Starting phenix.real_space_refine on Sat Mar 7 14:29:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ytl_10919/03_2026/6ytl_10919.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ytl_10919/03_2026/6ytl_10919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ytl_10919/03_2026/6ytl_10919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ytl_10919/03_2026/6ytl_10919.map" model { file = "/net/cci-nas-00/data/ceres_data/6ytl_10919/03_2026/6ytl_10919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ytl_10919/03_2026/6ytl_10919.cif" } resolution = 3.82 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= 0.001 sd= 0.007 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 440 5.16 5 C 29480 2.51 5 N 7678 2.21 5 O 8184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 165 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45782 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "B" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "C" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "D" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "E" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "F" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "G" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "H" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "I" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "J" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "K" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "L" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "M" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "N" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "O" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "P" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "Q" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "R" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "S" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "T" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "U" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "V" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Time building chain proxies: 10.40, per 1000 atoms: 0.23 Number of scatterers: 45782 At special positions: 0 Unit cell: (140.7, 140.7, 207.7, 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 440 16.00 O 8184 8.00 N 7678 7.00 C 29480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 162 " distance=2.04 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 131 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 131 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 131 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 162 " distance=2.03 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 131 " distance=2.03 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 131 " distance=2.03 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 131 " distance=2.03 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 162 " distance=2.03 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 131 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 162 " distance=2.03 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 131 " distance=2.03 Simple disulfide: pdb=" SG CYS M 43 " - pdb=" SG CYS M 162 " distance=2.03 Simple disulfide: pdb=" SG CYS N 41 " - pdb=" SG CYS N 131 " distance=2.03 Simple disulfide: pdb=" SG CYS N 43 " - pdb=" SG CYS N 162 " distance=2.03 Simple disulfide: pdb=" SG CYS O 41 " - pdb=" SG CYS O 131 " distance=2.03 Simple disulfide: pdb=" SG CYS O 43 " - pdb=" SG CYS O 162 " distance=2.03 Simple disulfide: pdb=" SG CYS P 41 " - pdb=" SG CYS P 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 43 " - pdb=" SG CYS P 162 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 41 " - pdb=" SG CYS Q 131 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 43 " - pdb=" SG CYS Q 162 " distance=2.03 Simple disulfide: pdb=" SG CYS R 41 " - pdb=" SG CYS R 131 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 162 " distance=2.03 Simple disulfide: pdb=" SG CYS S 41 " - pdb=" SG CYS S 131 " distance=2.03 Simple disulfide: pdb=" SG CYS S 43 " - pdb=" SG CYS S 162 " distance=2.03 Simple disulfide: pdb=" SG CYS T 41 " - pdb=" SG CYS T 131 " distance=2.03 Simple disulfide: pdb=" SG CYS T 43 " - pdb=" SG CYS T 162 " distance=2.03 Simple disulfide: pdb=" SG CYS U 41 " - pdb=" SG CYS U 131 " distance=2.03 Simple disulfide: pdb=" SG CYS U 43 " - pdb=" SG CYS U 162 " distance=2.03 Simple disulfide: pdb=" SG CYS V 41 " - pdb=" SG CYS V 131 " distance=2.03 Simple disulfide: pdb=" SG CYS V 43 " - pdb=" SG CYS V 162 " distance=2.03 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: 3.57 Conformation dependent library (CDL) restraints added in 1.7 seconds 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11176 Finding SS restraints... Secondary structure from input PDB file: 242 helices and 0 sheets defined 80.