Starting phenix.real_space_refine on Fri Feb 14 17:16:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l1u_0803/02_2025/6l1u_0803.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l1u_0803/02_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_0803/02_2025/6l1u_0803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l1u_0803/02_2025/6l1u_0803.map" model { file = "/net/cci-nas-00/data/ceres_data/6l1u_0803/02_2025/6l1u_0803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l1u_0803/02_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 2.86, per 1000 atoms: 0.27 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: 2.47 Conformation dependent library (CDL) restraints added in 1.2 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: 1.54 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: 2.93 Time building geometry restraints manager: 2.85 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: 0.10 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: 1.830 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: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 21.790 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- 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= 0.773 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 *********************** 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 : 1.133 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: 0.2136 time to fit residues: 98.5300 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 : 1.521 ------------------------------------------------------------------------------- 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 = 0.119963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.102923 restraints weight = 18450.592| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.83 r_work: 0.3578 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2366 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= 0.225 Angle : 0.616 8.197 14205 Z= 0.338 Chirality : 0.051 0.133 1770 Planarity : 0.002 0.014 1770 Dihedral : 9.329 51.978 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: -5.53 (0.11), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.09), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 50 PHE 0.019 0.003 PHE L 94 *********************** 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 : 1.302 Fit side-chains revert: symmetry clash REVERT: C 8 LEU cc_start: 0.8912 (mm) cc_final: 0.8623 (mm) REVERT: C 13 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7422 (mm-30) REVERT: E 61 GLU cc_start: 0.9020 (tt0) cc_final: 0.8240 (pm20) REVERT: G 57 GLU cc_start: 0.8298 (tp30) cc_final: 0.7859 (mm-30) REVERT: G 60 LYS cc_start: 0.7934 (mmtt) cc_final: 0.7628 (ttmm) REVERT: H 2 ASP cc_start: 0.8111 (p0) cc_final: 0.7863 (p0) REVERT: H 44 THR cc_start: 0.9428 (t) cc_final: 0.9184 (t) REVERT: H 57 GLU cc_start: 0.8458 (tp30) cc_final: 0.8126 (mm-30) REVERT: I 2 ASP cc_start: 0.8507 (p0) cc_final: 0.7953 (p0) REVERT: I 57 GLU cc_start: 0.8481 (tp30) cc_final: 0.8262 (mm-30) REVERT: I 60 LYS cc_start: 0.7842 (mptt) cc_final: 0.7473 (ttpt) REVERT: J 2 ASP cc_start: 0.7858 (p0) cc_final: 0.7605 (p0) REVERT: J 60 LYS cc_start: 0.7724 (mmtt) cc_final: 0.6954 (pttm) REVERT: K 2 ASP cc_start: 0.7660 (p0) cc_final: 0.6427 (m-30) REVERT: K 4 PHE cc_start: 0.6990 (t80) cc_final: 0.6683 (t80) REVERT: K 97 LYS cc_start: 0.8307 (mttt) cc_final: 0.7699 (mmtt) REVERT: K 100 LEU cc_start: 0.8398 (tt) cc_final: 0.8115 (pt) REVERT: L 12 LYS cc_start: 0.8800 (tptt) cc_final: 0.8353 (tppt) REVERT: L 99 GLN cc_start: 0.8704 (mt0) cc_final: 0.8064 (tm-30) REVERT: M 12 LYS cc_start: 0.8801 (tptp) cc_final: 0.8463 (mptt) REVERT: M 21 LYS cc_start: 0.8910 (mttt) cc_final: 0.8483 (mttp) REVERT: M 24 GLN cc_start: 0.7704 (mt0) cc_final: 0.7411 (mt0) REVERT: M 92 THR cc_start: 0.8555 (m) cc_final: 0.8336 (t) REVERT: N 24 GLN cc_start: 0.7730 (mt0) cc_final: 0.7521 (mt0) REVERT: N 92 THR cc_start: 0.8390 (m) cc_final: 0.8161 (t) REVERT: N 99 GLN cc_start: 0.8626 (mt0) cc_final: 0.8246 (tm-30) REVERT: N 100 LEU cc_start: 0.8168 (tt) cc_final: 0.7849 (tt) outliers start: 45 outliers final: 37 residues processed: 351 average time/residue: 0.1768 time to fit residues: 91.9805 Evaluate side-chains 327 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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: 3.9990 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: 