Starting phenix.real_space_refine on Fri Sep 11 16:53:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6l1u_0803/09_2026/6l1u_0803.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l1u_0803/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6l1u_0803/09_2026/6l1u_0803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l1u_0803/09_2026/6l1u_0803.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6l1u_0803/09_2026/6l1u_0803.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6l1u_0803/09_2026/6l1u_0803.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6l1u_0803/09_2026/6l1u_0803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l1u_0803/09_2026/6l1u_0803.map" } 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-2.2.1-6174/lib/python3.11/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: 3 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: 1.44, per 1000 atoms: 0.14 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: 0.91 Conformation dependent library (CDL) restraints added in 473.5 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: 0.47 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: 1.65 Time building geometry restraints manager: 1.24 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: 13743 1.90 - 3.80: 342 3.80 - 5.70: 75 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: 5715 17.25 - 34.50: 405 34.50 - 51.75: 120 51.75 - 69.00: 15 69.00 - 86.25: 30 Dihedral angle restraints: 6285 sinusoidal: 2220 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 6282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1210 0.056 - 0.113: 456 0.113 - 0.169: 89 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: 0.000 Normalize map: mean=0, sd=1: 3.020 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.970 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 : 0.901 9.499 14205 Z= 0.449 Chirality : 0.063 0.281 1770 Planarity : 0.002 0.010 1770 Dihedral : 15.318 86.255 3705 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/Z covalent geometry : bond 0.01123 / 0.51 (10560) covalent geometry : angle 0.90130 / 0.45 (14205) hydrogen bonds : bond 0.26099 / 17.91 ( 143) hydrogen bonds : angle 9.67119 / 6.19 ( 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 : 0.371 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: 0.0889 time to fit residues: 41.8944 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 : 0.410 ------------------------------------------------------------------------------- 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: 4.9990 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... 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 = 0.3975 r_free = 0.3975 target = 0.122037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.104935 restraints weight = 18421.636| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.85 r_work: 0.3623 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2373 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= 0.123 Angle : 0.582 7.898 14205 Z= 0.324 Chirality : 0.050 0.138 1770 Planarity : 0.002 0.014 1770 Dihedral : 6.206 29.644 1515 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.05 % Favored : 86.95 % Rotamer: Outliers : 3.33 % Allowed : 19.51 % Favored : 77.16 % 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 0.018 0.003 PHE N 4 HIS 0.002 0.001 HIS K 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (10560) covalent geometry : angle 0.58175 / 0.32 (14205) hydrogen bonds : bond 0.03514 / 2.36 ( 143) hydrogen bonds : angle 6.66004 / 4.28 ( 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 : 0.412 Fit side-chains revert: symmetry clash REVERT: C 8 LEU cc_start: 0.8814 (mm) cc_final: 0.8552 (mm) REVERT: C 13 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7405 (mm-30) REVERT: C 57 GLU cc_start: 0.8844 (tp30) cc_final: 0.8545 (tp30) REVERT: E 61 GLU cc_start: 0.8994 (tt0) cc_final: 0.8188 (pm20) REVERT: G 60 LYS cc_start: 0.7896 (mmtt) cc_final: 0.7607 (ttmm) REVERT: H 2 ASP cc_start: 0.8086 (p0) cc_final: 0.7841 (p0) REVERT: H 57 GLU cc_start: 0.8459 (tp30) cc_final: 0.8178 (mm-30) REVERT: I 2 ASP cc_start: 0.8484 (p0) cc_final: 0.7944 (p0) REVERT: I 57 GLU cc_start: 0.8446 (tp30) cc_final: 0.8224 (mm-30) REVERT: I 60 LYS cc_start: 0.7842 (mptt) cc_final: 0.7479 (ttpt) REVERT: J 2 ASP cc_start: 0.7802 (p0) cc_final: 0.7587 (p0) REVERT: J 60 LYS cc_start: 0.7689 (mmtt) cc_final: 0.7076 (pttm) REVERT: K 2 ASP cc_start: 0.7647 (p0) cc_final: 0.6412 (m-30) REVERT: K 4 PHE cc_start: 0.6955 (t80) cc_final: 0.6654 (t80) REVERT: K 13 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8037 (mm-30) REVERT: K 97 LYS cc_start: 0.8278 (mttt) cc_final: 0.7690 (mmtt) REVERT: K 100 LEU cc_start: 