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 70 removed outlier: 3.725A pdb=" N PHE A 55 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 167 through 211 Processing helix chain 'A' and resid 216 through 253 Processing helix chain 'A' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 70 removed outlier: 3.724A pdb=" N PHE B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 158 Processing helix chain 'B' and resid 167 through 211 Processing helix chain 'B' and resid 216 through 253 Processing helix chain 'B' and resid 268 through 276 removed outlier: 4.099A pdb=" N TRP B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 70 removed outlier: 3.724A pdb=" N PHE C 55 " --> pdb=" O TYR C 51 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 112 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 167 through 211 Processing helix chain 'C' and resid 216 through 253 Processing helix chain 'C' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 70 removed outlier: 3.724A pdb=" N PHE D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP D 75 " --> pdb=" O ARG D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 112 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS D 131 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 158 Processing helix chain 'D' and resid 167 through 211 Processing helix chain 'D' and resid 216 through 253 Processing helix chain 'D' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS D 273 " --> pdb=" O CYS D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 70 removed outlier: 3.724A pdb=" N PHE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP E 75 " --> pdb=" O ARG E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 112 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.552A pdb=" N LEU E 116 " --> pdb=" O VAL E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS E 131 " --> pdb=" O THR E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 167 through 211 Processing helix chain 'E' and resid 216 through 253 Processing helix chain 'E' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP E 272 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS E 273 " --> pdb=" O CYS E 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 70 removed outlier: 3.725A pdb=" N PHE F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 71 through 82 removed outlier: 3.730A pdb=" N TRP F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 112 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS F 131 " --> pdb=" O THR F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 158 Processing helix chain 'F' and resid 167 through 211 Processing helix chain 'F' and resid 216 through 253 Processing helix chain 'F' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP F 272 " --> pdb=" O SER F 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS F 273 " --> pdb=" O CYS F 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 15 through 39 removed outlier: 3.591A pdb=" N PHE G 39 " --> pdb=" O SER G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 70 removed outlier: 3.725A pdb=" N PHE G 55 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 112 Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU G 116 " --> pdb=" O VAL G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 133 removed outlier: 3.741A pdb=" N CYS G 131 " --> pdb=" O THR G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 158 Processing helix chain 'G' and resid 167 through 211 Processing helix chain 'G' and resid 216 through 253 Processing helix chain 'G' and resid 268 through 276 removed outlier: 4.097A pdb=" N TRP G 272 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS G 273 " --> pdb=" O CYS G 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 