8.9990 chunk 71 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 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 F 99 GLN K 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.114032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.096707 restraints weight = 18924.219| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.90 r_work: 0.3462 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 10560 Z= 0.443 Angle : 0.699 5.734 14205 Z= 0.379 Chirality : 0.052 0.146 1770 Planarity : 0.003 0.015 1770 Dihedral : 9.718 52.425 1650 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.35 % Favored : 83.65 % Rotamer: Outliers : 8.82 % Allowed : 17.94 % Favored : 73.24 % 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: -5.28 (0.12), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.09), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 50 PHE 0.020 0.003 PHE L 94 *********************** 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 391 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 301 time to evaluate : 1.283 Fit side-chains REVERT: C 13 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7744 (mm-30) REVERT: C 57 GLU cc_start: 0.8955 (tp30) cc_final: 0.8634 (tp30) REVERT: E 61 GLU cc_start: 0.9189 (tt0) cc_final: 0.8328 (pm20) REVERT: G 57 GLU cc_start: 0.8401 (tp30) cc_final: 0.8082 (mm-30) REVERT: G 60 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7755 (ttmm) REVERT: G 72 THR cc_start: 0.9557 (OUTLIER) cc_final: 0.9243 (p) REVERT: G 83 GLU cc_start: 0.8867 (tt0) cc_final: 0.8630 (tt0) REVERT: H 2 ASP cc_start: 0.8074 (p0) cc_final: 0.7841 (p0) REVERT: H 57 GLU cc_start: 0.8427 (tp30) cc_final: 0.8158 (mm-30) REVERT: I 2 ASP cc_start: 0.8186 (p0) cc_final: 0.7555 (p0) REVERT: I 57 GLU cc_start: 0.8580 (tp30) cc_final: 0.8350 (mm-30) REVERT: I 60 LYS cc_start: 0.8014 (mptt) cc_final: 0.7586 (ttpt) REVERT: J 2 ASP cc_start: 0.8238 (p0) cc_final: 0.7836 (p0) REVERT: J 60 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7080 (pttm) REVERT: J 61 GLU cc_start: 0.8761 (tt0) cc_final: 0.8237 (pm20) REVERT: J 83 GLU cc_start: 0.4972 (pm20) cc_final: 0.4573 (pm20) REVERT: K 2 ASP cc_start: 0.7607 (p0) cc_final: 0.6447 (m-30) REVERT: K 4 PHE cc_start: 0.7352 (t80) cc_final: 0.7014 (t80) REVERT: K 5 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8190 (ptm) REVERT: K 97 LYS cc_start: 0.8440 (mttt) cc_final: 0.7655 (mmtt) REVERT: K 100 LEU cc_start: 0.8443 (tt) cc_final: 0.8129 (pt) REVERT: L 12 LYS cc_start: 0.8873 (tptt) cc_final: 0.8580 (tppt) REVERT: L 55 VAL cc_start: 0.9311 (OUTLIER) cc_final: 0.9065 (p) REVERT: L 57 GLU cc_start: 0.8713 (tp30) cc_final: 0.8495 (tp30) REVERT: L 99 GLN cc_start: 0.8629 (mt0) cc_final: 0.8350 (tm-30) REVERT: M 12 LYS cc_start: 0.8832 (tptp) cc_final: 0.8379 (mptt) REVERT: M 21 LYS cc_start: 0.8916 (mttt) cc_final: 0.8546 (mttp) REVERT: M 38 LEU cc_start: 0.9399 (tt) cc_final: 0.9188 (tt) REVERT: N 99 GLN cc_start: 0.8716 (mt0) cc_final: 0.8196 (tm-30) outliers start: 90 outliers final: 69 residues processed: 360 average time/residue: 0.1780 time to fit residues: 96.5632 Evaluate side-chains 358 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 286 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain C residue 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 74 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 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 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: 6.9990 chunk 100 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 49 optimal weight: 6.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- 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 = 0.119384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.103207 restraints weight = 17706.919| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.73 r_work: 0.3527 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 10560 Z= 0.517 Angle : 0.741 8.045 14205 Z= 0.399 Chirality : 0.054 0.151 1770 Planarity : 0.003 0.014 1770 Dihedral : 10.049 55.291 1650 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.19 % Favored : 82.81 % Rotamer: Outliers : 10.29 % Allowed : 18.24 % 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: -5.18 (0.13), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS O 50 PHE 0.021 0.004 PHE L 94 *********************** 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 396 