Starting phenix.real_space_refine on Thu Nov 20 20:51:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5kyh_8298/11_2025/5kyh_8298.cif Found real_map, /net/cci-nas-00/data/ceres_data/5kyh_8298/11_2025/5kyh_8298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5kyh_8298/11_2025/5kyh_8298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5kyh_8298/11_2025/5kyh_8298.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5kyh_8298/11_2025/5kyh_8298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5kyh_8298/11_2025/5kyh_8298.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.951 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 25053 2.51 5 N 6321 2.21 5 O 7413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 342 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38892 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "B" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "C" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "D" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "E" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "F" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "G" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "H" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "I" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "J" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "K" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "L" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "M" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "N" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "O" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "P" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "Q" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "R" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "S" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "T" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "U" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1852 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Time building chain proxies: 8.83, per 1000 atoms: 0.23 Number of scatterers: 38892 At special positions: 0 Unit cell: (143.64, 145.8, 228.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 7413 8.00 N 6321 7.00 C 25053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 271 " distance=2.05 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 271 " distance=2.05 Simple disulfide: pdb=" SG CYS C 104 " - pdb=" SG CYS C 271 " distance=2.05 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 271 " distance=2.05 Simple disulfide: pdb=" SG CYS E 104 " - pdb=" SG CYS E 271 " distance=2.05 Simple disulfide: pdb=" SG CYS F 104 " - pdb=" SG CYS F 271 " distance=2.05 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 271 " distance=2.05 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 271 " distance=2.05 Simple disulfide: pdb=" SG CYS I 104 " - pdb=" SG CYS I 271 " distance=2.05 Simple disulfide: pdb=" SG CYS J 104 " - pdb=" SG CYS J 271 " distance=2.05 Simple disulfide: pdb=" SG CYS K 104 " - pdb=" SG CYS K 271 " distance=2.05 Simple disulfide: pdb=" SG CYS L 104 " - pdb=" SG CYS L 271 " distance=2.05 Simple disulfide: pdb=" SG CYS M 104 " - pdb=" SG CYS M 271 " distance=2.05 Simple disulfide: pdb=" SG CYS N 104 " - pdb=" SG CYS N 271 " distance=2.05 Simple disulfide: pdb=" SG CYS O 104 " - pdb=" SG CYS O 271 " distance=2.05 Simple disulfide: pdb=" SG CYS P 104 " - pdb=" SG CYS P 271 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 104 " - pdb=" SG CYS Q 271 " distance=2.05 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 271 " distance=2.05 Simple disulfide: pdb=" SG CYS S 104 " - pdb=" SG CYS S 271 " distance=2.05 Simple disulfide: pdb=" SG CYS T 104 " - pdb=" SG CYS T 271 " distance=2.05 Simple disulfide: pdb=" SG CYS U 104 " - pdb=" SG CYS U 271 " distance=2.05 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: 3.33 Conformation dependent library (CDL) restraints added in 1.8 seconds 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9576 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 126 sheets defined 16.1% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 1 through 29 removed outlier: 3.632A pdb=" N LEU A 8 " --> pdb=" O VAL A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE A 65 " --> pdb=" O LYS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU B 8 " --> pdb=" O VAL B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE B 65 " --> pdb=" O LYS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU C 8 " --> pdb=" O VAL C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE C 65 " --> pdb=" O LYS C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU D 8 " --> pdb=" O VAL D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE D 65 " --> pdb=" O LYS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU E 8 " --> pdb=" O VAL E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE E 65 " --> pdb=" O LYS E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY E 120 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU F 8 " --> pdb=" O VAL F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE F 65 " --> pdb=" O LYS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY F 120 " --> pdb=" O LYS F 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU G 8 " --> pdb=" O VAL G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE G 65 " --> pdb=" O LYS G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY G 120 " --> pdb=" O LYS G 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU H 8 " --> pdb=" O VAL H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE H 65 " --> pdb=" O LYS H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU I 8 " --> pdb=" O VAL I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE I 65 " --> pdb=" O LYS I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY I 120 " --> pdb=" O LYS I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU J 8 " --> pdb=" O VAL J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE J 65 " --> pdb=" O LYS J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY J 120 " --> pdb=" O LYS J 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU K 8 " --> pdb=" O VAL K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE K 65 " --> pdb=" O LYS K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY K 120 " --> pdb=" O LYS K 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU L 8 " --> pdb=" O VAL L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE L 65 " --> pdb=" O LYS L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY L 120 " --> pdb=" O LYS L 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU M 8 " --> pdb=" O VAL M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE M 65 " --> pdb=" O LYS M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY M 120 " --> pdb=" O LYS M 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU N 8 " --> pdb=" O VAL N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE N 65 " --> pdb=" O LYS N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY N 120 " --> pdb=" O LYS N 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU O 8 " --> pdb=" O VAL O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE O 65 " --> pdb=" O LYS O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY O 120 " --> pdb=" O LYS O 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU P 8 " --> pdb=" O VAL P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE P 65 " --> pdb=" O LYS P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY P 120 " --> pdb=" O LYS P 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 29 removed outlier: 3.633A pdb=" N LEU Q 8 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE Q 65 " --> pdb=" O LYS Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY Q 120 " --> pdb=" O LYS Q 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU R 8 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE R 65 " --> pdb=" O LYS R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY R 120 " --> pdb=" O LYS R 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU S 8 " --> pdb=" O VAL S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE S 65 " --> pdb=" O LYS S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY S 120 " --> pdb=" O LYS S 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU T 8 " --> pdb=" O VAL T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 61 through 65 removed outlier: 3.714A pdb=" N PHE T 65 " --> pdb=" O LYS T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 120 removed outlier: 4.380A pdb=" N GLY T 120 " --> pdb=" O LYS T 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 29 removed outlier: 3.632A pdb=" N LEU U 8 " --> pdb=" O VAL U 4 " (cutoff:3.500A) Processing helix chain 'U' and resid 61 through 65 removed outlier: 3.713A pdb=" N PHE U 65 " --> pdb=" O LYS U 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 115 through 120 removed outlier: 4.379A pdb=" N GLY U 120 " --> pdb=" O LYS U 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU A 44 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN A 77 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 46 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL A 96 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS A 105 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE A 94 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL A 96 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS A 105 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE A 94 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA5, first strand: chain 'A' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR A 127 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL A 252 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER A 243 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 209 through 215 Processing sheet with id=AA7, first strand: chain 'B' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU B 44 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN B 77 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 46 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL B 96 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS B 105 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE B 94 " --> pdb=" O HIS B 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL B 96 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS B 105 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE B 94 " --> pdb=" O HIS B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AB2, first strand: chain 'B' and resid 122 through 123 removed outlier: 5.795A pdb=" N THR B 127 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL B 252 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER B 243 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 209 through 215 Processing sheet with id=AB4, first strand: chain 'C' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU C 44 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN C 77 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C 46 " --> pdb=" O SER C 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL C 96 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS C 105 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE C 94 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL C 96 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS C 105 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE C 94 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 109 through 110 Processing sheet with id=AB8, first strand: chain 'C' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR C 127 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL C 252 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER C 243 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 209 through 215 Processing sheet with id=AC1, first strand: chain 'D' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU D 44 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN D 77 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN D 46 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL D 96 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS D 105 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE D 94 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL D 96 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS D 105 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE D 94 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AC5, first strand: chain 'D' and resid 122 through 123 removed outlier: 5.795A pdb=" N THR D 127 " --> pdb=" O GLY D 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL D 252 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER D 243 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 209 through 215 Processing sheet with id=AC7, first strand: chain 'E' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU E 44 " --> pdb=" O GLN E 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN E 77 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN E 46 " --> pdb=" O SER E 75 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.941A pdb=" N VAL E 96 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS E 105 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE E 94 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.941A pdb=" N VAL E 96 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS E 105 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE E 94 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AD2, first strand: chain 'E' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR E 127 " --> pdb=" O GLY E 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL E 252 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER E 243 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 209 through 215 Processing sheet with id=AD4, first strand: chain 'F' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU F 44 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN F 77 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN F 46 " --> pdb=" O SER F 75 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL F 96 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS F 105 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE F 94 " --> pdb=" O HIS F 105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL F 96 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS F 105 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE F 94 " --> pdb=" O HIS F 105 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 109 through 110 Processing sheet with id=AD8, first strand: chain 'F' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR F 127 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL F 252 " --> pdb=" O SER F 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER F 243 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 209 through 215 Processing sheet with id=AE1, first strand: chain 'G' and resid 43 through 50 removed outlier: 5.891A pdb=" N LEU G 44 " --> pdb=" O GLN G 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN G 77 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN G 46 " --> pdb=" O SER G 75 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL G 96 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS G 105 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE G 94 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL G 96 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS G 105 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE G 94 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 109 through 110 Processing sheet with id=AE5, first strand: chain 'G' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR G 127 " --> pdb=" O GLY G 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL G 252 " --> pdb=" O SER G 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER G 243 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 209 through 215 Processing sheet with id=AE7, first strand: chain 'H' and resid 43 through 50 removed outlier: 5.891A pdb=" N LEU H 44 " --> pdb=" O GLN H 77 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLN H 77 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN H 46 " --> pdb=" O SER H 75 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL H 96 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS H 105 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE H 94 " --> pdb=" O HIS H 105 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL H 96 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS H 105 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE H 94 " --> pdb=" O HIS H 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 109 through 110 Processing sheet with id=AF2, first strand: chain 'H' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR H 127 " --> pdb=" O GLY H 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL H 252 " --> pdb=" O SER H 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER H 243 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 209 through 215 Processing sheet with id=AF4, first strand: chain 'I' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU I 44 " --> pdb=" O GLN I 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN I 77 " --> pdb=" O LEU I 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN I 46 " --> pdb=" O SER I 75 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL I 96 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS I 105 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE I 94 " --> pdb=" O HIS I 105 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL I 96 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS I 105 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE I 94 " --> pdb=" O HIS I 105 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 109 through 110 Processing sheet with id=AF8, first strand: chain 'I' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR I 127 " --> pdb=" O GLY I 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL I 252 " --> pdb=" O SER I 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER I 243 " --> pdb=" O VAL I 252 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 209 through 215 Processing sheet with id=AG1, first strand: chain 'J' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU J 44 " --> pdb=" O GLN J 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN J 77 " --> pdb=" O LEU J 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN J 46 " --> pdb=" O SER J 75 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL J 96 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS J 105 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE J 94 " --> pdb=" O HIS J 105 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL J 96 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS J 105 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE J 94 " --> pdb=" O HIS J 105 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 109 through 110 Processing sheet with id=AG5, first strand: chain 'J' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR J 127 " --> pdb=" O GLY J 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL J 252 " --> pdb=" O SER J 243 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER J 243 " --> pdb=" O VAL J 252 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 209 through 215 Processing sheet with id=AG7, first strand: chain 'K' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU K 44 " --> pdb=" O GLN K 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN K 77 " --> pdb=" O LEU K 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN K 46 " --> pdb=" O SER K 75 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL K 96 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS K 105 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE K 94 " --> pdb=" O HIS K 105 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL K 96 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS K 105 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE K 94 " --> pdb=" O HIS K 105 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 109 through 110 Processing sheet with id=AH2, first strand: chain 'K' and resid 122 through 123 removed outlier: 5.795A pdb=" N THR K 127 " --> pdb=" O GLY K 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL K 252 " --> pdb=" O SER K 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER K 243 " --> pdb=" O VAL K 252 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 209 through 215 Processing sheet with id=AH4, first strand: chain 'L' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU L 44 " --> pdb=" O GLN L 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN L 77 " --> pdb=" O LEU L 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN L 46 " --> pdb=" O SER L 75 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL L 96 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS L 105 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE L 94 " --> pdb=" O HIS L 105 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL L 96 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS L 105 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE L 94 " --> pdb=" O HIS L 105 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 109 through 110 Processing sheet with id=AH8, first strand: chain 'L' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR L 127 " --> pdb=" O GLY L 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL L 252 " --> pdb=" O SER L 243 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER L 243 " --> pdb=" O VAL L 252 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 209 through 215 Processing sheet with id=AI1, first strand: chain 'M' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU M 44 " --> pdb=" O GLN M 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN M 77 " --> pdb=" O LEU M 44 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN M 46 " --> pdb=" O SER M 75 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL M 96 " --> pdb=" O VAL M 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS M 105 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE M 94 " --> pdb=" O HIS M 105 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL M 96 " --> pdb=" O VAL M 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS M 105 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE M 94 " --> pdb=" O HIS M 105 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 109 through 110 Processing sheet with id=AI5, first strand: chain 'M' and resid 122 through 123 removed outlier: 5.797A pdb=" N THR M 127 " --> pdb=" O GLY M 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL M 252 " --> pdb=" O SER M 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER M 243 " --> pdb=" O VAL M 252 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 209 through 215 Processing sheet with id=AI7, first strand: chain 'N' and resid 43 through 50 removed outlier: 5.891A pdb=" N LEU N 44 " --> pdb=" O GLN N 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN N 77 " --> pdb=" O LEU N 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN N 46 " --> pdb=" O SER N 75 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL N 96 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS N 105 " --> pdb=" O ILE N 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE N 94 " --> pdb=" O HIS N 105 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL N 96 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS N 105 " --> pdb=" O ILE N 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE N 94 " --> pdb=" O HIS N 105 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 109 through 110 Processing sheet with id=AJ2, first strand: chain 'N' and resid 122 through 123 removed outlier: 5.797A pdb=" N THR N 127 " --> pdb=" O GLY N 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL N 252 " --> pdb=" O SER N 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER N 243 " --> pdb=" O VAL N 252 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'N' and resid 209 through 215 Processing sheet with id=AJ4, first strand: chain 'O' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU O 44 " --> pdb=" O GLN O 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN O 77 " --> pdb=" O LEU O 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN O 46 " --> pdb=" O SER O 75 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'O' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL O 96 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS O 105 " --> pdb=" O ILE O 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE O 94 " --> pdb=" O HIS O 105 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'O' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL O 96 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS O 105 " --> pdb=" O ILE O 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE O 94 " --> pdb=" O HIS O 105 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'O' and resid 109 through 110 Processing sheet with id=AJ8, first strand: chain 'O' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR O 127 " --> pdb=" O GLY O 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL O 252 " --> pdb=" O SER O 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER O 243 " --> pdb=" O VAL O 252 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'O' and resid 209 through 215 Processing sheet with id=AK1, first strand: chain 'P' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU P 44 " --> pdb=" O GLN P 77 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLN P 77 " --> pdb=" O LEU P 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN P 46 " --> pdb=" O SER P 75 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'P' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL P 96 " --> pdb=" O VAL P 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS P 105 " --> pdb=" O ILE P 94 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE P 94 " --> pdb=" O HIS P 105 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'P' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL P 96 " --> pdb=" O VAL P 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS P 105 " --> pdb=" O ILE P 94 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE P 94 " --> pdb=" O HIS P 105 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'P' and resid 109 through 110 Processing sheet with id=AK5, first strand: chain 'P' and resid 122 through 123 removed outlier: 5.795A pdb=" N THR P 127 " --> pdb=" O GLY P 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL P 252 " --> pdb=" O SER P 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER P 243 " --> pdb=" O VAL P 252 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'P' and resid 209 through 215 Processing sheet with id=AK7, first strand: chain 'Q' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU Q 44 " --> pdb=" O GLN Q 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN Q 77 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN Q 46 " --> pdb=" O SER Q 75 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'Q' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL Q 96 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS Q 105 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE Q 94 " --> pdb=" O HIS Q 105 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'Q' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL Q 96 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS Q 105 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE Q 94 " --> pdb=" O HIS Q 105 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'Q' and resid 109 through 110 Processing sheet with id=AL2, first strand: chain 'Q' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR Q 127 " --> pdb=" O GLY Q 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL Q 252 " --> pdb=" O SER Q 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER Q 243 " --> pdb=" O VAL Q 252 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'Q' and resid 209 through 215 Processing sheet with id=AL4, first strand: chain 'R' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU R 44 " --> pdb=" O GLN R 77 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLN R 77 " --> pdb=" O LEU R 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN R 46 " --> pdb=" O SER R 75 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'R' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL R 96 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS R 105 " --> pdb=" O ILE R 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE R 94 " --> pdb=" O HIS R 105 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'R' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL R 96 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS R 105 " --> pdb=" O ILE R 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE R 94 " --> pdb=" O HIS R 105 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'R' and resid 109 through 110 Processing sheet with id=AL8, first strand: chain 'R' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR R 127 " --> pdb=" O GLY R 251 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL R 252 " --> pdb=" O SER R 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER R 243 " --> pdb=" O VAL R 252 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'R' and resid 209 through 215 Processing sheet with id=AM1, first strand: chain 'S' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU S 44 " --> pdb=" O GLN S 77 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLN S 77 " --> pdb=" O LEU S 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN S 46 " --> pdb=" O SER S 75 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'S' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL S 96 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS S 105 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE S 94 " --> pdb=" O HIS S 105 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'S' and resid 101 through 106 removed outlier: 6.939A pdb=" N VAL S 96 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS S 105 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE S 94 " --> pdb=" O HIS S 105 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'S' and resid 109 through 110 Processing sheet with id=AM5, first strand: chain 'S' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR S 127 " --> pdb=" O GLY S 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL S 252 " --> pdb=" O SER S 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER S 243 " --> pdb=" O VAL S 252 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'S' and resid 209 through 215 Processing sheet with id=AM7, first strand: chain 'T' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU T 44 " --> pdb=" O GLN T 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN T 77 " --> pdb=" O LEU T 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN T 46 " --> pdb=" O SER T 75 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'T' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL T 96 " --> pdb=" O VAL T 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS T 105 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE T 94 " --> pdb=" O HIS T 105 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'T' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL T 96 " --> pdb=" O VAL T 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS T 105 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE T 94 " --> pdb=" O HIS T 105 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'T' and resid 109 through 110 Processing sheet with id=AN2, first strand: chain 'T' and resid 122 through 123 removed outlier: 5.796A pdb=" N THR T 127 " --> pdb=" O GLY T 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL T 252 " --> pdb=" O SER T 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER T 243 " --> pdb=" O VAL T 252 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'T' and resid 209 through 215 Processing sheet with id=AN4, first strand: chain 'U' and resid 43 through 50 removed outlier: 5.890A pdb=" N LEU U 44 " --> pdb=" O GLN U 77 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN U 77 " --> pdb=" O LEU U 44 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN U 46 " --> pdb=" O SER U 75 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'U' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL U 96 " --> pdb=" O VAL U 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS U 105 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE U 94 " --> pdb=" O HIS U 105 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'U' and resid 101 through 106 removed outlier: 6.940A pdb=" N VAL U 96 " --> pdb=" O VAL U 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS U 105 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE U 94 " --> pdb=" O HIS U 105 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'U' and resid 109 through 110 Processing sheet with id=AN8, first strand: chain 'U' and resid 122 through 123 removed outlier: 5.795A pdb=" N THR U 127 " --> pdb=" O GLY U 251 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL U 252 " --> pdb=" O SER U 243 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER U 243 " --> pdb=" O VAL U 252 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'U' and resid 209 through 215 1639 hydrogen bonds defined for protein. 