0.8345 (tt) cc_final: 0.8091 (pt) REVERT: L 12 LYS cc_start: 0.8738 (tptt) cc_final: 0.8285 (tppt) REVERT: L 99 GLN cc_start: 0.8651 (mt0) cc_final: 0.8050 (tm-30) REVERT: M 2 ASP cc_start: 0.7964 (p0) cc_final: 0.7440 (p0) REVERT: M 12 LYS cc_start: 0.8803 (tptp) cc_final: 0.8465 (mptt) REVERT: M 21 LYS cc_start: 0.8889 (mttt) cc_final: 0.8502 (mttp) REVERT: M 24 GLN cc_start: 0.7645 (mt0) cc_final: 0.7365 (mt0) REVERT: N 24 GLN cc_start: 0.7709 (mt0) cc_final: 0.7488 (mt0) REVERT: N 100 LEU cc_start: 0.8219 (tt) cc_final: 0.7939 (tt) REVERT: O 12 LYS cc_start: 0.5302 (pttm) cc_final: 0.4723 (pttm) outliers start: 34 outliers final: 25 residues processed: 352 average time/residue: 0.0773 time to fit residues: 41.0450 Evaluate side-chains 314 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 289 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 141 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3841 r_free = 0.3841 target = 0.113342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.096021 restraints weight = 18861.383| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.89 r_work: 0.3461 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3041 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= 0.294 Angle : 0.700 6.177 14205 Z= 0.381 Chirality : 0.052 0.154 1770 Planarity : 0.003 0.015 1770 Dihedral : 6.566 26.360 1515 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.63 % Favored : 83.37 % Rotamer: Outliers : 9.71 % Allowed : 17.65 % Favored : 72.65 % 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: -5.28 (0.12), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.09), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.004 PHE L 94 HIS 0.004 0.001 HIS O 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.29 (10560) covalent geometry : angle 0.70006 / 0.38 (14205) hydrogen bonds : bond 0.04726 / 3.15 ( 143) hydrogen bonds : angle 6.35924 / 4.05 ( 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 395 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 296 time to evaluate : 0.359 Fit side-chains REVERT: C 13 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7760 (mm-30) REVERT: C 57 GLU cc_start: 0.8946 (tp30) cc_final: 0.8625 (tp30) REVERT: E 61 GLU cc_start: 0.9180 (tt0) cc_final: 0.8329 (pm20) REVERT: G 57 GLU cc_start: 0.8444 (tp30) cc_final: 0.8052 (mm-30) REVERT: G 60 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7751 (ttmm) REVERT: G 72 THR cc_start: 0.9525 (OUTLIER) cc_final: 0.9219 (p) REVERT: H 2 ASP cc_start: 0.8083 (p0) cc_final: 0.7854 (p0) REVERT: H 57 GLU cc_start: 0.8438 (tp30) cc_final: 0.8176 (mm-30) REVERT: I 2 ASP cc_start: 0.8197 (p0) cc_final: 0.7572 (p0) REVERT: I 57 GLU cc_start: 0.8584 (tp30) cc_final: 0.8353 (mm-30) REVERT: I 60 LYS cc_start: 0.8023 (mptt) cc_final: 0.7595 (ttpt) REVERT: J 2 ASP cc_start: 0.8238 (p0) cc_final: 0.7821 (p0) REVERT: J 60 LYS cc_start: 0.7855 (mmtt) cc_final: 0.7083 (pttm) REVERT: J 61 GLU cc_start: 0.8744 (tt0) cc_final: 0.8235 (pm20) REVERT: J 83 GLU cc_start: 0.4952 (pm20) cc_final: 0.4719 (pm20) REVERT: K 2 ASP cc_start: 0.7617 (p0) cc_final: 0.6452 (m-30) REVERT: K 4 PHE cc_start: 0.7416 (t80) cc_final: 0.7079 (t80) REVERT: K 5 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8203 (ptm) REVERT: K 97 LYS cc_start: 0.8381 (mttt) cc_final: 0.7616 (mmtt) REVERT: K 100 LEU cc_start: 0.8430 (tt) cc_final: 0.8115 (pt) REVERT: L 12 LYS cc_start: 0.8890 (tptt) cc_final: 0.8596 (tppt) REVERT: L 55 VAL cc_start: 0.9308 (OUTLIER) cc_final: 0.9068 (p) REVERT: L 99 GLN cc_start: 0.8642 (mt0) cc_final: 0.8364 (tm-30) REVERT: M 12 LYS cc_start: 0.8833 (tptp) cc_final: 0.8383 (mptt) REVERT: M 21 LYS cc_start: 0.8903 (mttt) cc_final: 0.8550 (mttp) REVERT: M 38 LEU cc_start: 0.9453 (tt) cc_final: 0.9213 (tt) outliers start: 99 outliers final: 76 residues processed: 357 average time/residue: 0.0757 time to fit residues: 41.3858 Evaluate side-chains 358 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 279 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 66 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 63 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR 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 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 5 MET 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 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 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 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: 5.9990 chunk 95 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3904 r_free = 0.3904 target = 0.117398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.100293 restraints weight = 