.883A pdb=" N VAL K 74 " --> pdb=" O GLY L 73 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR L 75 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA K 76 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL L 77 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA K 78 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLN L 79 " --> pdb=" O ALA K 78 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS K 80 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR L 81 " --> pdb=" O LYS K 80 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL K 82 " --> pdb=" O THR L 81 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL L 74 " --> pdb=" O GLY M 73 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR M 75 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA L 76 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL M 77 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA L 78 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN M 79 " --> pdb=" O ALA L 78 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS L 80 " --> pdb=" O GLN M 79 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR M 81 " --> pdb=" O LYS L 80 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL L 82 " --> pdb=" O THR M 81 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL M 74 " --> pdb=" O GLY N 73 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR N 75 " --> pdb=" O VAL M 74 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA M 76 " --> pdb=" O THR N 75 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL N 77 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA M 78 " --> pdb=" O VAL N 77 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLN N 79 " --> pdb=" O ALA M 78 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS M 80 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR N 81 " --> pdb=" O LYS M 80 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL M 82 " --> pdb=" O THR N 81 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL N 74 " --> pdb=" O GLY O 73 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR O 75 " --> pdb=" O VAL N 74 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA N 76 " --> pdb=" O THR O 75 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL O 77 " --> pdb=" O ALA N 76 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA N 78 " --> pdb=" O VAL O 77 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN O 79 " --> pdb=" O ALA N 78 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS N 80 " --> pdb=" O GLN O 79 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR O 81 " --> pdb=" O LYS N 80 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL N 82 " --> pdb=" O THR O 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 88 through 89 removed outlier: 6.721A pdb=" N ILE K 88 " --> pdb=" O ALA L 89 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE L 88 " --> pdb=" O ALA M 89 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE M 88 " --> pdb=" O ALA N 89 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE N 88 " --> pdb=" O ALA O 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'K' and resid 95 through 96 removed outlier: 8.674A pdb=" N THR L 92 " --> pdb=" O GLY M 93 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL M 95 " --> pdb=" O THR L 92 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N PHE L 94 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N THR M 92 " --> pdb=" O GLY N 93 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL N 95 " --> pdb=" O THR M 92 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N PHE M 94 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N THR N 92 " --> pdb=" O GLY O 93 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL O 95 " --> pdb=" O THR N 92 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N PHE N 94 " --> pdb=" O VAL O 95 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 450 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: 1.50 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3465 1.33 - 1.45: 810 1.45 - 1.57: 6240 1.57 - 1.68: 15 1.68 - 1.80: 30 Bond restraints: 10560 Sorted by residual: bond pdb=" OH PTR G 39 " pdb=" P PTR G 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" OH PTR N 39 " pdb=" P PTR N 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" OH PTR D 39 " pdb=" P PTR D 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" OH PTR M 39 " pdb=" P PTR M 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" OH PTR C 39 " pdb=" P PTR C 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.93e+01 ... (remaining 10555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 13728 1.90 - 3.80: 342 3.80 - 5.70: 90 5.70 - 7.60: 30 7.60 - 9.50: 15 Bond angle restraints: 14205 Sorted by residual: angle pdb=" OH PTR K 39 " pdb=" P PTR K 39 " pdb=" O2P PTR K 39 " ideal model delta sigma weight residual 99.92 109.42 -9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" OH PTR M 39 " pdb=" P PTR M 39 " pdb=" O2P PTR M 39 " ideal model delta sigma weight residual 99.92 109.40 -9.48 3.00e+00 1.11e-01 