4224 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: 10.77 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10622 1.33 - 1.46: 9341 1.46 - 1.59: 19664 1.59 - 1.71: 42 1.71 - 1.84: 168 Bond restraints: 39837 Sorted by residual: bond pdb=" CG GLU F 222 " pdb=" CD GLU F 222 " ideal model delta sigma weight residual 1.516 1.630 -0.114 2.50e-02 1.60e+03 2.10e+01 bond pdb=" CG GLU S 222 " pdb=" CD GLU S 222 " ideal model delta sigma weight residual 1.516 1.630 -0.114 2.50e-02 1.60e+03 2.09e+01 bond pdb=" CG GLU H 222 " pdb=" CD GLU H 222 " ideal model delta sigma weight residual 1.516 1.630 -0.114 2.50e-02 1.60e+03 2.09e+01 bond pdb=" CG GLU U 222 " pdb=" CD GLU U 222 " ideal model delta sigma weight residual 1.516 1.630 -0.114 2.50e-02 1.60e+03 2.09e+01 bond pdb=" CG GLU L 222 " pdb=" CD GLU L 222 " ideal model delta sigma weight residual 1.516 1.630 -0.114 2.50e-02 1.60e+03 2.08e+01 ... (remaining 39832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 49823 2.90 - 5.80: 3891 5.80 - 8.70: 718 8.70 - 11.60: 189 11.60 - 14.50: 42 Bond angle restraints: 54663 Sorted by residual: angle pdb=" O PRO T 78 " pdb=" C PRO T 78 " pdb=" N PRO T 79 " ideal model delta sigma weight residual 121.15 124.41 -3.26 4.70e-01 4.53e+00 4.82e+01 angle pdb=" O PRO D 78 " pdb=" C PRO D 78 " pdb=" N PRO D 79 " ideal model delta sigma weight residual 121.15 124.41 -3.26 4.70e-01 4.53e+00 4.81e+01 angle pdb=" O PRO K 78 " pdb=" C PRO K 78 " pdb=" N PRO K 79 " ideal model delta sigma weight residual 121.15 124.41 -3.26 4.70e-01 4.53e+00 4.81e+01 angle pdb=" O PRO C 78 " pdb=" C PRO C 78 " pdb=" N PRO C 79 " ideal model delta sigma weight residual 121.15 124.41 -3.26 4.70e-01 4.53e+00 4.80e+01 angle pdb=" O PRO N 78 " pdb=" C PRO N 78 " pdb=" N PRO N 79 " ideal model delta sigma weight residual 121.15 124.40 -3.25 4.70e-01 4.53e+00 4.79e+01 ... (remaining 54658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 21467 16.00 - 32.01: 1108 32.01 - 48.01: 399 48.01 - 64.02: 84 64.02 - 80.02: 21 Dihedral angle restraints: 23079 sinusoidal: 8295 harmonic: 14784 Sorted by residual: dihedral pdb=" CB CYS A 104 " pdb=" SG CYS A 104 " pdb=" SG CYS A 271 " pdb=" CB CYS A 271 " ideal model delta sinusoidal sigma weight residual -86.00 -145.17 59.17 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS L 104 " pdb=" SG CYS L 104 " pdb=" SG CYS L 271 " pdb=" CB CYS L 271 " ideal model delta sinusoidal sigma weight residual -86.00 -145.16 59.16 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS N 104 " pdb=" SG CYS N 104 " pdb=" SG CYS N 271 " pdb=" CB CYS N 271 " ideal model delta sinusoidal sigma weight residual -86.00 -145.15 59.15 1 1.00e+01 1.00e-02 4.68e+01 ... (remaining 23076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3487 0.076 - 0.151: 1917 0.151 - 0.227: 866 0.227 - 0.303: 261 0.303 - 0.379: 21 Chirality restraints: 6552 Sorted by residual: chirality pdb=" CA TRP K 270 " pdb=" N TRP K 270 " pdb=" C TRP K 270 " pdb=" CB TRP K 270 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA TRP R 270 " pdb=" N TRP R 270 " pdb=" C TRP R 270 " pdb=" CB TRP R 270 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA TRP C 270 " pdb=" N TRP C 270 " pdb=" C TRP C 270 " pdb=" CB TRP C 270 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 6549 not shown) Planarity restraints: 6909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 215 " -0.110 2.00e-02 2.50e+03 5.80e-02 6.72e+01 pdb=" CG TYR E 215 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR E 215 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR E 215 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR E 215 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR E 215 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR E 215 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 215 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR U 215 " -0.110 2.00e-02 2.50e+03 5.80e-02 6.72e+01 pdb=" CG TYR U 215 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR U 215 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR U 215 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR U 215 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR U 215 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR U 215 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR U 215 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 215 " -0.110 2.00e-02 2.50e+03 5.80e-02 6.72e+01 pdb=" CG TYR B 215 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 215 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR B 215 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR B 215 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR B 215 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR B 215 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 215 " -0.083 2.00e-02 2.50e+03 ... (remaining 6906 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 280 2.33 - 2.98: 20739 2.98 - 3.62: 51009 3.62 - 4.26: 80703 4.26 - 4.90: 133906 Nonbonded interactions: 286637 Sorted by model distance: nonbonded pdb=" OH TYR K 117 " pdb=" CD1 ILE R 302 " model vdw 1.692 3.460 nonbonded pdb=" OH TYR H 117 " pdb=" CD1 ILE O 302 " model vdw 1.711 3.460 nonbonded pdb=" OH TYR G 117 " pdb=" CD1 ILE N 302 " model vdw 1.725 3.460 nonbonded pdb=" OH TYR E 117 " pdb=" CD1 ILE L 302 " model vdw 1.729 3.460 nonbonded pdb=" OH TYR I 117 " pdb=" CD1 ILE P 302 " model vdw 1.732 3.460 ... (remaining 286632 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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 group one per residue 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: 0.920 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: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 39.240 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.014 0.114 39858 Z= 0.821 Angle : 1.824 14.502 54705 Z= 1.176 Chirality : 0.110 0.379 6552 Planarity : 0.012 0.081 6909 Dihedral : 11.444 80.024 13440 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 34.37 Ramachandran Plot: Outliers : 1.26 % Allowed : 2.52 % Favored : 96.22 % Rotamer: Outliers : 3.90 % Allowed : 5.85 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.68 (0.10), residues: 4998 helix: -0.10 (0.17), residues: 714 sheet: 0.66 (0.14), residues: 1155 loop : -0.99 (0.09), residues: 3129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.005 ARG L 67 TYR 0.110 0.016 TYR U 215 PHE 0.060 0.012 PHE Q 133 TRP 0.068 0.019 TRP U 294 HIS 0.006 0.002 HIS J 118 Details of bonding type rmsd covalent geometry : bond 0.01381 (39837) covalent geometry : angle 1.82360 (54663) SS BOND : bond 0.02037 ( 21) SS BOND : angle 2.32427 ( 42) hydrogen bonds : bond 0.30760 ( 1576) hydrogen bonds : angle 7.96759 ( 4224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1804 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 1636 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8630 (m-30) cc_final: 0.8351 (t70) REVERT: A 107 ASP cc_start: 0.7472 (p0) cc_final: 0.6915 (t0) REVERT: A 115 ASP cc_start: 0.8693 (t0) cc_final: 0.8268 (t0) REVERT: A 200 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8566 (mm110) REVERT: A 232 ILE cc_start: 0.9227 (mt) cc_final: 0.8535 (mt) REVERT: A 233 LYS cc_start: 0.8483 (mttt) cc_final: 0.7923 (mmmm) REVERT: A 239 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8605 (p0) REVERT: A 282 VAL cc_start: 0.9555 (m) cc_final: 0.9311 (m) REVERT: A 286 MET cc_start: 0.9188 (mtt) cc_final: 0.8877 (mtp) REVERT: B 63 ASP cc_start: 0.8799 (m-30) cc_final: 0.8406 (t70) REVERT: B 89 ILE cc_start: 0.8330 (mm) cc_final: 0.8118 (mt) REVERT: B 107 ASP cc_start: 0.7423 (p0) cc_final: 0.6744 (t0) REVERT: B 114 ASP cc_start: 0.8673 (t0) cc_final: 0.8134 (m-30) REVERT: B 115 ASP cc_start: 0.8467 (t0) cc_final: 0.8053 (t0) REVERT: B 198 ASP cc_start: 0.8727 (t0) cc_final: 0.8435 (t0) REVERT: B 232 ILE cc_start: 0.9230 (mt) cc_final: 0.8481 (mm) REVERT: B 233 LYS cc_start: 0.8399 (mttt) cc_final: 0.7937 (mmmm) REVERT: B 239 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8561 (p0) REVERT: B 267 VAL cc_start: 0.9245 (t) cc_final: 0.8985 (m) REVERT: B 279 MET cc_start: 0.8829 (mtt) cc_final: 0.8171 (mtt) REVERT: B 282 VAL cc_start: 0.9551 (m) cc_final: 0.9265 (m) REVERT: B 286 MET cc_start: 0.9135 (mtt) cc_final: 0.8867 (mtm) REVERT: C 107 ASP cc_start: 0.7391 (p0) cc_final: 0.6776 (t0) REVERT: C 114 ASP cc_start: 0.8557 (t0) cc_final: 0.8148 (m-30) REVERT: C 115 ASP cc_start: 0.8581 (t0) cc_final: 0.7800 (t0) REVERT: C 198 ASP cc_start: 0.8419 (t0) cc_final: 0.8109 (t0) REVERT: C 201 TYR cc_start: 0.8895 (m-80) cc_final: 0.8403 (m-80) REVERT: C 233 LYS cc_start: 0.8498 (mttt) cc_final: 0.8205 (mmmm) REVERT: C 249 ASN cc_start: 0.9323 (m-40) cc_final: 0.8968 (m110) REVERT: C 274 VAL cc_start: 0.9269 (t) cc_final: 0.9031 (p) REVERT: C 279 MET cc_start: 0.8528 (mtt) cc_final: 0.7824 (mtt) REVERT: C 282 VAL cc_start: 0.9446 (m) cc_final: 0.9146 (m) REVERT: D 62 LYS cc_start: 0.8540 (pttp) cc_final: 0.7906 (mttp) REVERT: D 107 ASP cc_start: 0.7406 (p0) cc_final: 0.7154 (t0) REVERT: D 114 ASP cc_start: 0.8881 (t0) cc_final: 0.8656 (t0) REVERT: D 115 ASP cc_start: 0.8563 (t0) cc_final: 0.8340 (t0) REVERT: D 233 LYS cc_start: 0.8441 (mttt) cc_final: 0.8067 (mmmm) REVERT: D 239 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8547 (p0) REVERT: D 282 VAL cc_start: 0.9439 (m) cc_final: 0.9145 (m) REVERT: E 75 SER cc_start: 0.8854 (t) cc_final: 0.8639 (t) REVERT: E 91 ILE cc_start: 0.9327 (mt) cc_final: 0.9088 (mt) REVERT: E 114 ASP cc_start: 0.8579 (t0) cc_final: 0.8059 (m-30) REVERT: E 115 ASP cc_start: 0.8377 (t0) cc_final: 0.8076 (t70) REVERT: E 233 LYS cc_start: 0.8086 (mttt) cc_final: 0.7495 (mmmm) REVERT: E 239 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8380 (p0) REVERT: E 249 ASN cc_start: 0.9239 (m-40) cc_final: 0.9014 (m-40) REVERT: E 279 MET cc_start: 0.8474 (mtt) cc_final: 0.8214 (mtt) REVERT: E 282 VAL cc_start: 0.9486 (m) cc_final: 0.9244 (m) REVERT: E 286 MET cc_start: 0.9183 (mtt) cc_final: 0.8851 (mtm) REVERT: F 83 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6742 (mt) REVERT: F 107 ASP cc_start: 0.7688 (p0) cc_final: 0.7049 (t0) REVERT: F 114 ASP cc_start: 0.8601 (t0) cc_final: 0.8080 (m-30) REVERT: F 232 ILE cc_start: 0.9074 (mt) cc_final: 0.8665 (mt) REVERT: F 233 LYS cc_start: 0.8366 (mttt) cc_final: 0.7933 (mmmm) REVERT: F 239 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8368 (p0) REVERT: F 279 MET cc_start: 0.8406 (mtt) cc_final: 0.7972 (mtt) REVERT: F 286 MET cc_start: 0.9152 (mtt) cc_final: 0.8894 (mtm) REVERT: G 8 LEU cc_start: 0.9032 (tp) cc_final: 0.8719 (tt) REVERT: G 62 LYS cc_start: 0.8398 (pttp) cc_final: 0.7973 (mttt) REVERT: G 107 ASP cc_start: 0.7722 (p0) cc_final: 0.7296 (t0) REVERT: G 111 MET cc_start: 0.8265 (ttp) cc_final: 0.8047 (ttt) REVERT: G 114 ASP cc_start: 0.8745 (t0) cc_final: 0.8491 (t0) REVERT: G 115 ASP cc_start: 0.8404 (t0) cc_final: 0.8073 (t0) REVERT: G 233 LYS cc_start: 0.8433 (mttt) cc_final: 0.7881 (mmmm) REVERT: G 282 VAL cc_start: 0.9493 (m) cc_final: 0.9184 (m) REVERT: H 8 LEU cc_start: 0.9071 (tp) cc_final: 0.8812 (tp) REVERT: H 91 ILE cc_start: 0.9389 (mt) cc_final: 0.9165 (mt) REVERT: H 107 ASP cc_start: 0.7397 (p0) cc_final: 0.7000 (t0) REVERT: H 114 ASP cc_start: 0.8671 (t0) cc_final: 0.8009 (m-30) REVERT: H 115 ASP cc_start: 0.8502 (t0) cc_final: 0.7946 (t0) REVERT: H 198 ASP cc_start: 0.8482 (t0) cc_final: 0.8239 (t0) REVERT: H 201 TYR cc_start: 0.8936 (m-80) cc_final: 0.8270 (m-80) REVERT: H 206 ILE cc_start: 0.9309 (mm) cc_final: 0.9060 (mm) REVERT: H 232 ILE cc_start: 0.9052 (mt) cc_final: 0.8770 (mt) REVERT: H 233 LYS cc_start: 0.8305 (mttt) cc_final: 0.7958 (mmmm) REVERT: H 239 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8650 (p0) REVERT: H 267 VAL cc_start: 0.9206 (t) cc_final: 0.9005 (m) REVERT: H 274 VAL cc_start: 0.9330 (t) cc_final: 0.9089 (p) REVERT: H 279 MET cc_start: 0.8496 (mtt) cc_final: 0.7539 (mtt) REVERT: H 282 VAL cc_start: 0.9345 (m) cc_final: 0.8997 (m) REVERT: I 8 LEU cc_start: 0.9084 (tp) cc_final: 0.8824 (tp) REVERT: I 62 LYS cc_start: 0.8197 (pttp) cc_final: 0.7678 (mttt) REVERT: I 63 ASP cc_start: 0.8624 (m-30) cc_final: 0.8420 (t0) REVERT: I 107 ASP cc_start: 0.7515 (p0) cc_final: 0.6956 (t0) REVERT: I 114 ASP cc_start: 0.8475 (t0) cc_final: 0.8238 (t0) REVERT: I 115 ASP cc_start: 0.8833 (t0) cc_final: 0.8469 (t70) REVERT: I 226 ARG cc_start: 0.8907 (ttm-80) cc_final: 0.8635 (tpp80) REVERT: I 232 ILE cc_start: 0.9061 (mt) cc_final: 0.8760 (mt) REVERT: I 233 LYS cc_start: 0.8138 (mttt) cc_final: 0.7698 (mmmm) REVERT: I 267 VAL cc_start: 0.9228 (t) cc_final: 0.8958 (m) REVERT: I 282 VAL cc_start: 0.9514 (m) cc_final: 0.9212 (m) REVERT: J 8 LEU cc_start: 0.9074 (tp) cc_final: 0.8802 (tp) REVERT: J 62 LYS cc_start: 0.8188 (pttp) cc_final: 0.7914 (mttp) REVERT: J 63 ASP cc_start: 0.8686 (m-30) cc_final: 0.8345 (t70) REVERT: J 107 ASP cc_start: 0.7606 (p0) cc_final: 0.7202 (t0) REVERT: J 206 ILE cc_start: 0.9437 (mm) cc_final: 0.9211 (mt) REVERT: J 232 ILE cc_start: 0.9126 (mt) cc_final: 0.8772 (mt) REVERT: J 233 LYS cc_start: 0.8338 (mttt) cc_final: 0.7706 (mmmm) REVERT: J 239 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8672 (p0) REVERT: J 267 VAL cc_start: 0.8955 (t) cc_final: 0.8699 (m) REVERT: J 279 MET cc_start: 0.8328 (mtt) cc_final: 0.7977 (mtt) REVERT: J 282 VAL cc_start: 0.9519 (m) cc_final: 0.9284 (m) REVERT: K 8 LEU cc_start: 0.9048 (tp) cc_final: 0.8822 (tp) REVERT: K 62 LYS cc_start: 0.8305 (pttp) cc_final: 0.7739 (mttt) REVERT: K 63 ASP cc_start: 0.8518 (m-30) cc_final: 0.8120 (t70) REVERT: K 107 ASP cc_start: 0.7576 (p0) cc_final: 0.7047 (t0) REVERT: K 233 LYS cc_start: 0.8338 (mttt) cc_final: 0.7876 (mmmm) REVERT: K 267 VAL cc_start: 0.9346 (t) cc_final: 0.8990 (m) REVERT: K 279 MET cc_start: 0.8352 (mtt) cc_final: 0.7793 (mtt) REVERT: K 282 VAL cc_start: 0.9374 (m) cc_final: 0.9124 (m) REVERT: L 62 LYS cc_start: 0.8733 (pttp) cc_final: 0.8225 (mttp) REVERT: L 69 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8517 (mmmt) REVERT: L 107 ASP cc_start: 0.7513 (p0) cc_final: 0.6836 (t0) REVERT: L 111 MET cc_start: 0.8300 (ttp) cc_final: 0.8045 (ttm) REVERT: L 114 ASP cc_start: 0.8595 (t0) cc_final: 0.8025 (m-30) REVERT: L 115 ASP cc_start: 0.8614 (t0) cc_final: 0.8300 (t70) REVERT: L 206 ILE cc_start: 0.9467 (mm) cc_final: 0.9259 (mt) REVERT: L 232 ILE cc_start: 0.9234 (mt) cc_final: 0.8570 (mt) REVERT: L 233 LYS cc_start: 0.8305 (mttt) cc_final: 0.7705 (mmmm) REVERT: L 279 MET cc_start: 0.8559 (mtt) cc_final: 0.8274 (mtt) REVERT: L 282 VAL cc_start: 0.9558 (m) cc_final: 0.9354 (m) REVERT: M 62 LYS cc_start: 0.8482 (pttp) cc_final: 0.8039 (mttp) REVERT: M 107 ASP cc_start: 0.7634 (p0) cc_final: 0.6971 (t0) REVERT: M 111 MET cc_start: 0.8348 (ttp) cc_final: 0.8066 (ttt) REVERT: M 206 ILE cc_start: 0.9469 (mm) cc_final: 0.9250 (mt) REVERT: M 232 ILE cc_start: 0.9247 (mt) cc_final: 0.8899 (mt) REVERT: M 233 LYS cc_start: 0.8332 (mttt) cc_final: 0.7723 (mmmm) REVERT: M 267 VAL cc_start: 0.9203 (t) cc_final: 0.8811 (m) REVERT: M 274 VAL cc_start: 0.9219 (t) cc_final: 0.9002 (p) REVERT: M 279 MET cc_start: 0.8500 (mtt) cc_final: 0.7696 (mtt) REVERT: N 62 LYS cc_start: 0.8477 (pttp) cc_final: 0.8161 (mttp) REVERT: N 74 LEU cc_start: 0.9619 (mt) cc_final: 0.9419 (mt) REVERT: N 107 ASP cc_start: 0.7641 (p0) cc_final: 0.7105 (t0) REVERT: N 201 TYR cc_start: 0.8813 (m-80) cc_final: 0.8607 (m-80) REVERT: N 232 ILE cc_start: 0.9319 (mt) cc_final: 0.9013 (mp) REVERT: N 233 LYS cc_start: 0.8307 (mttt) cc_final: 0.7626 (mmmm) REVERT: N 262 GLN cc_start: 0.8712 (pt0) cc_final: 0.8482 (pm20) REVERT: N 267 VAL cc_start: 0.9310 (t) cc_final: 0.9036 (m) REVERT: N 282 VAL cc_start: 0.9456 (m) cc_final: 0.9138 (m) REVERT: O 62 LYS cc_start: 0.8524 (pttp) cc_final: 0.8018 (mttp) REVERT: O 77 GLN cc_start: 0.8818 (tp40) cc_final: 0.8096 (tm-30) REVERT: O 107 ASP cc_start: 0.7475 (p0) cc_final: 0.6815 (t0) REVERT: O 116 LYS cc_start: 0.8713 (mttt) cc_final: 0.8314 (pttt) REVERT: O 132 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8326 (m) REVERT: O 232 ILE cc_start: 0.9269 (mt) cc_final: 0.9064 (mt) REVERT: O 233 LYS cc_start: 0.8505 (mttt) cc_final: 0.8294 (mmmm) REVERT: O 279 MET cc_start: 0.8462 (mtt) cc_final: 0.8205 (mtt) REVERT: O 282 VAL cc_start: 0.9439 (m) cc_final: 0.9196 (m) REVERT: P 29 SER cc_start: 0.9289 (t) cc_final: 0.9080 (p) REVERT: P 62 LYS cc_start: 0.8378 (pttp) cc_final: 0.8023 (mttp) REVERT: P 63 ASP cc_start: 0.8584 (m-30) cc_final: 0.8290 (t70) REVERT: P 75 SER cc_start: 0.8861 (t) cc_final: 0.8541 (t) REVERT: P 107 ASP cc_start: 0.7612 (p0) cc_final: 0.7167 (t0) REVERT: P 114 ASP cc_start: 0.8599 (t0) cc_final: 0.8362 (t0) REVERT: P 116 LYS cc_start: 0.8591 (mttt) cc_final: 0.8238 (pttt) REVERT: P 232 ILE cc_start: 0.9181 (mt) cc_final: 0.8844 (mt) REVERT: P 233 LYS cc_start: 0.8408 (mttt) cc_final: 0.7911 (mmmm) REVERT: P 267 VAL cc_start: 0.9203 (t) cc_final: 0.8925 (m) REVERT: P 279 MET cc_start: 0.8378 (mtt) cc_final: 0.7564 (mtt) REVERT: P 290 ASP cc_start: 0.8554 (p0) cc_final: 0.8290 (p0) REVERT: Q 8 LEU cc_start: 0.9046 (tp) cc_final: 0.8791 (tp) REVERT: Q 107 ASP cc_start: 0.7388 (p0) cc_final: 0.7110 (t0) REVERT: Q 116 LYS cc_start: 0.8677 (mttt) cc_final: 0.8237 (pttt) REVERT: Q 232 ILE cc_start: 0.9131 (mt) cc_final: 0.8632 (mt) REVERT: Q 233 LYS cc_start: 0.8483 (mttt) cc_final: 0.8117 (mmmm) REVERT: Q 267 VAL cc_start: 0.9420 (t) cc_final: 0.9217 (m) REVERT: Q 279 MET cc_start: 0.8375 (mtt) cc_final: 0.7747 (mtt) REVERT: Q 282 VAL cc_start: 0.9523 (m) cc_final: 0.9271 (m) REVERT: R 62 LYS cc_start: 0.8643 (pttp) cc_final: 0.7977 (mttp) REVERT: R 107 ASP cc_start: 0.7362 (p0) cc_final: 0.6664 (t0) REVERT: R 232 ILE cc_start: 0.9306 (mt) cc_final: 0.8749 (mt) REVERT: R 233 LYS cc_start: 0.8451 (mttt) cc_final: 0.8054 (mmmm) REVERT: R 239 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8615 (p0) REVERT: R 267 VAL cc_start: 0.9294 (t) cc_final: 0.9081 (m) REVERT: S 55 ASN cc_start: 0.8722 (m-40) cc_final: 0.7835 (p0) REVERT: S 62 LYS cc_start: 0.8229 (pttp) cc_final: 0.7678 (mttp) REVERT: S 77 GLN cc_start: 0.8706 (tp40) cc_final: 0.8307 (tm-30) REVERT: S 91 ILE cc_start: 0.9351 (mt) cc_final: 0.9096 (mt) REVERT: S 111 MET cc_start: 0.8206 (ttp) cc_final: 0.7955 (ttm) REVERT: S 115 ASP cc_start: 0.8628 (t0) cc_final: 0.8371 (t70) REVERT: S 116 LYS cc_start: 0.8598 (mttt) cc_final: 0.8374 (pttt) REVERT: S 121 GLN cc_start: 0.7350 (mt0) cc_final: 0.7130 (mt0) REVERT: S 232 ILE cc_start: 0.9230 (mt) cc_final: 0.8917 (mt) REVERT: S 253 PRO cc_start: 0.9425 (Cg_exo) cc_final: 0.8841 (Cg_endo) REVERT: S 274 VAL cc_start: 0.9412 (t) cc_final: 0.9172 (p) REVERT: S 275 ASN cc_start: 0.8715 (t0) cc_final: 0.8071 (t0) REVERT: S 279 MET cc_start: 0.8436 (mtt) cc_final: 0.7659 (mtt) REVERT: S 286 MET cc_start: 0.9170 (mtt) cc_final: 0.8891 (mtm) REVERT: T 54 THR cc_start: 0.8473 (p) cc_final: 0.8260 (p) REVERT: T 55 ASN cc_start: 0.8491 (m-40) cc_final: 0.7849 (p0) REVERT: T 62 LYS cc_start: 0.8559 (pttp) cc_final: 0.7883 (mttp) REVERT: T 77 GLN cc_start: 0.8594 (tp40) cc_final: 0.7894 (tm-30) REVERT: T 116 LYS cc_start: 0.8610 (mttt) cc_final: 0.8242 (pttt) REVERT: T 117 TYR cc_start: 0.8774 (t80) cc_final: 0.8531 (t80) REVERT: T 232 ILE cc_start: 0.9257 (mt) cc_final: 0.8574 (mt) REVERT: T 233 LYS cc_start: 0.8393 (mttt) cc_final: 0.8149 (mmmm) REVERT: T 248 ASN cc_start: 0.8730 (m-40) cc_final: 0.8453 (m110) REVERT: T 275 ASN cc_start: 0.8838 (t0) cc_final: 0.8167 (t0) REVERT: T 279 MET cc_start: 0.8678 (mtt) cc_final: 0.8075 (mtt) REVERT: T 282 VAL cc_start: 0.9505 (m) cc_final: 0.9305 (m) REVERT: T 300 LEU cc_start: 0.9108 (tt) cc_final: 0.8894 (tt) REVERT: U 55 ASN cc_start: 0.8208 (m-40) cc_final: 0.7947 (p0) REVERT: U 115 ASP cc_start: 0.8566 (t0) cc_final: 0.8301 (t70) REVERT: U 116 LYS cc_start: 0.8751 (mttt) cc_final: 0.8305 (pttt) REVERT: U 214 ASN cc_start: 0.8767 (t0) cc_final: 0.8371 (t0) REVERT: U 224 ASN cc_start: 0.8465 (t0) cc_final: 0.8169 (t0) REVERT: U 232 ILE cc_start: 0.9226 (mt) cc_final: 0.8765 (mp) REVERT: U 287 VAL cc_start: 0.9229 (t) cc_final: 0.8843 (p) REVERT: U 300 LEU cc_start: 0.8964 (tt) cc_final: 0.8759 (tt) outliers start: 168 outliers final: 86 residues processed: 1733 average time/residue: 0.2267 time to fit residues: 653.9410 Evaluate side-chains 1124 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1028 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 239 ASN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 239 ASN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 239 ASN Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 240 THR Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 239 ASN Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain O residue 48 THR Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 240 THR Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 240 THR Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain Q residue 94 ILE Chi-restraints excluded: chain Q residue 239 ASN Chi-restraints excluded: chain Q residue 240 THR Chi-restraints excluded: chain Q residue 257 VAL Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 239 ASN Chi-restraints excluded: chain R residue 240 THR Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 239 ASN Chi-restraints excluded: chain S residue 240 THR Chi-restraints excluded: chain S residue 257 VAL Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 240 THR Chi-restraints excluded: chain T residue 257 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 240 THR Chi-restraints excluded: chain U residue 257 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 40.0000 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 494 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 77 GLN B 46 GLN B 77 GLN B 121 GLN B 264 ASN C 46 GLN C 77 GLN C 118 HIS C 264 ASN D 46 GLN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN G 118 HIS G 247 GLN H 46 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 GLN ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 ASN J 247 GLN J 262 GLN ** J 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN K 99 GLN K 118 HIS L 118 HIS L 239 ASN M 46 GLN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN ** M 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 HIS N 219 ASN N 247 GLN ** N 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 ASN O 239 ASN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 262 GLN ** P 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 46 GLN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 46 GLN R 219 ASN R 264 ASN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 277 ASN T 46 GLN ** T 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 219 ASN ** T 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN U 99 GLN U 239 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100807 restraints weight = 96965.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102614 restraints weight = 55168.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104133 restraints weight = 35074.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104585 restraints weight = 24695.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105236 restraints weight = 20977.101| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 39858 Z= 0.220 Angle : 0.780 8.982 54705 Z= 0.421 Chirality : 0.049 0.188 6552 Planarity : 0.005 0.067 6909 Dihedral : 7.002 56.587 5452 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.06 % Favored : 96.84 % Rotamer: Outliers : 4.32 % Allowed : 14.12 % Favored : 81.56 % 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: 0.29 (0.11), residues: 4998 helix: 2.24 (0.18), residues: 714 sheet: 0.68 (0.11), residues: 1722 loop : -0.76 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 236 TYR 0.024 0.003 TYR L 22 PHE 0.015 0.002 PHE F 197 TRP 0.021 0.002 TRP H 211 HIS 0.006 0.002 HIS Q 105 Details of bonding type rmsd covalent geometry : bond 0.00482 (39837) covalent geometry : angle 0.78006 (54663) SS BOND : bond 0.00852 ( 21) SS BOND : angle 0.80800 ( 42) hydrogen bonds : bond 0.08353 ( 1576) hydrogen bonds : angle 6.40542 ( 4224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 1063 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7467 (pm20) REVERT: A 115 ASP cc_start: 0.8682 (t0) cc_final: 0.8261 (t0) REVERT: A 239 ASN cc_start: 0.8517 (m-40) cc_final: 0.7847 (p0) REVERT: A 286 MET cc_start: 0.8971 (mtt) cc_final: 0.8712 (mtp) REVERT: B 63 ASP cc_start: 0.8535 (m-30) cc_final: 0.8287 (t70) REVERT: B 105 HIS cc_start: 0.8480 (t70) cc_final: 0.8217 (t70) REVERT: B 115 ASP cc_start: 0.8636 (t0) cc_final: 0.8399 (t0) REVERT: B 198 ASP cc_start: 0.8588 (t0) cc_final: 0.8304 (t0) REVERT: B 201 TYR cc_start: 0.8746 (m-80) cc_final: 0.8476 (m-80) REVERT: B 236 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7149 (ttm-80) REVERT: B 279 MET cc_start: 0.8657 (mtt) cc_final: 0.7990 (mtt) REVERT: C 81 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7482 (pm20) REVERT: C 107 ASP cc_start: 0.7391 (p0) cc_final: 0.6860 (t0) REVERT: C 115 ASP cc_start: 0.8641 (t0) cc_final: 0.8399 (t0) REVERT: C 201 TYR cc_start: 0.8824 (m-80) cc_final: 0.8475 (m-80) REVERT: C 249 ASN cc_start: 0.9094 (m-40) cc_final: 0.8878 (m110) REVERT: C 274 VAL cc_start: 0.9239 (t) cc_final: 0.9001 (p) REVERT: C 279 MET cc_start: 0.8367 (mtt) cc_final: 0.7360 (mtt) REVERT: D 62 LYS cc_start: 0.8507 (pttp) cc_final: 0.8000 (mttp) REVERT: D 107 ASP cc_start: 0.7512 (p0) cc_final: 0.6915 (t0) REVERT: D 114 ASP cc_start: 0.8713 (t0) cc_final: 0.8502 (t0) REVERT: D 115 ASP cc_start: 0.8707 (t0) cc_final: 0.8346 (t0) REVERT: D 201 TYR cc_start: 0.8909 (m-10) cc_final: 0.8627 (m-10) REVERT: E 115 ASP cc_start: 0.8657 (t0) cc_final: 0.8124 (t0) REVERT: E 201 TYR cc_start: 0.8863 (m-10) cc_final: 0.8645 (m-10) REVERT: E 233 LYS cc_start: 0.7712 (mttt) cc_final: 0.7469 (mmmm) REVERT: E 239 ASN cc_start: 0.8791 (m-40) cc_final: 0.7997 (p0) REVERT: E 279 MET cc_start: 0.8444 (mtt) cc_final: 0.8053 (mtt) REVERT: F 114 ASP cc_start: 0.8422 (t0) cc_final: 0.8101 (m-30) REVERT: F 116 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8300 (mmtt) REVERT: F 239 ASN cc_start: 0.8854 (m-40) cc_final: 0.8184 (p0) REVERT: F 279 MET cc_start: 0.8073 (mtt) cc_final: 0.7873 (mtt) REVERT: G 62 LYS cc_start: 0.8363 (pttp) cc_final: 0.8018 (mttt) REVERT: G 114 ASP cc_start: 0.8681 (t0) cc_final: 0.8446 (t0) REVERT: G 115 ASP cc_start: 0.8707 (t0) cc_final: 0.8297 (t0) REVERT: H 114 ASP cc_start: 0.8714 (t0) cc_final: 0.8359 (t0) REVERT: H 115 ASP cc_start: 0.8773 (t0) cc_final: 0.8385 (t0) REVERT: H 239 ASN cc_start: 0.9086 (m-40) cc_final: 0.8373 (p0) REVERT: I 54 THR cc_start: 0.8472 (p) cc_final: 0.8254 (t) REVERT: I 62 LYS cc_start: 0.8219 (pttp) cc_final: 0.7712 (mttp) REVERT: I 83 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6801 (tp) REVERT: J 62 LYS cc_start: 0.8341 (pttp) cc_final: 0.8030 (mttp) REVERT: J 63 ASP cc_start: 0.8594 (m-30) cc_final: 0.8325 (t70) REVERT: J 239 ASN cc_start: 0.9126 (m-40) cc_final: 0.8413 (p0) REVERT: J 279 MET cc_start: 0.8223 (mtt) cc_final: 0.7280 (mtt) REVERT: J 295 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7902 (mt-10) REVERT: K 62 LYS cc_start: 0.8358 (pttp) cc_final: 0.7887 (mttt) REVERT: K 63 ASP cc_start: 0.8473 (m-30) cc_final: 0.8182 (t70) REVERT: K 198 ASP cc_start: 0.8455 (t0) cc_final: 0.8144 (t70) REVERT: K 201 TYR cc_start: 0.8958 (m-80) cc_final: 0.8444 (m-80) REVERT: K 236 ARG cc_start: 0.6824 (ttm-80) cc_final: 0.6389 (ttm-80) REVERT: K 239 ASN cc_start: 0.8539 (m-40) cc_final: 0.7872 (p0) REVERT: K 279 MET cc_start: 0.7974 (mtt) cc_final: 0.7740 (mtt) REVERT: L 62 LYS cc_start: 0.8703 (pttp) cc_final: 0.8196 (mttp) REVERT: L 114 ASP cc_start: 0.8800 (t0) cc_final: 0.8155 (m-30) REVERT: L 232 ILE cc_start: 0.9087 (mt) cc_final: 0.8758 (mt) REVERT: L 236 ARG cc_start: 0.7117 (ttm-80) cc_final: 0.6779 (ttm-80) REVERT: L 254 ILE cc_start: 0.9120 (mm) cc_final: 0.8869 (mt) REVERT: L 279 MET cc_start: 0.8167 (mtt) cc_final: 0.7928 (mtt) REVERT: M 62 LYS cc_start: 0.8368 (pttp) cc_final: 0.7988 (mttp) REVERT: M 83 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6463 (tp) REVERT: M 233 LYS cc_start: 0.7996 (mttt) cc_final: 0.7755 (mmmm) REVERT: M 262 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8058 (pm20) REVERT: M 264 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7957 (m110) REVERT: M 279 MET cc_start: 0.8303 (mtt) cc_final: 0.7737 (mtt) REVERT: N 62 LYS cc_start: 0.8536 (pttp) cc_final: 0.8132 (mttp) REVERT: N 233 LYS cc_start: 0.7842 (mttt) cc_final: 0.7422 (mmmm) REVERT: N 267 VAL cc_start: 0.9198 (t) cc_final: 0.8899 (m) REVERT: N 279 MET cc_start: 0.8137 (mtt) cc_final: 0.7117 (mtt) REVERT: N 300 LEU cc_start: 0.8970 (tp) cc_final: 0.8722 (tp) REVERT: O 62 LYS cc_start: 0.8341 (pttp) cc_final: 0.7886 (mttt) REVERT: O 214 ASN cc_start: 0.8641 (t0) cc_final: 0.8363 (t0) REVERT: O 215 TYR cc_start: 0.8340 (m-80) cc_final: 0.8124 (m-80) REVERT: O 233 LYS cc_start: 0.8094 (mttt) cc_final: 0.7792 (mmmm) REVERT: O 236 ARG cc_start: 0.4512 (tpt170) cc_final: 0.3695 (tpt170) REVERT: O 262 GLN cc_start: 0.8497 (pt0) cc_final: 0.8237 (pm20) REVERT: O 279 MET cc_start: 0.8121 (mtt) cc_final: 0.7920 (mtt) REVERT: P 62 LYS cc_start: 0.8365 (pttp) cc_final: 0.7895 (mttt) REVERT: P 63 ASP cc_start: 0.8643 (m-30) cc_final: 0.8260 (t70) REVERT: P 114 ASP cc_start: 0.8747 (t0) cc_final: 0.8498 (t70) REVERT: P 116 LYS cc_start: 0.8723 (mttt) cc_final: 0.8459 (pttt) REVERT: P 233 LYS cc_start: 0.7941 (mttt) cc_final: 0.7465 (mmmm) REVERT: Q 107 ASP cc_start: 0.7357 (p0) cc_final: 0.7108 (t0) REVERT: Q 116 LYS cc_start: 0.8725 (mttt) cc_final: 0.8465 (pttt) REVERT: R 46 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: R 62 LYS cc_start: 0.8449 (pttp) cc_final: 0.7926 (mttp) REVERT: R 63 ASP cc_start: 0.8503 (t70) cc_final: 0.8204 (t70) REVERT: R 239 ASN cc_start: 0.9043 (m-40) cc_final: 0.8452 (p0) REVERT: S 62 LYS cc_start: 0.8178 (pttp) cc_final: 0.7599 (mttp) REVERT: S 91 ILE cc_start: 0.9393 (mt) cc_final: 0.9066 (mt) REVERT: S 111 MET cc_start: 0.7919 (ttp) cc_final: 0.7682 (ttm) REVERT: S 116 LYS cc_start: 0.8727 (mttt) cc_final: 0.8406 (pttt) REVERT: S 198 ASP cc_start: 0.8183 (t0) cc_final: 0.7308 (t0) REVERT: S 232 ILE cc_start: 0.9019 (mt) cc_final: 0.8755 (mt) REVERT: S 253 PRO cc_start: 0.9290 (Cg_exo) cc_final: 0.8845 (Cg_endo) REVERT: S 262 GLN cc_start: 0.8524 (pm20) cc_final: 0.8178 (pm20) REVERT: S 286 MET cc_start: 0.9029 (mtt) cc_final: 0.8764 (mtm) REVERT: S 287 VAL cc_start: 0.9457 (t) cc_final: 0.9155 (p) REVERT: T 62 LYS cc_start: 0.8152 (pttp) cc_final: 0.7859 (mttp) REVERT: T 63 ASP cc_start: 0.8568 (t70) cc_final: 0.8342 (t70) REVERT: T 116 LYS cc_start: 0.8681 (mttt) cc_final: 0.8389 (pttt) REVERT: T 232 ILE cc_start: 0.9076 (mt) cc_final: 0.8850 (mp) REVERT: T 275 ASN cc_start: 0.8722 (t0) cc_final: 0.8406 (t0) REVERT: T 279 MET cc_start: 0.8362 (mtt) cc_final: 0.8150 (mtt) REVERT: U 89 ILE cc_start: 0.7890 (mm) cc_final: 0.7658 (mt) REVERT: U 115 ASP cc_start: 0.8813 (t0) cc_final: 0.8421 (t0) REVERT: U 116 LYS cc_start: 0.8836 (mttt) cc_final: 0.8409 (pttt) outliers start: 186 outliers final: 97 residues processed: 1161 average time/residue: 0.2206 time to fit residues: 434.9922 Evaluate side-chains 956 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 854 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 198 ASP Chi-restraints excluded: chain G residue 264 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 264 ASN Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 264 ASN Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 264 ASN Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 262 GLN Chi-restraints excluded: chain P residue 264 ASN Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 46 GLN Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 293 THR Chi-restraints excluded: chain T residue 1 VAL Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain U residue 1 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 460 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 383 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 196 optimal weight: 20.0000 chunk 217 optimal weight: 5.9990 chunk 457 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN ** L 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 239 ASN ** P 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 46 GLN ** R 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN S 118 HIS ** T 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100638 restraints weight = 97228.