18702.924| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.86 r_work: 0.3543 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3319 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= 0.163 Angle : 0.598 6.936 14205 Z= 0.328 Chirality : 0.050 0.138 1770 Planarity : 0.002 0.012 1770 Dihedral : 6.249 27.153 1515 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.05 % Favored : 86.95 % Rotamer: Outliers : 8.14 % Allowed : 20.98 % Favored : 70.88 % 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: -5.09 (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/Z covalent geometry : bond 0.00377 / 0.16 (10560) covalent geometry : angle 0.59788 / 0.33 (14205) hydrogen bonds : bond 0.03685 / 2.48 ( 143) hydrogen bonds : angle 6.07137 / 3.88 ( 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 385 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 302 time to evaluate : 0.301 Fit side-chains REVERT: A 98 ASP cc_start: 0.8366 (p0) cc_final: 0.7618 (p0) REVERT: C 57 GLU cc_start: 0.8849 (tp30) cc_final: 0.8377 (tp30) REVERT: E 61 GLU cc_start: 0.9154 (tt0) cc_final: 0.8349 (pm20) REVERT: G 57 GLU cc_start: 0.8287 (tp30) cc_final: 0.7847 (mm-30) REVERT: G 60 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7698 (ttmm) REVERT: H 2 ASP cc_start: 0.8064 (p0) cc_final: 0.7831 (p0) REVERT: H 57 GLU cc_start: 0.8383 (tp30) cc_final: 0.8154 (mm-30) REVERT: I 2 ASP cc_start: 0.8175 (p0) cc_final: 0.7538 (p0) REVERT: I 12 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8278 (ttpt) REVERT: I 57 GLU cc_start: 0.8535 (tp30) cc_final: 0.8267 (mm-30) REVERT: I 60 LYS cc_start: 0.7919 (mptt) cc_final: 0.7535 (ttpt) REVERT: J 2 ASP cc_start: 0.8178 (p0) cc_final: 0.7798 (p0) REVERT: J 13 GLU cc_start: 0.5655 (pm20) cc_final: 0.5339 (pm20) REVERT: J 60 LYS cc_start: 0.7937 (mmtt) cc_final: 0.7093 (pttm) REVERT: J 61 GLU cc_start: 0.8639 (tt0) cc_final: 0.8229 (pm20) REVERT: K 2 ASP cc_start: 0.7584 (p0) cc_final: 0.6429 (m-30) REVERT: K 4 PHE cc_start: 0.7275 (t80) cc_final: 0.6936 (t80) REVERT: K 97 LYS cc_start: 0.8363 (mttt) cc_final: 0.7594 (mmtt) REVERT: K 100 LEU cc_start: 0.8449 (tt) cc_final: 0.8132 (pt) REVERT: L 12 LYS cc_start: 0.8877 (tptt) cc_final: 0.8604 (tppt) REVERT: L 55 VAL cc_start: 0.9318 (OUTLIER) cc_final: 0.9056 (p) REVERT: L 57 GLU cc_start: 0.8711 (tp30) cc_final: 0.8498 (tp30) REVERT: L 99 GLN cc_start: 0.8635 (mt0) cc_final: 0.8357 (tm-30) REVERT: M 12 LYS cc_start: 0.8832 (tptp) cc_final: 0.8396 (mptt) REVERT: M 21 LYS cc_start: 0.8889 (mttt) cc_final: 0.8508 (mttp) REVERT: M 38 LEU cc_start: 0.9470 (tt) cc_final: 0.9251 (tt) REVERT: M 57 GLU cc_start: 0.8840 (tp30) cc_final: 0.8558 (tp30) REVERT: M 99 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7129 (tm-30) outliers start: 83 outliers final: 69 residues processed: 350 average time/residue: 0.0747 time to fit residues: 39.6420 Evaluate side-chains 358 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 288 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 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 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 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 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 63 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 77 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 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 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 M residue 20 GLU 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 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 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: 10.0000 chunk 85 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 54 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3855 r_free = 0.3855 target = 0.114720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.097645 restraints weight = 18988.764| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.91 r_work: 0.3490 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3519 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= 0.276 Angle : 0.679 7.111 14205 Z= 0.369 Chirality : 0.052 0.143 1770 Planarity : 0.002 0.012 1770 Dihedral : 6.511 26.414 1515 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.42 % Favored : 83.58 % Rotamer: Outliers : 9.41 % Allowed : 20.10 % Favored : 70.49 % 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: -5.00 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.003 PHE L 94 HIS 0.004 0.001 HIS O 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.28 (10560) covalent geometry : angle 0.67912 / 0.37 (14205) hydrogen bonds : bond 0.04398 / 2.96 ( 143) hydrogen bonds : angle 6.09982 / 3.90 ( 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 