9.98e+00 angle pdb=" OH PTR J 39 " pdb=" P PTR J 39 " pdb=" O2P PTR J 39 " ideal model delta sigma weight residual 99.92 109.40 -9.48 3.00e+00 1.11e-01 9.98e+00 angle pdb=" OH PTR L 39 " pdb=" P PTR L 39 " pdb=" O2P PTR L 39 " ideal model delta sigma weight residual 99.92 109.39 -9.47 3.00e+00 1.11e-01 9.96e+00 angle pdb=" OH PTR C 39 " pdb=" P PTR C 39 " pdb=" O2P PTR C 39 " ideal model delta sigma weight residual 99.92 109.39 -9.47 3.00e+00 1.11e-01 9.96e+00 ... (remaining 14200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 5775 17.25 - 34.50: 465 34.50 - 51.75: 135 51.75 - 69.00: 15 69.00 - 86.25: 30 Dihedral angle restraints: 6420 sinusoidal: 2355 harmonic: 4065 Sorted by residual: dihedral pdb=" CA ALA G 29 " pdb=" C ALA G 29 " pdb=" N ALA G 30 " pdb=" CA ALA G 30 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ALA J 29 " pdb=" C ALA J 29 " pdb=" N ALA J 30 " pdb=" CA ALA J 30 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ALA E 29 " pdb=" C ALA E 29 " pdb=" N ALA E 30 " pdb=" CA ALA E 30 " ideal model delta harmonic sigma weight residual 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 6417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1195 0.056 - 0.113: 456 0.113 - 0.169: 104 0.169 - 0.225: 0 0.225 - 0.281: 15 Chirality restraints: 1770 Sorted by residual: chirality pdb=" CB VAL F 77 " pdb=" CA VAL F 77 " pdb=" CG1 VAL F 77 " pdb=" CG2 VAL F 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB VAL L 77 " pdb=" CA VAL L 77 " pdb=" CG1 VAL L 77 " pdb=" CG2 VAL L 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL N 77 " pdb=" CA VAL N 77 " pdb=" CG1 VAL N 77 " pdb=" CG2 VAL N 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1767 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 13 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" CD GLU D 13 " 0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU D 13 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU D 13 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU L 13 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" CD GLU L 13 " 0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU L 13 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU L 13 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU M 13 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.03e+00 pdb=" CD GLU M 13 " 0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU M 13 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU M 13 " -0.006 2.00e-02 2.50e+03 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 408 2.69 - 3.24: 10149 3.24 - 3.79: 15394 3.79 - 4.35: 18717 4.35 - 4.90: 37388 Nonbonded interactions: 82056 Sorted by model distance: nonbonded pdb=" O SER D 9 " pdb=" OG SER D 9 " model vdw 2.138 3.040 nonbonded pdb=" O SER A 9 " pdb=" OG SER A 9 " model vdw 2.138 3.040 nonbonded pdb=" O SER N 9 " pdb=" OG SER N 9 " model vdw 2.138 3.040 nonbonded pdb=" O SER J 9 " pdb=" OG SER J 9 " model vdw 2.138 3.040 nonbonded pdb=" O SER G 9 " pdb=" OG SER G 9 " model vdw 2.138 3.040 ... (remaining 82051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.860 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.167 10560 Z= 0.515 Angle : 0.915 9.499 14205 Z= 0.450 Chirality : 0.064 0.281 1770 Planarity : 0.002 0.010 1770 Dihedral : 15.744 86.255 3840 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 0.00 % Allowed : 17.65 % Favored : 82.35 % 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: -6.06 (0.10), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.61 (0.08), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.003 PHE F 94 HIS 0.001 0.000 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.01123 (10560) covalent geometry : angle 0.91508 (14205) hydrogen bonds : bond 0.26099 ( 143) hydrogen bonds : angle 9.67119 ( 450) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 THR cc_start: 0.8952 (m) cc_final: 0.8744 (t) REVERT: E 61 GLU cc_start: 0.8368 (tt0) cc_final: 0.7794 (pm20) REVERT: F 4 PHE cc_start: 0.7955 (t80) cc_final: 0.7608 (t80) REVERT: G 60 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7499 (ttmm) REVERT: H 2 ASP cc_start: 0.7968 (p0) cc_final: 0.7749 (p0) REVERT: H 6 LYS cc_start: 0.8954 (ptmm) cc_final: 0.8750 (ptmt) REVERT: H 57 GLU cc_start: 0.8115 (tp30) cc_final: 0.7880 (tp30) REVERT: I 2 ASP cc_start: 0.8146 (p0) cc_final: 0.7866 (p0) REVERT: J 2 ASP cc_start: 0.7756 (p0) cc_final: 0.7482 (p0) REVERT: J 60 LYS cc_start: 0.7329 (mmtt) cc_final: 0.7049 (pttm) REVERT: K 2 ASP cc_start: 0.7505 (p0) cc_final: 0.6343 (m-30) REVERT: K 4 PHE cc_start: 0.7937 (t80) cc_final: 0.7634 (t80) REVERT: K 75 THR cc_start: 0.8870 (m) cc_final: 0.8594 (p) REVERT: K 97 LYS cc_start: 0.8276 (mttt) cc_final: 0.7513 (mmmt) REVERT: K 100 LEU cc_start: 0.8152 (tt) cc_final: 0.7758 (pt) REVERT: L 75 THR cc_start: 0.8635 (m) cc_final: 0.8344 (m) REVERT: L 100 LEU cc_start: 0.7930 (tt) cc_final: 0.7475 (tp) REVERT: M 21 LYS cc_start: 0.8553 (mttt) cc_final: 0.8269 (mttp) REVERT: M 24 GLN cc_start: 0.7805 (mt0) cc_final: 0.7601 (mt0) REVERT: N 12 LYS cc_start: 0.8469 (tptp) cc_final: 