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102473 restraints weight = 56016.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103556 restraints weight = 34707.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104690 restraints weight = 24940.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104785 restraints weight = 19527.396| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 39858 Z= 0.192 Angle : 0.703 7.963 54705 Z= 0.376 Chirality : 0.047 0.172 6552 Planarity : 0.004 0.029 6909 Dihedral : 6.007 54.836 5355 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.51 % Allowed : 15.87 % Favored : 79.63 % 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: 0.29 (0.12), residues: 4998 helix: 2.55 (0.18), residues: 714 sheet: 0.50 (0.12), residues: 1764 loop : -0.73 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 236 TYR 0.019 0.002 TYR S 22 PHE 0.014 0.001 PHE S 237 TRP 0.020 0.002 TRP Q 211 HIS 0.006 0.001 HIS K 105 Details of bonding type rmsd covalent geometry : bond 0.00430 (39837) covalent geometry : angle 0.70338 (54663) SS BOND : bond 0.00671 ( 21) SS BOND : angle 0.70467 ( 42) hydrogen bonds : bond 0.06930 ( 1576) hydrogen bonds : angle 5.90447 ( 4224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 898 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7472 (pm20) REVERT: A 115 ASP cc_start: 0.8730 (t0) cc_final: 0.8317 (t0) REVERT: A 239 ASN cc_start: 0.8577 (m-40) cc_final: 0.7913 (p0) REVERT: A 286 MET cc_start: 0.8978 (mtt) cc_final: 0.8745 (mtp) REVERT: B 81 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7515 (pm20) REVERT: B 279 MET cc_start: 0.8461 (mtt) cc_final: 0.7937 (mtt) REVERT: C 81 GLN cc_start: 0.7486 (tm-30) cc_final: 0.7161 (pm20) REVERT: C 111 MET cc_start: 0.7993 (ttm) cc_final: 0.7776 (ttm) REVERT: C 279 MET cc_start: 0.8381 (mtt) cc_final: 0.7457 (mtt) REVERT: C 283 ASP cc_start: 0.8560 (m-30) cc_final: 0.8358 (m-30) REVERT: D 114 ASP cc_start: 0.8855 (t0) cc_final: 0.8615 (t70) REVERT: D 115 ASP cc_start: 0.8792 (t0) cc_final: 0.8445 (t0) REVERT: D 201 TYR cc_start: 0.8887 (m-10) cc_final: 0.8567 (m-10) REVERT: E 20 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8855 (tt) REVERT: E 201 TYR cc_start: 0.8884 (m-10) cc_final: 0.8611 (m-10) REVERT: E 233 LYS cc_start: 0.7941 (mttt) cc_final: 0.7601 (mmmm) REVERT: E 239 ASN cc_start: 0.8740 (m-40) cc_final: 0.7993 (p0) REVERT: E 279 MET cc_start: 0.8295 (mtt) cc_final: 0.8089 (mtt) REVERT: F 114 ASP cc_start: 0.8497 (t0) cc_final: 0.8098 (t0) REVERT: F 116 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8434 (mmtt) REVERT: F 239 ASN cc_start: 0.8895 (m-40) cc_final: 0.8212 (p0) REVERT: F 279 MET cc_start: 0.8206 (mtt) cc_final: 0.7930 (mtt) REVERT: G 62 LYS cc_start: 0.8401 (pttp) cc_final: 0.8198 (mttt) REVERT: G 114 ASP cc_start: 0.8732 (t0) cc_final: 0.8454 (t0) REVERT: G 115 ASP cc_start: 0.8751 (t0) cc_final: 0.8281 (t0) REVERT: H 114 ASP cc_start: 0.8752 (t0) cc_final: 0.8436 (t0) REVERT: H 201 TYR cc_start: 0.8936 (m-80) cc_final: 0.8700 (m-10) REVERT: H 239 ASN cc_start: 0.9118 (m-40) cc_final: 0.8301 (p0) REVERT: I 54 THR cc_start: 0.8521 (p) cc_final: 0.8281 (t) REVERT: I 62 LYS cc_start: 0.8180 (pttp) cc_final: 0.7779 (mttp) REVERT: I 198 ASP cc_start: 0.7874 (t70) cc_final: 0.7626 (p0) REVERT: I 201 TYR cc_start: 0.8865 (m-80) cc_final: 0.8328 (m-80) REVERT: J 62 LYS cc_start: 0.8396 (pttp) cc_final: 0.8086 (mttp) REVERT: J 63 ASP cc_start: 0.8563 (m-30) cc_final: 0.8292 (t70) REVERT: J 236 ARG cc_start: 0.7213 (ttm-80) cc_final: 0.6880 (ttm-80) REVERT: J 239 ASN cc_start: 0.9079 (m-40) cc_final: 0.8263 (p0) REVERT: J 279 MET cc_start: 0.8243 (mtt) cc_final: 0.8004 (mtt) REVERT: K 62 LYS cc_start: 0.8629 (pttp) cc_final: 0.8004 (mttt) REVERT: K 63 ASP cc_start: 0.8427 (m-30) cc_final: 0.8181 (t70) REVERT: K 239 ASN cc_start: 0.8494 (m-40) cc_final: 0.7780 (p0) REVERT: K 279 MET cc_start: 0.7795 (mtt) cc_final: 0.7450 (mtt) REVERT: K 290 ASP cc_start: 0.8213 (p0) cc_final: 0.7988 (p0) REVERT: L 62 LYS cc_start: 0.8699 (pttp) cc_final: 0.8225 (mttp) REVERT: L 83 LEU cc_start: 0.7547 (mt) cc_final: 0.7085 (tp) REVERT: L 236 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.7135 (ttm-80) REVERT: L 262 GLN cc_start: 0.8203 (pm20) cc_final: 0.7247 (pm20) REVERT: M 233 LYS cc_start: 0.8232 (mttt) cc_final: 0.7882 (mmmm) REVERT: N 62 LYS cc_start: 0.8344 (pttp) cc_final: 0.8032 (mttp) REVERT: N 233 LYS cc_start: 0.8023 (mttt) cc_final: 0.7521 (mmmm) REVERT: N 279 MET cc_start: 0.8171 (mtt) cc_final: 0.7302 (mtt) REVERT: O 62 LYS cc_start: 0.8395 (pttp) cc_final: 0.8107 (mttp) REVERT: O 94 ILE cc_start: 0.9280 (mt) cc_final: 0.8960 (tt) REVERT: O 236 ARG cc_start: 0.4102 (tpt170) cc_final: 0.3445 (tpt170) REVERT: O 262 GLN cc_start: 0.8486 (pt0) cc_final: 0.8116 (pm20) REVERT: P 62 LYS cc_start: 0.8440 (pttp) cc_final: 0.8051 (mttt) REVERT: P 63 ASP cc_start: 0.8655 (m-30) cc_final: 0.8336 (t70) REVERT: P 114 ASP cc_start: 0.8766 (t0) cc_final: 0.8508 (t70) REVERT: P 116 LYS cc_start: 0.8854 (mttt) cc_final: 0.8505 (pttt) REVERT: P 232 ILE cc_start: 0.9190 (mt) cc_final: 0.8924 (mm) REVERT: P 233 LYS cc_start: 0.8044 (mttt) cc_final: 0.7529 (mmmm) REVERT: P 262 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7675 (pp30) REVERT: Q 116 LYS cc_start: 0.8813 (mttt) cc_final: 0.8526 (pttt) REVERT: Q 279 MET cc_start: 0.8053 (mtt) cc_final: 0.7647 (mtt) REVERT: Q 300 LEU cc_start: 0.8951 (tp) cc_final: 0.8712 (tp) REVERT: R 62 LYS cc_start: 0.8544 (pttp) cc_final: 0.8032 (mttp) REVERT: R 63 ASP cc_start: 0.8627 (t70) cc_final: 0.8332 (t70) REVERT: R 239 ASN cc_start: 0.8953 (m-40) cc_final: 0.8379 (p0) REVERT: R 279 MET cc_start: 0.8291 (mtt) cc_final: 0.7768 (mtt) REVERT: S 62 LYS cc_start: 0.8092 (pttp) cc_final: 0.7571 (mttp) REVERT: S 91 ILE cc_start: 0.9447 (mt) cc_final: 0.9134 (mt) REVERT: S 111 MET cc_start: 0.7986 (ttp) cc_final: 0.7769 (ttm) REVERT: S 116 LYS cc_start: 0.8794 (mttt) cc_final: 0.8542 (pttt) REVERT: S 253 PRO cc_start: 0.9275 (Cg_exo) cc_final: 0.8924 (Cg_endo) REVERT: S 262 GLN cc_start: 0.8585 (pm20) cc_final: 0.8062 (pm20) REVERT: S 279 MET cc_start: 0.8067 (mtt) cc_final: 0.7346 (mtt) REVERT: S 286 MET cc_start: 0.9103 (mtt) cc_final: 0.8853 (mtm) REVERT: T 46 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: T 62 LYS cc_start: 0.8139 (pttp) cc_final: 0.7889 (mttp) REVERT: T 63 ASP cc_start: 0.8573 (t70) cc_final: 0.8362 (t70) REVERT: T 116 LYS cc_start: 0.8742 (mttt) cc_final: 0.8409 (pttt) REVERT: T 232 ILE cc_start: 0.9003 (mt) cc_final: 0.8689 (mt) REVERT: T 275 ASN cc_start: 0.8722 (t0) cc_final: 0.8408 (t0) REVERT: T 279 MET cc_start: 0.8444 (mtt) cc_final: 0.8222 (mtt) REVERT: U 115 ASP cc_start: 0.8740 (t0) cc_final: 0.8377 (t0) REVERT: U 116 LYS cc_start: 0.8934 (mttt) cc_final: 0.8454 (pttt) outliers start: 194 outliers final: 139 residues processed: 1025 average time/residue: 0.2186 time to fit residues: 378.3937 Evaluate side-chains 971 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 829 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 46 GLN Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain H residue 293 THR Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 264 ASN Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 262 GLN Chi-restraints excluded: chain P residue 264 ASN Chi-restraints excluded: chain P residue 293 THR Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 257 VAL Chi-restraints excluded: chain Q residue 293 THR Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 293 THR Chi-restraints excluded: chain S residue 1 VAL Chi-restraints excluded: chain S residue 13 ILE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 126 LEU Chi-restraints excluded: chain S residue 257 VAL Chi-restraints excluded: chain S residue 293 THR Chi-restraints excluded: chain T residue 1 VAL Chi-restraints excluded: chain T residue 13 ILE Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 46 GLN Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 238 VAL Chi-restraints excluded: chain T residue 257 VAL Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 238 VAL Chi-restraints excluded: chain U residue 257 VAL Chi-restraints excluded: chain U residue 293 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 336 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 368 optimal weight: 9.9990 chunk 492 optimal weight: 0.9980 chunk 384 optimal weight: 0.9980 chunk 329 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 480 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 471 optimal weight: 10.0000 chunk 288 optimal weight: 0.8980 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN F 118 HIS G 46 GLN H 118 HIS I 46 GLN I 219 ASN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN M 118 HIS ** M 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 GLN O 200 GLN P 219 ASN P 239 ASN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 GLN ** T 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102354 restraints weight = 95817.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.104489 restraints weight = 55343.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.105540 restraints weight = 32659.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106438 restraints weight = 23875.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.106991 restraints weight = 18817.760| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 39858 Z= 0.140 Angle : 0.648 8.516 54705 Z= 0.339 Chirality : 0.046 0.185 6552 Planarity : 0.003 0.026 6909 Dihedral : 5.659 53.110 5345 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.65 % Allowed : 18.30 % Favored : 78.05 % 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: 0.47 (0.12), residues: 4998 helix: 2.94 (0.19), residues: 714 sheet: 0.58 (0.12), residues: 1764 loop : -0.65 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG T 226 TYR 0.023 0.002 TYR S 98 PHE 0.010 0.001 PHE U 237 TRP 0.015 0.001 TRP O 211 HIS 0.006 0.001 HIS J 105 Details of bonding type rmsd covalent geometry : bond 0.00309 (39837) covalent geometry : angle 0.64788 (54663) SS BOND : bond 0.00861 ( 21) SS BOND : angle 0.59802 ( 42) hydrogen bonds : bond 0.05848 ( 1576) hydrogen bonds : angle 5.57943 ( 4224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 878 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7469 (tm-30) cc_final: 0.7221 (pm20) REVERT: A 239 ASN cc_start: 0.8603 (m-40) cc_final: 0.7878 (p0) REVERT: A 286 MET cc_start: 0.8927 (mtt) cc_final: 0.8703 (mtp) REVERT: B 81 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7455 (pm20) REVERT: B 198 ASP cc_start: 0.8555 (t0) cc_final: 0.8319 (t0) REVERT: B 279 MET cc_start: 0.8403 (mtt) cc_final: 0.7901 (mtt) REVERT: C 81 GLN cc_start: 0.7472 (tm-30) cc_final: 0.7199 (pm20) REVERT: C 201 TYR cc_start: 0.8769 (m-80) cc_final: 0.8358 (m-80) REVERT: C 279 MET cc_start: 0.8292 (mtt) cc_final: 0.7401 (mtt) REVERT: D 114 ASP cc_start: 0.8909 (t0) cc_final: 0.8657 (t70) REVERT: D 115 ASP cc_start: 0.8837 (t0) cc_final: 0.8396 (t0) REVERT: D 201 TYR cc_start: 0.8871 (m-10) cc_final: 0.8564 (m-10) REVERT: D 267 VAL cc_start: 0.9352 (t) cc_final: 0.9138 (m) REVERT: E 115 ASP cc_start: 0.8691 (t0) cc_final: 0.8270 (t0) REVERT: E 233 LYS cc_start: 0.7937 (mttt) cc_final: 0.7719 (mmmm) REVERT: E 239 ASN cc_start: 0.8714 (m-40) cc_final: 0.7974 (p0) REVERT: F 114 ASP cc_start: 0.8419 (t0) cc_final: 0.8017 (t0) REVERT: F 116 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8421 (mmtt) REVERT: F 239 ASN cc_start: 0.8831 (m-40) cc_final: 0.8141 (p0) REVERT: F 267 VAL cc_start: 0.8951 (t) cc_final: 0.8656 (m) REVERT: F 279 MET cc_start: 0.8180 (mtt) cc_final: 0.7906 (mtt) REVERT: G 62 LYS cc_start: 0.8417 (pttp) cc_final: 0.8157 (mttt) REVERT: G 114 ASP cc_start: 0.8748 (t0) cc_final: 0.8444 (t0) REVERT: G 115 ASP cc_start: 0.8727 (t0) cc_final: 0.8355 (t0) REVERT: G 233 LYS cc_start: 0.8039 (mmmm) cc_final: 0.7559 (mmmm) REVERT: H 114 ASP cc_start: 0.8702 (t0) cc_final: 0.8363 (t0) REVERT: H 201 TYR cc_start: 0.8848 (m-80) cc_final: 0.8501 (m-10) REVERT: H 233 LYS cc_start: 0.7644 (mmmm) cc_final: 0.7364 (mmmm) REVERT: H 239 ASN cc_start: 0.8973 (m-40) cc_final: 0.8196 (p0) REVERT: H 279 MET cc_start: 0.8190 (mtt) cc_final: 0.7897 (mtp) REVERT: I 62 LYS cc_start: 0.8131 (pttp) cc_final: 0.7815 (mttt) REVERT: I 198 ASP cc_start: 0.7914 (t70) cc_final: 0.7584 (p0) REVERT: I 201 TYR cc_start: 0.8812 (m-80) cc_final: 0.8193 (m-80) REVERT: I 267 VAL cc_start: 0.9095 (t) cc_final: 0.8882 (m) REVERT: J 62 LYS cc_start: 0.8413 (pttp) cc_final: 0.8132 (mttp) REVERT: J 239 ASN cc_start: 0.9035 (m-40) cc_final: 0.8246 (p0) REVERT: J 279 MET cc_start: 0.8164 (mtt) cc_final: 0.7940 (mtt) REVERT: K 62 LYS cc_start: 0.8657 (pttp) cc_final: 0.7982 (mttt) REVERT: K 63 ASP cc_start: 0.8407 (m-30) cc_final: 0.8185 (t70) REVERT: K 198 ASP cc_start: 0.8509 (t0) cc_final: 0.8155 (p0) REVERT: K 201 TYR cc_start: 0.8908 (m-80) cc_final: 0.8396 (m-80) REVERT: K 239 ASN cc_start: 0.8453 (m-40) cc_final: 0.7748 (p0) REVERT: K 267 VAL cc_start: 0.9174 (t) cc_final: 0.8878 (m) REVERT: L 62 LYS cc_start: 0.8667 (pttp) cc_final: 0.8200 (mttp) REVERT: L 236 ARG cc_start: 0.7522 (ttm-80) cc_final: 0.7225 (ttm-80) REVERT: L 262 GLN cc_start: 0.8240 (pm20) cc_final: 0.7330 (pm20) REVERT: L 279 MET cc_start: 0.8147 (mtt) cc_final: 0.7832 (mtp) REVERT: M 233 LYS cc_start: 0.8294 (mttt) cc_final: 0.7907 (mmmm) REVERT: M 267 VAL cc_start: 0.8996 (t) cc_final: 0.8622 (m) REVERT: M 279 MET cc_start: 0.8207 (mtt) cc_final: 0.7695 (mtt) REVERT: N 62 LYS cc_start: 0.8165 (pttp) cc_final: 0.7858 (mttp) REVERT: N 233 LYS cc_start: 0.7948 (mttt) cc_final: 0.7512 (mmmm) REVERT: N 279 MET cc_start: 0.7955 (mtt) cc_final: 0.7304 (mtt) REVERT: O 62 LYS cc_start: 0.8567 (pttp) cc_final: 0.8188 (mttp) REVERT: O 94 ILE cc_start: 0.9284 (mt) cc_final: 0.8973 (tt) REVERT: O 236 ARG cc_start: 0.4043 (tpt170) cc_final: 0.3321 (tpt170) REVERT: O 262 GLN cc_start: 0.8480 (pt0) cc_final: 0.8133 (pm20) REVERT: O 279 MET cc_start: 0.7690 (mtt) cc_final: 0.6924 (mtt) REVERT: P 63 ASP cc_start: 0.8661 (m-30) cc_final: 0.8294 (t70) REVERT: P 116 LYS cc_start: 0.8787 (mttt) cc_final: 0.8496 (pttt) REVERT: P 214 ASN cc_start: 0.8769 (t0) cc_final: 0.8555 (t0) REVERT: P 233 LYS cc_start: 0.8011 (mttt) cc_final: 0.7490 (mmmm) REVERT: P 262 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7507 (pp30) REVERT: Q 116 LYS cc_start: 0.8836 (mttt) cc_final: 0.8535 (pttt) REVERT: Q 279 MET cc_start: 0.8038 (mtt) cc_final: 0.7578 (mtt) REVERT: R 62 LYS cc_start: 0.8571 (pttp) cc_final: 0.8050 (mttp) REVERT: R 63 ASP cc_start: 0.8650 (t70) cc_final: 0.8358 (t70) REVERT: R 225 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8311 (t80) REVERT: R 239 ASN cc_start: 0.8887 (m-40) cc_final: 0.8306 (p0) REVERT: S 62 LYS cc_start: 0.8129 (pttp) cc_final: 0.7613 (mttp) REVERT: S 111 MET cc_start: 0.8019 (ttp) cc_final: 0.7791 (ttm) REVERT: S 116 LYS cc_start: 0.8780 (mttt) cc_final: 0.8512 (pttt) REVERT: S 253 PRO cc_start: 0.9195 (Cg_exo) cc_final: 0.8810 (Cg_endo) REVERT: S 262 GLN cc_start: 0.8641 (pm20) cc_final: 0.8130 (pm20) REVERT: S 279 MET cc_start: 0.8032 (mtt) cc_final: 0.7358 (mtt) REVERT: T 62 LYS cc_start: 0.8132 (pttp) cc_final: 0.7879 (mttp) REVERT: T 63 ASP cc_start: 0.8597 (t70) cc_final: 0.8383 (t70) REVERT: T 116 LYS cc_start: 0.8732 (mttt) cc_final: 0.8415 (pttt) REVERT: T 225 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8356 (t80) REVERT: T 275 ASN cc_start: 0.8748 (t0) cc_final: 0.8473 (t0) REVERT: T 279 MET cc_start: 0.8416 (mtt) cc_final: 0.8202 (mtt) REVERT: U 115 ASP cc_start: 0.8698 (t0) cc_final: 0.8299 (t0) REVERT: U 116 LYS cc_start: 0.8924 (mttt) cc_final: 0.8431 (pttt) outliers start: 157 outliers final: 124 residues processed: 986 average time/residue: 0.2211 time to fit residues: 366.6021 Evaluate side-chains 927 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 800 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 225 PHE Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 46 GLN Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 225 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 262 GLN Chi-restraints excluded: chain P residue 293 THR Chi-restraints excluded: chain P residue 297 SER Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 293 THR Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 126 LEU Chi-restraints excluded: chain S residue 293 THR Chi-restraints excluded: chain S residue 297 SER Chi-restraints excluded: chain T residue 13 ILE Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 225 PHE Chi-restraints excluded: chain T residue 238 VAL Chi-restraints excluded: chain T residue 257 VAL Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 238 VAL Chi-restraints excluded: chain U residue 257 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 60 optimal weight: 0.0070 chunk 386 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 chunk 264 optimal weight: 0.9980 chunk 309 optimal weight: 9.9990 chunk 445 optimal weight: 0.0870 chunk 457 optimal weight: 5.9990 chunk 37 optimal weight: 0.0270 chunk 368 optimal weight: 20.0000 chunk 358 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 overall best weight: 0.4234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN C 46 GLN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN G 46 GLN I 46 GLN K 219 ASN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 ASN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 GLN O 46 GLN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 GLN P 239 ASN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 219 ASN R 280 GLN S 121 GLN ** T 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 99 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105317 restraints weight = 94025.