Starting phenix.real_space_refine on Tue Aug 4 18:16:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36qd_77765/08_2026/36qd_77765.cif Found real_map, /net/cci-nas-00/data/ceres_data/36qd_77765/08_2026/36qd_77765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/36qd_77765/08_2026/36qd_77765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36qd_77765/08_2026/36qd_77765.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/36qd_77765/08_2026/36qd_77765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36qd_77765/08_2026/36qd_77765.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.146 sd= 0.806 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: 3 Type Number sf(0) Gaussians C 3720 2.51 5 N 1044 2.21 5 O 1188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5952 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "B" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "C" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "E" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "F" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "G" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "H" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "I" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "J" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "K" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "L" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Time building chain proxies: 1.44, per 1000 atoms: 0.24 Number of scatterers: 5952 At special positions: 0 Unit cell: (125.19, 80.25, 52.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1188 8.00 N 1044 7.00 C 3720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 234.8 milliseconds 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 80.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 15 through 23 removed outlier: 6.468A pdb=" N VAL B 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ALA C 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N GLU C 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N THR C 22 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS B 21 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLN C 24 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS B 23 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL E 15 " --> pdb=" O VAL F 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 15 through 23 removed outlier: 6.468A pdb=" N VAL B 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ALA C 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N GLU C 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N THR C 22 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS B 21 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLN C 24 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS B 23 " --> pdb=" O GLN C 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 37 through 55 removed outlier: 6.437A pdb=" N LEU B 38 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N GLY C 41 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL B 40 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N LYS C 43 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER B 42 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N LYS C 45 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N THR B 44 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N GLY C 47 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N GLU B 46 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 10.318A pdb=" N VAL C 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N VAL B 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N GLY C 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N HIS B 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ALA C 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL C 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR B 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLU C 46 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY D 47 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 48 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL D 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N HIS C 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY D 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLU D 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY A 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL D 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N HIS D 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY A 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU A 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLY E 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LYS E 43 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER A 42 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N LYS E 45 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N THR A 44 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLY E 47 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N GLU A 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N VAL E 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N VAL A 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N GLY E 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N HIS A 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ALA E 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL E 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR A 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU E 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLY F 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL E 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N LYS F 43 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER E 42 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LYS F 45 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N THR E 44 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLY F 47 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N GLU E 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N VAL F 49 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N VAL E 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N GLY F 51 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N HIS E 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N