388 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 292 time to evaluate : 0.330 Fit side-chains REVERT: A 20 GLU cc_start: 0.8844 (pt0) cc_final: 0.8480 (pt0) REVERT: A 98 ASP cc_start: 0.8336 (p0) cc_final: 0.7728 (p0) REVERT: E 2 ASP cc_start: 0.8744 (p0) cc_final: 0.8487 (p0) REVERT: E 61 GLU cc_start: 0.9177 (tt0) cc_final: 0.8358 (pm20) REVERT: F 8 LEU cc_start: 0.9213 (tp) cc_final: 0.9001 (tp) REVERT: G 57 GLU cc_start: 0.8442 (tp30) cc_final: 0.7991 (mm-30) REVERT: G 60 LYS cc_start: 0.8274 (mmtt) cc_final: 0.7730 (ttmm) REVERT: H 2 ASP cc_start: 0.8039 (p0) cc_final: 0.7822 (p0) REVERT: H 46 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8440 (tt0) REVERT: H 57 GLU cc_start: 0.8368 (tp30) cc_final: 0.8139 (mm-30) REVERT: I 2 ASP cc_start: 0.8190 (p0) cc_final: 0.7552 (p0) REVERT: I 12 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8209 (ttpt) REVERT: I 57 GLU cc_start: 0.8509 (tp30) cc_final: 0.8305 (mm-30) REVERT: J 13 GLU cc_start: 0.6108 (pm20) cc_final: 0.5836 (pm20) REVERT: J 60 LYS cc_start: 0.8080 (mmtt) cc_final: 0.7281 (pttm) REVERT: J 61 GLU cc_start: 0.8782 (tt0) cc_final: 0.8560 (pm20) REVERT: K 2 ASP cc_start: 0.7433 (p0) cc_final: 0.6339 (m-30) REVERT: K 4 PHE cc_start: 0.7355 (t80) cc_final: 0.7038 (t80) REVERT: K 97 LYS cc_start: 0.8441 (mttt) cc_final: 0.7593 (mmmt) REVERT: K 100 LEU cc_start: 0.8412 (tt) cc_final: 0.8089 (pt) REVERT: L 12 LYS cc_start: 0.8952 (tptt) cc_final: 0.8582 (tppt) REVERT: L 55 VAL cc_start: 0.9291 (OUTLIER) cc_final: 0.9008 (p) REVERT: L 99 GLN cc_start: 0.8728 (mt0) cc_final: 0.8394 (tm-30) REVERT: M 12 LYS cc_start: 0.8786 (tptp) cc_final: 0.8534 (tppt) REVERT: M 21 LYS cc_start: 0.8883 (mttt) cc_final: 0.8520 (mttp) REVERT: M 38 LEU cc_start: 0.9439 (tt) cc_final: 0.9207 (tt) REVERT: M 99 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7341 (tm-30) outliers start: 96 outliers final: 85 residues processed: 352 average time/residue: 0.0773 time to fit residues: 41.2580 Evaluate side-chains 371 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 285 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 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 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 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 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 22 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 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 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 74 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: 10.0000 chunk 100 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3851 r_free = 0.3851 target = 0.114371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.097611 restraints weight = 19217.654| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.82 r_work: 0.3487 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 10560 Z= 0.308 Angle : 0.713 8.053 14205 Z= 0.386 Chirality : 0.053 0.169 1770 Planarity : 0.003 0.013 1770 Dihedral : 6.654 27.230 1515 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 11.27 % Allowed : 18.92 % 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: -4.99 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.004 PHE L 94 HIS 0.004 0.001 HIS O 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.31 (10560) covalent geometry : angle 0.71283 / 0.39 (14205) hydrogen bonds : bond 0.04539 / 3.03 ( 143) hydrogen bonds : angle 6.15692 / 3.93 ( 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 406 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 291 time to evaluate : 0.400 Fit side-chains REVERT: A 20 GLU cc_start: 0.8826 (pt0) cc_final: 0.8426 (pt0) REVERT: A 98 ASP cc_start: 0.8235 (p0) cc_final: 0.7719 (p0) REVERT: D 20 GLU cc_start: 0.9064 (pt0) cc_final: 0.8794 (pt0) REVERT: E 2 ASP cc_start: 0.8700 (p0) cc_final: 0.8475 (p0) REVERT: E 61 GLU cc_start: 0.9155 (tt0) cc_final: 0.8385 (pm20) REVERT: F 8 LEU cc_start: 0.9250 (tp) cc_final: 0.9049 (tp) REVERT: G 57 GLU cc_start: 0.8417 (tp30) cc_final: 0.7972 (mm-30) REVERT: G 60 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7810 (ttmm) REVERT: H 2 ASP cc_start: 0.8155 (p0) cc_final: 0.7910 (p0) REVERT: H 57 GLU cc_start: 0.8328 (tp30) cc_final: 0.8101 (mm-30) REVERT: I 2 ASP cc_start: 0.8204 (p0) cc_final: 0.7577 (p0) REVERT: I 12 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8266 (ttpt) REVERT: I 57 GLU cc_start: 0.8499 (tp30) cc_final: 0.8296 (mm-30) REVERT: J 13 GLU cc_start: 0.5736 (pm20) cc_final: 0.5452 (pm20) REVERT: J 20 GLU cc_start: 0.4607 (pm20) cc_final: 0.2424 (tp30) REVERT: J 60 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7348 (pttm) REVERT: K 2 ASP cc_start: 0.7442 (p0) cc_final: 