Starting phenix.real_space_refine on Mon Jul 28 14:51:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l1u_0803/07_2025/6l1u_0803.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l1u_0803/07_2025/6l1u_0803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6l1u_0803/07_2025/6l1u_0803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l1u_0803/07_2025/6l1u_0803.map" model { file = "/net/cci-nas-00/data/ceres_data/6l1u_0803/07_2025/6l1u_0803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l1u_0803/07_2025/6l1u_0803.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10515 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N Time building chain proxies: 3.36, per 1000 atoms: 0.32 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.03 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: 2.78 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3465 1.33 - 1.45: 810 1.45 - 1.57: 6240 1.57 - 1.68: 15 1.68 - 1.80: 30 Bond restraints: 10560 Sorted by residual: bond pdb=" OH PTR G 39 " pdb=" P PTR G 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" OH PTR N 39 " pdb=" P PTR N 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" OH PTR D 39 " pdb=" P PTR D 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" OH PTR M 39 " pdb=" P PTR M 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" OH PTR C 39 " pdb=" P PTR C 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.93e+01 ... (remaining 10555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 13728 1.90 - 3.80: 342 3.80 - 5.70: 90 5.70 - 7.60: 30 7.60 - 9.50: 15 Bond angle restraints: 14205 Sorted by residual: angle pdb=" OH PTR K 39 " pdb=" P PTR K 39 " pdb=" O2P PTR K 39 " ideal model delta sigma weight residual 99.92 109.42 -9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" OH PTR M 39 " pdb=" P PTR M 39 " pdb=" O2P PTR M 39 " ideal model delta sigma weight residual 99.92 109.40 -9.48 3.00e+00 1.11e-01 9.98e+00 angle pdb=" OH PTR J 39 " pdb=" P PTR J 39 " pdb=" O2P PTR J 39 " ideal model delta sigma weight residual 99.92 109.40 -9.48 3.00e+00 1.11e-01 9.98e+00 angle pdb=" OH PTR L 39 " pdb=" P PTR L 39 " pdb=" O2P PTR L 39 " ideal model delta sigma weight residual 99.92 109.39 -9.47 3.00e+00 1.11e-01 9.96e+00 angle pdb=" OH PTR C 39 " pdb=" P PTR C 39 " pdb=" O2P PTR C 39 " ideal model delta sigma weight residual 99.92 109.39 -9.47 3.00e+00 1.11e-01 9.96e+00 ... (remaining 14200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 5775 17.25 - 34.50: 465 34.50 - 51.75: 135 51.75 - 69.00: 15 69.00 - 86.25: 30 Dihedral angle restraints: 6420 sinusoidal: 2355 harmonic: 4065 Sorted by residual: dihedral pdb=" CA ALA G 29 " pdb=" C ALA G 29 " pdb=" N ALA G 30 " pdb=" CA ALA G 30 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ALA J 29 " pdb=" C ALA J 29 " pdb=" N ALA J 30 " pdb=" CA ALA J 30 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ALA E 29 " pdb=" C ALA E 29 " pdb=" N ALA E 30 " pdb=" CA ALA E 30 " ideal model delta harmonic sigma weight residual 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 6417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1195 0.056 - 0.113: 456 0.113 - 0.169: 104 0.169 - 0.225: 0 0.225 - 0.281: 15 Chirality restraints: 1770 Sorted by residual: chirality pdb=" CB VAL F 77 " pdb=" CA VAL F 77 " pdb=" CG1 VAL F 77 " pdb=" CG2 VAL F 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB VAL L 77 " pdb=" CA VAL L 77 " pdb=" CG1 VAL L 77 " pdb=" CG2 VAL L 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL N 77 " pdb=" CA VAL N 77 " pdb=" CG1 VAL N 77 " pdb=" CG2 VAL N 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1767 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 13 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" CD GLU D 13 " 0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU D 13 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU D 13 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU L 13 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" CD GLU L 13 " 0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU L 13 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU L 13 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU M 13 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.03e+00 pdb=" CD GLU M 13 " 0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU M 13 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU M 13 " -0.006 2.00e-02 2.50e+03 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 408 2.69 - 3.24: 10149 3.24 - 3.79: 15394 3.79 - 4.35: 18717 4.35 - 4.90: 37388 Nonbonded interactions: 82056 Sorted by model distance: nonbonded pdb=" O SER D 9 " pdb=" OG SER D 9 " model vdw 2.138 3.040 nonbonded pdb=" O SER A 9 " pdb=" OG SER A 9 " model vdw 2.138 3.040 nonbonded pdb=" O SER N 9 " pdb=" OG SER N 9 " model vdw 2.138 3.040 nonbonded pdb=" O SER J 9 " pdb=" OG SER J 9 " model vdw 2.138 3.040 nonbonded pdb=" O SER G 9 " pdb=" OG SER G 9 " model vdw 2.138 3.040 ... (remaining 82051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' } 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: 3.230 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.530 Find NCS groups from input model: 0.240 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.167 10560 Z= 0.515 Angle : 0.915 9.499 14205 Z= 0.450 Chirality : 0.064 0.281 1770 