0.8245 (tptp) REVERT: N 92 THR cc_start: 0.8475 (m) cc_final: 0.8203 (t) REVERT: N 100 LEU cc_start: 0.8214 (tt) cc_final: 0.7981 (tt) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.0892 time to fit residues: 41.6649 Evaluate side-chains 256 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 62 GLN B 99 GLN C 62 GLN C 99 GLN D 62 GLN D 99 GLN E 62 GLN E 99 GLN F 62 GLN F 99 GLN G 62 GLN H 62 GLN I 62 GLN J 62 GLN K 62 GLN L 62 GLN M 62 GLN N 62 GLN O 62 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.122187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105081 restraints weight = 18433.410| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.84 r_work: 0.3626 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10560 Z= 0.124 Angle : 0.595 8.130 14205 Z= 0.328 Chirality : 0.051 0.139 1770 Planarity : 0.002 0.014 1770 Dihedral : 9.244 52.378 1650 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.19 % Favored : 86.81 % Rotamer: Outliers : 3.33 % Allowed : 19.71 % Favored : 76.96 % 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: -5.53 (0.11), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.09), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.003 PHE N 4 HIS 0.002 0.001 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00274 (10560) covalent geometry : angle 0.59538 (14205) hydrogen bonds : bond 0.03547 ( 143) hydrogen bonds : angle 6.67917 ( 450) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 335 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: C 8 LEU cc_start: 0.8841 (mm) cc_final: 0.8592 (mm) REVERT: C 13 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7435 (mm-30) REVERT: C 57 GLU cc_start: 0.8838 (tp30) cc_final: 0.8542 (tp30) REVERT: E 61 GLU cc_start: 0.8991 (tt0) cc_final: 0.8187 (pm20) REVERT: G 60 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7608 (ttmm) REVERT: H 2 ASP cc_start: 0.8095 (p0) cc_final: 0.7847 (p0) REVERT: H 57 GLU cc_start: 0.8450 (tp30) cc_final: 0.8168 (mm-30) REVERT: I 2 ASP cc_start: 0.8486 (p0) cc_final: 0.7955 (p0) REVERT: I 57 GLU cc_start: 0.8442 (tp30) cc_final: 0.8220 (mm-30) REVERT: I 60 LYS cc_start: 0.7838 (mptt) cc_final: 0.7507 (ttpt) REVERT: J 2 ASP cc_start: 0.7817 (p0) cc_final: 0.7564 (p0) REVERT: J 60 LYS cc_start: 0.7694 (mmtt) cc_final: 0.7064 (pttm) REVERT: K 2 ASP cc_start: 0.7652 (p0) cc_final: 0.6420 (m-30) REVERT: K 4 PHE cc_start: 0.6952 (t80) cc_final: 0.6660 (t80) REVERT: K 13 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8083 (mm-30) REVERT: K 97 LYS cc_start: 0.8272 (mttt) cc_final: 0.7702 (mmtt) REVERT: K 100 LEU cc_start: 0.8340 (tt) cc_final: 0.8090 (pt) REVERT: L 12 LYS cc_start: 0.8732 (tptt) cc_final: 0.8297 (tppt) REVERT: L 99 GLN cc_start: 0.8648 (mt0) cc_final: 0.8070 (tm-30) REVERT: M 2 ASP cc_start: 0.7970 (p0) cc_final: 0.7448 (p0) REVERT: M 12 LYS cc_start: 0.8802 (tptp) cc_final: 0.8466 (mptt) REVERT: M 21 LYS cc_start: 0.8891 (mttt) cc_final: 0.8503 (mttp) REVERT: M 24 GLN cc_start: 0.7630 (mt0) cc_final: 0.7396 (mt0) REVERT: M 99 GLN cc_start: 0.8518 (mt0) cc_final: 0.8260 (tm-30) REVERT: N 24 GLN cc_start: 0.7771 (mt0) cc_final: 0.7512 (mt0) REVERT: N 100 LEU cc_start: 0.8209 (tt) cc_final: 0.8007 (mt) REVERT: O 12 LYS cc_start: 0.5305 (pttm) cc_final: 0.4723 (pttm) outliers start: 34 outliers final: 24 residues processed: 353 average time/residue: 0.0765 time to fit residues: 40.7640 Evaluate side-chains 314 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 290 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain O residue 5 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 141 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN E 99 GLN F 99 GLN K 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.112088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094742 restraints weight = 18996.063| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.90 r_work: 0.3440 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 10560 Z= 0.315 Angle : 0.731 6.161 14205 Z= 0.394 Chirality : 0.054 0.168 1770 Planarity : 0.003 0.015 1770 Dihedral : 9.891 52.128 1650 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.84 % Favored : 83.16 % Rotamer: Outliers : 9.80 % Allowed : 18.14 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.26 (0.12), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.09), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.004 PHE C 94 HIS 0.005 0.001 HIS O 50 Details of bonding type rmsd covalent geometry : bond 0.00738 (10560) covalent geometry : angle 0.73093 (14205) hydrogen bonds : bond 0.04999 ( 143) hydrogen bonds : angle 6.37708 ( 450) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 296 time to evaluate : 0.317 Fit side-chains REVERT: C 13 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7765 (mm-30) REVERT: C 57 GLU cc_start: 0.8954 (tp30) cc_final: 0.8627 (tp30) REVERT: E 61 GLU cc_start: 0.9196 (tt0) cc_final: 0.8333 (pm20) REVERT: G 57 GLU cc_start: 0.8463 (tp30) cc_final: 0.8093 (mm-30) REVERT: G 60 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7775 (ttmm) REVERT: G 72 THR cc_start: 0.9552 (OUTLIER) cc_final: 0.9246 (p) REVERT: H 2 ASP cc_start: 0.8089 (p0) cc_final: 0.7862 (p0) REVERT: H 57 GLU cc_start: 0.8447 (tp30) cc_final: 0.8124 (mm-30) REVERT: I 2 ASP cc_start: 0.8618 (p0) cc_final: 0.8038 (p0) REVERT: I 57 GLU cc_start: 0.8586 (tp30) cc_final: 0.8293 (mm-30) REVERT: I 60 LYS cc_start: 0.7898 (mptt) cc_final: 0.7471 (ttpt) REVERT: I 83 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8587 (tm-30) REVERT: J 2 ASP cc_start: 0.8241 (p0) cc_final: 0.7829 (p0) REVERT: J 60 LYS cc_start: 0.7858 (mmtt) cc_final: 0.7098 (pttm) REVERT: J 61 GLU cc_start: 0.8757 (tt0) cc_final: 0.8240 (pm20) REVERT: J 83 GLU cc_start: 0.5057 (pm20) cc_final: 0.4747 (pm20) REVERT: K 2 ASP cc_start: 0.7616 (p0) cc_final: 0.6453 (m-30) REVERT: K 4 PHE cc_start: 0.7363 (t80) cc_final: 0.7043 (t80) REVERT: K 97 LYS cc_start: 0.8419 (mttt) cc_final: 0.7623 (mmtt) REVERT: K 100 LEU cc_start: 0.8441 (tt) cc_final: 0.8104 (pt) REVERT: L 12 LYS cc_start: 0.8892 (tptt) cc_final: 0.8644 (tppt) REVERT: L 55 VAL cc_start: 0.9314 (OUTLIER) cc_final: 0.9072 (p) REVERT: L 57 GLU cc_start: 0.8723 (tp30) cc_final: 0.8512 (tp30) REVERT: L 99 GLN cc_start: 0.8653 (mt0) cc_final: 0.8377 (tm-30) REVERT: M 12 LYS cc_start: 0.8832 (tptp) cc_final: 0.8381 (mptt) REVERT: M 21 LYS cc_start: 0.8900 (mttt) cc_final: 0.8549 (mttp) REVERT: M 38 LEU cc_start: 0.9450 (tt) cc_final: 0.9230 (tt) REVERT: M 99 GLN cc_start: 0.8726 (mt0) cc_final: 0.8488 (tm-30) REVERT: N 100 LEU cc_start: 0.8093 (tt) cc_final: 0.7882 (tt) outliers start: 100 outliers final: 77 residues processed: 359 average time/residue: 0.0752 time to fit residues: 41.0720 Evaluate side-chains 360 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 280 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 5 MET Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.117540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.100404 restraints weight = 18741.503| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.86 r_work: 0.3545 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10560 Z= 0.164 Angle : 0.607 6.957 14205 Z= 0.330 Chirality : 0.051 0.139 1770 Planarity : 0.002 0.013 1770 Dihedral : 9.354 52.485 1650 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 7.45 % Allowed : 20.98 % Favored : 71.57 % 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: -5.08 (0.13), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.003 PHE N 4 HIS 0.003 0.001 HIS O 50 Details of bonding type rmsd covalent geometry : bond 0.00380 (10560) covalent geometry : angle 0.60657 (14205) hydrogen bonds : bond 0.03650 ( 143) hydrogen bonds : angle 6.06998 ( 450) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 305 time to evaluate : 0.374 Fit side-chains REVERT: A 98 ASP cc_start: 0.8372 (p0) cc_final: 0.7638 (p0) REVERT: B 57 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8503 (mm-30) REVERT: C 57 GLU cc_start: 0.8860 (tp30) cc_final: 0.8367 (tp30) REVERT: E 2 ASP cc_start: 0.8655 (p0) cc_final: 0.8422 (p0) REVERT: E 61 GLU cc_start: 0.9148 (tt0) cc_final: 0.8351 (pm20) REVERT: G 57 GLU cc_start: 0.8302 (tp30) cc_final: 0.7862 (mm-30) REVERT: G 60 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7712 (ttmm) REVERT: H 2 ASP cc_start: 0.8066 (p0) cc_final: 0.7826 (p0) REVERT: H 57 GLU cc_start: 0.8374 (tp30) cc_final: 0.8143 (mm-30) REVERT: I 2 ASP cc_start: 0.8178 (p0) cc_final: 0.7541 (p0) REVERT: I 57 GLU cc_start: 0.8538 (tp30) cc_final: 0.8273 (mm-30) REVERT: I 60 LYS cc_start: 0.7991 (mptt) cc_final: 0.7597 (ttpt) REVERT: J 2 ASP cc_start: 0.8193 (p0) cc_final: 0.7800 (p0) REVERT: J 13 GLU cc_start: 0.5451 (pm20) cc_final: 0.5100 (pm20) REVERT: J 60 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7202 (pttm) REVERT: J 61 GLU cc_start: 0.8703 (tt0) cc_final: 0.8283 (pm20) REVERT: J 83 GLU cc_start: 0.5006 (pm20) cc_final: 0.4766 (pm20) REVERT: K 2 ASP cc_start: 0.7577 (p0) cc_final: 0.6428 (m-30) REVERT: K 4 PHE cc_start: 0.7424 (t80) cc_final: 0.7086 (t80) REVERT: K 97 LYS cc_start: 0.8350 (mttt) cc_final: 0.7603 (mmtt) REVERT: K 100 LEU cc_start: 0.8397 (tt) cc_final: 0.8134 (pt) REVERT: L 12 LYS cc_start: 0.8941 (tptt) cc_final: 0.8662 (tppt) REVERT: L 44 THR cc_start: 0.8919 (t) cc_final: 0.8716 (t) REVERT: L 55 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.9027 (p) REVERT: L 57 GLU cc_start: 0.8709 (tp30) cc_final: 0.8507 (tp30) REVERT: L 99 GLN cc_start: 0.8786 (mt0) cc_final: 0.8290 (tm-30) REVERT: M 12 LYS cc_start: 0.8809 (tptp) cc_final: 0.8501 (mptt) REVERT: M 21 LYS cc_start: 0.8881 (mttt) cc_final: 0.8501 (mttp) REVERT: M 38 LEU cc_start: 0.9465 (tt) cc_final: 0.9242 (tt) REVERT: M 57 GLU cc_start: 0.8844 (tp30) cc_final: 0.8565 (tp30) REVERT: M 99 GLN cc_start: 0.8621 (mt0) cc_final: 0.8405 (tm-30) REVERT: N 100 LEU cc_start: 0.8085 (tt) cc_final: 0.7878 (tt) outliers start: 76 outliers final: 63 residues processed: 353 average time/residue: 0.0753 time to fit residues: 40.6645 Evaluate side-chains 356 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 291 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 