0.6364 (m-30) REVERT: K 4 PHE cc_start: 0.7485 (t80) cc_final: 0.7185 (t80) REVERT: K 100 LEU cc_start: 0.8456 (tt) cc_final: 0.8071 (pt) REVERT: L 4 PHE cc_start: 0.7564 (t80) cc_final: 0.7355 (t80) REVERT: L 12 LYS cc_start: 0.8981 (tptt) cc_final: 0.8745 (tppt) REVERT: L 55 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.9038 (p) REVERT: L 99 GLN cc_start: 0.8666 (mt0) cc_final: 0.8426 (tm-30) REVERT: M 21 LYS cc_start: 0.8895 (mttt) cc_final: 0.8553 (mttp) REVERT: M 38 LEU cc_start: 0.9465 (tt) cc_final: 0.9243 (tt) REVERT: M 99 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7412 (tm-30) REVERT: N 99 GLN cc_start: 0.7618 (tm-30) cc_final: 0.7366 (tm-30) outliers start: 115 outliers final: 103 residues processed: 359 average time/residue: 0.0727 time to fit residues: 40.2368 Evaluate side-chains 391 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 287 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 64 THR 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 28 GLU 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 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 88 ILE Chi-restraints excluded: chain E residue 92 THR 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 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 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 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 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 8 LEU 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 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 74 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 74 VAL 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: 4.9990 chunk 93 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.114934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.097876 restraints weight = 18759.311| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.82 r_work: 0.3503 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10560 Z= 0.232 Angle : 0.642 7.261 14205 Z= 0.350 Chirality : 0.051 0.164 1770 Planarity : 0.002 0.012 1770 Dihedral : 6.438 25.620 1515 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.72 % Favored : 84.28 % Rotamer: Outliers : 10.88 % Allowed : 19.71 % 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: -4.92 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.003 PHE L 94 HIS 0.004 0.001 HIS O 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (10560) covalent geometry : angle 0.64157 / 0.35 (14205) hydrogen bonds : bond 0.04036 / 2.71 ( 143) hydrogen bonds : angle 6.03102 / 3.86 ( 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 401 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 290 time to evaluate : 0.377 Fit side-chains REVERT: A 20 GLU cc_start: 0.8817 (pt0) cc_final: 0.8551 (pt0) REVERT: A 98 ASP cc_start: 0.7993 (p0) cc_final: 0.7624 (p0) REVERT: C 13 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7799 (mm-30) REVERT: E 61 GLU cc_start: 0.9187 (tt0) cc_final: 0.8449 (pm20) REVERT: F 8 LEU cc_start: 0.9193 (tp) cc_final: 0.8990 (tp) REVERT: G 57 GLU cc_start: 0.8384 (tp30) cc_final: 0.8001 (mm-30) REVERT: G 60 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7707 (ttmm) REVERT: H 2 ASP cc_start: 0.8195 (p0) cc_final: 0.7923 (p0) REVERT: H 57 GLU cc_start: 0.8374 (tp30) cc_final: 0.8114 (mm-30) REVERT: H 75 THR cc_start: 0.8969 (m) cc_final: 0.8562 (p) REVERT: I 2 ASP cc_start: 0.8178 (p0) cc_final: 0.7541 (p0) REVERT: I 12 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8236 (ttpt) REVERT: J 13 GLU cc_start: 0.5606 (pm20) cc_final: 0.5340 (pm20) REVERT: J 20 GLU cc_start: 0.4226 (pm20) cc_final: 0.2315 (tp30) REVERT: J 60 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7378 (pttm) REVERT: K 2 ASP cc_start: 0.7444 (p0) cc_final: 0.6332 (m-30) REVERT: K 4 PHE cc_start: 0.7479 (t80) cc_final: 0.7218 (t80) REVERT: K 13 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7441 (mm-30) REVERT: K 100 LEU cc_start: 0.8452 (tt) cc_final: 0.8076 (pt) REVERT: L 12 LYS cc_start: 0.8731 (tptt) cc_final: 0.8493 (tppt) REVERT: L 55 VAL cc_start: 0.9262 (OUTLIER) cc_final: 0.9028 (p) REVERT: L 99 GLN cc_start: 0.8740 (mt0) cc_final: 0.8442 (tm-30) REVERT: M 21 LYS cc_start: 0.8881 (mttt) cc_final: 0.8541 (mttp) REVERT: M 99 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7321 (tm-30) REVERT: N 99 GLN cc_start: 0.7605 (tm-30) cc_final: 0.7313 (tm-30) outliers start: 111 outliers final: 97 residues processed: 354 average time/residue: 0.0717 time to fit residues: 39.0496 Evaluate side-chains 381 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 283 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET 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 