Planarity : 0.002 0.010 1770 Dihedral : 15.744 86.255 3840 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 0.00 % Allowed : 17.65 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.001 0.000 HIS H 50 PHE 0.015 0.003 PHE F 94 Details of bonding type rmsd hydrogen bonds : bond 0.26099 ( 143) hydrogen bonds : angle 9.67119 ( 450) covalent geometry : bond 0.01123 (10560) covalent geometry : angle 0.91508 (14205) *********************** 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 : 1.212 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: 0.7795 (pm20) REVERT: F 4 PHE cc_start: 0.7955 (t80) cc_final: 0.7609 (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: 0.8114 (tp30) cc_final: 0.7880 (tp30) REVERT: I 2 ASP cc_start: 0.8147 (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: 0.6344 (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: 0.8593 (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: 0.7600 (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 99 GLN cc_start: 0.8442 (mt0) cc_final: 0.8242 (tm-30) 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: 0.2168 time to fit residues: 99.6219 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 : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 62 GLN B 99 GLN C 62 GLN C 99 GLN D 62 GLN D 99 GLN E 62 GLN E 99 GLN F 62 GLN F 99 GLN G 62 GLN H 62 GLN I 62 GLN J 62 GLN K 62 GLN L 62 GLN M 62 GLN N 62 GLN O 62 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.119955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.102914 restraints weight = 18449.183| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.84 r_work: 0.3581 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10560 Z= 0.149 Angle : 0.616 8.196 14205 Z= 0.338 Chirality : 0.051 0.133 1770 Planarity : 0.002 0.014 1770 Dihedral : 9.331 52.008 1650 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.96 % Favored : 86.04 % Rotamer: Outliers : 4.41 % Allowed : 18.53 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.54 (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 HIS 0.002 0.001 HIS K 50 PHE 0.019 0.003 PHE L 94 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 143) hydrogen bonds : angle 6.63044 ( 450) covalent geometry : bond 0.00337 (10560) covalent geometry : angle 0.61616 (14205) *********************** 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 368 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 323 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: C 8 LEU cc_start: 0.8914 (mm) cc_final: 0.8619 (mm) REVERT: C 13 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7430 (mm-30) REVERT: E 61 GLU cc_start: 0.9016 (tt0) cc_final: 0.8233 (pm20) REVERT: G 57 GLU cc_start: 0.8296 (tp30) cc_final: 0.7854 (mm-30) REVERT: G 60 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7617 (ttmm) REVERT: H 2 ASP cc_start: 0.8096 (p0) cc_final: 0.7849 (p0) REVERT: H 44 THR cc_start: 0.9431 (t) cc_final: 0.9187 (t) REVERT: H 57 GLU cc_start: 0.8455 (tp30) cc_final: 0.8122 (mm-30) REVERT: I 2 ASP cc_start: 0.8498 (p0) cc_final: 0.7941 (p0) REVERT: I 57 GLU cc_start: 0.8493 (tp30) cc_final: 0.8257 (mm-30) REVERT: I 60 LYS cc_start: 0.7838 (mptt) cc_final: 0.7460 (ttpt) REVERT: J 2 ASP cc_start: 0.7849 (p0) cc_final: 0.7596 (p0) REVERT: J 60 LYS cc_start: 0.7722 (mmtt) cc_final: 0.6946 (pttm) REVERT: K 2 ASP cc_start: 0.7654 (p0) cc_final: 0.6423 (m-30) REVERT: K 4 PHE cc_start: 0.6982 (t80) cc_final: 0.6681 (t80) REVERT: K 97 LYS cc_start: 0.8303 (mttt) cc_final: 0.7698 (mmtt) REVERT: K 100 LEU cc_start: 0.8392 (tt) cc_final: 0.8113 (pt) REVERT: L 12 LYS cc_start: 0.8799 (tptt) cc_final: 0.8356 (tppt) REVERT: L 99 GLN cc_start: 0.8694 (mt0) cc_final: 0.8072 (tm-30) REVERT: M 12 LYS cc_start: 0.8800 (tptp) cc_final: 0.8466 (mptt) REVERT: M 21 LYS cc_start: 0.8907 (mttt) cc_final: 0.8477 (mttp) REVERT: M 24 GLN cc_start: 0.7701 (mt0) cc_final: 0.7395 (mt0) REVERT: M 92 THR cc_start: 0.8553 (m) cc_final: 0.8332 (t) REVERT: N 92 THR cc_start: 0.8387 (m) cc_final: 0.8158 (t) REVERT: N 99 GLN cc_start: 0.8612 (mt0) cc_final: 0.8251 (tm-30) REVERT: N 100 LEU cc_start: 0.8166 (tt) cc_final: 0.7848 (tt) outliers start: 45 outliers final: 37 residues processed: 351 average time/residue: 0.1823 time to fit residues: 94.8406 Evaluate side-chains 326 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 289 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 33 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL 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 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 59 THR 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 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 I residue 63 VAL Chi-restraints excluded: chain J 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 M residue 20 GLU Chi-restraints excluded: chain M residue 63 VAL 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 32 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN E 99 GLN F 99 GLN K 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.117122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.100802 restraints weight = 18165.934| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.77 r_work: 0.3466 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.055 10560 Z= 0.428 Angle : 0.831 6.214 14205 Z= 0.446 Chirality : 0.057 0.188 1770 Planarity : 0.003 0.016 1770 Dihedral : 10.377 59.208 1650 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.04 % Favored : 81.96 % Rotamer: Outliers : 9.12 % Allowed : 18.