ALA F 53 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL E 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL F 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N THR E 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 66 removed outlier: 6.500A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N THR D 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL D 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN A 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 72 removed outlier: 6.153A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLY C 73 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR B 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR C 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL D 70 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 71 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR D 72 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY C 73 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL D 74 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N VAL A 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 10.175A pdb=" N GLY D 73 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N THR A 72 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N THR D 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 74 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL D 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA A 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N GLN D 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL E 70 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A 71 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR E 72 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY A 73 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL E 74 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 75 through 79 removed outlier: 6.137A pdb=" N THR B 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ALA C 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL D 70 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 71 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR D 72 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY C 73 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL D 74 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N VAL A 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 10.175A pdb=" N GLY D 73 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N THR A 72 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N THR D 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 74 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL D 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA A 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N GLN D 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL E 70 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A 71 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR E 72 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY A 73 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL E 74 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 95 removed outlier: 6.892A pdb=" N SER C 87 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE B 88 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA C 89 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA B 90 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA C 91 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR B 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY C 93 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N GLY C 86 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N ALA D 89 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N ILE C 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N ALA D 91 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N ALA C 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N GLY D 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR C 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N VAL D 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE C 94 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N SER A 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N ALA D 90 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N ALA A 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N THR D 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N ALA A 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N PHE D 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY A 93 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N GLY A 86 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 10.389A pdb=" N ALA E 89 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ILE A 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N ALA E 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N ALA A 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 10.146A pdb=" N GLY E 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR A 92 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N VAL E 95 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE A 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER E 87 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ALA F 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA E 89 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N THR F 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA E 91 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE F 94 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY E 93 " --> pdb=" O PHE F 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 15 through 18 removed outlier: 6.514A pdb=" N VAL G 15 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ALA H 18 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA G 17 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N GLU H 20 " --> pdb=" O ALA G 17 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 15 through 18 removed outlier: 6.514A pdb=" N VAL G 15 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ALA H 18 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA G 17 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N GLU H 20 " --> pdb=" O ALA G 17 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 