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 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 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 28 GLU 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 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 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 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 83 GLU 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 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 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 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 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 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 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 74 VAL 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: 10.0000 chunk 79 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 66 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.115369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.098278 restraints weight = 18786.617| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.82 r_work: 0.3513 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10560 Z= 0.225 Angle : 0.651 6.694 14205 Z= 0.352 Chirality : 0.051 0.159 1770 Planarity : 0.002 0.011 1770 Dihedral : 6.424 24.826 1515 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.95 % Favored : 85.05 % Rotamer: Outliers : 10.69 % Allowed : 19.41 % 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: -4.89 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.003 PHE M 4 HIS 0.003 0.001 HIS O 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (10560) covalent geometry : angle 0.65072 / 0.35 (14205) hydrogen bonds : bond 0.04006 / 2.70 ( 143) hydrogen bonds : angle 5.99269 / 3.83 ( 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 399 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 290 time to evaluate : 0.402 Fit side-chains REVERT: A 20 GLU cc_start: 0.8824 (pt0) cc_final: 0.8555 (pt0) REVERT: A 98 ASP cc_start: 0.7986 (p0) cc_final: 0.7648 (p0) REVERT: D 20 GLU cc_start: 0.9018 (pt0) cc_final: 0.8742 (pt0) REVERT: E 13 GLU cc_start: 0.3853 (OUTLIER) cc_final: 0.2316 (pm20) REVERT: E 61 GLU cc_start: 0.9186 (tt0) cc_final: 0.8459 (pm20) REVERT: E 83 GLU cc_start: 0.4844 (pm20) cc_final: 0.4600 (pm20) REVERT: F 13 GLU cc_start: 0.7861 (mp0) cc_final: 0.7585 (mp0) REVERT: G 57 GLU cc_start: 0.8371 (tp30) cc_final: 0.7977 (mm-30) REVERT: G 60 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7703 (ttmm) REVERT: H 2 ASP cc_start: 0.8204 (p0) cc_final: 0.7928 (p0) REVERT: H 57 GLU cc_start: 0.8314 (tp30) cc_final: 0.8037 (mm-30) REVERT: H 75 THR cc_start: 0.8964 (m) cc_final: 0.8563 (p) REVERT: I 2 ASP cc_start: 0.8183 (p0) cc_final: 0.7555 (p0) REVERT: I 12 LYS cc_start: 0.8610 (ttmt) cc_final: 0.8386 (ttpt) REVERT: I 60 LYS cc_start: 0.7928 (mptt) cc_final: 0.7562 (ttpt) REVERT: J 13 GLU cc_start: 0.5442 (pm20) cc_final: 0.5152 (pm20) REVERT: J 20 GLU cc_start: 0.4162 (pm20) cc_final: 0.2369 (tp30) REVERT: J 60 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7346 (pttm) REVERT: K 2 ASP cc_start: 0.7449 (p0) cc_final: 0.6314 (m-30) REVERT: K 4 PHE cc_start: 0.7480 (t80) cc_final: 0.7182 (t80) REVERT: K 97 LYS cc_start: 0.8447 (mttt) cc_final: 0.7602 (mmmt) REVERT: K 100 LEU cc_start: 0.8300 (tt) cc_final: 0.7925 (pt) REVERT: L 44 THR cc_start: 0.8952 (t) cc_final: 0.8646 (t) REVERT: L 55 VAL cc_start: 0.9251 (OUTLIER) cc_final: 0.8992 (p) REVERT: L 99 GLN cc_start: 0.8657 (mt0) cc_final: 0.8320 (tm-30) REVERT: M 21 LYS cc_start: 0.8883 (mttt) cc_final: 0.8548 (mttp) REVERT: M 99 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7253 (tm-30) REVERT: N 59 THR cc_start: 0.9053 (t) cc_final: 0.8732 (t) REVERT: N 99 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7260 (tm-30) outliers start: 109 outliers final: 104 residues processed: 353 average time/residue: 0.0722 time to fit residues: 39.0955 Evaluate side-chains 393 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 287 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET 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 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 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 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 28 GLU 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 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 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 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 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 77 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 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 