70 removed outlier: 3.723A pdb=" N PHE H 55 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 112 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS H 131 " --> pdb=" O THR H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 158 Processing helix chain 'H' and resid 167 through 211 Processing helix chain 'H' and resid 216 through 253 Processing helix chain 'H' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP H 272 " --> pdb=" O SER H 268 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS H 273 " --> pdb=" O CYS H 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 15 through 39 removed outlier: 3.591A pdb=" N PHE I 39 " --> pdb=" O SER I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 70 removed outlier: 3.724A pdb=" N PHE I 55 " --> pdb=" O TYR I 51 " (cutoff:3.500A) Proline residue: I 59 - end of helix Processing helix chain 'I' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP I 75 " --> pdb=" O ARG I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 112 Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.552A pdb=" N LEU I 116 " --> pdb=" O VAL I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS I 131 " --> pdb=" O THR I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 158 Processing helix chain 'I' and resid 167 through 211 Processing helix chain 'I' and resid 216 through 253 Processing helix chain 'I' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP I 272 " --> pdb=" O SER I 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS I 273 " --> pdb=" O CYS I 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE J 39 " --> pdb=" O SER J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 70 removed outlier: 3.723A pdb=" N PHE J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) Proline residue: J 59 - end of helix Processing helix chain 'J' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 112 Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU J 116 " --> pdb=" O VAL J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS J 131 " --> pdb=" O THR J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 158 Processing helix chain 'J' and resid 167 through 211 Processing helix chain 'J' and resid 216 through 253 Processing helix chain 'J' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP J 272 " --> pdb=" O SER J 268 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS J 273 " --> pdb=" O CYS J 269 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 15 through 39 removed outlier: 3.591A pdb=" N PHE K 39 " --> pdb=" O SER K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 70 removed outlier: 3.725A pdb=" N PHE K 55 " --> pdb=" O TYR K 51 " (cutoff:3.500A) Proline residue: K 59 - end of helix Processing helix chain 'K' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 112 Processing helix chain 'K' and resid 112 through 126 removed outlier: 3.552A pdb=" N LEU K 116 " --> pdb=" O VAL K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS K 131 " --> pdb=" O THR K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 158 Processing helix chain 'K' and resid 167 through 211 Processing helix chain 'K' and resid 216 through 253 Processing helix chain 'K' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP K 272 " --> pdb=" O SER K 268 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS K 273 " --> pdb=" O CYS K 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE L 39 " --> pdb=" O SER L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE L 55 " --> pdb=" O TYR L 51 " (cutoff:3.500A) Proline residue: L 59 - end of helix Processing helix chain 'L' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP L 75 " --> pdb=" O ARG L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 112 Processing helix chain 'L' and resid 112 through 126 removed outlier: 3.575A pdb=" N LEU L 116 " --> pdb=" O VAL L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.741A pdb=" N CYS L 131 " --> pdb=" O THR L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 158 Processing helix chain 'L' and resid 167 through 211 Processing helix chain 'L' and resid 216 through 253 Processing helix chain 'L' and resid 268 through 276 removed outlier: 4.070A pdb=" N TRP L 272 " --> pdb=" O SER L 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS L 