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107484 restraints weight = 54019.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108451 restraints weight = 32020.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109366 restraints weight = 24376.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110250 restraints weight = 19272.447| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 39858 Z= 0.123 Angle : 0.618 9.219 54705 Z= 0.317 Chirality : 0.046 0.183 6552 Planarity : 0.003 0.027 6909 Dihedral : 5.075 51.951 5341 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.56 % Allowed : 20.05 % Favored : 77.40 % 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: 0.70 (0.12), residues: 4998 helix: 3.06 (0.19), residues: 714 sheet: 0.86 (0.13), residues: 1659 loop : -0.53 (0.12), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 101 TYR 0.024 0.001 TYR I 22 PHE 0.018 0.001 PHE S 237 TRP 0.019 0.001 TRP O 211 HIS 0.004 0.001 HIS O 105 Details of bonding type rmsd covalent geometry : bond 0.00265 (39837) covalent geometry : angle 0.61861 (54663) SS BOND : bond 0.00116 ( 21) SS BOND : angle 0.40830 ( 42) hydrogen bonds : bond 0.04632 ( 1576) hydrogen bonds : angle 5.19388 ( 4224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 893 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ASN cc_start: 0.8504 (m-40) cc_final: 0.7842 (p0) REVERT: A 279 MET cc_start: 0.8283 (mtt) cc_final: 0.8072 (mtt) REVERT: B 81 GLN cc_start: 0.7504 (tm-30) cc_final: 0.7254 (pm20) REVERT: B 279 MET cc_start: 0.8342 (mtt) cc_final: 0.7872 (mtt) REVERT: C 279 MET cc_start: 0.8193 (mtt) cc_final: 0.7303 (mtt) REVERT: D 114 ASP cc_start: 0.8855 (t0) cc_final: 0.8636 (t70) REVERT: D 115 ASP cc_start: 0.8822 (t0) cc_final: 0.8299 (t0) REVERT: E 115 ASP cc_start: 0.8518 (t0) cc_final: 0.8295 (t70) REVERT: E 239 ASN cc_start: 0.8704 (m-40) cc_final: 0.7940 (p0) REVERT: F 114 ASP cc_start: 0.8325 (t0) cc_final: 0.7974 (t0) REVERT: F 116 LYS cc_start: 0.8460 (mmtt) cc_final: 0.8227 (mmtt) REVERT: F 198 ASP cc_start: 0.8357 (t0) cc_final: 0.7976 (p0) REVERT: F 233 LYS cc_start: 0.7720 (mmmm) cc_final: 0.7469 (mmmm) REVERT: F 239 ASN cc_start: 0.8779 (m-40) cc_final: 0.8107 (p0) REVERT: F 267 VAL cc_start: 0.8931 (t) cc_final: 0.8670 (m) REVERT: F 279 MET cc_start: 0.8153 (mtt) cc_final: 0.7861 (mtt) REVERT: G 62 LYS cc_start: 0.8424 (pttp) cc_final: 0.8133 (mttt) REVERT: G 107 ASP cc_start: 0.7594 (p0) cc_final: 0.7339 (t0) REVERT: G 115 ASP cc_start: 0.8581 (t0) cc_final: 0.8105 (t0) REVERT: G 201 TYR cc_start: 0.9074 (m-80) cc_final: 0.8608 (m-80) REVERT: H 114 ASP cc_start: 0.8640 (t0) cc_final: 0.8385 (t0) REVERT: H 239 ASN cc_start: 0.8920 (m-40) cc_final: 0.8189 (p0) REVERT: H 279 MET cc_start: 0.8132 (mtt) cc_final: 0.7874 (mtp) REVERT: I 62 LYS cc_start: 0.8148 (pttp) cc_final: 0.7840 (mttt) REVERT: I 198 ASP cc_start: 0.7879 (t70) cc_final: 0.7423 (p0) REVERT: I 201 TYR cc_start: 0.8741 (m-80) cc_final: 0.8103 (m-80) REVERT: I 233 LYS cc_start: 0.7660 (mmmm) cc_final: 0.7398 (mmmm) REVERT: I 290 ASP cc_start: 0.8275 (p0) cc_final: 0.7944 (p0) REVERT: J 63 ASP cc_start: 0.8691 (t70) cc_final: 0.8395 (t70) REVERT: J 115 ASP cc_start: 0.8646 (t0) cc_final: 0.8005 (t0) REVERT: J 233 LYS cc_start: 0.7671 (mmmm) cc_final: 0.7294 (mmmm) REVERT: J 239 ASN cc_start: 0.9005 (m-40) cc_final: 0.8230 (p0) REVERT: J 267 VAL cc_start: 0.8820 (t) cc_final: 0.8593 (m) REVERT: J 279 MET cc_start: 0.8218 (mtt) cc_final: 0.7356 (mtt) REVERT: K 62 LYS cc_start: 0.8359 (pttp) cc_final: 0.7948 (mttt) REVERT: K 63 ASP cc_start: 0.8392 (m-30) cc_final: 0.8165 (t70) REVERT: K 198 ASP cc_start: 0.8508 (t0) cc_final: 0.8074 (p0) REVERT: K 201 TYR cc_start: 0.8881 (m-80) cc_final: 0.8304 (m-80) REVERT: K 239 ASN cc_start: 0.8429 (m-40) cc_final: 0.7747 (p0) REVERT: K 267 VAL cc_start: 0.9145 (t) cc_final: 0.8868 (m) REVERT: L 62 LYS cc_start: 0.8640 (pttp) cc_final: 0.8199 (mttp) REVERT: L 262 GLN cc_start: 0.8217 (pm20) cc_final: 0.7364 (pm20) REVERT: M 198 ASP cc_start: 0.7963 (t0) cc_final: 0.7341 (t0) REVERT: M 201 TYR cc_start: 0.8572 (m-10) cc_final: 0.8357 (m-80) REVERT: M 233 LYS cc_start: 0.8160 (mttt) cc_final: 0.7843 (mmmm) REVERT: M 279 MET cc_start: 0.8065 (mtt) cc_final: 0.7509 (mtt) REVERT: N 46 GLN cc_start: 0.8435 (pt0) cc_final: 0.8164 (pp30) REVERT: N 62 LYS cc_start: 0.8179 (pttp) cc_final: 0.7911 (mttp) REVERT: N 233 LYS cc_start: 0.7888 (mttt) cc_final: 0.7522 (mmmm) REVERT: O 62 LYS cc_start: 0.8510 (pttp) cc_final: 0.8164 (mttp) REVERT: O 94 ILE cc_start: 0.9269 (mt) cc_final: 0.9051 (tt) REVERT: O 111 MET cc_start: 0.7886 (ttt) cc_final: 0.7678 (ttm) REVERT: O 236 ARG cc_start: 0.3776 (tpt170) cc_final: 0.3082 (tpt170) REVERT: O 262 GLN cc_start: 0.8496 (pp30) cc_final: 0.8220 (pm20) REVERT: P 46 GLN cc_start: 0.8056 (pm20) cc_final: 0.7735 (pm20) REVERT: P 116 LYS cc_start: 0.8669 (mttt) cc_final: 0.8421 (pttt) REVERT: P 198 ASP cc_start: 0.8609 (t0) cc_final: 0.8137 (p0) REVERT: P 201 TYR cc_start: 0.8789 (m-80) cc_final: 0.8466 (m-80) REVERT: P 233 LYS cc_start: 0.7943 (mttt) cc_final: 0.7477 (mmmm) REVERT: Q 116 LYS cc_start: 0.8704 (mttt) cc_final: 0.8430 (pttt) REVERT: Q 279 MET cc_start: 0.7925 (mtt) cc_final: 0.7621 (mtt) REVERT: R 62 LYS cc_start: 0.8542 (pttp) cc_final: 0.8011 (mttp) REVERT: R 63 ASP cc_start: 0.8522 (t70) cc_final: 0.8251 (t70) REVERT: R 225 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8355 (t80) REVERT: R 239 ASN cc_start: 0.8864 (m-40) cc_final: 0.8339 (p0) REVERT: S 62 LYS cc_start: 0.8087 (pttp) cc_final: 0.7539 (mttp) REVERT: S 111 MET cc_start: 0.7978 (ttp) cc_final: 0.7734 (ttm) REVERT: S 116 LYS cc_start: 0.8728 (mttt) cc_final: 0.8499 (pttt) REVERT: S 253 PRO cc_start: 0.9190 (Cg_exo) cc_final: 0.8803 (Cg_endo) REVERT: S 262 GLN cc_start: 0.8647 (pm20) cc_final: 0.8139 (pm20) REVERT: S 279 MET cc_start: 0.8063 (mtt) cc_final: 0.7210 (mtt) REVERT: S 287 VAL cc_start: 0.9389 (t) cc_final: 0.9070 (p) REVERT: S 290 ASP cc_start: 0.8530 (p0) cc_final: 0.8132 (p0) REVERT: T 46 GLN cc_start: 0.8489 (pm20) cc_final: 0.8262 (pm20) REVERT: T 62 LYS cc_start: 0.8116 (pttp) cc_final: 0.7890 (mttp) REVERT: T 99 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8280 (mm-40) REVERT: T 116 LYS cc_start: 0.8723 (mttt) cc_final: 0.8383 (pttt) REVERT: T 121 GLN cc_start: 0.7712 (mt0) cc_final: 0.7282 (mp10) REVERT: T 225 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8150 (t80) REVERT: T 275 ASN cc_start: 0.8672 (t0) cc_final: 0.8439 (t0) REVERT: U 115 ASP cc_start: 0.8644 (t0) cc_final: 0.8400 (t0) REVERT: U 116 LYS cc_start: 0.8839 (mttt) cc_final: 0.8327 (pttt) outliers start: 110 outliers final: 83 residues processed: 980 average time/residue: 0.2295 time to fit residues: 377.7810 Evaluate side-chains 887 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 802 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 1 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 225 PHE Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 297 SER Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 225 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 104 CYS Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 126 LEU Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 108 SER Chi-restraints excluded: chain T residue 225 PHE Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 81 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 418 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 318 optimal weight: 9.9990 chunk 390 optimal weight: 10.0000 chunk 477 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN H 46 GLN I 46 GLN ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN ** M 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 121 GLN O 200 GLN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 239 ASN Q 46 GLN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 46 GLN ** T 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.102053 restraints weight = 96736.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103861 restraints weight = 53415.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105042 restraints weight = 32157.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105872 restraints weight = 22232.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106434 restraints weight = 17120.991| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 39858 Z= 0.189 Angle : 0.669 9.464 54705 Z= 0.351 Chirality : 0.047 0.218 6552 Planarity : 0.003 0.028 6909 Dihedral : 5.266 49.363 5341 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.18 % Allowed : 21.25 % Favored : 75.56 % 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: 0.36 (0.12), residues: 4998 helix: 2.63 (0.19), residues: 714 sheet: 0.58 (0.12), residues: 1806 loop : -0.74 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 226 TYR 0.029 0.002 TYR M 98 PHE 0.016 0.001 PHE S 237 TRP 0.014 0.002 TRP S 294 HIS 0.011 0.001 HIS M 105 Details of bonding type rmsd covalent geometry : bond 0.00433 (39837) covalent geometry : angle 0.66858 (54663) SS BOND : bond 0.00698 ( 21) SS BOND : angle 0.66838 ( 42) hydrogen bonds : bond 0.05405 ( 1576) hydrogen bonds : angle 5.38020 ( 4224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 803 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ASN cc_start: 0.8565 (m-40) cc_final: 0.7774 (p0) REVERT: B 63 ASP cc_start: 0.8261 (m-30) cc_final: 0.7999 (t70) REVERT: B 81 GLN cc_start: 0.7582 (tm-30) cc_final: 0.7305 (pm20) REVERT: B 279 MET cc_start: 0.8393 (mtt) cc_final: 0.7906 (mtt) REVERT: B 290 ASP cc_start: 0.8354 (p0) cc_final: 0.8118 (p0) REVERT: C 279 MET cc_start: 0.8268 (mtt) cc_final: 0.7351 (mtt) REVERT: D 114 ASP cc_start: 0.8853 (t0) cc_final: 0.8629 (t70) REVERT: D 115 ASP cc_start: 0.8889 (t0) cc_final: 0.8490 (t0) REVERT: E 233 LYS cc_start: 0.7806 (mmmm) cc_final: 0.7449 (mmmm) REVERT: E 239 ASN cc_start: 0.8677 (m-40) cc_final: 0.7903 (p0) REVERT: F 114 ASP cc_start: 0.8385 (t0) cc_final: 0.7991 (t0) REVERT: F 233 LYS cc_start: 0.7780 (mmmm) cc_final: 0.7525 (mmmm) REVERT: F 239 ASN cc_start: 0.8810 (m-40) cc_final: 0.8097 (p0) REVERT: F 267 VAL cc_start: 0.8931 (t) cc_final: 0.8652 (m) REVERT: G 114 ASP cc_start: 0.8661 (t70) cc_final: 0.8352 (t0) REVERT: G 115 ASP cc_start: 0.8828 (t0) cc_final: 0.8470 (t0) REVERT: G 201 TYR cc_start: 0.9087 (m-80) cc_final: 0.8668 (m-80) REVERT: G 233 LYS cc_start: 0.8109 (mmmm) cc_final: 0.7647 (mmmm) REVERT: H 114 ASP cc_start: 0.8632 (t0) cc_final: 0.8362 (t0) REVERT: H 239 ASN cc_start: 0.8903 (m-40) cc_final: 0.8170 (p0) REVERT: I 62 LYS cc_start: 0.8329 (pttp) cc_final: 0.7925 (mttt) REVERT: I 198 ASP cc_start: 0.7919 (t70) cc_final: 0.6971 (p0) REVERT: I 201 TYR cc_start: 0.8823 (m-80) cc_final: 0.8088 (m-80) REVERT: I 290 ASP cc_start: 0.8240 (p0) cc_final: 0.7994 (p0) REVERT: J 233 LYS cc_start: 0.7691 (mmmm) cc_final: 0.7356 (mmmm) REVERT: J 239 ASN cc_start: 0.8996 (m-40) cc_final: 0.8232 (p0) REVERT: J 267 VAL cc_start: 0.8877 (t) cc_final: 0.8618 (m) REVERT: K 62 LYS cc_start: 0.8398 (pttp) cc_final: 0.8022 (mttt) REVERT: K 239 ASN cc_start: 0.8339 (m-40) cc_final: 0.7709 (p0) REVERT: K 267 VAL cc_start: 0.9177 (t) cc_final: 0.8862 (m) REVERT: K 279 MET cc_start: 0.8015 (mtt) cc_final: 0.7792 (mtt) REVERT: L 62 LYS cc_start: 0.8834 (pttp) cc_final: 0.8159 (mttp) REVERT: M 233 LYS cc_start: 0.8370 (mttt) cc_final: 0.7971 (mmmm) REVERT: M 267 VAL cc_start: 0.9072 (t) cc_final: 0.8740 (m) REVERT: M 279 MET cc_start: 0.8349 (mtt) cc_final: 0.7749 (mtt) REVERT: N 62 LYS cc_start: 0.8131 (pttp) cc_final: 0.7890 (mttp) REVERT: N 201 TYR cc_start: 0.8551 (m-80) cc_final: 0.8291 (m-80) REVERT: N 233 LYS cc_start: 0.7986 (mttt) cc_final: 0.7534 (mmmm) REVERT: N 279 MET cc_start: 0.8135 (mtt) cc_final: 0.7522 (mtt) REVERT: N 290 ASP cc_start: 0.8373 (p0) cc_final: 0.8116 (p0) REVERT: O 46 GLN cc_start: 0.8399 (pm20) cc_final: 0.7961 (pm20) REVERT: O 62 LYS cc_start: 0.8539 (pttp) cc_final: 0.8196 (mttp) REVERT: O 94 ILE cc_start: 0.9301 (mt) cc_final: 0.9092 (tt) REVERT: O 236 ARG cc_start: 0.3920 (tpt170) cc_final: 0.3076 (tpt170) REVERT: O 262 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8194 (pm20) REVERT: P 116 LYS cc_start: 0.8965 (mttt) cc_final: 0.8551 (pttt) REVERT: P 198 ASP cc_start: 0.8655 (t0) cc_final: 0.8393 (t0) REVERT: P 233 LYS cc_start: 0.7958 (mttt) cc_final: 0.7460 (mmmm) REVERT: Q 116 LYS cc_start: 0.8835 (mttt) cc_final: 0.8571 (pttt) REVERT: Q 236 ARG cc_start: 0.4685 (tpt170) cc_final: 0.4185 (tpp-160) REVERT: Q 279 MET cc_start: 0.8107 (mtt) cc_final: 0.7674 (mtt) REVERT: R 62 LYS cc_start: 0.8787 (pttp) cc_final: 0.8066 (mttp) REVERT: R 63 ASP cc_start: 0.8638 (t70) cc_final: 0.8338 (t70) REVERT: R 225 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8354 (t80) REVERT: R 239 ASN cc_start: 0.8818 (m-40) cc_final: 0.8273 (p0) REVERT: R 279 MET cc_start: 0.8526 (mtt) cc_final: 0.8175 (mtm) REVERT: S 62 LYS cc_start: 0.8342 (pttp) cc_final: 0.7704 (mttp) REVERT: S 116 LYS cc_start: 0.8811 (mttt) cc_final: 0.8479 (pttt) REVERT: S 200 GLN cc_start: 0.8344 (mp10) cc_final: 0.8126 (pt0) REVERT: S 253 PRO cc_start: 0.9337 (Cg_exo) cc_final: 0.9007 (Cg_endo) REVERT: S 262 GLN cc_start: 0.8721 (pm20) cc_final: 0.8110 (pm20) REVERT: S 290 ASP cc_start: 0.8621 (p0) cc_final: 0.8281 (p0) REVERT: T 62 LYS cc_start: 0.8206 (pttp) cc_final: 0.7954 (mttp) REVERT: T 116 LYS cc_start: 0.8815 (mttt) cc_final: 0.8498 (pttt) REVERT: T 225 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.8286 (t80) REVERT: T 275 ASN cc_start: 0.8695 (t0) cc_final: 0.8413 (t0) REVERT: T 279 MET cc_start: 0.8514 (mtt) cc_final: 0.8075 (mtt) REVERT: U 116 LYS cc_start: 0.9047 (mttt) cc_final: 0.8542 (pttt) outliers start: 137 outliers final: 116 residues processed: 898 average time/residue: 0.2259 time to fit residues: 341.3223 Evaluate side-chains 884 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 765 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 46 GLN Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 225 PHE Chi-restraints excluded: chain H residue 293 THR Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 293 THR Chi-restraints excluded: chain L residue 297 SER Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 23 THR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 121 GLN Chi-restraints excluded: chain O residue 225 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 262 GLN Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain P residue 1 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 293 THR Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 293 THR Chi-restraints excluded: chain S residue 1 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 293 THR Chi-restraints excluded: chain T residue 13 ILE Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 91 ILE Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 225 PHE Chi-restraints excluded: chain T residue 238 VAL Chi-restraints excluded: chain T residue 293 THR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 102 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 403 optimal weight: 20.0000 chunk 341 optimal weight: 20.0000 chunk 401 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 317 optimal weight: 0.6980 chunk 333 optimal weight: 40.0000 chunk 95 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 328 optimal weight: 1.9990 chunk 362 optimal weight: 8.9990 chunk 178 optimal weight: 20.