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.33 (0.12), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.09), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS O 50 PHE 0.025 0.005 PHE F 94 Details of bonding type rmsd hydrogen bonds : bond 0.05539 ( 143) hydrogen bonds : angle 6.55645 ( 450) covalent geometry : bond 0.01007 (10560) covalent geometry : angle 0.83087 (14205) *********************** 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 379 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 286 time to evaluate : 1.191 Fit side-chains REVERT: A 20 GLU cc_start: 0.8963 (tt0) cc_final: 0.8708 (pt0) REVERT: C 8 LEU cc_start: 0.9039 (mm) cc_final: 0.8812 (mm) REVERT: C 13 GLU cc_start: 0.8595 (mm-30) cc_final: 0.7930 (mm-30) REVERT: E 61 GLU cc_start: 0.9303 (tt0) cc_final: 0.8350 (pm20) REVERT: E 83 GLU cc_start: 0.8725 (tt0) cc_final: 0.8381 (pm20) REVERT: G 57 GLU cc_start: 0.8677 (tp30) cc_final: 0.8210 (mm-30) REVERT: G 60 LYS cc_start: 0.8355 (mmtt) cc_final: 0.7803 (ttmm) REVERT: G 72 THR cc_start: 0.9543 (OUTLIER) cc_final: 0.9239 (p) REVERT: G 83 GLU cc_start: 0.9032 (tt0) cc_final: 0.8810 (tt0) REVERT: H 2 ASP cc_start: 0.8090 (p0) cc_final: 0.7874 (p0) REVERT: H 57 GLU cc_start: 0.8648 (tp30) cc_final: 0.8358 (mm-30) REVERT: I 2 ASP cc_start: 0.8627 (p0) cc_final: 0.8040 (p0) REVERT: I 12 LYS cc_start: 0.8591 (ttmt) cc_final: 0.7987 (ttpp) REVERT: I 57 GLU cc_start: 0.8770 (tp30) cc_final: 0.8502 (mm-30) REVERT: I 60 LYS cc_start: 0.8097 (mptt) cc_final: 0.7547 (ttpt) REVERT: J 13 GLU cc_start: 0.5953 (pm20) cc_final: 0.5436 (pm20) REVERT: J 60 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7108 (pttm) REVERT: J 61 GLU cc_start: 0.8958 (tt0) cc_final: 0.8440 (pm20) REVERT: K 2 ASP cc_start: 0.7483 (p0) cc_final: 0.6360 (m-30) REVERT: K 4 PHE cc_start: 0.7506 (t80) cc_final: 0.7172 (t80) REVERT: K 5 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8265 (ptm) REVERT: K 97 LYS cc_start: 0.8521 (mttt) cc_final: 0.7634 (mmmt) REVERT: K 100 LEU cc_start: 0.8360 (tt) cc_final: 0.8117 (pt) REVERT: L 12 LYS cc_start: 0.8931 (tptt) cc_final: 0.8596 (tppt) REVERT: L 55 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.9050 (p) REVERT: L 99 GLN cc_start: 0.8787 (mt0) cc_final: 0.8409 (tm-30) REVERT: M 12 LYS cc_start: 0.8858 (tptp) cc_final: 0.8420 (mptt) REVERT: M 21 LYS cc_start: 0.8933 (mttt) cc_final: 0.8592 (mttp) REVERT: N 57 GLU cc_start: 0.8827 (tp30) cc_final: 0.8602 (tp30) outliers start: 93 outliers final: 75 residues processed: 348 average time/residue: 0.1778 time to fit residues: 92.9089 Evaluate side-chains 348 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 270 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 70 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 33 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 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 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 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 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 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 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 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 74 VAL 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 121 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.122637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.106664 restraints weight = 17535.917| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.70 r_work: 0.3573 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10560 Z= 0.236 Angle : 0.670 7.360 14205 Z= 0.362 Chirality : 0.052 0.141 1770 Planarity : 0.002 0.013 1770 Dihedral : 9.733 52.481 1650 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.11 % Favored : 85.89 % Rotamer: Outliers : 8.73 % Allowed : 19.80 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.19 (0.13), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 50 PHE 0.018 0.003 PHE L 94 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 143) hydrogen bonds : angle 6.20525 ( 450) covalent geometry : bond 0.00550 (10560) covalent geometry : angle 0.67030 (14205) *********************** 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 390 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 301 time to evaluate : 1.189 Fit side-chains REVERT: A 9 SER cc_start: 0.8104 (p) cc_final: 0.7874 (p) REVERT: C 13 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8173 (mm-30) REVERT: E 61 GLU cc_start: 0.9262 (tt0) cc_final: 0.8372 (pm20) REVERT: E 83 GLU cc_start: 0.8670 (tt0) cc_final: 0.8424 (pm20) REVERT: G 57 GLU cc_start: 0.8532 (tp30) cc_final: 0.8089 (mm-30) REVERT: G 60 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7733 (ttmm) REVERT: G 72 THR cc_start: 0.9542 (OUTLIER) cc_final: 0.9218 (p) REVERT: G 83 GLU cc_start: 0.8997 (tt0) cc_final: 0.8600 (tt0) REVERT: H 2 ASP cc_start: 0.8070 (p0) cc_final: 0.7850 (p0) REVERT: H 57 GLU cc_start: 0.8580 (tp30) cc_final: 0.8359 (mm-30) REVERT: I 2 ASP cc_start: 0.8158 (p0) cc_final: 0.7524 (p0) REVERT: I 12 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8140 (ttpt) REVERT: J 13 GLU cc_start: 0.6066 (pm20) cc_final: 0.5533 (pm20) REVERT: J 60 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7313 (pttm) REVERT: J 61 GLU cc_start: 0.8942 (tt0) cc_final: 0.8415 (pm20) REVERT: K 2 ASP cc_start: 0.7444 (p0) cc_final: 0.6309 (m-30) REVERT: K 4 PHE cc_start: 0.7413 (t80) cc_final: 0.7091 (t80) REVERT: K 97 LYS cc_start: 0.8452 (mttt) cc_final: 0.7559 (mmmt) REVERT: K 100 LEU cc_start: 0.8427 (tt) cc_final: 0.8126 (pt) REVERT: L 2 ASP cc_start: 0.7786 (p0) cc_final: 0.7562 (p0) REVERT: L 12 LYS cc_start: 0.8971 (tptt) cc_final: 0.8647 (tppt) REVERT: L 44 THR cc_start: 0.9018 (t) cc_final: 0.8794 (t) REVERT: L 55 VAL cc_start: 0.9312 (OUTLIER) cc_final: 0.8988 (p) REVERT: L 99 GLN cc_start: 0.8724 (mt0) cc_final: 0.8370 (tm-30) REVERT: M 12 LYS cc_start: 0.8854 (tptp) cc_final: 0.8395 (mptt) REVERT: M 21 LYS cc_start: 0.8841 (mttt) cc_final: 0.8501 (mttp) REVERT: M 24 GLN cc_start: 0.8025 (mt0) cc_final: 0.7731 (mt0) REVERT: M 57 GLU cc_start: 0.8904 (tp30) cc_final: 0.8660 (tp30) outliers start: 89 outliers final: 71 residues processed: 353 average time/residue: 0.1758 time to fit residues: 92.5530 Evaluate side-chains 364 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 291 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL 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 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 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 74 VAL 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 72 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 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 33 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain 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 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 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 O residue 5 MET Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 84 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN L 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.120151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.103052 restraints weight = 18300.104| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.80 r_work: 0.3589 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10560 Z= 0.119 Angle : 0.561 6.719 14205 Z= 0.307 Chirality : 0.050 0.140 1770 Planarity : 0.002 0.011 1770 Dihedral : 9.162 53.176 1650 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.40 % Favored : 86.60 % Rotamer: Outliers : 6.08 % Allowed : 23.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS O 50 PHE 0.016 0.002 PHE M 4 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 143) hydrogen bonds : angle 5.85838 ( 450) covalent geometry : bond 0.00267 (10560) covalent geometry : angle 0.56144 (14205) *********************** 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 371 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 309 time to evaluate : 1.238 Fit side-chains REVERT: A 98 ASP cc_start: 0.8359 (p0) cc_final: 0.7610 (p0) REVERT: C 57 GLU cc_start: 0.8821 (tp30) cc_final: 0.8376 (tp30) REVERT: E 61 GLU cc_start: 0.9126 (tt0) cc_final: 0.8370 (pm20) REVERT: G 57 GLU cc_start: 0.8282 (tp30) cc_final: 0.7879 (mm-30) REVERT: G 60 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7606 (ttmm) REVERT: G 83 GLU cc_start: 0.8692 (tt0) cc_final: 0.8331 (tt0) REVERT: H 2 ASP cc_start: 0.7972 (p0) cc_final: 0.7742 (p0) REVERT: H 57 GLU cc_start: 0.8306 (tp30) cc_final: 0.8082 (mm-30) REVERT: H 75 THR cc_start: 0.8954 (m) cc_final: 0.8567 (p) REVERT: I 2 ASP cc_start: 0.8110 (p0) cc_final: 0.7479 (p0) REVERT: I 12 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8203 (ttpt) REVERT: I 60 LYS cc_start: 0.7972 (mptt) cc_final: 0.7592 (ttpt) REVERT: J 13 GLU cc_start: 0.5313 (pm20) cc_final: 0.5012 (pm20) REVERT: J 20 GLU cc_start: 0.3529 (pm20) cc_final: 0.2289 (tt0) REVERT: J 60 LYS cc_start: 0.8077 (mmtt) cc_final: 0.7211 (pttm) REVERT: J 61 GLU cc_start: 0.8750 (tt0) cc_final: 0.8345 (pm20) REVERT: K 2 ASP cc_start: 0.7521 (p0) cc_final: 0.6311 (m-30) REVERT: K 4 PHE cc_start: 0.7374 (t80) cc_final: 0.6992 (t80) REVERT: K 46 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8478 (mt-10) REVERT: K 97 LYS cc_start: 0.8380 (mttt) cc_final: 0.7583 (mmmt) REVERT: K 100 LEU cc_start: 0.8414 (tt) cc_final: 0.8078 (pt) REVERT: L 12 LYS cc_start: 0.8871 (tptt) cc_final: 0.8544 (tppt) REVERT: L 44 THR cc_start: 0.8791 (t) cc_final: 0.8542 (t) REVERT: L 55 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.9004 (p) REVERT: L 99 GLN cc_start: 0.8682 (mt0) cc_final: 0.8368 (tm-30) REVERT: M 12 LYS cc_start: 0.8806 (tptp) cc_final: 0.8489 (mptt) REVERT: M 21 LYS cc_start: 0.8802 (mttt) cc_final: 0.8519 (mttp) REVERT: M 99 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7247 (tm-30) REVERT: N 60 LYS cc_start: 0.8125 (mptt) cc_final: 0.6593 (ttmt) REVERT: N 99 GLN cc_start: 0.8812 (mt0) cc_final: 0.8256 (tm-30) REVERT: O 98 ASP cc_start: 0.7315 (p0) cc_final: 0.6811 (m-30) outliers start: 62 outliers final: 51 residues processed: 343 average time/residue: 0.1822 time to fit residues: 93.1963 Evaluate side-chains 348 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 296 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 72 THR Chi-restraints excluded: chain B residue 5 MET 