37 through 55 removed outlier: 9.310A pdb=" N VAL G 37 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N VAL H 40 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N SER H 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N GLY G 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N THR H 44 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N LYS G 43 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N GLU H 46 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LYS G 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N VAL H 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY G 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N HIS H 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL G 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL H 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLY G 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N THR H 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ALA G 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU H 38 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLY I 41 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL H 40 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N LYS I 43 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER H 42 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N LYS I 45 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N THR H 44 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLY I 47 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N GLU H 46 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N VAL I 49 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N VAL H 48 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N GLY I 51 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N HIS H 50 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ALA I 53 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL H 52 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL I 55 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N THR H 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU I 46 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY J 47 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL I 48 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL J 49 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N HIS I 50 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY J 51 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU J 38 " --> pdb=" O TYR K 39 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY K 41 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL J 40 " --> pdb=" O GLY K 41 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N LYS K 43 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER J 42 " --> pdb=" O LYS K 43 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N LYS K 45 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N THR J 44 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLY K 47 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N GLU J 46 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N VAL K 49 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N VAL J 48 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 10.274A pdb=" N GLY K 51 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N HIS J 50 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ALA K 53 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL J 52 " --> pdb=" O ALA K 53 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL K 55 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR J 54 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU K 38 " --> pdb=" O TYR L 39 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLY L 41 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL K 40 " --> pdb=" O GLY L 41 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N LYS L 43 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER K 42 " --> pdb=" O LYS L 43 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N LYS L 45 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N THR K 44 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLY L 47 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N GLU K 46 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N VAL L 49 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N VAL K 48 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 10.232A pdb=" N GLY L 51 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N HIS K 50 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ALA L 53 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL K 52 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL L 55 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR K 54 " --> pdb=" O VAL L 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 61 through 66 removed outlier: 6.404A pdb=" N GLN G 62 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASN H 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR G 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN K 62 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ASN L 65 " --> pdb=" O GLN K 62 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR K 64 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 69 through 72 removed outlier: 6.204A pdb=" N VAL G 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N GLY H 73 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR G 72 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR H 75 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL H 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N GLY I 73 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR H 72 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR I 75 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL H 74 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N VAL I 77 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA H 76 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N GLN I 79 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N ALA H 78 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL J 70 " --> pdb=" O ALA I 69 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL I 71 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR J 72 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY I 73 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL J 74 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL K 70 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL J 71 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR K 72 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY J 73 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL K 74 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL K 70 " --> pdb=" O VAL L 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 75 through 79 removed outlier: 6.213A pdb=" N THR G 75 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ALA H 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL G 77 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL H 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N GLY I 73 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR H 72 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR I 75 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL H 74 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N VAL I 77 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA H 76 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N GLN I 79 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N ALA H 78 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL J 70 " --> pdb=" O ALA I 69 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL I 71 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR J 72 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY I 73 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL J 74 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL K 70 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL J 71 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR K 72 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY J 73 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL K 74 " --> pdb=" O GLY J 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 86 through 95 removed outlier: 6.552A pdb=" N SER G 87 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ALA H 90 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA G 89 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR H 92 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA G 91 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE H 94 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLY G 93 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N GLY H 86 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N ALA I 89 " --> pdb=" O GLY H 86 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ILE H 88 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N ALA I 91 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N ALA H 90 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N GLY I 93 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR H 92 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N VAL I 95 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE H 94 " --> pdb=" O VAL I 95 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER I 87 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA J 90 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA I 89 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N THR J 92 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA I 91 " --> pdb=" O THR J 92 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE J 94 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLY I 93 " --> pdb=" O PHE J 94 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N GLY J 86 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N ALA K 89 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N ILE J 88 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 9.990A pdb=" N ALA K 91 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N ALA J 90 " --> pdb=" O ALA K 91 " (cutoff:3.500A) removed outlier: 10.201A pdb=" N GLY K 93 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR J 92 " --> pdb=" O GLY K 93 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL K 95 " --> pdb=" O THR J 92 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE J 94 " --> pdb=" O VAL K 95 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE L 94 " --> pdb=" O GLY K 93 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL K 95 " --> pdb=" O PHE L 94 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 618 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: 0.87 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 1044 1.30 - 1.38: 1037 1.38 - 1.45: 362 1.45 - 1.53: 2941 1.53 - 1.60: 580 Bond restraints: 5964 Sorted by residual: bond pdb=" CA GLN G 24 " pdb=" CB GLN G 24 " ideal model delta sigma weight residual 1.524 1.603 -0.080 1.33e-02 5.65e+03 3.59e+01 bond pdb=" CA GLN A 24 " pdb=" CB GLN A 24 " ideal model delta sigma weight residual 1.527 1.489 0.039 2.48e-02 1.63e+03 2.42e+00 bond pdb=" CA GLN F 24 " pdb=" CB GLN F 24 " ideal model delta sigma weight residual 1.527 1.490 0.037 2.48e-02 1.63e+03 2.21e+00 bond pdb=" CA GLN B 24 " pdb=" CB GLN B 24 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.31e-02 5.83e+03 1.46e+00 bond pdb=" CB LYS G 58 " pdb=" CG LYS G 58 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.19e+00 ... (remaining 5959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 7708 1.29 - 2.58: 286 2.58 - 3.87: 27 3.87 - 5.16: 11 5.16 - 6.45: 8 Bond angle restraints: 8040 Sorted by residual: angle pdb=" N GLY C 67 " pdb=" CA GLY C 67 " pdb=" C GLY C 67 " ideal model delta sigma weight residual 115.66 110.42 5.24 1.56e+00 4.11e-01 1.13e+01 angle pdb=" N GLY B 67 " pdb=" CA GLY B 67 " pdb=" C GLY B 67 " ideal model delta sigma weight residual 115.66 110.44 5.22 1.56e+00 4.11e-01 1.12e+01 angle pdb=" N GLY J 67 " pdb=" CA GLY J 67 " pdb=" C GLY J 67 " ideal model delta sigma weight residual 115.66 110.59 5.07 1.56e+00 4.11e-01 1.06e+01 angle pdb=" CA LYS H 23 " pdb=" CB LYS H 23 " pdb=" CG LYS H 23 " ideal model delta sigma weight residual 114.10 120.55 -6.45 2.00e+00 2.50e-01 1.04e+01 angle pdb=" N VAL C 82 " pdb=" CA VAL C 82 " pdb=" C VAL C 82 " ideal model delta sigma weight residual 106.85 110.83 -3.98 1.42e+00 4.96e-01 7.86e+00 ... (remaining 8035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 3027 17.87 - 35.74: 306 35.74 - 53.62: 92 53.62 - 71.49: 36 71.49 - 89.36: 7 Dihedral angle restraints: 3468 sinusoidal: 1140 harmonic: 2328 Sorted by residual: dihedral pdb=" CA ALA D 56 " pdb=" C ALA D 56 " pdb=" N GLU D 57 " pdb=" CA GLU D 57 " ideal model delta harmonic sigma weight residual 180.00 163.00 17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA LYS K 80 " pdb=" C LYS K 80 " pdb=" N THR K 81 " pdb=" CA THR K 81 " ideal model delta harmonic sigma weight residual -180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ALA H 56 " pdb=" C ALA H 56 " pdb=" N GLU H 57 " pdb=" CA GLU H 57 " ideal model delta harmonic sigma weight residual 180.00 163.45 16.55 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 3465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 491 0.029 - 0.058: 330 0.058 - 0.087: 51 0.087 - 0.115: 176 0.115 - 0.144: 8 Chirality restraints: 1056 Sorted by residual: chirality pdb=" CA ILE G 88 " pdb=" N ILE G 88 " pdb=" C ILE G 88 " pdb=" CB ILE G 88 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ILE I 88 " pdb=" N ILE I 88 " pdb=" C ILE I 88 " pdb=" CB ILE I 88 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE H 88 " pdb=" N ILE H 88 " pdb=" C ILE H 88 " pdb=" CB ILE H 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1053 not shown) Planarity restraints: 996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 24 " 0.004 2.00e-02 2.50e+03 7.76e-03 6.02e-01 pdb=" C GLN B 24 " -0.013 2.00e-02 2.50e+03 pdb=" O GLN B 24 " 0.005 2.00e-02 2.50e+03 pdb=" N GLY B 25 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 73 " -0.003 2.00e-02 2.50e+03 6.96e-03 4.84e-01 pdb=" C GLY D 73 " 0.012 2.00e-02 2.50e+03 pdb=" O GLY D 73 " -0.005 2.00e-02 2.50e+03 pdb=" N VAL D 74 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY I 73 " 0.003 2.00e-02 2.50e+03 6.61e-03 4.37e-01 pdb=" C GLY I 73 " -0.011 2.00e-02 2.50e+03 pdb=" O GLY I 73 " 0.004 2.00e-02 2.50e+03 pdb=" N VAL I 74 " 0.004 2.00e-02 2.50e+03 ... (remaining 993 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 629 2.76 - 3.30: 4952 3.30 - 3.83: 9550 3.83 - 4.37: 10688 4.37 - 4.90: 20658 Nonbonded interactions: 46477 Sorted by model distance: nonbonded pdb=" NZ LYS K 23 " pdb=" O GLY K 25 " model vdw 2.228 3.120 nonbonded pdb=" NZ LYS B 80 " pdb=" OE1 GLU B 83 " model vdw 2.254 3.120 nonbonded pdb=" O LYS E 96 " pdb=" NZ LYS E 96 " model vdw 2.278 3.120 nonbonded pdb=" O LYS A 96 " pdb=" NZ LYS A 96 " model vdw 2.295 3.120 nonbonded pdb=" O LYS L 23 " pdb=" NE2 GLN L 24 " model vdw 2.296 3.120 ... (remaining 46472 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.410 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.370 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 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 : 0.006 0.080 5964 Z= 0.273 Angle : 0.615 6.445 8040 Z= 0.351 Chirality : 0.052 0.144 1056 Planarity : 0.002 0.008 996 Dihedral : 17.901 89.360 2004 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.34 % Allowed : 28.91 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.25), residues: 828 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR K 39 PHE 0.006 0.001 PHE I 94 HIS 0.003 0.001 HIS K 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.27 ( 5964) covalent geometry : angle 0.61519 / 0.35 ( 8040) hydrogen bonds : bond 0.16418 / 11.63 ( 163) hydrogen bonds : angle 7.39410 / 5.08 ( 618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.234 Fit side-chains REVERT: E 61 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8692 (mt-10) REVERT: I 23 LYS cc_start: 0.7838 (tmtt) cc_final: 0.7569 (tmtt) outliers start: 2 outliers final: 0 residues processed: 75 average time/residue: 0.1272 time to fit residues: 11.5368 Evaluate side-chains 75 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.054310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.051198 restraints weight = 31337.868| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.07 r_work: 0.3239 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.052 5964 Z= 0.392 Angle : 0.667 5.413 8040 Z= 0.375 Chirality : 0.054 0.154 1056 Planarity : 0.003 0.011 996 Dihedral : 5.944 54.428 867 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.40 % Allowed : 29.08 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.24), residues: 828 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR K 39 PHE 0.009 0.002 PHE H 94 HIS 0.004 0.002 HIS K 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00912 / 0.39 ( 5964) covalent geometry : angle 0.66728 / 0.37 ( 8040) hydrogen bonds : bond 0.03369 / 2.34 ( 163) hydrogen bonds : angle 5.19411 / 3.58 ( 618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.263 Fit side-chains REVERT: H 23 LYS cc_start: 0.8702 (tmtt) cc_final: 0.8463 (tmtt) outliers start: 20 outliers final: 11 residues processed: 83 average time/residue: 0.1432 time to fit residues: 14.3994 Evaluate side-chains 80 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.055346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.052246 restraints weight = 30653.779| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.05 r_work: 0.3272 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5964 Z= 0.270 Angle : 0.556 4.431 8040 Z= 0.314 Chirality : 0.052 0.150 1056 Planarity : 0.002 0.008 996 Dihedral : 5.235 17.098 864 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.23 % Allowed : 31.29 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.24), residues: 828 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR K 39 PHE 0.006 0.002 PHE K 94 HIS 0.002 0.001 HIS K 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.27 ( 5964) covalent geometry : angle 0.55616 / 0.31 ( 8040) hydrogen bonds : bond 0.02747 / 1.88 ( 163) hydrogen bonds : angle 4.63723 / 3.20 ( 618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.213 Fit side-chains REVERT: B 21 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.8997 (tttt) REVERT: E 58 LYS cc_start: 0.9579 (OUTLIER) cc_final: 0.9329 (mtmm) REVERT: H 23 LYS cc_start: 0.8519 (tmtt) cc_final: 0.7697 (tmtt) outliers start: 19 outliers final: 11 residues processed: 87 average time/residue: 0.1239 time to fit residues: 13.0920 Evaluate side-chains 84 