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 GLN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN H 46 GLN I 46 GLN J 46 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 99 GLN P 239 ASN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 84 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102075 restraints weight = 96904.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104232 restraints weight = 55569.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105395 restraints weight = 33017.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105902 restraints weight = 22968.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106447 restraints weight = 19236.920| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 39858 Z= 0.169 Angle : 0.656 10.044 54705 Z= 0.342 Chirality : 0.046 0.252 6552 Planarity : 0.003 0.029 6909 Dihedral : 5.282 50.447 5339 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.14 % Allowed : 22.00 % Favored : 74.87 % 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: 0.31 (0.12), residues: 4998 helix: 2.61 (0.19), residues: 714 sheet: 0.64 (0.12), residues: 1701 loop : -0.79 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 226 TYR 0.030 0.002 TYR C 22 PHE 0.017 0.001 PHE S 237 TRP 0.014 0.002 TRP J 211 HIS 0.004 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00388 (39837) covalent geometry : angle 0.65625 (54663) SS BOND : bond 0.00554 ( 21) SS BOND : angle 0.57852 ( 42) hydrogen bonds : bond 0.05363 ( 1576) hydrogen bonds : angle 5.37455 ( 4224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 772 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ASN cc_start: 0.8618 (m-40) cc_final: 0.7762 (p0) REVERT: B 267 VAL cc_start: 0.9091 (t) cc_final: 0.8837 (m) REVERT: B 279 MET cc_start: 0.8349 (mtt) cc_final: 0.7780 (mtt) REVERT: C 279 MET cc_start: 0.8168 (mtt) cc_final: 0.7261 (mtt) REVERT: D 107 ASP cc_start: 0.7352 (p0) cc_final: 0.7040 (t0) REVERT: D 114 ASP cc_start: 0.8868 (t0) cc_final: 0.8642 (t70) REVERT: D 115 ASP cc_start: 0.8884 (t0) cc_final: 0.8483 (t0) REVERT: E 233 LYS cc_start: 0.7781 (mmmm) cc_final: 0.7462 (mmmm) REVERT: E 239 ASN cc_start: 0.8687 (m-40) cc_final: 0.7911 (p0) REVERT: F 114 ASP cc_start: 0.8415 (t0) cc_final: 0.7988 (t0) REVERT: F 233 LYS cc_start: 0.7801 (mmmm) cc_final: 0.7577 (mmmm) REVERT: F 239 ASN cc_start: 0.8830 (m-40) cc_final: 0.8069 (p0) REVERT: F 267 VAL cc_start: 0.8936 (t) cc_final: 0.8661 (m) REVERT: G 114 ASP cc_start: 0.8693 (t70) cc_final: 0.8392 (t0) REVERT: G 115 ASP cc_start: 0.8813 (t0) cc_final: 0.8467 (t0) REVERT: G 201 TYR cc_start: 0.9070 (m-80) cc_final: 0.8607 (m-80) REVERT: G 233 LYS cc_start: 0.8107 (mmmm) cc_final: 0.7658 (mmmm) REVERT: H 114 ASP cc_start: 0.8690 (t0) cc_final: 0.8416 (t0) REVERT: H 233 LYS cc_start: 0.7678 (mmmm) cc_final: 0.7362 (mmmm) REVERT: H 239 ASN cc_start: 0.8922 (m-40) cc_final: 0.8187 (p0) REVERT: I 62 LYS cc_start: 0.8320 (pttp) cc_final: 0.7901 (mttt) REVERT: I 201 TYR cc_start: 0.8781 (m-80) cc_final: 0.8394 (m-80) REVERT: I 290 ASP cc_start: 0.8265 (p0) cc_final: 0.8009 (p0) REVERT: J 233 LYS cc_start: 0.7803 (mmmm) cc_final: 0.7498 (mmmm) REVERT: J 239 ASN cc_start: 0.8982 (m-40) cc_final: 0.8220 (p0) REVERT: J 267 VAL cc_start: 0.8868 (t) cc_final: 0.8607 (m) REVERT: J 279 MET cc_start: 0.8248 (mtt) cc_final: 0.7998 (mtt) REVERT: K 62 LYS cc_start: 0.8294 (pttp) cc_final: 0.7979 (mttt) REVERT: K 63 ASP cc_start: 0.8653 (t70) cc_final: 0.8436 (t70) REVERT: K 201 TYR cc_start: 0.8946 (m-80) cc_final: 0.8604 (m-80) REVERT: K 239 ASN cc_start: 0.8347 (m-40) cc_final: 0.7716 (p0) REVERT: K 279 MET cc_start: 0.8017 (mtt) cc_final: 0.7773 (mtt) REVERT: L 62 LYS cc_start: 0.8795 (pttp) cc_final: 0.8135 (mttp) REVERT: L 286 MET cc_start: 0.9111 (mtm) cc_final: 0.8881 (mtm) REVERT: M 267 VAL cc_start: 0.9109 (t) cc_final: 0.8791 (m) REVERT: M 279 MET cc_start: 0.8352 (mtt) cc_final: 0.7727 (mtt) REVERT: N 62 LYS cc_start: 0.8144 (pttp) cc_final: 0.7863 (mttp) REVERT: N 201 TYR cc_start: 0.8583 (m-80) cc_final: 0.8269 (m-80) REVERT: N 233 LYS cc_start: 0.8031 (mttt) cc_final: 0.7558 (mmmm) REVERT: N 279 MET cc_start: 0.8098 (mtt) cc_final: 0.7415 (mtt) REVERT: N 290 ASP cc_start: 0.8407 (p0) cc_final: 0.8147 (p0) REVERT: O 62 LYS cc_start: 0.8690 (pttp) cc_final: 0.8221 (mttt) REVERT: O 94 ILE cc_start: 0.9293 (mt) cc_final: 0.9084 (tt) REVERT: O 121 GLN cc_start: 0.6396 (OUTLIER) cc_final: 0.6004 (mt0) REVERT: O 236 ARG cc_start: 0.3751 (tpt170) cc_final: 0.2855 (tpt170) REVERT: O 262 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8224 (pm20) REVERT: P 46 GLN cc_start: 0.8208 (pm20) cc_final: 0.7878 (pm20) REVERT: P 116 LYS cc_start: 0.9027 (mttt) cc_final: 0.8534 (pttt) REVERT: P 233 LYS cc_start: 0.7996 (mttt) cc_final: 0.7458 (mmmm) REVERT: P 262 GLN cc_start: 0.7797 (pm20) cc_final: 0.7483 (pm20) REVERT: Q 116 LYS cc_start: 0.8854 (mttt) cc_final: 0.8559 (pttt) REVERT: Q 236 ARG cc_start: 0.4730 (tpt170) cc_final: 0.4253 (tpp-160) REVERT: Q 279 MET cc_start: 0.8118 (mtt) cc_final: 0.7682 (mtt) REVERT: R 62 LYS cc_start: 0.8887 (pttp) cc_final: 0.8083 (mttp) REVERT: R 63 ASP cc_start: 0.8565 (t70) cc_final: 0.8289 (t70) REVERT: R 225 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8333 (t80) REVERT: R 239 ASN cc_start: 0.8837 (m-40) cc_final: 0.8193 (p0) REVERT: R 279 MET cc_start: 0.8594 (mtt) cc_final: 0.8235 (mtm) REVERT: S 62 LYS cc_start: 0.8385 (pttp) cc_final: 0.7713 (mttp) REVERT: S 116 LYS cc_start: 0.8758 (mttt) cc_final: 0.8464 (pttt) REVERT: S 200 GLN cc_start: 0.8323 (mp10) cc_final: 0.8111 (pt0) REVERT: S 262 GLN cc_start: 0.8722 (pm20) cc_final: 0.8097 (pm20) REVERT: S 290 ASP cc_start: 0.8622 (p0) cc_final: 0.8271 (p0) REVERT: T 62 LYS cc_start: 0.8154 (pttp) cc_final: 0.7929 (mttp) REVERT: T 116 LYS cc_start: 0.8847 (mttt) cc_final: 0.8488 (pttt) REVERT: T 225 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8405 (t80) REVERT: T 275 ASN cc_start: 0.8754 (t0) cc_final: 0.8497 (t0) REVERT: T 279 MET cc_start: 0.8533 (mtt) cc_final: 0.8317 (mtt) REVERT: U 116 LYS cc_start: 0.9108 (mttt) cc_final: 0.8557 (pttt) outliers start: 135 outliers final: 117 residues processed: 866 average time/residue: 0.2271 time to fit residues: 328.8292 Evaluate side-chains 884 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 763 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 46 GLN Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 297 SER Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 225 PHE Chi-restraints excluded: chain H residue 293 THR Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 297 SER Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 121 GLN Chi-restraints excluded: chain O residue 225 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 262 GLN Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain P residue 1 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 293 THR Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 293 THR Chi-restraints excluded: chain S residue 1 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 293 THR Chi-restraints excluded: chain S residue 297 SER Chi-restraints excluded: chain T residue 13 ILE Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 23 THR Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 75 SER Chi-restraints excluded: chain T residue 91 ILE Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 225 PHE Chi-restraints excluded: chain T residue 257 VAL Chi-restraints excluded: chain T residue 293 THR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 102 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 327 optimal weight: 20.0000 chunk 234 optimal weight: 30.0000 chunk 177 optimal weight: 20.0000 chunk 450 optimal weight: 20.0000 chunk 402 optimal weight: 0.0980 chunk 69 optimal weight: 20.0000 chunk 413 optimal weight: 20.0000 chunk 320 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 21 optimal weight: 0.0370 overall best weight: 4.8264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 46 GLN ** M 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 GLN P 239 ASN Q 46 GLN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.109628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102150 restraints weight = 96336.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104097 restraints weight = 54267.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105247 restraints weight = 32590.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105981 restraints weight = 23493.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.106007 restraints weight = 19218.618| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 39858 Z= 0.162 Angle : 0.661 12.813 54705 Z= 0.341 Chirality : 0.047 0.244 6552 Planarity : 0.003 0.030 6909 Dihedral : 5.235 50.414 5339 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.23 % Allowed : 21.93 % Favored : 74.84 % 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: 0.28 (0.12), residues: 4998 helix: 2.64 (0.19), residues: 714 sheet: 0.60 (0.12), residues: 1701 loop : -0.82 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 226 TYR 0.025 0.002 TYR D 22 PHE 0.017 0.001 PHE S 237 TRP 0.015 0.002 TRP A 211 HIS 0.012 0.001 HIS M 105 Details of bonding type rmsd covalent geometry : bond 0.00374 (39837) covalent geometry : angle 0.66080 (54663) SS BOND : bond 0.00515 ( 21) SS BOND : angle 0.56286 ( 42) hydrogen bonds : bond 0.05296 ( 1576) hydrogen bonds : angle 5.34750 ( 4224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 774 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ASN cc_start: 0.8618 (m-40) cc_final: 0.7753 (p0) REVERT: B 63 ASP cc_start: 0.8290 (m-30) cc_final: 0.8064 (t70) REVERT: B 115 ASP cc_start: 0.8529 (t0) cc_final: 0.8199 (t0) REVERT: B 279 MET cc_start: 0.8428 (mtt) cc_final: 0.7859 (mtt) REVERT: C 294 TRP cc_start: 0.8187 (t-100) cc_final: 0.7816 (t60) REVERT: D 114 ASP cc_start: 0.8883 (t0) cc_final: 0.8647 (t70) REVERT: D 115 ASP cc_start: 0.8887 (t0) cc_final: 0.8489 (t0) REVERT: E 233 LYS cc_start: 0.7839 (mmmm) cc_final: 0.7509 (mmmm) REVERT: E 239 ASN cc_start: 0.8682 (m-40) cc_final: 0.7948 (p0) REVERT: E 279 MET cc_start: 0.8261 (mtt) cc_final: 0.7994 (mtm) REVERT: F 114 ASP cc_start: 0.8448 (t0) cc_final: 0.8017 (t0) REVERT: F 233 LYS cc_start: 0.7866 (mmmm) cc_final: 0.7610 (mmmm) REVERT: F 239 ASN cc_start: 0.8786 (m-40) cc_final: 0.8014 (p0) REVERT: F 267 VAL cc_start: 0.8941 (t) cc_final: 0.8660 (m) REVERT: G 115 ASP cc_start: 0.8808 (t0) cc_final: 0.8469 (t0) REVERT: G 201 TYR cc_start: 0.9080 (m-80) cc_final: 0.8552 (m-80) REVERT: G 233 LYS cc_start: 0.8111 (mmmm) cc_final: 0.7665 (mmmm) REVERT: H 114 ASP cc_start: 0.8698 (t0) cc_final: 0.8417 (t0) REVERT: H 233 LYS cc_start: 0.7689 (mmmm) cc_final: 0.7387 (mmmm) REVERT: H 239 ASN cc_start: 0.8941 (m-40) cc_final: 0.8189 (p0) REVERT: I 62 LYS cc_start: 0.8312 (pttp) cc_final: 0.7872 (mttt) REVERT: I 201 TYR cc_start: 0.8855 (m-80) cc_final: 0.8515 (m-80) REVERT: I 290 ASP cc_start: 0.8268 (p0) cc_final: 0.8016 (p0) REVERT: J 115 ASP cc_start: 0.8928 (t0) cc_final: 0.8366 (t0) REVERT: J 233 LYS cc_start: 0.7843 (mmmm) cc_final: 0.7500 (mmmm) REVERT: J 239 ASN cc_start: 0.8964 (m-40) cc_final: 0.8204 (p0) REVERT: J 267 VAL cc_start: 0.8854 (t) cc_final: 0.8635 (m) REVERT: K 62 LYS cc_start: 0.8320 (pttp) cc_final: 0.7958 (mttt) REVERT: K 63 ASP cc_start: 0.8670 (t70) cc_final: 0.8468 (t70) REVERT: K 201 TYR cc_start: 0.8957 (m-80) cc_final: 0.8590 (m-80) REVERT: K 239 ASN cc_start: 0.8347 (m-40) cc_final: 0.7737 (p0) REVERT: L 62 LYS cc_start: 0.8775 (pttp) cc_final: 0.8067 (mttp) REVERT: L 279 MET cc_start: 0.8546 (mtp) cc_final: 0.7459 (mtp) REVERT: L 286 MET cc_start: 0.9133 (mtm) cc_final: 0.8904 (mtm) REVERT: M 233 LYS cc_start: 0.8065 (mmmm) cc_final: 0.7499 (mmmm) REVERT: M 267 VAL cc_start: 0.9112 (t) cc_final: 0.8805 (m) REVERT: M 279 MET cc_start: 0.8340 (mtt) cc_final: 0.7781 (mtt) REVERT: N 201 TYR cc_start: 0.8588 (m-80) cc_final: 0.8300 (m-80) REVERT: N 233 LYS cc_start: 0.8069 (mttt) cc_final: 0.7584 (mmmm) REVERT: N 279 MET cc_start: 0.8164 (mtt) cc_final: 0.7547 (mtt) REVERT: N 290 ASP cc_start: 0.8420 (p0) cc_final: 0.8183 (p0) REVERT: O 62 LYS cc_start: 0.8694 (pttp) cc_final: 0.8209 (mttt) REVERT: O 94 ILE cc_start: 0.9290 (mt) cc_final: 0.9076 (tt) REVERT: O 121 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.5876 (mt0) REVERT: O 236 ARG cc_start: 0.3839 (tpt170) cc_final: 0.2767 (tpt-90) REVERT: O 262 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8181 (pm20) REVERT: P 46 GLN cc_start: 0.8175 (pm20) cc_final: 0.7869 (pm20) REVERT: P 116 LYS cc_start: 0.9036 (mttt) cc_final: 0.8512 (pttt) REVERT: P 198 ASP cc_start: 0.8795 (t0) cc_final: 0.8253 (p0) REVERT: P 233 LYS cc_start: 0.8024 (mttt) cc_final: 0.7477 (mmmm) REVERT: Q 116 LYS cc_start: 0.8865 (mttt) cc_final: 0.8588 (pttt) REVERT: Q 236 ARG cc_start: 0.4798 (tpt170) cc_final: 0.4342 (tpp-160) REVERT: Q 279 MET cc_start: 0.8182 (mtt) cc_final: 0.7799 (mtt) REVERT: R 62 LYS cc_start: 0.8896 (pttp) cc_final: 0.8071 (mttp) REVERT: R 63 ASP cc_start: 0.8587 (t70) cc_final: 0.8314 (t70) REVERT: R 225 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8395 (t80) REVERT: R 239 ASN cc_start: 0.8835 (m-40) cc_final: 0.8165 (p0) REVERT: R 279 MET cc_start: 0.8587 (mtt) cc_final: 0.8171 (mtm) REVERT: S 62 LYS cc_start: 0.8396 (pttp) cc_final: 0.7709 (mttp) REVERT: S 116 LYS cc_start: 0.8747 (mttt) cc_final: 0.8452 (pttt) REVERT: S 262 GLN cc_start: 0.8731 (pm20) cc_final: 0.8089 (pm20) REVERT: S 290 ASP cc_start: 0.8632 (p0) cc_final: 0.8288 (p0) REVERT: T 62 LYS cc_start: 0.8212 (pttp) cc_final: 0.7928 (mttp) REVERT: T 116 LYS cc_start: 0.8880 (mttt) cc_final: 0.8506 (pttt) REVERT: T 225 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8400 (t80) REVERT: T 275 ASN cc_start: 0.8752 (t0) cc_final: 0.8514 (t0) REVERT: U 116 LYS cc_start: 0.9139 (mttt) cc_final: 0.8569 (pttt) REVERT: U 236 ARG cc_start: 0.3166 (tpt170) cc_final: 0.2800 (tpt170) outliers start: 139 outliers final: 122 residues processed: 875 average time/residue: 0.2275 time to fit residues: 334.3252 Evaluate side-chains 883 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 757 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 297 SER Chi-restraints excluded: chain H residue 1 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 225 PHE Chi-restraints excluded: chain H residue 293 THR Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 297 SER Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 121 GLN Chi-restraints excluded: chain O residue 225 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 262 GLN Chi-restraints excluded: chain O residue 293 THR Chi-restraints excluded: chain P residue 1 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 293 THR Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 293 THR Chi-restraints excluded: chain S residue 1 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 257 VAL Chi-restraints excluded: chain S residue 293 THR Chi-restraints excluded: chain S residue 297 SER Chi-restraints excluded: chain T residue 13 ILE Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 23 THR Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 75 SER Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 225 PHE Chi-restraints excluded: chain T residue 238 VAL Chi-restraints excluded: chain T residue 257 VAL Chi-restraints excluded: chain T residue 293 THR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 102 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 468 optimal weight: 0.1980 chunk 168 optimal weight: 1.9990 chunk 353 optimal weight: 7.9990 chunk 93 optimal weight: 0.0670 chunk 257 optimal weight: 7.9990 chunk 464 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 380 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 379 optimal weight: 7.9990 overall best weight: 2.6524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 46 GLN L 219 ASN N 46 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 200 GLN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 239 ASN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN U 84 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103793 restraints weight = 95335.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105734 restraints weight = 53333.