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 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 8 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 63 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 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 74 VAL 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 55 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 102 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 99 GLN C 99 GLN F 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.114011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.097139 restraints weight = 19178.881| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.80 r_work: 0.3474 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 10560 Z= 0.337 Angle : 0.749 7.859 14205 Z= 0.400 Chirality : 0.054 0.158 1770 Planarity : 0.003 0.013 1770 Dihedral : 10.023 52.565 1650 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.91 % Favored : 83.09 % Rotamer: Outliers : 10.78 % Allowed : 18.43 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS O 50 PHE 0.023 0.004 PHE C 94 Details of bonding type rmsd hydrogen bonds : bond 0.04709 ( 143) hydrogen bonds : angle 6.11902 ( 450) covalent geometry : bond 0.00790 (10560) covalent geometry : angle 0.74882 (14205) *********************** 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 409 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 299 time to evaluate : 1.179 Fit side-chains REVERT: A 20 GLU cc_start: 0.8815 (pt0) cc_final: 0.8464 (pt0) REVERT: A 98 ASP cc_start: 0.8368 (p0) cc_final: 0.7723 (p0) REVERT: D 20 GLU cc_start: 0.9017 (pt0) cc_final: 0.8786 (pt0) REVERT: E 61 GLU cc_start: 0.9180 (tt0) cc_final: 0.8457 (pm20) REVERT: G 57 GLU cc_start: 0.8423 (tp30) cc_final: 0.7968 (mm-30) REVERT: G 60 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7789 (ttmm) REVERT: G 83 GLU cc_start: 0.8623 (tt0) cc_final: 0.8379 (tt0) REVERT: H 2 ASP cc_start: 0.8130 (p0) cc_final: 0.7907 (p0) REVERT: H 57 GLU cc_start: 0.8293 (tp30) cc_final: 0.8043 (mm-30) REVERT: I 2 ASP cc_start: 0.8222 (p0) cc_final: 0.7596 (p0) REVERT: I 12 LYS cc_start: 0.8613 (ttmt) cc_final: 0.8367 (ttpt) REVERT: J 13 GLU cc_start: 0.5723 (pm20) cc_final: 0.5395 (pm20) REVERT: J 20 GLU cc_start: 0.4582 (pm20) cc_final: 0.2258 (tp30) REVERT: J 60 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7375 (pttm) REVERT: K 2 ASP cc_start: 0.7418 (p0) cc_final: 0.6343 (m-30) REVERT: K 4 PHE cc_start: 0.7577 (t80) cc_final: 0.7283 (t80) REVERT: K 100 LEU cc_start: 0.8420 (tt) cc_final: 0.8022 (pt) REVERT: L 44 THR cc_start: 0.8949 (t) cc_final: 0.8731 (t) REVERT: L 55 VAL cc_start: 0.9279 (OUTLIER) cc_final: 0.9051 (p) REVERT: L 99 GLN cc_start: 0.8706 (mt0) cc_final: 0.8420 (tm-30) REVERT: M 12 LYS cc_start: 0.8790 (tptp) cc_final: 0.8391 (mttt) REVERT: M 21 LYS cc_start: 0.8889 (mttt) cc_final: 0.8565 (mttp) REVERT: O 98 ASP cc_start: 0.7467 (p0) cc_final: 0.6950 (m-30) outliers start: 110 outliers final: 103 residues processed: 367 average time/residue: 0.1703 time to fit residues: 94.6085 Evaluate side-chains 393 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 289 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL 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 8 LEU Chi-restraints excluded: chain D residue 33 THR 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 D residue 77 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 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 H residue 5 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 70 VAL 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 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 77 VAL 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 L residue 81 THR Chi-restraints excluded: chain M residue 20 GLU 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 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 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 115 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 91 optimal weight: 0.1980 chunk 144 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.115292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.098251 restraints weight = 19114.247| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.83 r_work: 0.3513 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3760 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= 0.226 Angle : 0.661 7.593 14205 Z= 0.355 Chirality : 0.052 0.135 1770 Planarity : 0.002 0.014 1770 Dihedral : 9.688 53.350 1650 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 9.71 % Allowed : 20.29 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS O 50 PHE 0.019 0.003 PHE M 4 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 143) hydrogen bonds : angle 5.96463 ( 450) covalent geometry : bond 0.00529 (10560) covalent geometry : angle 0.66084 (14205) *********************** 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 396 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 297 time to evaluate : 1.204 Fit side-chains REVERT: A 20 GLU cc_start: 0.8823 (pt0) cc_final: 0.8416 (pt0) REVERT: A 83 GLU cc_start: 0.8641 (tt0) cc_final: 0.8418 (tt0) REVERT: A 98 ASP cc_start: 0.8255 (p0) cc_final: 0.7681 (p0) REVERT: B 35 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7828 (mm-30) REVERT: C 57 GLU