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 291 time to evaluate : 1.174 Fit side-chains REVERT: A 20 GLU cc_start: 0.8956 (tt0) cc_final: 0.8739 (pt0) REVERT: C 13 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8228 (mm-30) REVERT: C 57 GLU cc_start: 0.9170 (tp30) cc_final: 0.8818 (tp30) REVERT: D 13 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7928 (mm-30) REVERT: E 61 GLU cc_start: 0.9293 (tt0) cc_final: 0.8394 (pm20) REVERT: E 83 GLU cc_start: 0.8739 (tt0) cc_final: 0.8449 (pm20) REVERT: G 57 GLU cc_start: 0.8586 (tp30) cc_final: 0.8123 (mm-30) REVERT: G 60 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7767 (ttmm) REVERT: G 72 THR cc_start: 0.9541 (OUTLIER) cc_final: 0.9224 (p) REVERT: G 83 GLU cc_start: 0.9038 (tt0) cc_final: 0.8640 (tt0) REVERT: H 2 ASP cc_start: 0.8140 (p0) cc_final: 0.7910 (p0) REVERT: H 57 GLU cc_start: 0.8636 (tp30) cc_final: 0.8382 (mm-30) REVERT: I 2 ASP cc_start: 0.8164 (p0) cc_final: 0.7531 (p0) REVERT: I 12 LYS cc_start: 0.8549 (ttmt) cc_final: 0.8141 (ttpt) REVERT: J 13 GLU cc_start: 0.5726 (pm20) cc_final: 0.5039 (pm20) REVERT: J 60 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7323 (pttm) REVERT: J 61 GLU cc_start: 0.8960 (tt0) cc_final: 0.8614 (pm20) REVERT: K 2 ASP cc_start: 0.7449 (p0) cc_final: 0.6323 (m-30) REVERT: K 4 PHE cc_start: 0.7543 (t80) cc_final: 0.7211 (t80) REVERT: K 100 LEU cc_start: 0.8428 (tt) cc_final: 0.8179 (pt) REVERT: L 2 ASP cc_start: 0.7762 (p0) cc_final: 0.7562 (p0) REVERT: L 12 LYS cc_start: 0.8972 (tptt) cc_final: 0.8629 (tppt) REVERT: L 23 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8177 (mtpt) REVERT: L 44 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8766 (t) REVERT: L 55 VAL cc_start: 0.9369 (OUTLIER) cc_final: 0.9044 (p) REVERT: L 99 GLN cc_start: 0.8739 (mt0) cc_final: 0.8377 (tm-30) REVERT: M 12 LYS cc_start: 0.8844 (tptp) cc_final: 0.8389 (mttt) REVERT: M 21 LYS cc_start: 0.8913 (mttt) cc_final: 0.8554 (mttp) REVERT: M 99 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7494 (tm-30) REVERT: O 12 LYS cc_start: 0.5181 (OUTLIER) cc_final: 0.4606 (pttm) outliers start: 105 outliers final: 88 residues processed: 356 average time/residue: 0.1917 time to fit residues: 102.8576 Evaluate side-chains 378 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 285 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain 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 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 72 THR 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 38 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain 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 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 23 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain 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 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.124049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.108163 restraints weight = 17503.404| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.67 r_work: 0.3579 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10560 Z= 0.325 Angle : 0.638 7.480 14205 Z= 0.344 Chirality : 0.051 0.155 1770 Planarity : 0.002 0.011 1770 Dihedral : 9.567 52.663 1650 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.16 % Favored : 84.84 % Rotamer: Outliers : 8.63 % Allowed : 20.39 % Favored : 70.98 % 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: -5.05 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS O 50 PHE 0.017 0.003 PHE L 94 *********************** 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 389 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 301 time to evaluate : 1.110 Fit side-chains REVERT: A 98 ASP cc_start: 0.8543 (p0) cc_final: 0.7855 (p0) REVERT: C 13 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8146 (mm-30) REVERT: D 13 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7864 (mm-30) REVERT: D 20 GLU cc_start: 0.9169 (pt0) cc_final: 0.8944 (pt0) REVERT: E 2 ASP cc_start: 0.8718 (p0) cc_final: 0.8463 (p0) REVERT: E 61 GLU cc_start: 0.9280 (tt0) cc_final: 0.8480 (pm20) REVERT: E 83 GLU cc_start: 0.8575 (tt0) cc_final: 0.8373 (pm20) REVERT: G 57 GLU cc_start: 0.8535 (tp30) cc_final: 0.8073 (mm-30) REVERT: G 60 LYS cc_start: 0.8273 (mmtt) cc_final: 0.7703 (ttmm) REVERT: G 72 THR cc_start: 0.9534 (OUTLIER) cc_final: 0.9198 (p) REVERT: G 83 GLU cc_start: 0.8895 (tt0) cc_final: 0.8572 (tt0) REVERT: H 2 ASP cc_start: 0.8049 (p0) cc_final: 0.7822 (p0) REVERT: H 57 GLU cc_start: 0.8576 (tp30) cc_final: 0.8327 (mm-30) REVERT: I 2 ASP cc_start: 0.8171 (p0) cc_final: 0.7542 (p0) REVERT: I 12 LYS cc_start: 0.8527 (ttmt) cc_final: 0.8168 (ttpt) REVERT: I 60 LYS cc_start: 0.8070 (mptt) cc_final: 0.7406 (ttpt) REVERT: J 13 GLU cc_start: 0.5862 (pm20) cc_final: 0.5206 (pm20) REVERT: J 20 GLU cc_start: 0.4552 (pm20) cc_final: 0.2505 (tp30) REVERT: J 60 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7188 (pttm) REVERT: J 61 GLU cc_start: 0.8911 (tt0) cc_final: 0.8379 (pm20) REVERT: K 2 ASP cc_start: 0.7437 (p0) cc_final: 0.6285 (m-30) REVERT: K 4 PHE cc_start: 0.7600 (t80) cc_final: 0.7254 (t80) REVERT: K 46 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8494 (mt-10) REVERT: K 97 LYS cc_start: 0.8454 (mttt) cc_final: 0.7581 (mmmt) REVERT: K 100 LEU cc_start: 0.8436 (tt) cc_final: 0.8084 (pt) REVERT: L 12 LYS cc_start: 0.8935 (tptt) cc_final: 0.8607 (tppt) REVERT: L 44 THR cc_start: 0.9011 (t) cc_final: 0.8709 (t) REVERT: L 55 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8951 (p) REVERT: L 99 GLN cc_start: 0.8700 (mt0) cc_final: 0.8392 (tm-30) REVERT: M 12 LYS cc_start: 0.8809 (tptp) cc_final: 0.8366 (mptt) REVERT: M 21 LYS cc_start: 0.8897 (mttt) cc_final: 0.8557 (mttp) REVERT: M 99 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7507 (tm-30) REVERT: N 99 GLN cc_start: 0.8839 (mt0) cc_final: 0.8189 (tm-30) REVERT: O 12 LYS cc_start: 0.4972 (OUTLIER) cc_final: 0.4489 (pttm) outliers start: 88 outliers final: 76 residues processed: 347 average time/residue: 0.1761 time to fit residues: 91.1428 Evaluate side-chains 371 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 292 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 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 74 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain 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 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 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 102 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.119048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.102393 restraints weight = 18763.436| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.75 r_work: 0.3567 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10560 Z= 0.255 Angle : 0.598 7.047 14205 Z= 0.324 Chirality : 0.050 0.135 1770 Planarity : 0.002 0.010 1770 Dihedral : 9.345 52.746 1650 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.67 % Favored : 85.33 % Rotamer: Outliers : 8.14 % Allowed : 20.78 % Favored : 71.08 % 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: -4.93 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (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 N 4 *********************** 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 386 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 303 time to evaluate : 1.091 Fit side-chains REVERT: A 13 GLU cc_start: 0.5959 (mm-30) cc_final: 0.5579 (mm-30) REVERT: A 98 ASP cc_start: 0.8230 (p0) cc_final: 0.7657 (p0) REVERT: C 57 GLU cc_start: 0.9005 (tp30) cc_final: 0.8629 (tp30) REVERT: E 61 GLU cc_start: 0.9284 (tt0) cc_final: 0.8542 (pm20) REVERT: G 57 GLU cc_start: 0.8500 (tp30) cc_final: 0.8083 (mm-30) REVERT: G 60 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7783 (ttmm) REVERT: G 72 THR cc_start: 0.9522 (OUTLIER) cc_final: 0.9206 (p) REVERT: G 83 GLU cc_start: 0.8741 (tt0) cc_final: 0.8465 (tt0) REVERT: H 2 ASP cc_start: 0.8135 (p0) cc_final: 0.7908 (p0) REVERT: H 57 GLU cc_start: 0.8470 (tp30) cc_final: 0.8241 (mm-30) REVERT: H 75 THR cc_start: 0.9056 (m) cc_final: 0.8655 (p) REVERT: I 2 ASP cc_start: 0.8252 (p0) cc_final: 0.7623 (p0) REVERT: I 12 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8231 (ttpt) REVERT: I 60 LYS cc_start: 0.8104 (mptt) cc_final: 0.7516 (ttpt) REVERT: J 13 GLU cc_start: 0.5627 (pm20) cc_final: 0.4950 (pm20) REVERT: J 20 GLU cc_start: 0.4344 (pm20) cc_final: 0.2623 (tt0) REVERT: J 60 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7245 (pttm) REVERT: J 61 GLU cc_start: 0.8913 (tt0) cc_final: 0.8495 (pm20) REVERT: K 2 ASP cc_start: 0.7428 (p0) cc_final: 0.6310 (m-30) REVERT: K 4 PHE cc_start: 0.7513 (t80) cc_final: 0.7129 (t80) REVERT: K 97 LYS cc_start: 0.8466 (mttt) cc_final: 0.7622 (mmmt) REVERT: K 100 LEU cc_start: 0.8399 (tt) cc_final: 0.8040 (pt) REVERT: L 12 LYS