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.055650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.052687 restraints weight = 30941.618| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.95 r_work: 0.3303 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5964 Z= 0.216 Angle : 0.505 5.860 8040 Z= 0.285 Chirality : 0.052 0.148 1056 Planarity : 0.002 0.008 996 Dihedral : 5.003 15.867 864 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.42 % Allowed : 31.29 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.25), residues: 828 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR K 39 PHE 0.004 0.001 PHE C 94 HIS 0.002 0.001 HIS K 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 ( 5964) covalent geometry : angle 0.50530 / 0.29 ( 8040) hydrogen bonds : bond 0.02325 / 1.56 ( 163) hydrogen bonds : angle 4.31808 / 2.97 ( 618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.230 Fit side-chains REVERT: A 58 LYS cc_start: 0.9473 (mtmm) cc_final: 0.9171 (mtmm) REVERT: B 21 LYS cc_start: 0.9485 (OUTLIER) cc_final: 0.8991 (tttt) REVERT: E 58 LYS cc_start: 0.9562 (OUTLIER) cc_final: 0.9343 (mtmm) REVERT: G 23 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6727 (tptt) REVERT: H 23 LYS cc_start: 0.8464 (tmtt) cc_final: 0.7795 (tmtt) REVERT: I 23 LYS cc_start: 0.8768 (tmtt) cc_final: 0.8485 (tmtt) outliers start: 26 outliers final: 16 residues processed: 94 average time/residue: 0.1296 time to fit residues: 14.7161 Evaluate side-chains 93 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 96 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 53 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.054606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.051590 restraints weight = 31543.342| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.97 r_work: 0.3256 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.051 5964 Z= 0.389 Angle : 0.646 4.695 8040 Z= 0.361 Chirality : 0.053 0.151 1056 Planarity : 0.002 0.010 996 Dihedral : 5.553 19.047 864 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 5.44 % Allowed : 30.78 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.24), residues: 828 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR K 39 PHE 0.008 0.002 PHE K 94 HIS 0.003 0.002 HIS K 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00906 / 0.39 ( 5964) covalent geometry : angle 0.64649 / 0.36 ( 8040) hydrogen bonds : bond 0.02976 / 2.00 ( 163) hydrogen bonds : angle 4.51986 / 3.11 ( 618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.234 Fit side-chains REVERT: D 23 LYS cc_start: 0.8475 (tmtt) cc_final: 0.8237 (tptt) REVERT: E 58 LYS cc_start: 0.9580 (OUTLIER) cc_final: 0.9289 (mtmm) REVERT: F 23 LYS cc_start: 0.6095 (OUTLIER) cc_final: 0.4658 (pttm) REVERT: G 23 LYS cc_start: 0.6482 (OUTLIER) cc_final: 0.6195 (tptt) REVERT: H 23 LYS cc_start: 0.8615 (tmtt) cc_final: 0.8108 (tmtt) outliers start: 32 outliers final: 21 residues processed: 88 average time/residue: 0.1213 time to fit residues: 12.9012 Evaluate side-chains 89 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 96 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.056302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.053282 restraints weight = 31063.208| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.98 r_work: 0.3322 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5964 Z= 0.148 Angle : 0.463 4.874 8040 Z= 0.260 Chirality : 0.052 0.144 1056 Planarity : 0.002 0.007 996 Dihedral : 4.747 14.840 864 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.91 % Allowed : 32.31 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.25), residues: 828 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR K 39 PHE 0.003 0.001 PHE A 94 HIS 0.001 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 5964) covalent geometry : angle 0.46256 / 0.26 ( 8040) hydrogen bonds : bond 0.01915 / 1.27 ( 163) hydrogen bonds : angle 3.98612 / 2.75 ( 618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.135 Fit side-chains REVERT: E 58 LYS cc_start: 0.9542 (OUTLIER) cc_final: 0.9311 (mtmm) REVERT: F 23 LYS cc_start: 0.5931 (OUTLIER) cc_final: 0.4480 (pttm) REVERT: G 23 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6564 (tptt) REVERT: H 23 LYS cc_start: 0.8484 (tmtt) cc_final: 0.7953 (tmtt) REVERT: I 61 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8136 (mt-10) outliers start: 23 outliers final: 15 residues processed: 94 average time/residue: 0.1165 time to fit residues: 13.4094 Evaluate side-chains 93 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 96 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.054533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.051548 restraints weight = 31622.578| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.00 r_work: 0.3264 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.054 5964 Z= 0.379 Angle : 0.639 5.712 8040 Z= 0.355 Chirality : 0.053 0.148 1056 Planarity : 0.002 0.009 996 Dihedral : 5.459 19.027 864 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 5.78 % Allowed : 30.10 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.24), residues: 828 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR G 39 PHE 0.008 0.002 PHE H 94 HIS 0.003 0.002 HIS K 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00885 / 0.38 ( 5964) covalent geometry : angle 0.63905 / 0.35 ( 8040) hydrogen bonds : bond 0.02865 / 1.92 ( 163) hydrogen bonds : angle 4.37025 / 3.00 ( 618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 0.241 Fit side-chains REVERT: A 58 LYS cc_start: 0.9544 (mtpp) cc_final: 0.9292 (mtmm) REVERT: E 58 LYS cc_start: 0.9552 (OUTLIER) cc_final: 0.9281 (mtmm) REVERT: F 23 LYS cc_start: 0.5748 (OUTLIER) cc_final: 0.4387 (pttm) REVERT: G 23 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6722 (tptt) REVERT: H 23 LYS cc_start: 0.8568 (tmtt) cc_final: 0.7939 (tmtt) REVERT: I 61 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8452 (mt-10) outliers start: 34 outliers final: 25 residues processed: 92 average time/residue: 0.1184 time to fit residues: 13.3779 Evaluate side-chains 90 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 96 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.056088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.053109 