cc_start: 0.8909 (tp30) cc_final: 0.8500 (tp30) REVERT: D 20 GLU cc_start: 0.9012 (pt0) cc_final: 0.8794 (pt0) REVERT: E 61 GLU cc_start: 0.9179 (tt0) cc_final: 0.8453 (pm20) REVERT: G 57 GLU cc_start: 0.8366 (tp30) cc_final: 0.7915 (mm-30) REVERT: G 60 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7684 (ttmm) REVERT: G 83 GLU cc_start: 0.8601 (tt0) cc_final: 0.8338 (tt0) REVERT: H 2 ASP cc_start: 0.8073 (p0) cc_final: 0.7843 (p0) REVERT: H 57 GLU cc_start: 0.8293 (tp30) cc_final: 0.8034 (mm-30) REVERT: H 75 THR cc_start: 0.8965 (m) cc_final: 0.8573 (p) REVERT: I 2 ASP cc_start: 0.8189 (p0) cc_final: 0.7563 (p0) REVERT: I 12 LYS cc_start: 0.8501 (ttmt) cc_final: 0.8275 (ttpt) REVERT: J 13 GLU cc_start: 0.5462 (pm20) cc_final: 0.5146 (pm20) REVERT: J 20 GLU cc_start: 0.4355 (pm20) cc_final: 0.2384 (tp30) REVERT: J 60 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7397 (pttm) REVERT: K 2 ASP cc_start: 0.7380 (p0) cc_final: 0.6305 (m-30) REVERT: K 4 PHE cc_start: 0.7516 (t80) cc_final: 0.7133 (t80) REVERT: K 5 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.8048 (ptm) REVERT: K 100 LEU cc_start: 0.8393 (tt) cc_final: 0.8014 (pt) REVERT: L 12 LYS cc_start: 0.8835 (tptt) cc_final: 0.8578 (tppt) REVERT: L 44 THR cc_start: 0.8904 (t) cc_final: 0.8670 (t) REVERT: L 55 VAL cc_start: 0.9255 (OUTLIER) cc_final: 0.9011 (p) REVERT: L 99 GLN cc_start: 0.8694 (mt0) cc_final: 0.8442 (tm-30) REVERT: M 12 LYS cc_start: 0.8716 (tptp) cc_final: 0.8504 (tppt) REVERT: M 21 LYS cc_start: 0.8791 (mttt) cc_final: 0.8456 (mttp) REVERT: N 59 THR cc_start: 0.9053 (t) cc_final: 0.8737 (t) REVERT: O 72 THR cc_start: 0.9219 (t) cc_final: 0.8968 (m) REVERT: O 98 ASP cc_start: 0.7441 (p0) cc_final: 0.6914 (m-30) outliers start: 99 outliers final: 93 residues processed: 354 average time/residue: 0.1701 time to fit residues: 90.7177 Evaluate side-chains 389 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 294 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 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 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 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 F residue 77 VAL Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain 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 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 33 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 5 MET 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 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL 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 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 52 optimal weight: 0.0770 chunk 41 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 82 optimal weight: 6.9990 chunk 40 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 99 GLN C 99 GLN F 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.122059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.105265 restraints weight = 18326.607| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.76 r_work: 0.3637 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10560 Z= 0.098 Angle : 0.559 6.917 14205 Z= 0.303 Chirality : 0.050 0.135 1770 Planarity : 0.002 0.012 1770 Dihedral : 9.164 54.941 1650 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer: Outliers : 7.65 % Allowed : 22.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 50 PHE 0.023 0.002 PHE N 4 Details of bonding type rmsd hydrogen bonds : bond 0.02837 ( 143) hydrogen bonds : angle 5.73841 ( 450) covalent geometry : bond 0.00218 (10560) covalent geometry : angle 0.55868 (14205) *********************** 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 395 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 317 time to evaluate : 1.073 Fit side-chains REVERT: A 20 GLU cc_start: 0.8777 (pt0) cc_final: 0.8444 (pt0) REVERT: A 98 ASP cc_start: 0.7930 (p0) cc_final: 0.7445 (p0) REVERT: C 13 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7590 (mm-30) REVERT: C 57 GLU cc_start: 0.8811 (tp30) cc_final: 0.8347 (tp30) REVERT: D 20 GLU cc_start: 0.9044 (pt0) cc_final: 0.8772 (pt0) REVERT: E 61 GLU cc_start: 0.9091 (tt0) cc_final: 0.8437 (pm20) REVERT: G 57 GLU cc_start: 0.8238 (tp30) cc_final: 0.7821 (mm-30) REVERT: G 60 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7526 (ttmm) REVERT: G 83 GLU cc_start: 0.8634 (tt0) cc_final: 0.8401 (tt0) REVERT: H 2 ASP cc_start: 0.8001 (p0) cc_final: 0.7771 (p0) REVERT: H 57 GLU cc_start: 0.8229 (tp30) cc_final: 0.7983 (mm-30) REVERT: H 75 THR cc_start: 0.8944 (m) cc_final: 0.8628 (p) REVERT: H 87 SER cc_start: 0.8593 (t) cc_final: 0.8217 (m) REVERT: I 2 ASP cc_start: 0.8103 (p0) cc_final: 0.7482 (p0) REVERT: I 12 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8272 (ttpt) REVERT: I 60 LYS cc_start: 0.7989 (mptt) cc_final: 0.7611 (ttpt) REVERT: J 20 GLU cc_start: 0.4009 (pm20) cc_final: 0.2870 (tt0) REVERT: J 60 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7323 (pttm) REVERT: K 2 ASP cc_start: 0.7355 (p0) cc_final: 0.6219 (m-30) REVERT: K 4 PHE cc_start: 0.7363 (t80) cc_final: 0.6946 (t80) REVERT: K 5 MET cc_start: 0.8147 (ptm) cc_final: 0.7522 (ptm) REVERT: K 97 LYS cc_start: 0.8338 (mttt) cc_final: 0.7558 (mmmt) REVERT: K 100 LEU cc_start: 0.8328 (tt) cc_final: 0.8013 (pt) REVERT: L 12 LYS cc_start: 0.8708 (tptt) cc_final: 0.8449 (tppt) REVERT: L 44 THR cc_start: 0.8726 (t) cc_final: 0.8443 (t) REVERT: L 99 GLN cc_start: 0.8662 (mt0) cc_final: 0.8383 (tm-30) REVERT: M 21 LYS cc_start: 0.8866 (mttt) cc_final: 0.8501 (mttp) REVERT: N 79 GLN cc_start: 0.9217 (pt0) cc_final: 0.8992 (pt0) REVERT: O 72 THR cc_start: 0.9072 (t) cc_final: 0.8780 (m) REVERT: O 98 ASP cc_start: 0.7171 (p0) cc_final: 0.6657 (m-30) outliers start: 78 outliers final: 64 residues processed: 359 average time/residue: 0.1849 time to fit residues: 99.0174 Evaluate side-chains 366 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 302 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 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 74 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 63 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 44 THR 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 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 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 74 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 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 74 VAL Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain N residue 5 MET Chi-restraints excluded: chain N residue 63 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 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 88 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN E 99 GLN F 99 GLN H 99 GLN M 24 GLN ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.111492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.094260 restraints weight = 19269.020| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.87 r_work: 0.3455 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.056 10560 Z= 0.408 Angle : 0.810 8.971 14205 Z= 0.428 Chirality : 0.056 0.203 1770 Planarity : 0.003 0.014 1770 Dihedral : 10.262 56.220 1650 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.82 % Favored : 82.18 % Rotamer: Outliers : 9.41 % Allowed : 20.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS O 50 PHE 0.023 0.004 PHE B 94 Details of bonding type rmsd hydrogen bonds : bond 0.04710 ( 143) hydrogen bonds : angle 6.07473 ( 450) covalent geometry : bond 0.00956 (10560) covalent geometry : angle 0.80956 (14205) *********************** 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 388 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 292 time to evaluate : 1.110 Fit side-chains REVERT: A 20 GLU cc_start: 0.8871 (pt0) cc_final: 0.8452 (pt0) REVERT: A 98 ASP cc_start: 0.8241 (p0) cc_final: 0.7747 (p0) REVERT: C 13 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7807 (mm-30) REVERT: D 20 GLU cc_start: 0.9046 (pt0) cc_final: 0.8785 (pt0) REVERT: E 13 GLU cc_start: 0.3652 (OUTLIER) cc_final: 0.1988 (pm20) REVERT: E 61 GLU cc_start: 0.9216 (tt0) cc_final: 0.8429 (pm20) REVERT: F 28 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8591 (mt-10) REVERT: G 57 GLU cc_start: 0.8448 (tp30) cc_final: 0.7988 (mm-30) REVERT: G 60 LYS cc_start: 0.8273 (mmtt) cc_final: 0.7766 (ttmm) REVERT: G 83 GLU cc_start: 0.8734 (tt0) cc_final: 0.8507 (tt0) REVERT: H 2 ASP cc_start: 0.8132 (p0) cc_final: 0.7904 (p0) REVERT: H 57 GLU cc_start: 0.8358 (tp30) cc_final: 0.8069 (mm-30) REVERT: I 2 ASP cc_start: 0.8212 (p0) cc_final: 0.7585 (p0) REVERT: I 12 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8363 (ttpt) REVERT: J 13 GLU cc_start: 0.6122 (pm20) cc_final: 0.5723 (pm20) REVERT: J 20 GLU cc_start: 0.4625 (pm20) cc_final: 0.2205 (tp30) REVERT: J 60 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7344 (pttm) REVERT: K 2 ASP cc_start: 0.7396 (p0) cc_final: 0.6320 (m-30) REVERT: K 4 PHE cc_start: 0.7582 (t80) cc_final: 0.7185 (t80) REVERT: K 5 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8132 (ptm) REVERT: K 46 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8370 (mt-10) REVERT: K 100 LEU cc_start: 0.8305 (tt) cc_final: 0.7941 (pt) REVERT: L 4 PHE cc_start: 0.7705 (t80) cc_final: 0.7441 (t80) REVERT: M 21 LYS cc_start: 0.8836 (mttt) cc_final: 0.8609 (mttp) REVERT: M 46 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8416 (mt-10) REVERT: N 59 THR cc_start: 0.9128 (t) cc_final: 0.8821 (t) REVERT: O 98 ASP cc_start: 0.7346 (p0) cc_final: 0.6809 (m-30) REVERT: O 99 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7920 (tm-30) outliers start: 96 outliers final: 90 residues processed: 352 average time/residue: 0.1747 time to fit residues: 91.9007 Evaluate side-chains 375 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 282 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 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 44 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 74 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 55 VAL 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 44 THR Chi-restraints excluded: chain D residue 55 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 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 F residue 22 THR Chi-restraints excluded: chain F residue 26 VAL 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 F residue 77 VAL 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 H residue 5 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 64 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 74 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 5 