cc_start: 0.8924 (tptt) cc_final: 0.8635 (tppt) REVERT: L 44 THR cc_start: 0.8898 (t) cc_final: 0.8652 (t) REVERT: L 55 VAL cc_start: 0.9304 (OUTLIER) cc_final: 0.9070 (p) REVERT: L 99 GLN cc_start: 0.8612 (mt0) cc_final: 0.8383 (tm-30) REVERT: M 21 LYS cc_start: 0.8952 (mttt) cc_final: 0.8625 (mttp) REVERT: M 99 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7562 (tm-30) REVERT: N 99 GLN cc_start: 0.8751 (mt0) cc_final: 0.8233 (tm-30) REVERT: O 98 ASP cc_start: 0.7458 (p0) cc_final: 0.6927 (m-30) outliers start: 83 outliers final: 76 residues processed: 347 average time/residue: 0.1780 time to fit residues: 92.1428 Evaluate side-chains 371 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 293 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 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 57 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 8 LEU 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 E residue 88 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 72 THR 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 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 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 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 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 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 63 VAL Chi-restraints excluded: chain N residue 70 VAL 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 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: 9.9990 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.113085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.095715 restraints weight = 19178.303| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.87 r_work: 0.3461 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 10560 Z= 0.469 Angle : 0.711 6.605 14205 Z= 0.382 Chirality : 0.053 0.193 1770 Planarity : 0.002 0.012 1770 Dihedral : 9.862 52.750 1650 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.77 % Favored : 83.23 % Rotamer: Outliers : 11.47 % Allowed : 17.55 % Favored : 70.98 % 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: -4.94 (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 0.004 0.001 HIS O 50 PHE 0.020 0.004 PHE C 94 *********************** 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 408 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 291 time to evaluate : 1.175 Fit side-chains REVERT: A 20 GLU cc_start: 0.8855 (pt0) cc_final: 0.8461 (pt0) REVERT: A 98 ASP cc_start: 0.8286 (p0) cc_final: 0.7719 (p0) REVERT: D 8 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8716 (mm) REVERT: D 20 GLU cc_start: 0.9037 (pt0) cc_final: 0.8762 (pt0) REVERT: E 13 GLU cc_start: 0.3744 (OUTLIER) cc_final: 0.2030 (pm20) REVERT: E 61 GLU cc_start: 0.9184 (tt0) cc_final: 0.8437 (pm20) REVERT: G 57 GLU cc_start: 0.8403 (tp30) cc_final: 0.8013 (mm-30) REVERT: G 60 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7734 (ttmm) REVERT: G 72 THR cc_start: 0.9504 (OUTLIER) cc_final: 0.9192 (p) REVERT: G 83 GLU cc_start: 0.8633 (tt0) cc_final: 0.8391 (tt0) REVERT: H 2 ASP cc_start: 0.8089 (p0) cc_final: 0.7862 (p0) REVERT: H 57 GLU cc_start: 0.8305 (tp30) cc_final: 0.8023 (mm-30) REVERT: I 2 ASP cc_start: 0.8191 (p0) cc_final: 0.7565 (p0) REVERT: I 12 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8327 (ttpt) REVERT: J 13 GLU cc_start: 0.5601 (pm20) cc_final: 0.5331 (pm20) REVERT: J 20 GLU cc_start: 0.4426 (pm20) cc_final: 0.2335 (tp30) REVERT: J 60 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7358 (pttm) REVERT: K 2 ASP cc_start: 0.7397 (p0) cc_final: 0.6317 (m-30) REVERT: K 4 PHE cc_start: 0.7509 (t80) cc_final: 0.7202 (t80) REVERT: K 100 LEU cc_start: 0.8437 (tt) cc_final: 0.8002 (pt) REVERT: L 12 LYS cc_start: 0.8654 (tptt) cc_final: 0.8386 (tppt) REVERT: L 44 THR cc_start: 0.8968 (t) cc_final: 0.8734 (t) REVERT: L 55 VAL cc_start: 0.9284 (OUTLIER) cc_final: 0.9057 (p) REVERT: L 99 GLN cc_start: 0.8709 (mt0) cc_final: 0.8425 (tm-30) REVERT: M 21 LYS cc_start: 0.8860 (mttt) cc_final: 0.8528 (mttp) REVERT: M 99 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7530 (tm-30) REVERT: N 59 THR cc_start: 0.9069 (t) cc_final: 0.8743 (t) REVERT: N 99 GLN cc_start: 0.8827 (mt0) cc_final: 0.8229 (tm-30) REVERT: O 98 ASP cc_start: 0.7440 (p0) cc_final: 0.6923 (m-30) outliers start: 117 outliers final: 106 residues processed: 362 average time/residue: 0.1648 time to fit residues: 