5 MET Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.114393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.097474 restraints weight = 19102.052| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.81 r_work: 0.3480 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 10560 Z= 0.299 Angle : 0.704 7.728 14205 Z= 0.379 Chirality : 0.053 0.147 1770 Planarity : 0.002 0.012 1770 Dihedral : 9.833 52.302 1650 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.98 % Favored : 83.02 % Rotamer: Outliers : 10.29 % Allowed : 18.92 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.01 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.004 PHE L 94 HIS 0.005 0.001 HIS O 50 Details of bonding type rmsd covalent geometry : bond 0.00702 (10560) covalent geometry : angle 0.70392 (14205) hydrogen bonds : bond 0.04511 ( 143) hydrogen bonds : angle 6.12428 ( 450) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 294 time to evaluate : 0.369 Fit side-chains REVERT: A 20 GLU cc_start: 0.8794 (pt0) cc_final: 0.8432 (pt0) REVERT: A 98 ASP cc_start: 0.8313 (p0) cc_final: 0.7705 (p0) REVERT: E 2 ASP cc_start: 0.8838 (p0) cc_final: 0.8562 (p0) REVERT: E 61 GLU cc_start: 0.9159 (tt0) cc_final: 0.8389 (pm20) REVERT: G 57 GLU cc_start: 0.8402 (tp30) cc_final: 0.7965 (mm-30) REVERT: G 60 LYS cc_start: 0.8271 (mmtt) cc_final: 0.7806 (ttmm) REVERT: H 2 ASP cc_start: 0.8104 (p0) cc_final: 0.7886 (p0) REVERT: H 46 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8397 (tt0) REVERT: H 57 GLU cc_start: 0.8319 (tp30) cc_final: 0.8090 (mm-30) REVERT: I 2 ASP cc_start: 0.8233 (p0) cc_final: 0.7607 (p0) REVERT: I 12 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8204 (ttpt) REVERT: I 57 GLU cc_start: 0.8457 (tp30) cc_final: 0.8255 (mm-30) REVERT: J 13 GLU cc_start: 0.5937 (pm20) cc_final: 0.5694 (pm20) REVERT: J 20 GLU cc_start: 0.4183 (pm20) cc_final: 0.2605 (tp30) REVERT: J 60 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7331 (pttm) REVERT: K 2 ASP cc_start: 0.7466 (p0) cc_final: 0.6386 (m-30) REVERT: K 4 PHE cc_start: 0.7558 (t80) cc_final: 0.7261 (t80) REVERT: K 97 LYS cc_start: 0.8502 (mttt) cc_final: 0.7642 (mmmt) REVERT: K 100 LEU cc_start: 0.8419 (tt) cc_final: 0.8114 (pt) REVERT: L 12 LYS cc_start: 0.8914 (tptt) cc_final: 0.8679 (tppt) REVERT: L 44 THR cc_start: 0.9029 (t) cc_final: 0.8778 (t) REVERT: L 55 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.9076 (p) REVERT: L 99 GLN cc_start: 0.8691 (mt0) cc_final: 0.8451 (tm-30) REVERT: M 21 LYS cc_start: 0.8923 (mttt) cc_final: 0.8566 (mttp) REVERT: M 38 LEU cc_start: 0.9471 (tt) cc_final: 0.9254 (tt) REVERT: N 99 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7198 (tm-30) REVERT: N 100 LEU cc_start: 0.8186 (tt) cc_final: 0.7975 (tt) outliers start: 105 outliers final: 95 residues processed: 357 average time/residue: 0.0713 time to fit residues: 38.8580 Evaluate side-chains 384 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 288 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 5 MET Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 123 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.114764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.097743 restraints weight = 19144.185| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.84 r_work: 0.3503 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10560 Z= 0.236 Angle : 0.666 6.959 14205 Z= 0.359 Chirality : 0.052 0.160 1770 Planarity : 0.002 0.013 1770 Dihedral : 9.676 52.540 1650 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % Rotamer: Outliers : 10.10 % Allowed : 20.10 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.95 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.003 PHE N 4 HIS 0.003 0.001 HIS O 50 Details of bonding type rmsd covalent geometry : bond 0.00553 (10560) covalent geometry : angle 0.66587 (14205) hydrogen bonds : bond 0.04082 ( 143) hydrogen bonds : angle 6.01599 ( 450) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 294 time to evaluate : 0.327 Fit side-chains REVERT: A 20 GLU cc_start: 0.8844 (pt0) cc_final: 0.8430 (pt0) REVERT: A 98 ASP cc_start: 0.8258 (p0) cc_final: 0.7744 (p0) REVERT: E 2 ASP cc_start: 0.8695 (p0) cc_final: 0.8469 (p0) REVERT: E 61 GLU cc_start: 0.9167 (tt0) cc_final: 0.8409 (pm20) REVERT: G 57 GLU cc_start: 0.8397 (tp30) cc_final: 0.7961 (mm-30) REVERT: G 60 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7736 (ttmm) REVERT: H 2 ASP cc_start: 0.8106 (p0) cc_final: 0.7854 (p0) REVERT: H 57 GLU cc_start: 0.8349 (tp30) cc_final: 0.8102 (mm-30) REVERT: I 2 ASP cc_start: 0.8200 (p0) cc_final: 0.7565 (p0) REVERT: I 12 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8235 (ttpt) REVERT: J 13 GLU cc_start: 0.6016 (pm20) cc_final: 0.5766 (pm20) REVERT: J 20 GLU cc_start: 0.4176 (pm20) cc_final: 0.2387 (tp30) REVERT: J 60 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7383 (pttm) REVERT: K 2 ASP cc_start: 0.7436 (p0) cc_final: 0.6329 (m-30) REVERT: K 4 PHE cc_start: 0.7581 (t80) cc_final: 0.7208 (t80) REVERT: K 97 LYS cc_start: 0.8467 (mttt) cc_final: 