MET Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 GLU 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 77 VAL Chi-restraints excluded: chain N residue 5 MET 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 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 91 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 141 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN L 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.119824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.103045 restraints weight = 18641.558| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.75 r_work: 0.3609 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10560 Z= 0.125 Angle : 0.598 8.578 14205 Z= 0.321 Chirality : 0.050 0.156 1770 Planarity : 0.002 0.010 1770 Dihedral : 9.360 56.272 1650 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 6.47 % Allowed : 24.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 50 PHE 0.023 0.003 PHE N 4 Details of bonding type rmsd hydrogen bonds : bond 0.03006 ( 143) hydrogen bonds : angle 5.77288 ( 450) covalent geometry : bond 0.00286 (10560) covalent geometry : angle 0.59829 (14205) ********************** 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 373 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 307 time to evaluate : 1.114 Fit side-chains REVERT: A 20 GLU cc_start: 0.8753 (pt0) cc_final: 0.8409 (pt0) REVERT: A 83 GLU cc_start: 0.8585 (tt0) cc_final: 0.8187 (tt0) REVERT: A 98 ASP cc_start: 0.7888 (p0) cc_final: 0.7465 (p0) REVERT: C 13 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7579 (mm-30) REVERT: D 20 GLU cc_start: 0.9052 (pt0) cc_final: 0.8762 (pt0) REVERT: E 61 GLU cc_start: 0.9078 (tt0) cc_final: 0.8425 (pm20) REVERT: E 83 GLU cc_start: 0.4066 (pm20) cc_final: 0.3772 (pm20) REVERT: G 57 GLU cc_start: 0.8259 (tp30) cc_final: 0.7895 (mm-30) REVERT: G 60 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7585 (ttmm) REVERT: G 83 GLU cc_start: 0.8630 (tt0) cc_final: 0.8396 (tt0) REVERT: H 2 ASP cc_start: 0.8063 (p0) cc_final: 0.7820 (p0) REVERT: H 57 GLU cc_start: 0.8252 (tp30) cc_final: 0.7976 (mm-30) REVERT: H 75 THR cc_start: 0.8945 (m) cc_final: 0.8608 (p) REVERT: I 2 ASP cc_start: 0.8081 (p0) cc_final: 0.7471 (p0) REVERT: I 12 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8252 (ttpt) REVERT: I 60 LYS cc_start: 0.7811 (mptt) cc_final: 0.7554 (ttpt) REVERT: J 20 GLU cc_start: 0.3728 (pm20) cc_final: 0.2640 (tp30) REVERT: J 60 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7338 (pttm) REVERT: K 2 ASP cc_start: 0.7477 (p0) cc_final: 0.6367 (m-30) REVERT: K 4 PHE cc_start: 0.7428 (t80) cc_final: 0.7119 (t80) REVERT: K 21 LYS cc_start: 0.8478 (mttp) cc_final: 0.8245 (mttp) REVERT: K 46 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8232 (mt-10) REVERT: K 97 LYS cc_start: 0.8373 (mttt) cc_final: 0.7571 (mmmt) REVERT: K 100 LEU cc_start: 0.8150 (tt) cc_final: 0.7868 (pt) REVERT: L 4 PHE cc_start: 0.7554 (t80) cc_final: 0.7277 (t80) REVERT: L 99 GLN cc_start: 0.8708 (mt0) cc_final: 0.8438 (tm-30) REVERT: M 21 LYS cc_start: 0.8759 (mttt) cc_final: 0.8417 (mttp) REVERT: M 46 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8420 (mt-10) REVERT: N 59 THR cc_start: 0.9010 (t) cc_final: 0.8709 (t) REVERT: O 72 THR cc_start: 0.9059 (t) cc_final: 0.8773 (m) REVERT: O 98 ASP cc_start: 0.7226 (p0) cc_final: 0.6697 (m-30) REVERT: O 99 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7814 (tm-30) outliers start: 66 outliers final: 66 residues processed: 346 average time/residue: 0.1875 time to fit residues: 97.4824 Evaluate side-chains 364 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 298 time to evaluate : 1.801 ------------------------------------------------------------------------------- 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 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL 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 44 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain 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 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 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 74 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain N residue 5 MET 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 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 125 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN E 99 GLN F 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.114299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.097173 restraints weight = 18745.346| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.79 r_work: 0.3507 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10560 Z= 0.276 Angle : 0.707 8.172 14205 Z= 0.374 Chirality : 0.053 0.194 1770 Planarity : 0.002 0.011 1770 Dihedral : 9.815 53.485 1650 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.49 % Favored : 83.51 % Rotamer: Outliers : 8.82 % Allowed : 22.55 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 50 PHE 0.020 0.003 PHE D 4 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 143) hydrogen bonds : angle 5.89936 ( 450) covalent geometry : bond 0.00646 (10560) covalent geometry : angle 0.70701 (14205) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5438.21 seconds wall clock time: 96 minutes 19.31 seconds (5779.31 seconds total)