90.2181 Evaluate side-chains 397 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 287 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 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 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 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 E residue 92 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 74 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 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 22 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain 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: 3.9990 chunk 41 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.116603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.099580 restraints weight = 18637.073| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.79 r_work: 0.3530 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10560 Z= 0.275 Angle : 0.623 6.998 14205 Z= 0.336 Chirality : 0.051 0.173 1770 Planarity : 0.002 0.011 1770 Dihedral : 9.479 53.358 1650 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.61 % Favored : 86.39 % Rotamer: Outliers : 9.71 % Allowed : 19.71 % Favored : 70.59 % 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: -4.86 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS O 50 PHE 0.020 0.003 PHE N 4 *********************** 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: 99 poor density : 296 time to evaluate : 1.344 Fit side-chains REVERT: A 20 GLU cc_start: 0.8819 (pt0) cc_final: 0.8417 (pt0) REVERT: A 98 ASP cc_start: 0.7983 (p0) cc_final: 0.7503 (p0) REVERT: C 57 GLU cc_start: 0.8909 (tp30) cc_final: 0.8541 (tp30) REVERT: D 8 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8732 (mm) REVERT: D 20 GLU cc_start: 0.9021 (pt0) cc_final: 0.8735 (pt0) REVERT: E 61 GLU cc_start: 0.9144 (tt0) cc_final: 0.8427 (pm20) REVERT: G 57 GLU cc_start: 0.8314 (tp30) cc_final: 0.7943 (mm-30) REVERT: G 60 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7666 (ttmm) REVERT: G 72 THR cc_start: 0.9504 (OUTLIER) cc_final: 0.9173 (p) REVERT: G 83 GLU cc_start: 0.8585 (tt0) cc_final: 0.8328 (tt0) REVERT: H 2 ASP cc_start: 0.8056 (p0) cc_final: 0.7815 (p0) REVERT: H 57 GLU cc_start: 0.8314 (tp30) cc_final: 0.8043 (mm-30) REVERT: H 75 THR cc_start: 0.8942 (m) cc_final: 0.8565 (p) REVERT: I 2 ASP cc_start: 0.8171 (p0) cc_final: 0.7548 (p0) REVERT: J 13 GLU cc_start: 0.5888 (pm20) cc_final: 0.5634 (pm20) REVERT: J 20 GLU cc_start: 0.4112 (pm20) cc_final: 0.2706 (tp30) REVERT: J 60 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7371 (pttm) REVERT: K 2 ASP cc_start: 0.7461 (p0) cc_final: 0.6403 (m-30) REVERT: K 4 PHE cc_start: 0.7441 (t80) cc_final: 0.7114 (t80) REVERT: K 97 LYS cc_start: 0.8435 (mttt) cc_final: 0.7601 (mmmt) REVERT: K 100 LEU cc_start: 0.8354 (tt) cc_final: 0.7983 (pt) REVERT: L 44 THR cc_start: 0.8887 (t) cc_final: 0.8629 (t) REVERT: L 55 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.9012 (p) REVERT: L 99 GLN cc_start: 0.8881 (mt0) cc_final: 0.8377 (tm-30) REVERT: M 21 LYS cc_start: 0.8847 (mttt) cc_final: 0.8511 (mttp) REVERT: M 46 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8420 (mt-10) REVERT: M 99 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7383 (tm-30) REVERT: N 59 THR cc_start: 0.9032 (t) cc_final: 0.8718 (t) REVERT: N 99 GLN cc_start: 0.8886 (mt0) cc_final: 0.8263 (tm-30) REVERT: O 98 ASP cc_start: 0.7407 (p0) cc_final: 0.6893 (m-30) REVERT: O 99 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7692 (tm-30) outliers start: 99 outliers final: 90 residues processed: 353 average time/residue: 0.1799 time to fit residues: 96.2138 Evaluate side-chains 383 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 290 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 92 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 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 63 VAL Chi-restraints excluded: chain G residue 72 THR 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 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 81 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR 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 74 VAL Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 5 MET Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 88 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN ** O 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.111429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.094230 