restraints weight = 30971.631| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.99 r_work: 0.3321 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5964 Z= 0.163 Angle : 0.479 6.558 8040 Z= 0.265 Chirality : 0.052 0.142 1056 Planarity : 0.002 0.007 996 Dihedral : 4.762 15.051 864 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.91 % Allowed : 31.46 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.25), residues: 828 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR K 39 PHE 0.003 0.001 PHE L 94 HIS 0.002 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 5964) covalent geometry : angle 0.47881 / 0.27 ( 8040) hydrogen bonds : bond 0.01903 / 1.27 ( 163) hydrogen bonds : angle 3.94532 / 2.71 ( 618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.238 Fit side-chains REVERT: A 58 LYS cc_start: 0.9492 (mtpp) cc_final: 0.9281 (mtmm) REVERT: E 58 LYS cc_start: 0.9535 (OUTLIER) cc_final: 0.9301 (mtmm) REVERT: F 23 LYS cc_start: 0.5975 (OUTLIER) cc_final: 0.4561 (pttm) REVERT: G 23 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6649 (tptt) REVERT: H 23 LYS cc_start: 0.8578 (tmtt) cc_final: 0.7968 (tmtt) REVERT: I 61 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8083 (mt-10) REVERT: J 58 LYS cc_start: 0.9229 (mtmm) cc_final: 0.8698 (mtmm) REVERT: K 23 LYS cc_start: 0.8506 (tmtt) cc_final: 0.8151 (ttpt) REVERT: K 58 LYS cc_start: 0.9545 (mtpp) cc_final: 0.9267 (mtmm) outliers start: 23 outliers final: 18 residues processed: 94 average time/residue: 0.1095 time to fit residues: 12.6399 Evaluate side-chains 99 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 96 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 31 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 35 optimal weight: 0.0670 chunk 15 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 overall best weight: 4.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.055637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.052656 restraints weight = 31422.637| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.99 r_work: 0.3305 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5964 Z= 0.212 Angle : 0.515 6.619 8040 Z= 0.285 Chirality : 0.052 0.146 1056 Planarity : 0.002 0.007 996 Dihedral : 4.905 16.110 864 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.25 % Allowed : 31.29 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.25), residues: 828 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR K 39 PHE 0.004 0.001 PHE L 94 HIS 0.002 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 ( 5964) covalent geometry : angle 0.51545 / 0.29 ( 8040) hydrogen bonds : bond 0.02177 / 1.45 ( 163) hydrogen bonds : angle 4.00928 / 2.75 ( 618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.238 Fit side-chains REVERT: A 58 LYS cc_start: 0.9523 (mtpp) cc_final: 0.9312 (mtmm) REVERT: E 58 LYS cc_start: 0.9549 (OUTLIER) cc_final: 0.9311 (mtmm) REVERT: F 23 LYS cc_start: 0.5965 (OUTLIER) cc_final: 0.4534 (pttm) REVERT: H 23 LYS cc_start: 0.8562 (tmtt) cc_final: 0.7872 (tmtt) REVERT: I 61 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8214 (mt-10) outliers start: 25 outliers final: 20 residues processed: 99 average time/residue: 0.1132 time to fit residues: 13.8017 Evaluate side-chains 99 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 96 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 83 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 0.0470 chunk 51 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 overall best weight: 5.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.055498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.052517 restraints weight = 31577.664| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.01 r_work: 0.3303 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5964 Z= 0.223 Angle : 0.523 6.542 8040 Z= 0.290 Chirality : 0.052 0.146 1056 Planarity : 0.002 0.007 996 Dihedral : 4.933 16.548 864 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.42 % Allowed : 31.29 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.25), residues: 828 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR K 39 PHE 0.005 0.001 PHE C 94 HIS 0.002 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 ( 5964) covalent geometry : angle 0.52273 / 0.29 ( 8040) hydrogen bonds : bond 0.02210 / 1.47 ( 163) hydrogen bonds : angle 4.02515 / 2.77 ( 618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.234 Fit side-chains REVERT: A 58 LYS cc_start: 0.9528 (mtpp) cc_final: 0.9320 (mtmm) REVERT: E 58 LYS cc_start: 0.9552 (OUTLIER) cc_final: 0.9313 (mtmm) REVERT: F 23 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.4554 (pttm) REVERT: H 23 LYS cc_start: 0.8583 (tmtt) cc_final: 0.7925 (tmtt) REVERT: I 61 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8241 (mt-10) REVERT: K 58 LYS cc_start: 0.9545 (mtpp) cc_final: 0.9294 (mtmm) outliers start: 26 outliers final: 22 residues processed: 97 average time/residue: 0.1166 time to fit residues: 13.9231 Evaluate side-chains 100 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 96 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 50 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.055563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.052542 restraints weight = 31224.891| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.03 r_work: 0.3297 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5964 Z= 0.238 Angle : 0.536 6.427 8040 Z= 0.298 Chirality : 0.052 0.153 1056 Planarity : 0.002 0.007 996 Dihedral : 4.999 17.392 864 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.42 % Allowed : 31.12 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.25), residues: 828 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR K 39 PHE 0.005 0.001 PHE C 94 HIS 0.002 0.001 HIS K 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 ( 5964) covalent geometry : angle 0.53609 / 0.30 ( 8040) hydrogen bonds : bond 0.02280 / 1.52 ( 163) hydrogen bonds : angle 4.06230 / 2.79 ( 618) =============================================================================== Job complete usr+sys time: 1219.89 seconds wall clock time: 21 minutes 46.36 seconds (1306.36 seconds total)