273 " --> pdb=" O CYS L 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 15 Processing helix chain 'M' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE M 55 " --> pdb=" O TYR M 51 " (cutoff:3.500A) Proline residue: M 59 - end of helix Processing helix chain 'M' and resid 71 through 82 removed outlier: 3.747A pdb=" N TRP M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 112 Processing helix chain 'M' and resid 112 through 126 removed outlier: 3.576A pdb=" N LEU M 116 " --> pdb=" O VAL M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 133 removed outlier: 3.742A pdb=" N CYS M 131 " --> pdb=" O THR M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 158 Processing helix chain 'M' and resid 167 through 211 Processing helix chain 'M' and resid 216 through 253 Processing helix chain 'M' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP M 272 " --> pdb=" O SER M 268 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS M 273 " --> pdb=" O CYS M 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 15 Processing helix chain 'N' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE N 39 " --> pdb=" O SER N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 70 removed outlier: 3.714A pdb=" N PHE N 55 " --> pdb=" O TYR N 51 " (cutoff:3.500A) Proline residue: N 59 - end of helix Processing helix chain 'N' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP N 75 " --> pdb=" O ARG N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 112 Processing helix chain 'N' and resid 112 through 126 removed outlier: 3.575A pdb=" N LEU N 116 " --> pdb=" O VAL N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 133 removed outlier: 3.741A pdb=" N CYS N 131 " --> pdb=" O THR N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 158 Processing helix chain 'N' and resid 167 through 211 Processing helix chain 'N' and resid 216 through 253 Processing helix chain 'N' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP N 272 " --> pdb=" O SER N 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS N 273 " --> pdb=" O CYS N 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE O 39 " --> pdb=" O SER O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE O 55 " --> pdb=" O TYR O 51 " (cutoff:3.500A) Proline residue: O 59 - end of helix Processing helix chain 'O' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP O 75 " --> pdb=" O ARG O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 112 Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.575A pdb=" N LEU O 116 " --> pdb=" O VAL O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 133 removed outlier: 3.742A pdb=" N CYS O 131 " --> pdb=" O THR O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 158 Processing helix chain 'O' and resid 167 through 211 Processing helix chain 'O' and resid 216 through 253 Processing helix chain 'O' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP O 272 " --> pdb=" O SER O 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS O 273 " --> pdb=" O CYS O 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 15 Processing helix chain 'P' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE P 39 " --> pdb=" O SER P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE P 55 " --> pdb=" O TYR P 51 " (cutoff:3.500A) Proline residue: P 59 - end of helix Processing helix chain 'P' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP P 75 " --> pdb=" O ARG P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 112 Processing helix chain 'P' and resid 112 through 126 removed outlier: 3.576A pdb=" N LEU P 116 " --> pdb=" O VAL P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 133 removed outlier: 3.742A pdb=" N CYS P 131 " --> pdb=" O THR P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 158 Processing helix chain 'P' and resid 167 through 211 Processing helix chain 'P' and resid 216 through 253 Processing helix chain 'P' and resid 268 through 276 removed outlier: 4.070A pdb=" N TRP P 272 " --> pdb=" O SER P 268 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS P 273 " --> pdb=" O CYS P 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 15 Processing helix chain 'Q' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE Q 39 " --> pdb=" O SER Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE Q 