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107107 restraints weight = 32067.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108120 restraints weight = 22231.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108120 restraints weight = 17153.872| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 39858 Z= 0.127 Angle : 0.653 12.606 54705 Z= 0.330 Chirality : 0.046 0.251 6552 Planarity : 0.003 0.032 6909 Dihedral : 5.012 47.934 5339 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.60 % Allowed : 22.81 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.34 (0.12), residues: 4998 helix: 2.74 (0.19), residues: 714 sheet: 0.60 (0.12), residues: 1701 loop : -0.77 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 226 TYR 0.023 0.002 TYR D 22 PHE 0.018 0.001 PHE S 237 TRP 0.015 0.001 TRP D 211 HIS 0.004 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00289 (39837) covalent geometry : angle 0.65326 (54663) SS BOND : bond 0.00253 ( 21) SS BOND : angle 0.40644 ( 42) hydrogen bonds : bond 0.04795 ( 1576) hydrogen bonds : angle 5.19067 ( 4224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 787 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ASN cc_start: 0.8580 (m-40) cc_final: 0.7718 (p0) REVERT: B 63 ASP cc_start: 0.8279 (m-30) cc_final: 0.8060 (t70) REVERT: B 279 MET cc_start: 0.8430 (mtt) cc_final: 0.7873 (mtt) REVERT: C 279 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.6890 (mtt) REVERT: C 294 TRP cc_start: 0.8083 (t-100) cc_final: 0.7726 (t60) REVERT: D 114 ASP cc_start: 0.8843 (t0) cc_final: 0.8622 (t70) REVERT: D 115 ASP cc_start: 0.8788 (t0) cc_final: 0.8362 (t0) REVERT: E 233 LYS cc_start: 0.7796 (mmmm) cc_final: 0.7481 (mmmm) REVERT: E 239 ASN cc_start: 0.8663 (m-40) cc_final: 0.7939 (p0) REVERT: E 279 MET cc_start: 0.8286 (mtt) cc_final: 0.8039 (mtm) REVERT: F 114 ASP cc_start: 0.8402 (t0) cc_final: 0.7976 (t0) REVERT: F 201 TYR cc_start: 0.8624 (m-80) cc_final: 0.8308 (m-80) REVERT: F 233 LYS cc_start: 0.7843 (mmmm) cc_final: 0.7599 (mmmm) REVERT: F 239 ASN cc_start: 0.8769 (m-40) cc_final: 0.7999 (p0) REVERT: F 267 VAL cc_start: 0.8959 (t) cc_final: 0.8709 (m) REVERT: G 201 TYR cc_start: 0.9079 (m-80) cc_final: 0.7875 (m-80) REVERT: G 233 LYS cc_start: 0.8041 (mmmm) cc_final: 0.7666 (mmmm) REVERT: G 279 MET cc_start: 0.8468 (mtt) cc_final: 0.8108 (mtm) REVERT: H 114 ASP cc_start: 0.8655 (t0) cc_final: 0.8309 (t0) REVERT: H 233 LYS cc_start: 0.7658 (mmmm) cc_final: 0.7390 (mmmm) REVERT: H 239 ASN cc_start: 0.8928 (m-40) cc_final: 0.8172 (p0) REVERT: I 62 LYS cc_start: 0.8303 (pttp) cc_final: 0.7846 (mttt) REVERT: I 201 TYR cc_start: 0.8808 (m-80) cc_final: 0.8578 (m-80) REVERT: I 239 ASN cc_start: 0.8587 (m110) cc_final: 0.7934 (p0) REVERT: I 290 ASP cc_start: 0.8286 (p0) cc_final: 0.8014 (p0) REVERT: J 115 ASP cc_start: 0.8895 (t0) cc_final: 0.8590 (t70) REVERT: J 233 LYS cc_start: 0.7788 (mmmm) cc_final: 0.7474 (mmmm) REVERT: J 239 ASN cc_start: 0.8938 (m-40) cc_final: 0.8183 (p0) REVERT: J 267 VAL cc_start: 0.8862 (t) cc_final: 0.8642 (m) REVERT: K 26 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8313 (p) REVERT: K 62 LYS cc_start: 0.8303 (pttp) cc_final: 0.7950 (mttt) REVERT: K 63 ASP cc_start: 0.8622 (t70) cc_final: 0.8416 (t70) REVERT: K 201 TYR cc_start: 0.8926 (m-80) cc_final: 0.8641 (m-80) REVERT: K 239 ASN cc_start: 0.8387 (m-40) cc_final: 0.7748 (p0) REVERT: K 279 MET cc_start: 0.8073 (mtt) cc_final: 0.7228 (mtm) REVERT: L 62 LYS cc_start: 0.8760 (pttp) cc_final: 0.8037 (mttt) REVERT: L 279 MET cc_start: 0.8507 (mtp) cc_final: 0.7412 (mtp) REVERT: L 286 MET cc_start: 0.9134 (mtm) cc_final: 0.8895 (mtm) REVERT: M 233 LYS cc_start: 0.8085 (mmmm) cc_final: 0.7567 (mmmm) REVERT: M 267 VAL cc_start: 0.9119 (t) cc_final: 0.8832 (m) REVERT: M 279 MET cc_start: 0.8296 (mtt) cc_final: 0.7712 (mtt) REVERT: N 201 TYR cc_start: 0.8569 (m-80) cc_final: 0.8259 (m-80) REVERT: N 233 LYS cc_start: 0.8021 (mttt) cc_final: 0.7532 (mmmm) REVERT: N 290 ASP cc_start: 0.8354 (p0) cc_final: 0.8149 (p0) REVERT: O 62 LYS cc_start: 0.8688 (pttp) cc_final: 0.8213 (mttt) REVERT: O 94 ILE cc_start: 0.9255 (mt) cc_final: 0.9044 (tt) REVERT: O 121 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.5831 (mt0) REVERT: O 236 ARG cc_start: 0.3051 (tpt170) cc_final: 0.2125 (tpt-90) REVERT: O 262 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8094 (pm20) REVERT: O 279 MET cc_start: 0.7882 (mtt) cc_final: 0.7672 (mtt) REVERT: P 46 GLN cc_start: 0.8197 (pm20) cc_final: 0.7842 (pm20) REVERT: P 116 LYS cc_start: 0.8988 (mttt) cc_final: 0.8472 (pttt) REVERT: P 233 LYS cc_start: 0.8004 (mttt) cc_final: 0.7470 (mmmm) REVERT: P 279 MET cc_start: 0.8505 (mtt) cc_final: 0.8189 (mtm) REVERT: Q 116 LYS cc_start: 0.8848 (mttt) cc_final: 0.8553 (pttt) REVERT: Q 236 ARG cc_start: 0.4704 (tpt170) cc_final: 0.4257 (tpp-160) REVERT: Q 279 MET cc_start: 0.8203 (mtt) cc_final: 0.7815 (mtt) REVERT: R 62 LYS cc_start: 0.8756 (pttp) cc_final: 0.8032 (mttp) REVERT: R 63 ASP cc_start: 0.8549 (t70) cc_final: 0.8304 (t70) REVERT: R 225 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8373 (t80) REVERT: R 239 ASN cc_start: 0.8802 (m-40) cc_final: 0.8224 (p0) REVERT: R 279 MET cc_start: 0.8453 (mtt) cc_final: 0.8212 (mtm) REVERT: S 62 LYS cc_start: 0.8361 (pttp) cc_final: 0.7675 (mttp) REVERT: S 116 LYS cc_start: 0.8704 (mttt) cc_final: 0.8413 (pttt) REVERT: S 262 GLN cc_start: 0.8711 (pm20) cc_final: 0.8092 (pm20) REVERT: S 290 ASP cc_start: 0.8637 (p0) cc_final: 0.8258 (p0) REVERT: T 62 LYS cc_start: 0.8171 (pttp) cc_final: 0.7869 (mttp) REVERT: T 116 LYS cc_start: 0.8864 (mttt) cc_final: 0.8484 (pttt) REVERT: T 225 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8335 (t80) REVERT: U 116 LYS cc_start: 0.9083 (mttt) cc_final: 0.8513 (pttt) REVERT: U 236 ARG cc_start: 0.3198 (tpt170) cc_final: 0.2834 (tpt170) outliers start: 112 outliers final: 96 residues processed: 866 average time/residue: 0.2317 time to fit residues: 335.7950 Evaluate side-chains 852 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 750 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 297 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 225 PHE Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 297 SER Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 121 GLN Chi-restraints excluded: chain O residue 225 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 262 GLN Chi-restraints excluded: chain P residue 1 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 23 THR Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 225 PHE Chi-restraints excluded: chain T residue 257 VAL Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 203 optimal weight: 8.9990 chunk 368 optimal weight: 20.0000 chunk 198 optimal weight: 7.9990 chunk 490 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 326 optimal weight: 6.9990 chunk 133 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS G 46 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 HIS N 46 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 GLN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 239 ASN Q 46 GLN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102239 restraints weight = 96432.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.104476 restraints weight = 53717.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105314 restraints weight = 32282.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106130 restraints weight = 24418.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106746 restraints weight = 19323.379| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 39858 Z= 0.179 Angle : 0.687 12.255 54705 Z= 0.354 Chirality : 0.047 0.277 6552 Planarity : 0.003 0.034 6909 Dihedral : 5.077 47.391 5337 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.58 % Allowed : 22.93 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.12), residues: 4998 helix: 2.56 (0.19), residues: 714 sheet: 0.53 (0.12), residues: 1701 loop : -0.87 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 226 TYR 0.023 0.002 TYR M 98 PHE 0.015 0.001 PHE S 237 TRP 0.041 0.002 TRP D 294 HIS 0.004 0.001 HIS O 105 Details of bonding type rmsd covalent geometry : bond 0.00417 (39837) covalent geometry : angle 0.68742 (54663) SS BOND : bond 0.00611 ( 21) SS BOND : angle 0.59376 ( 42) hydrogen bonds : bond 0.05201 ( 1576) hydrogen bonds : angle 5.32664 ( 4224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9996 Ramachandran restraints generated. 4998 Oldfield, 0 Emsley, 4998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 762 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ASN cc_start: 0.8621 (m-40) cc_final: 0.7723 (p0) REVERT: B 279 MET cc_start: 0.8531 (mtt) cc_final: 0.7946 (mtt) REVERT: C 279 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.6981 (mtt) REVERT: C 294 TRP cc_start: 0.8292 (t-100) cc_final: 0.7711 (t60) REVERT: D 114 ASP cc_start: 0.8836 (t0) cc_final: 0.8634 (t70) REVERT: D 115 ASP cc_start: 0.8807 (t0) cc_final: 0.8426 (t0) REVERT: E 233 LYS cc_start: 0.7820 (mmmm) cc_final: 0.7462 (mmmm) REVERT: E 239 ASN cc_start: 0.8691 (m-40) cc_final: 0.7937 (p0) REVERT: E 279 MET cc_start: 0.8362 (mtt) cc_final: 0.8104 (mtm) REVERT: F 114 ASP cc_start: 0.8418 (t0) cc_final: 0.7991 (t0) REVERT: F 233 LYS cc_start: 0.7838 (mmmm) cc_final: 0.7568 (mmmm) REVERT: F 239 ASN cc_start: 0.8754 (m-40) cc_final: 0.7972 (p0) REVERT: F 267 VAL cc_start: 0.8959 (t) cc_final: 0.8687 (m) REVERT: G 201 TYR cc_start: 0.8984 (m-80) cc_final: 0.8780 (m-80) REVERT: G 212 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7243 (mt-10) REVERT: H 114 ASP cc_start: 0.8729 (t0) cc_final: 0.8369 (t0) REVERT: H 233 LYS cc_start: 0.7745 (mmmm) cc_final: 0.7438 (mmmm) REVERT: H 239 ASN cc_start: 0.8957 (m-40) cc_final: 0.8195 (p0) REVERT: I 62 LYS cc_start: 0.8320 (pttp) cc_final: 0.7869 (mttt) REVERT: I 201 TYR cc_start: 0.8861 (m-80) cc_final: 0.8600 (m-80) REVERT: I 233 LYS cc_start: 0.7566 (mmmm) cc_final: 0.7274 (mmmm) REVERT: I 239 ASN cc_start: 0.8616 (m110) cc_final: 0.7939 (p0) REVERT: I 290 ASP cc_start: 0.8274 (p0) cc_final: 0.8038 (p0) REVERT: J 115 ASP cc_start: 0.8916 (t0) cc_final: 0.8387 (t0) REVERT: J 233 LYS cc_start: 0.7798 (mmmm) cc_final: 0.7414 (mmmm) REVERT: J 239 ASN cc_start: 0.8920 (m-40) cc_final: 0.8154 (p0) REVERT: J 267 VAL cc_start: 0.8845 (t) cc_final: 0.8623 (m) REVERT: K 26 SER cc_start: 0.9046 (OUTLIER) cc_final: 0.8368 (p) REVERT: K 62 LYS cc_start: 0.8271 (pttp) cc_final: 0.7987 (mttt) REVERT: K 63 ASP cc_start: 0.8629 (t70) cc_final: 0.8415 (t70) REVERT: K 201 TYR cc_start: 0.8949 (m-80) cc_final: 0.8598 (m-80) REVERT: K 239 ASN cc_start: 0.8383 (m-40) cc_final: 0.7717 (p0) REVERT: K 279 MET cc_start: 0.8186 (mtt) cc_final: 0.7965 (mtm) REVERT: L 62 LYS cc_start: 0.8734 (pttp) cc_final: 0.7974 (mttt) REVERT: L 286 MET cc_start: 0.9131 (mtm) cc_final: 0.8897 (mtm) REVERT: M 233 LYS cc_start: 0.8094 (mmmm) cc_final: 0.7576 (mmmm) REVERT: M 267 VAL cc_start: 0.9119 (t) cc_final: 0.8838 (m) REVERT: M 279 MET cc_start: 0.8385 (mtt) cc_final: 0.7799 (mtt) REVERT: N 201 TYR cc_start: 0.8647 (m-80) cc_final: 0.8343 (m-80) REVERT: N 233 LYS cc_start: 0.8115 (mttt) cc_final: 0.7583 (mmmm) REVERT: N 290 ASP cc_start: 0.8439 (p0) cc_final: 0.8200 (p0) REVERT: O 62 LYS cc_start: 0.8685 (pttp) cc_final: 0.8203 (mttp) REVERT: O 94 ILE cc_start: 0.9264 (mt) cc_final: 0.9043 (tt) REVERT: O 121 GLN cc_start: 0.6479 (OUTLIER) cc_final: 0.5971 (mt0) REVERT: O 236 ARG cc_start: 0.3197 (tpt170) cc_final: 0.2184 (tpt-90) REVERT: O 262 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: O 279 MET cc_start: 0.8039 (mtt) cc_final: 0.7795 (mtt) REVERT: P 46 GLN cc_start: 0.8162 (pm20) cc_final: 0.7851 (pm20) REVERT: P 116 LYS cc_start: 0.9047 (mttt) cc_final: 0.8491 (pttt) REVERT: P 233 LYS cc_start: 0.8013 (mttt) cc_final: 0.7460 (mmmm) REVERT: P 279 MET cc_start: 0.8633 (mtt) cc_final: 0.8370 (mtm) REVERT: Q 116 LYS cc_start: 0.8893 (mttt) cc_final: 0.8544 (pttt) REVERT: Q 236 ARG cc_start: 0.4870 (tpt170) cc_final: 0.4460 (tpp-160) REVERT: Q 279 MET cc_start: 0.8307 (mtt) cc_final: 0.7938 (mtt) REVERT: R 62 LYS cc_start: 0.8891 (pttp) cc_final: 0.8079 (mttp) REVERT: R 63 ASP cc_start: 0.8574 (t70) cc_final: 0.8308 (t70) REVERT: R 225 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8315 (t80) REVERT: R 239 ASN cc_start: 0.8805 (m-40) cc_final: 0.8136 (p0) REVERT: R 279 MET cc_start: 0.8594 (mtt) cc_final: 0.8161 (mtm) REVERT: S 62 LYS cc_start: 0.8375 (pttp) cc_final: 0.7692 (mttp) REVERT: S 116 LYS cc_start: 0.8727 (mttt) cc_final: 0.8421 (pttt) REVERT: S 262 GLN cc_start: 0.8728 (pm20) cc_final: 0.8085 (pm20) REVERT: S 290 ASP cc_start: 0.8644 (p0) cc_final: 0.8301 (p0) REVERT: T 62 LYS cc_start: 0.8216 (pttp) cc_final: 0.7909 (mttp) REVERT: T 116 LYS cc_start: 0.8885 (mttt) cc_final: 0.8479 (pttt) REVERT: T 225 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8266 (t80) REVERT: U 116 LYS cc_start: 0.9153 (mttt) cc_final: 0.8561 (pttt) REVERT: U 236 ARG cc_start: 0.3110 (tpt170) cc_final: 0.2776 (tpt170) outliers start: 111 outliers final: 99 residues processed: 843 average time/residue: 0.2283 time to fit residues: 324.2587 Evaluate side-chains 849 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 744 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain D residue 1 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 46 GLN Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 297 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 225 PHE Chi-restraints excluded: chain H residue 293 THR Chi-restraints excluded: chain I residue 1 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 297 SER Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 297 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 46 GLN Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 121 GLN Chi-restraints excluded: chain O residue 225 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 262 GLN Chi-restraints excluded: chain P residue 1 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 102 VAL Chi-restraints excluded: chain P residue 216 VAL Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 46 GLN Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain S residue 1 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 257 VAL Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 23 THR Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain T residue 225 PHE Chi-restraints excluded: chain T residue 257 VAL Chi-restraints excluded: chain T residue 293 THR Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 46 GLN Chi-restraints excluded: chain U residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 468 optimal weight: 0.0670 chunk 78 optimal weight: 0.0770 chunk 448 optimal weight: 10.0000 chunk 279 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 360 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 338 optimal weight: 4.9990 overall best weight: 2.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 46 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 239 ASN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103859 restraints weight = 95438.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105856 restraints weight = 54664.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107111 restraints weight = 32282.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.108131 restraints weight = 22198.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108201 restraints weight = 17061.497| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 39858 Z= 0.130 Angle : 0.672 12.251 54705 Z= 0.339 Chirality : 0.047 0.262 6552 Planarity : 0.003 0.040 6909 Dihedral : 4.913 44.028 5335 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.28 % Allowed : 23.79 % Favored : 73.94 % 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: 0.24 (0.12), residues: 4998 helix: 2.58 (0.19), residues: 714 sheet: 0.55 (0.12), residues: 1701 loop : -0.81 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 226 TYR 0.023 0.002 TYR L 201 PHE 0.018 0.001 PHE S 237 TRP 0.034 0.002 TRP D 294 HIS 0.005 0.001 HIS O 105 Details of bonding type rmsd covalent geometry : bond 0.00298 (39837) covalent geometry : angle 0.67177 (54663) SS BOND : bond 0.00260 ( 21) SS BOND : angle 0.39976 ( 42) hydrogen bonds : bond 0.04819 ( 1576) hydrogen bonds : angle 5.23076 ( 4224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7383.61 seconds wall clock time: 128 minutes 5.08 seconds (7685.08 seconds total)