restraints weight = 19216.220| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.86 r_work: 0.3441 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 10560 Z= 0.614 Angle : 0.794 7.138 14205 Z= 0.422 Chirality : 0.055 0.183 1770 Planarity : 0.003 0.015 1770 Dihedral : 10.234 57.715 1650 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % Rotamer: Outliers : 11.27 % Allowed : 18.43 % Favored : 70.29 % 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: -4.92 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.11), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS O 50 PHE 0.023 0.004 PHE C 94 *********************** 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 402 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 287 time to evaluate : 1.109 Fit side-chains REVERT: A 20 GLU cc_start: 0.8907 (pt0) cc_final: 0.8475 (pt0) REVERT: A 98 ASP cc_start: 0.8430 (p0) cc_final: 0.7961 (p0) REVERT: C 57 GLU cc_start: 0.9109 (tp30) cc_final: 0.8784 (tp30) REVERT: D 8 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8721 (mm) REVERT: D 20 GLU cc_start: 0.9166 (pt0) cc_final: 0.8894 (pt0) REVERT: E 13 GLU cc_start: 0.3860 (OUTLIER) cc_final: 0.2056 (pm20) REVERT: E 61 GLU cc_start: 0.9364 (tt0) cc_final: 0.8528 (pm20) REVERT: F 28 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8724 (mt-10) REVERT: G 57 GLU cc_start: 0.8641 (tp30) cc_final: 0.8238 (mm-30) REVERT: G 60 LYS cc_start: 0.8420 (mmtt) cc_final: 0.7862 (ttmm) REVERT: G 72 THR cc_start: 0.9514 (OUTLIER) cc_final: 0.9211 (p) REVERT: G 83 GLU cc_start: 0.8834 (tt0) cc_final: 0.8613 (tt0) REVERT: H 2 ASP cc_start: 0.8170 (p0) cc_final: 0.7951 (p0) REVERT: H 57 GLU cc_start: 0.8586 (tp30) cc_final: 0.8298 (mm-30) REVERT: I 2 ASP cc_start: 0.8275 (p0) cc_final: 0.7654 (p0) REVERT: I 12 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8396 (ttpt) REVERT: J 13 GLU cc_start: 0.5920 (pm20) cc_final: 0.5352 (pm20) REVERT: J 20 GLU cc_start: 0.5042 (pm20) cc_final: 0.2295 (tp30) REVERT: J 60 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7440 (pttm) REVERT: K 2 ASP cc_start: 0.7526 (p0) cc_final: 0.6492 (m-30) REVERT: K 4 PHE cc_start: 0.7650 (t80) cc_final: 0.7273 (t80) REVERT: K 100 LEU cc_start: 0.8244 (tt) cc_final: 0.8008 (pt) REVERT: L 4 PHE cc_start: 0.7786 (t80) cc_final: 0.7430 (t80) REVERT: L 55 VAL cc_start: 0.9347 (OUTLIER) cc_final: 0.9096 (p) REVERT: M 21 LYS cc_start: 0.8907 (mttt) cc_final: 0.8616 (mttp) REVERT: M 46 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8631 (mt-10) REVERT: M 99 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7589 (tm-30) REVERT: N 59 THR cc_start: 0.9190 (t) cc_final: 0.8843 (t) REVERT: O 98 ASP cc_start: 0.7540 (p0) cc_final: 0.7000 (m-30) REVERT: O 99 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7946 (tm-30) outliers start: 115 outliers final: 104 residues processed: 360 average time/residue: 0.1730 time to fit residues: 94.0786 Evaluate side-chains 387 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 278 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 57 GLU 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 77 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 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 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 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 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 33 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 72 THR 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 63 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 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 22 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain N residue 5 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 91 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- 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 E 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.118610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.101681 restraints weight = 18635.680| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.79 r_work: 0.3575 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3931 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= 0.216 Angle : 0.612 7.516 14205 Z= 0.329 Chirality : 0.051 0.140 1770 Planarity : 0.002 0.010 1770 Dihedral : 9.415 56.240 1650 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer: Outliers : 8.14 % Allowed : 21.57 % Favored : 70.29 % 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: -4.82 (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 0.002 0.001 HIS C 50 PHE 0.021 0.003 PHE N 4 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 307 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8779 (pt0) cc_final: 0.8346 (pt0) REVERT: A 98 ASP cc_start: 0.7870 (p0) cc_final: 0.7410 (p0) REVERT: D 8 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8762 (mm) REVERT: D 20 GLU cc_start: 0.9025 (pt0) cc_final: 0.8702 (pt0) REVERT: E 61 GLU cc_start: 0.9139 (tt0) cc_final: 0.8454 (pm20) REVERT: E 83 GLU cc_start: 0.4399 (pm20) cc_final: 0.4157 (pm20) REVERT: G 57 GLU cc_start: 0.8276 (tp30) cc_final: 0.7898 (mm-30) REVERT: G 60 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7613 (ttmm) REVERT: G 72 THR cc_start: 0.9501 (OUTLIER) cc_final: 0.9171 (p) REVERT: G 83 GLU cc_start: 0.8598 (tt0) cc_final: 0.8361 (tt0) REVERT: H 2 ASP cc_start: 0.8091 (p0) cc_final: 0.7823 (p0) REVERT: H 57 GLU cc_start: 0.8239 (tp30) cc_final: 0.7956 (mm-30) REVERT: H 75 THR cc_start: 0.8924 (m) cc_final: 0.8557 (p) REVERT: I 2 ASP cc_start: 0.8180 (p0) cc_final: 0.7541 (p0) REVERT: I 12 LYS cc_start: 0.8459 (ttmt) cc_final: 0.8211 (ttpt) REVERT: I 60 LYS cc_start: 0.7897 (mptt) cc_final: 0.7578 (ttpt) REVERT: J 13 GLU cc_start: 0.5349 (pm20) cc_final: 0.5075 (pm20) REVERT: J 20 GLU cc_start: 0.3931 (pm20) cc_final: 0.2596 (tp30) REVERT: J 60 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7346 (pttm) REVERT: K 2 ASP cc_start: 0.7483 (p0) cc_final: 0.6397 (m-30) REVERT: K 4 PHE cc_start: 0.7535 (t80) cc_final: 0.7168 (t80) REVERT: K 97 LYS cc_start: 0.8379 (mttt) cc_final: 0.7565 (mmmt) REVERT: K 100 LEU cc_start: 0.8212 (tt) cc_final: 0.7914 (pt) REVERT: L 55 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.8996 (p) REVERT: L 60 LYS cc_start: 0.7943 (mptt) cc_final: 0.6956 (tttm) REVERT: L 99 GLN cc_start: 0.8931 (mt0) cc_final: 0.8370 (tm-30) REVERT: M 21 LYS cc_start: 0.8839 (mttt) cc_final: 0.8509 (mttp) REVERT: M 46 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8476 (mt-10) REVERT: M 99 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7464 (tm-30) REVERT: N 59 THR cc_start: 0.9038 (t) cc_final: 0.8744 (t) REVERT: N 79 GLN cc_start: 0.9262 (pt0) cc_final: 0.9012 (pt0) REVERT: O 72 THR cc_start: 0.9195 (t) cc_final: 0.8936 (m) REVERT: O 98 ASP cc_start: 0.7223 (p0) cc_final: 0.6713 (m-30) REVERT: O 99 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7794 (tm-30) outliers start: 83 outliers final: 74 residues processed: 349 average time/residue: 0.1734 time to fit residues: 90.5677 Evaluate side-chains 374 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 297 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain A residue 92 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 44 THR 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 8 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 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 83 GLU 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 G residue 74 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 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 55 VAL Chi-restraints excluded: chain L residue 59 THR 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 70 VAL Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 5 MET Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 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: 7.9990 chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 E 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.115700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.098542 restraints weight = 18549.317| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.79 r_work: 0.3517 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10560 Z= 0.341 Angle : 0.660 7.248 14205 Z= 0.351 Chirality : 0.052 0.171 1770 Planarity : 0.002 0.010 1770 Dihedral : 9.552 54.749 1650 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.65 % Favored : 84.35 % Rotamer: Outliers : 9.12 % Allowed : 20.49 % Favored : 70.39 % 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: -4.79 (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 0.003 0.001 HIS O 50 PHE 0.020 0.003 PHE E 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4731.31 seconds wall clock time: 85 minutes 23.29 seconds (5123.29 seconds total)