0.7603 (mmmt) REVERT: K 100 LEU cc_start: 0.8439 (tt) cc_final: 0.8099 (pt) REVERT: L 12 LYS cc_start: 0.8841 (tptt) cc_final: 0.8636 (tppt) REVERT: L 44 THR cc_start: 0.8970 (t) cc_final: 0.8732 (t) REVERT: L 55 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.9036 (p) REVERT: L 99 GLN cc_start: 0.8644 (mt0) cc_final: 0.8416 (tm-30) REVERT: M 21 LYS cc_start: 0.8890 (mttt) cc_final: 0.8538 (mttp) REVERT: M 38 LEU cc_start: 0.9468 (tt) cc_final: 0.9251 (tt) REVERT: M 100 LEU cc_start: 0.7633 (tt) cc_final: 0.7275 (tt) outliers start: 103 outliers final: 95 residues processed: 355 average time/residue: 0.0740 time to fit residues: 40.1572 Evaluate side-chains 385 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 289 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 5 MET Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 55 optimal weight: 0.0670 chunk 84 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 overall best weight: 2.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN F 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.116153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.099163 restraints weight = 18735.179| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.80 r_work: 0.3530 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10560 Z= 0.194 Angle : 0.625 6.688 14205 Z= 0.337 Chirality : 0.051 0.135 1770 Planarity : 0.002 0.012 1770 Dihedral : 9.472 52.777 1650 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.30 % Favored : 84.70 % Rotamer: Outliers : 10.20 % Allowed : 20.00 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.85 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.003 PHE L 94 HIS 0.003 0.001 HIS O 50 Details of bonding type rmsd covalent geometry : bond 0.00453 (10560) covalent geometry : angle 0.62512 (14205) hydrogen bonds : bond 0.03788 ( 143) hydrogen bonds : angle 5.91978 ( 450) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 293 time to evaluate : 0.396 Fit side-chains REVERT: A 20 GLU cc_start: 0.8798 (pt0) cc_final: 0.8406 (pt0) REVERT: A 98 ASP cc_start: 0.8250 (p0) cc_final: 0.7847 (p0) REVERT: C 13 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7766 (mm-30) REVERT: C 57 GLU cc_start: 0.8907 (tp30) cc_final: 0.8487 (tp30) REVERT: C 72 THR cc_start: 0.9388 (OUTLIER) cc_final: 0.9106 (p) REVERT: D 20 GLU cc_start: 0.9040 (pt0) cc_final: 0.8772 (pt0) REVERT: E 61 GLU cc_start: 0.9162 (tt0) cc_final: 0.8459 (pm20) REVERT: G 57 GLU cc_start: 0.8350 (tp30) cc_final: 0.7894 (mm-30) REVERT: G 60 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7697 (ttmm) REVERT: H 2 ASP cc_start: 0.8173 (p0) cc_final: 0.7899 (p0) REVERT: H 57 GLU cc_start: 0.8296 (tp30) cc_final: 0.8040 (mm-30) REVERT: H 75 THR cc_start: 0.8946 (m) cc_final: 0.8551 (p) REVERT: I 2 ASP cc_start: 0.8199 (p0) cc_final: 0.7557 (p0) REVERT: I 12 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8219 (ttpt) REVERT: I 60 LYS cc_start: 0.7916 (mptt) cc_final: 0.7553 (ttpt) REVERT: J 13 GLU cc_start: 0.5799 (pm20) cc_final: 0.5538 (pm20) REVERT: J 20 GLU cc_start: 0.4202 (pm20) cc_final: 0.2549 (tp30) REVERT: J 60 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7384 (pttm) REVERT: K 2 ASP cc_start: 0.7438 (p0) cc_final: 0.6307 (m-30) REVERT: K 4 PHE cc_start: 0.7456 (t80) cc_final: 0.7119 (t80) REVERT: K 97 LYS cc_start: 0.8424 (mttt) cc_final: 0.7591 (mmmt) REVERT: K 100 LEU cc_start: 0.8429 (tt) cc_final: 0.8087 (pt) REVERT: L 12 LYS cc_start: 0.8755 (tptt) cc_final: 0.8502 (tppt) REVERT: L 44 THR cc_start: 0.8831 (t) cc_final: 0.8593 (t) REVERT: L 55 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.9029 (p) REVERT: L 99 GLN cc_start: 0.8687 (mt0) cc_final: 0.8462 (tm-30) REVERT: M 21 LYS cc_start: 0.8856 (mttt) cc_final: 0.8523 (mttp) REVERT: M 38 LEU cc_start: 0.9468 (tt) cc_final: 0.9219 (tt) REVERT: M 100 LEU cc_start: 0.7399 (tt) cc_final: 0.7133 (tt) outliers start: 104 outliers final: 94 residues processed: 355 average time/residue: 0.0719 time to fit residues: 39.2112 Evaluate side-chains 382 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 286 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 5 MET Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN F 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.117012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.100055 restraints weight = 18734.017| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.80 r_work: 0.3544 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10560 Z= 0.177 Angle : 0.620 7.048 14205 Z= 0.334 Chirality : 0.051 0.195 1770 Planarity : 0.002 0.011 1770 Dihedral : 9.404 54.253 1650 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 9.71 % Allowed : 20.39 % Favored : 69.90 % 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: -4.80 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.003 PHE M 4 HIS 0.002 0.001 HIS O 50 Details of bonding type rmsd covalent geometry : bond 0.00414 (10560) covalent geometry : angle 0.62005 (14205) hydrogen bonds : bond 0.03661 ( 143) hydrogen bonds : angle 5.86752 ( 450) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 290 time to evaluate : 0.394 Fit side-chains REVERT: A 20 GLU cc_start: 0.8791 (pt0) cc_final: 0.8399 (pt0) REVERT: A 83 GLU cc_start: 0.8669 (tt0) cc_final: 0.8460 (tt0) REVERT: A 98 ASP cc_start: 0.8217 (p0) cc_final: 0.7839 (p0) REVERT: C 72 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.9099 (p) REVERT: D 20 GLU cc_start: 0.9034 (pt0) cc_final: 0.8748 (pt0) REVERT: E 61 GLU cc_start: 0.9156 (tt0) cc_final: 0.8473 (pm20) REVERT: G 57 GLU cc_start: 0.8324 (tp30) cc_final: 0.7886 (mm-30) REVERT: G 60 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7678 (ttmm) REVERT: H 2 ASP cc_start: 0.8046 (p0) cc_final: 0.7802 (p0) REVERT: H 57 GLU cc_start: 0.8288 (tp30) cc_final: 0.8027 (mm-30) REVERT: H 75 THR cc_start: 0.8935 (m) cc_final: 0.8567 (p) REVERT: I 2 ASP cc_start: 0.8191 (p0) cc_final: 0.7567 (p0) REVERT: I 60 LYS cc_start: 0.7920 (mptt) cc_final: 0.7573 (ttpt) REVERT: J 13 GLU cc_start: 0.5740 (pm20) cc_final: 0.5475 (pm20) REVERT: J 20 GLU cc_start: 0.3833 (pm20) cc_final: 0.2429 (tp30) REVERT: J 60 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7344 (pttm) REVERT: K 2 ASP cc_start: 0.7437 (p0) cc_final: 0.6288 (m-30) REVERT: K 4 PHE cc_start: 0.7527 (t80) cc_final: 0.7117 (t80) REVERT: K 13 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7318 (mm-30) REVERT: K 97 LYS cc_start: 0.8386 (mttt) cc_final: 0.7584 (mmmt) REVERT: K 100 LEU cc_start: 0.8333 (tt) cc_final: 0.7997 (pt) REVERT: L 44 THR cc_start: 0.8873 (t) cc_final: 0.8642 (t) REVERT: L 55 VAL cc_start: 0.9265 (OUTLIER) cc_final: 0.9040 (p) REVERT: L 99 GLN cc_start: 0.8818 (mt0) cc_final: 0.8360 (tm-30) REVERT: M 21 LYS cc_start: 0.8847 (mttt) cc_final: 0.8517 (mttp) REVERT: O 98 ASP cc_start: 0.7352 (p0) cc_final: 0.6834 (m-30) outliers start: 99 outliers final: 93 residues processed: 348 average time/residue: 0.0677 time to fit residues: 36.0816 Evaluate side-chains 380 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 285 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 5 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 5 MET Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 149 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.117640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.100663 restraints weight = 18752.115| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.80 r_work: 0.3557 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10560 Z= 0.170 Angle : 0.619 9.789 14205 Z= 0.332 Chirality : 0.051 0.192 1770 Planarity : 0.002 0.015 1770 Dihedral : 9.323 56.793 1650 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.46 % Favored : 85.54 % Rotamer: Outliers : 9.80 % Allowed : 20.98 % Favored : 69.22 % 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: -4.76 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.003 PHE M 4 HIS 0.003 0.001 HIS O 50 Details of bonding type rmsd covalent geometry : bond 0.00399 (10560) covalent geometry : angle 0.61860 (14205) hydrogen bonds : bond 0.03553 ( 143) hydrogen bonds : angle 5.81483 ( 450) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 296 time to evaluate : 0.376 Fit side-chains REVERT: A 20 GLU cc_start: 0.8800 (pt0) cc_final: 0.8417 (pt0) REVERT: A 98 ASP cc_start: 0.7950 (p0) cc_final: 0.7605 (p0) REVERT: C 13 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7596 (mm-30) REVERT: C 57 GLU cc_start: 0.8901 (tp30) cc_final: 0.8493 (tp30) REVERT: C 72 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.9078 (p) REVERT: D 20 GLU cc_start: 0.9033 (pt0) cc_final: 0.8734 (pt0) REVERT: E 13 GLU cc_start: 0.3770 (OUTLIER) cc_final: 0.2287 (pm20) REVERT: E 61 GLU cc_start: 0.9125 (tt0) cc_final: 0.8450 (pm20) REVERT: E 83 GLU cc_start: 0.4866 (pm20) cc_final: 0.4581 (pm20) REVERT: G 57 GLU cc_start: 0.8301 (tp30) cc_final: 0.7885 (mm-30) REVERT: G 60 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7635 (ttmm) REVERT: H 2 ASP cc_start: 0.8109 (p0) cc_final: 0.7862 (p0) REVERT: H 57 GLU cc_start: 0.8252 (tp30) cc_final: 0.7988 (mm-30) REVERT: H 75 THR cc_start: 0.8951 (m) cc_final: 0.8588 (p) REVERT: I 2 ASP cc_start: 0.8148 (p0) cc_final: 0.7525 (p0) REVERT: I 12 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8262 (ttpt) REVERT: I 60 LYS cc_start: 0.7793 (mptt) cc_final: 0.7470 (ttpt) REVERT: J 13 GLU cc_start: 0.5701 (pm20) cc_final: 0.5442 (pm20) REVERT: J 20 GLU cc_start: 0.3772 (pm20) cc_final: 0.2461 (tp30) REVERT: J 60 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7343 (pttm) REVERT: K 2 ASP cc_start: 0.7447 (p0) cc_final: 0.6273 (m-30) REVERT: K 4 PHE cc_start: 0.7547 (t80) cc_final: 0.7126 (t80) REVERT: K 5 MET cc_start: 0.8449 (ptm) cc_final: 0.8022 (ttp) REVERT: K 13 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7235 (mm-30) REVERT: K 97 LYS cc_start: 0.8361 (mttt) cc_final: 0.7635 (mmtt) REVERT: K 100 LEU cc_start: 0.8334 (tt) cc_final: 0.7982 (pt) REVERT: L 44 THR cc_start: 0.8876 (t) cc_final: 0.8644 (t) REVERT: L 55 VAL cc_start: 0.9293 (OUTLIER) cc_final: 0.9081 (p) REVERT: L 99 GLN cc_start: 0.8678 (mt0) cc_final: 0.8437 (tm-30) REVERT: M 21 LYS cc_start: 0.8850 (mttt) cc_final: 0.8515 (mttp) REVERT: M 46 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8406 (mt-10) REVERT: O 72 THR cc_start: 0.9189 (t) cc_final: 0.8939 (m) REVERT: O 98 ASP cc_start: 0.7335 (p0) cc_final: 0.6828 (m-30) outliers start: 100 outliers final: 92 residues processed: 355 average time/residue: 0.0747 time to fit residues: 40.7282 Evaluate side-chains 386 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 291 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 5 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 5 MET Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 138 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 75 optimal weight: 0.0030 chunk 89 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.115161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.098051 restraints weight = 18727.279| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.82 r_work: 0.3516 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10560 Z= 0.238 Angle : 0.680 8.557 14205 Z= 0.361 Chirality : 0.052 0.200 1770 Planarity : 0.002 0.013 1770 Dihedral : 9.592 55.535 1650 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.93 % Favored : 84.07 % Rotamer: Outliers : 10.29 % Allowed : 20.10 % Favored : 69.61 % 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: -4.81 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.003 PHE M 4 HIS 0.004 0.001 HIS O 50 Details of bonding type rmsd covalent geometry : bond 0.00560 (10560) covalent geometry : angle 0.67956 (14205) hydrogen bonds : bond 0.04012 ( 143) hydrogen bonds : angle 5.89605 ( 450) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 289 time to evaluate : 0.439 Fit side-chains REVERT: A 20 GLU cc_start: 0.8842 (pt0) cc_final: 0.8425 (pt0) REVERT: A 98 ASP cc_start: 0.8236 (p0) cc_final: 0.7875 (p0) REVERT: C 13 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7635 (mm-30) REVERT: C 72 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.9107 (p) REVERT: D 20 GLU cc_start: 0.9042 (pt0) cc_final: 0.8757 (pt0) REVERT: E 13 GLU cc_start: 0.3840 (OUTLIER) cc_final: 0.2351 (pm20) REVERT: E 61 GLU cc_start: 0.9172 (tt0) cc_final: 0.8442 (pm20) REVERT: G 57 GLU cc_start: 0.8363 (tp30) cc_final: 0.7915 (mm-30) REVERT: G 60 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7668 (ttmm) REVERT: H 2 ASP cc_start: 0.8146 (p0) cc_final: 0.7896 (p0) REVERT: H 57 GLU cc_start: 0.8304 (tp30) cc_final: 0.8028 (mm-30) REVERT: H 75 THR cc_start: 0.8988 (m) cc_final: 0.8589 (p) REVERT: I 2 ASP cc_start: 0.8159 (p0) cc_final: 0.7540 (p0) REVERT: I 12 LYS cc_start: 0.8503 (ttmt) cc_final: 0.8222 (ttpt) REVERT: I 60 LYS cc_start: 0.7804 (mptt) cc_final: 0.7458 (ttpt) REVERT: J 13 GLU cc_start: 0.5384 (pm20) cc_final: 0.5102 (pm20) REVERT: J 20 GLU cc_start: 0.4171 (pm20) cc_final: 0.2395 (tp30) REVERT: J 60 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7337 (pttm) REVERT: K 2 ASP cc_start: 0.7538 (p0) cc_final: 0.6414 (m-30) REVERT: K 4 PHE cc_start: 0.7566 (t80) cc_final: 0.7138 (t80) REVERT: K 5 MET cc_start: 0.8480 (ptm) cc_final: 0.8033 (ttp) REVERT: K 97 LYS cc_start: 0.8420 (mttt) cc_final: 0.7597 (mmmt) REVERT: K 100 LEU cc_start: 0.8058 (tt) cc_final: 0.7763 (pt) REVERT: L 44 THR cc_start: 0.8887 (t) cc_final: 0.8656 (t) REVERT: L 55 VAL cc_start: 0.9265 (OUTLIER) cc_final: 0.9034 (p) REVERT: L 99 GLN cc_start: 0.8654 (mt0) cc_final: 0.8389 (tm-30) REVERT: M 21 LYS cc_start: 0.8833 (mttt) cc_final: 0.8500 (mttp) REVERT: M 46 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8404 (mt-10) REVERT: N 59 THR cc_start: 0.9079 (t) cc_final: 0.8770 (t) REVERT: O 72 THR cc_start: 0.9186 (t) cc_final: 0.8942 (m) REVERT: O 98 ASP cc_start: 0.7407 (p0) cc_final: 0.6888 (m-30) outliers start: 105 outliers final: 100 residues processed: 351 average time/residue: 0.0733 time to fit residues: 39.4471 Evaluate side-chains 391 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 288 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 5 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 5 MET Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 113 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.117737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.100696 restraints weight = 18694.093| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.82 r_work: 0.3561 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10560 Z= 0.166 Angle : 0.618 8.611 14205 Z= 0.331 Chirality : 0.051 0.179 1770 Planarity : 0.002 0.013 1770 Dihedral : 9.329 58.990 1650 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.82 % Favored : 86.18 % Rotamer: Outliers : 10.20 % Allowed : 20.39 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.003 PHE M 4 HIS 0.002 0.001 HIS O 50 Details of bonding type rmsd covalent geometry : bond 0.00389 (10560) covalent geometry : angle 0.61838 (14205) hydrogen bonds : bond 0.03472 ( 143) hydrogen bonds : angle 5.79838 ( 450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2069.96 seconds wall clock time: 36 minutes 31.84 seconds (2191.84 seconds total)