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 63 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 81 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: 10.0000 chunk 138 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 ASN B 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.117609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.100615 restraints weight = 18691.879| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.80 r_work: 0.3557 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10560 Z= 0.165 Angle : 0.614 9.213 14205 Z= 0.331 Chirality : 0.050 0.142 1770 Planarity : 0.002 0.015 1770 Dihedral : 6.212 25.694 1515 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.46 % Favored : 85.54 % Rotamer: Outliers : 9.71 % Allowed : 20.69 % 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: -4.83 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (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/Z covalent geometry : bond 0.00386 / 0.17 (10560) covalent geometry : angle 0.61379 / 0.33 (14205) hydrogen bonds : bond 0.03538 / 2.40 ( 143) hydrogen bonds : angle 5.85796 / 3.76 ( 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 395 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 296 time to evaluate : 0.410 Fit side-chains REVERT: A 20 GLU cc_start: 0.8770 (pt0) cc_final: 0.8370 (pt0) REVERT: A 98 ASP cc_start: 0.7937 (p0) cc_final: 0.7613 (p0) REVERT: C 13 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7559 (mm-30) REVERT: C 57 GLU cc_start: 0.8897 (tp30) cc_final: 0.8497 (tp30) REVERT: D 20 GLU cc_start: 0.9026 (pt0) cc_final: 0.8740 (pt0) REVERT: E 13 GLU cc_start: 0.3788 (OUTLIER) cc_final: 0.2293 (pm20) REVERT: E 61 GLU cc_start: 0.9158 (tt0) cc_final: 0.8463 (pm20) REVERT: G 57 GLU cc_start: 0.8311 (tp30) cc_final: 0.7935 (mm-30) REVERT: G 60 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7672 (ttmm) REVERT: H 2 ASP cc_start: 0.8183 (p0) cc_final: 0.7907 (p0) REVERT: H 57 GLU cc_start: 0.8242 (tp30) cc_final: 0.7982 (mm-30) REVERT: H 75 THR cc_start: 0.8974 (m) cc_final: 0.8614 (p) REVERT: I 2 ASP cc_start: 0.8185 (p0) cc_final: 0.7559 (p0) REVERT: I 60 LYS cc_start: 0.7916 (mptt) cc_final: 0.7581 (ttpt) REVERT: J 13 GLU cc_start: 0.5293 (pm20) cc_final: 0.5023 (pm20) REVERT: J 20 GLU cc_start: 0.3862 (pm20) cc_final: 0.2350 (tp30) REVERT: J 60 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7340 (pttm) REVERT: K 2 ASP cc_start: 0.7541 (p0) cc_final: 0.6383 (m-30) REVERT: K 4 PHE cc_start: 0.7570 (t80) cc_final: 0.7197 (t80) REVERT: K 97 LYS cc_start: 0.8397 (mttt) cc_final: 0.7593 (mmmt) REVERT: K 100 LEU cc_start: 0.8280 (tt) cc_final: 0.7902 (pt) REVERT: L 2 ASP cc_start: 0.7839 (p0) cc_final: 0.7597 (p0) REVERT: L 44 THR cc_start: 0.8884 (t) cc_final: 0.8655 (t) REVERT: L 55 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.8994 (p) REVERT: L 99 GLN cc_start: 0.8710 (mt0) cc_final: 0.8456 (tm-30) REVERT: M 21 LYS cc_start: 0.8878 (mttt) cc_final: 0.8547 (mttp) REVERT: M 99 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7299 (tm-30) REVERT: N 59 THR cc_start: 0.9031 (t) cc_final: 0.8718 (t) REVERT: N 99 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7236 (tm-30) REVERT: O 72 THR cc_start: 0.9191 (t) cc_final: 0.8943 (m) REVERT: O 98 ASP cc_start: 0.7380 (p0) cc_final: 0.6876 (m-30) outliers start: 99 outliers final: 94 residues processed: 355 average time/residue: 0.0735 time to fit residues: 40.0768 Evaluate side-chains 381 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 285 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 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 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 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 28 GLU 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 92 THR 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 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 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 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 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 74 VAL 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: 10.0000 chunk 91 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 GLN E 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.114197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.097118 restraints weight = 18742.876| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.81 r_work: 0.3499 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3939 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= 0.271 Angle : 0.707 9.700 14205 Z= 0.376 Chirality : 0.052 0.217 1770 Planarity : 0.002 0.013 1770 Dihedral : 6.529 