55 " --> pdb=" O TYR Q 51 " (cutoff:3.500A) Proline residue: Q 59 - end of helix Processing helix chain 'Q' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP Q 75 " --> pdb=" O ARG Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 112 Processing helix chain 'Q' and resid 112 through 126 removed outlier: 3.576A pdb=" N LEU Q 116 " --> pdb=" O VAL Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 133 removed outlier: 3.742A pdb=" N CYS Q 131 " --> pdb=" O THR Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 158 Processing helix chain 'Q' and resid 167 through 211 Processing helix chain 'Q' and resid 216 through 253 Processing helix chain 'Q' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP Q 272 " --> pdb=" O SER Q 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS Q 273 " --> pdb=" O CYS Q 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 15 Processing helix chain 'R' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE R 39 " --> pdb=" O SER R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE R 55 " --> pdb=" O TYR R 51 " (cutoff:3.500A) Proline residue: R 59 - end of helix Processing helix chain 'R' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP R 75 " --> pdb=" O ARG R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 112 Processing helix chain 'R' and resid 112 through 126 removed outlier: 3.575A pdb=" N LEU R 116 " --> pdb=" O VAL R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 removed outlier: 3.741A pdb=" N CYS R 131 " --> pdb=" O THR R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 158 Processing helix chain 'R' and resid 167 through 211 Processing helix chain 'R' and resid 216 through 253 Processing helix chain 'R' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP R 272 " --> pdb=" O SER R 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS R 273 " --> pdb=" O CYS R 269 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 15 Processing helix chain 'S' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE S 39 " --> pdb=" O SER S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 70 removed outlier: 3.714A pdb=" N PHE S 55 " --> pdb=" O TYR S 51 " (cutoff:3.500A) Proline residue: S 59 - end of helix Processing helix chain 'S' and resid 71 through 82 removed outlier: 3.745A pdb=" N TRP S 75 " --> pdb=" O ARG S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 112 Processing helix chain 'S' and resid 112 through 126 removed outlier: 3.575A pdb=" N LEU S 116 " --> pdb=" O VAL S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 133 removed outlier: 3.742A pdb=" N CYS S 131 " --> pdb=" O THR S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 149 through 158 Processing helix chain 'S' and resid 167 through 211 Processing helix chain 'S' and resid 216 through 253 Processing helix chain 'S' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP S 272 " --> pdb=" O SER S 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS S 273 " --> pdb=" O CYS S 269 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 15 Processing helix chain 'T' and resid 15 through 39 removed outlier: 3.591A pdb=" N PHE T 39 " --> pdb=" O SER T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE T 55 " --> pdb=" O TYR T 51 " (cutoff:3.500A) Proline residue: T 59 - end of helix Processing helix chain 'T' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP T 75 " --> pdb=" O ARG T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 112 Processing helix chain 'T' and resid 112 through 126 removed outlier: 3.575A pdb=" N LEU T 116 " --> pdb=" O VAL T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 126 through 133 removed outlier: 3.741A pdb=" N CYS T 131 " --> pdb=" O THR T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 149 through 158 Processing helix chain 'T' and resid 167 through 211 Processing helix chain 'T' and resid 216 through 253 Processing helix chain 'T' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP T 272 " --> pdb=" O SER T 268 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS T 273 " --> pdb=" O CYS T 269 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 15 Processing helix chain 'U' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE U 39 " --> pdb=" O SER U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE U 55 " --> pdb=" O TYR U 51 " (cutoff:3.500A) Proline residue: U 59 - end of helix Processing helix chain 'U' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP U 75 " --> pdb=" O ARG U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 112 Processing helix chain 'U' and resid 112 through 126 removed outlier: 3.575A pdb=" N LEU U 116 " --> pdb=" O VAL U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 126 through 133 removed outlier: 3.742A pdb=" N CYS U 131 " --> pdb=" O THR U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 149 through 158 Processing helix chain 'U' and resid 167 through 211 Processing helix chain 'U' and resid 216 through 253 Processing helix chain 'U' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP U 272 " --> pdb=" O SER U 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS U 273 " --> pdb=" O CYS U 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 15 Processing helix chain 'V' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE V 39 " --> pdb=" O SER V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 47 through 70 removed outlier: 3.712A pdb=" N PHE V 55 " --> pdb=" O TYR V 51 " (cutoff:3.500A) Proline residue: V 59 - end of helix Processing helix chain 'V' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP V 75 " --> pdb=" O ARG V 71 " (cutoff:3.500A) Processing helix chain 'V' and resid 95 through 112 Processing helix chain 'V' and resid 112 through 126 removed outlier: 3.576A pdb=" N LEU V 116 " --> pdb=" O VAL V 112 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 133 removed outlier: 3.741A pdb=" N CYS V 131 " --> pdb=" O THR V 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 158 Processing helix chain 'V' and resid 167 through 211 Processing helix chain 'V' and resid 216 through 253 Processing helix chain 'V' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP V 272 " --> pdb=" O SER V 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS V 273 " --> pdb=" O CYS V 269 " (cutoff:3.500A) 3543 hydrogen bonds defined for protein. 10629 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: 8.54 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14476 1.34 - 1.46: 11338 1.46 - 1.58: 20474 1.58 - 1.71: 0 1.71 - 1.83: 550 Bond restraints: 46838 Sorted by residual: bond pdb=" CA ILE M 58 " pdb=" CB ILE M 58 " ideal model delta sigma weight residual 1.537 1.528 0.009 5.00e-03 4.00e+04 3.29e+00 bond pdb=" CA ILE V 58 " pdb=" CB ILE V 58 " ideal model delta sigma weight residual 1.537 1.528 0.009 5.00e-03 4.00e+04 3.29e+00 bond pdb=" CA ILE P 58 " pdb=" CB ILE P 58 " ideal model delta sigma weight residual 1.537 1.528 0.009 5.00e-03 4.00e+04 3.20e+00 bond pdb=" CA ILE N 58 " pdb=" CB ILE N 58 " ideal model delta sigma weight residual 1.537 1.528 0.009 5.00e-03 4.00e+04 3.14e+00 bond pdb=" CA ILE T 58 " pdb=" CB ILE T 58 " ideal model delta sigma weight residual 1.537 1.528 0.009 5.00e-03 4.00e+04 3.00e+00 ... (remaining 46833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 58494 1.22 - 2.45: 3875 2.45 - 3.67: 914 3.67 - 4.89: 213 4.89 - 6.12: 106 Bond angle restraints: 63602 Sorted by residual: angle pdb=" CA LYS R 262 " pdb=" CB LYS R 262 " pdb=" CG LYS R 262 " ideal model delta sigma weight residual 114.10 120.01 -5.91 2.00e+00 2.50e-01 8.74e+00 angle pdb=" CA LYS S 262 " pdb=" CB LYS S 262 " pdb=" CG LYS S 262 " ideal model delta sigma weight residual 114.10 120.01 -5.91 2.00e+00 2.50e-01 8.73e+00 angle pdb=" CA LYS V 262 " pdb=" CB LYS V 262 " pdb=" CG LYS V 262 " ideal model delta sigma weight residual 114.10 120.01 -5.91 2.00e+00 2.50e-01 8.72e+00 angle pdb=" CA LYS T 262 " pdb=" CB LYS T 262 " pdb=" CG LYS T 262 " ideal model delta sigma weight residual 114.10 120.00 -5.90 2.00e+00 2.50e-01 8.71e+00 angle pdb=" CA LYS M 262 " pdb=" CB LYS M 262 " pdb=" CG LYS M 262 " ideal model delta sigma weight residual 114.10 119.99 -5.89 2.00e+00 2.50e-01 8.69e+00 ... (remaining 63597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 25214 17.94 - 35.88: 2341 35.88 - 53.81: 319 53.81 - 71.75: 44 71.75 - 89.69: 66 Dihedral angle restraints: 27984 sinusoidal: 10802 harmonic: 17182 Sorted by residual: dihedral pdb=" CB CYS N 41 " pdb=" SG CYS N 41 " pdb=" SG CYS N 131 " pdb=" CB CYS N 131 " ideal model delta sinusoidal sigma weight residual -86.00 -170.40 84.40 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS O 41 " pdb=" SG CYS O 41 " pdb=" SG CYS O 131 " pdb=" CB CYS O 131 " ideal model delta sinusoidal sigma weight residual -86.00 -170.39 84.39 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS Q 41 " pdb=" SG CYS Q 41 " pdb=" SG CYS Q 131 " pdb=" CB CYS Q 131 " ideal model delta sinusoidal sigma weight residual -86.00 -170.38 84.38 1 1.00e+01 1.00e-02 8.66e+01 ... (remaining 27981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 5504 0.044 - 0.087: 1317 0.087 - 0.131: 483 0.131 - 0.174: 99 0.174 - 0.218: 11 Chirality restraints: 7414 Sorted by residual: chirality pdb=" CB VAL B 148 " pdb=" CA VAL B 148 " pdb=" CG1 VAL B 148 " pdb=" CG2 VAL B 148 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB VAL A 148 " pdb=" CA VAL A 148 " pdb=" CG1 VAL A 148 " pdb=" CG2 VAL A 148 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB VAL E 148 " pdb=" CA VAL E 148 " pdb=" CG1 VAL E 148 " pdb=" CG2 VAL E 148 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 7411 not shown) Planarity restraints: 7898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU J 228 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" CD GLU J 228 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU J 228 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU J 228 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 228 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" CD GLU B 228 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU B 228 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU B 228 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 228 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" CD GLU G 228 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU G 228 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU G 228 " -0.015 2.00e-02 2.50e+03 ... (remaining 7895 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 239 2.52 - 3.12: 36698 3.12 - 3.71: 71526 3.71 - 4.31: 87756 4.31 - 4.90: 154040 Nonbonded interactions: 350259 Sorted by model distance: nonbonded pdb=" OG SER I 40 " pdb=" NH1 ARG J 182 " model vdw 1.929 3.120 nonbonded pdb=" OG SER A 40 " pdb=" NH1 ARG B 182 " model vdw 2.028 3.120 nonbonded pdb=" OG SER R 40 " pdb=" NH1 ARG S 182 " model vdw 2.047 3.120 nonbonded pdb=" OG SER Q 40 " pdb=" NH1 ARG R 182 " model vdw 2.082 3.120 nonbonded pdb=" OG SER T 40 " pdb=" NH1 ARG U 182 " model vdw 2.140 3.120 ... (remaining 350254 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: 0.08 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' selection = chain 'V' } 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: 0.840 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: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 37.130 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.005 0.052 46882 Z= 0.234 Angle : 0.767 6.116 63690 Z= 0.443 Chirality : 0.046 0.218 7414 Planarity : 0.005 0.035 7898 Dihedral : 13.893 89.688 16676 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % 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: -0.15 (0.10), residues: 5786 helix: 0.69 (0.07), residues: 4466 sheet: None (None), residues: 0 loop : -2.76 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 247 TYR 0.011 0.002 TYR A 128 PHE 0.027 0.002 PHE N 55 TRP 0.019 0.002 TRP N 75 HIS 0.003 0.001 HIS M 239 Details of bonding type rmsd covalent geometry : bond 0.00527 (46838) covalent geometry : angle 0.76293 (63602) SS BOND : bond 0.00182 ( 44) SS BOND : angle 2.18437 ( 88) hydrogen bonds : bond 0.13515 ( 3543) hydrogen bonds : angle 5.18584 (10629) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1074 time to evaluate : 1.878 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 129 TYR cc_start: 0.9019 (t80) cc_final: 0.8763 (t80) REVERT: A 192 LEU cc_start: 0.9041 (tp) cc_final: 0.8810 (tt) REVERT: A 195 LEU cc_start: 0.8739 (tt) cc_final: 0.8412 (mm) REVERT: A 229 ARG cc_start: 0.8049 (tpt90) cc_final: 0.7659 (tpp80) REVERT: A 258 SER cc_start: 0.8505 (m) cc_final: 0.8076 (t) REVERT: B 14 ARG cc_start: 0.7727 (mtm110) cc_final: 0.6526 (ptm160) REVERT: B 74 MET cc_start: 0.8359 (tmm) cc_final: 0.7669 (tmm) REVERT: B 163 CYS cc_start: 0.6909 (p) cc_final: 0.6634 (t) REVERT: B 195 LEU cc_start: 0.8483 (tt) cc_final: 