26.319 1515 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.28 % Favored : 83.72 % Rotamer: Outliers : 10.00 % Allowed : 20.69 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.87 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.004 PHE M 4 HIS 0.004 0.001 HIS O 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.27 (10560) covalent geometry : angle 0.70653 / 0.38 (14205) hydrogen bonds : bond 0.04257 / 2.86 ( 143) hydrogen bonds : angle 5.99649 / 3.85 ( 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 390 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 288 time to evaluate : 0.395 Fit side-chains REVERT: A 20 GLU cc_start: 0.8898 (pt0) cc_final: 0.8499 (pt0) REVERT: A 98 ASP cc_start: 0.8153 (p0) cc_final: 0.7851 (p0) REVERT: C 13 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7745 (mm-30) REVERT: D 20 GLU cc_start: 0.9147 (pt0) cc_final: 0.8857 (pt0) REVERT: E 13 GLU cc_start: 0.4043 (OUTLIER) cc_final: 0.2376 (pm20) REVERT: E 61 GLU cc_start: 0.9351 (tt0) cc_final: 0.8531 (pm20) REVERT: G 57 GLU cc_start: 0.8621 (tp30) cc_final: 0.8229 (mm-30) REVERT: G 60 LYS cc_start: 0.8356 (mmtt) cc_final: 0.7789 (ttmm) REVERT: H 2 ASP cc_start: 0.8266 (p0) cc_final: 0.8006 (p0) REVERT: H 57 GLU cc_start: 0.8532 (tp30) cc_final: 0.8274 (mm-30) REVERT: H 75 THR cc_start: 0.9065 (m) cc_final: 0.8637 (p) REVERT: I 2 ASP cc_start: 0.8254 (p0) cc_final: 0.7623 (p0) REVERT: J 13 GLU cc_start: 0.5977 (pm20) cc_final: 0.5429 (pm20) REVERT: J 20 GLU cc_start: 0.4678 (pm20) cc_final: 0.2540 (tp30) REVERT: J 60 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7416 (pttm) REVERT: K 2 ASP cc_start: 0.7584 (p0) cc_final: 0.6420 (m-30) REVERT: K 4 PHE cc_start: 0.7636 (t80) cc_final: 0.7177 (t80) REVERT: K 5 MET cc_start: 0.8603 (ptm) cc_final: 0.8166 (ttp) REVERT: K 46 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8587 (mt-10) REVERT: K 97 LYS cc_start: 0.8491 (mttt) cc_final: 0.7630 (mmmt) REVERT: K 100 LEU cc_start: 0.8278 (tt) cc_final: 0.7881 (pt) REVERT: L 4 PHE cc_start: 0.7798 (t80) cc_final: 0.7548 (t80) REVERT: L 44 THR cc_start: 0.9111 (t) cc_final: 0.8832 (t) REVERT: L 55 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.9025 (p) REVERT: L 99 GLN cc_start: 0.8677 (mt0) cc_final: 0.8417 (tm-30) REVERT: M 21 LYS cc_start: 0.8820 (mttt) cc_final: 0.8532 (mttp) REVERT: M 46 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8614 (mt-10) REVERT: M 99 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7242 (tm-30) REVERT: N 59 THR cc_start: 0.9134 (t) cc_final: 0.8844 (t) REVERT: N 99 GLN cc_start: 0.7458 (tm-30) cc_final: 0.6894 (tm-30) outliers start: 102 outliers final: 99 residues processed: 347 average time/residue: 0.0743 time to fit residues: 39.6134 Evaluate side-chains 387 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 286 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 64 THR 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 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 28 GLU 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 92 THR 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 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 77 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 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 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 74 VAL Chi-restraints excluded: chain O residue 75 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: 5.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 111 optimal weight: 0.4980 chunk 127 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 96 optimal weight: 0.4980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 GLN E 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.120700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.103773 restraints weight = 18492.939| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.79 r_work: 0.3613 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10560 Z= 0.114 Angle : 0.578 7.955 14205 Z= 0.314 Chirality : 0.049 0.135 1770 Planarity : 0.002 0.014 1770 Dihedral : 6.019 26.860 1515 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.72 % Favored : 88.28 % Rotamer: Outliers : 7.45 % Allowed : 23.43 % Favored : 69.12 % 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: -4.74 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.002 PHE M 4 HIS 0.002 0.000 HIS O 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (10560) covalent geometry : angle 0.57790 / 0.31 (14205) hydrogen bonds : bond 0.03046 / 2.10 ( 143) hydrogen bonds : angle 5.77000 / 3.71 ( 450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2239.09 seconds wall clock time: 39 minutes 33.05 seconds (2373.05 seconds total)