0.8169 (mm) REVERT: B 208 LYS cc_start: 0.8627 (tptp) cc_final: 0.8316 (mmtp) REVERT: C 48 ASN cc_start: 0.8024 (t0) cc_final: 0.7568 (t0) REVERT: C 187 MET cc_start: 0.9262 (mmp) cc_final: 0.8401 (mmm) REVERT: C 191 ILE cc_start: 0.9266 (mt) cc_final: 0.8877 (mt) REVERT: C 195 LEU cc_start: 0.8763 (tt) cc_final: 0.8462 (mm) REVERT: C 229 ARG cc_start: 0.7984 (tpt90) cc_final: 0.7717 (tpp80) REVERT: D 31 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8249 (tm-30) REVERT: D 187 MET cc_start: 0.9244 (mmp) cc_final: 0.8852 (tpp) REVERT: D 208 LYS cc_start: 0.8703 (tptp) cc_final: 0.8323 (tppt) REVERT: D 215 SER cc_start: 0.8749 (t) cc_final: 0.8417 (p) REVERT: D 233 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7667 (tm-30) REVERT: D 237 GLU cc_start: 0.8251 (tm-30) cc_final: 0.8021 (tm-30) REVERT: E 50 TYR cc_start: 0.8584 (m-80) cc_final: 0.8327 (m-80) REVERT: E 187 MET cc_start: 0.8900 (mmp) cc_final: 0.8533 (mmm) REVERT: E 229 ARG cc_start: 0.7925 (tpt90) cc_final: 0.7453 (tpp80) REVERT: E 244 MET cc_start: 0.8147 (tpt) cc_final: 0.7913 (tpt) REVERT: F 141 HIS cc_start: 0.7637 (p-80) cc_final: 0.6951 (p-80) REVERT: F 192 LEU cc_start: 0.8676 (tp) cc_final: 0.8415 (tt) REVERT: F 195 LEU cc_start: 0.8585 (tt) cc_final: 0.8267 (mm) REVERT: F 208 LYS cc_start: 0.8718 (tptp) cc_final: 0.8219 (mmtm) REVERT: F 229 ARG cc_start: 0.7716 (tpt90) cc_final: 0.7434 (tpp80) REVERT: G 74 MET cc_start: 0.7526 (tmm) cc_final: 0.7220 (tmm) REVERT: G 141 HIS cc_start: 0.7198 (p-80) cc_final: 0.6612 (p-80) REVERT: G 187 MET cc_start: 0.9275 (mmp) cc_final: 0.8934 (mmm) REVERT: G 229 ARG cc_start: 0.8221 (tpt90) cc_final: 0.7799 (tpp80) REVERT: G 274 ASP cc_start: 0.7267 (m-30) cc_final: 0.7046 (m-30) REVERT: H 187 MET cc_start: 0.9212 (mmp) cc_final: 0.8997 (mmm) REVERT: H 195 LEU cc_start: 0.8661 (tt) cc_final: 0.8224 (mm) REVERT: H 208 LYS cc_start: 0.8719 (tptp) cc_final: 0.8360 (tppt) REVERT: H 229 ARG cc_start: 0.8206 (tpt90) cc_final: 0.7870 (tpp80) REVERT: H 258 SER cc_start: 0.8747 (m) cc_final: 0.8421 (t) REVERT: H 274 ASP cc_start: 0.7679 (m-30) cc_final: 0.7457 (m-30) REVERT: I 208 LYS cc_start: 0.8957 (tptp) cc_final: 0.8249 (mmtm) REVERT: I 229 ARG cc_start: 0.7872 (tpt90) cc_final: 0.7592 (tpp80) REVERT: J 14 ARG cc_start: 0.8044 (mtm110) cc_final: 0.6692 (ptm160) REVERT: J 155 GLU cc_start: 0.8445 (tp30) cc_final: 0.7985 (tm-30) REVERT: J 186 GLN cc_start: 0.7995 (mt0) cc_final: 0.7788 (mt0) REVERT: J 215 SER cc_start: 0.8752 (t) cc_final: 0.8188 (p) REVERT: K 31 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8348 (tm-30) REVERT: K 129 TYR cc_start: 0.8860 (t80) cc_final: 0.8537 (t80) REVERT: K 187 MET cc_start: 0.9126 (mmp) cc_final: 0.8854 (mmm) REVERT: K 229 ARG cc_start: 0.8007 (tpt90) cc_final: 0.7662 (tpp80) REVERT: K 258 SER cc_start: 0.8276 (m) cc_final: 0.8065 (t) REVERT: L 104 PHE cc_start: 0.8190 (t80) cc_final: 0.7966 (t80) REVERT: L 142 TYR cc_start: 0.6386 (m-80) cc_final: 0.6153 (m-10) REVERT: L 155 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7954 (tp30) REVERT: L 187 MET cc_start: 0.9323 (mmp) cc_final: 0.8990 (mmp) REVERT: L 195 LEU cc_start: 0.8674 (tt) cc_final: 0.8364 (mm) REVERT: L 208 LYS cc_start: 0.9051 (tptp) cc_final: 0.8472 (mmtm) REVERT: L 229 ARG cc_start: 0.7970 (tpt90) cc_final: 0.7621 (tpp80) REVERT: M 128 TYR cc_start: 0.9088 (m-10) cc_final: 0.8880 (m-10) REVERT: M 187 MET cc_start: 0.9258 (mmp) cc_final: 0.8948 (mmp) REVERT: M 195 LEU cc_start: 0.8659 (tt) cc_final: 0.8347 (mm) REVERT: M 208 LYS cc_start: 0.8991 (tptp) cc_final: 0.8342 (mmtm) REVERT: M 229 ARG cc_start: 0.8282 (tpt90) cc_final: 0.7811 (tpp80) REVERT: N 74 MET cc_start: 0.7695 (tmm) cc_final: 0.7451 (tmm) REVERT: N 195 LEU cc_start: 0.8708 (tt) cc_final: 0.8336 (mm) REVERT: N 208 LYS cc_start: 0.8941 (tptp) cc_final: 0.8667 (tppt) REVERT: N 229 ARG cc_start: 0.8087 (tpt90) cc_final: 0.7849 (tpp80) REVERT: N 258 SER cc_start: 0.8343 (m) cc_final: 0.7894 (t) REVERT: N 274 ASP cc_start: 0.8043 (m-30) cc_final: 0.7815 (m-30) REVERT: O 129 TYR cc_start: 0.9021 (t80) cc_final: 0.8628 (t80) REVERT: O 195 LEU cc_start: 0.8832 (tt) cc_final: 0.8462 (tp) REVERT: O 208 LYS cc_start: 0.8881 (tptp) cc_final: 0.8433 (mmtm) REVERT: O 229 ARG cc_start: 0.8050 (tpt90) cc_final: 0.7573 (tpp80) REVERT: O 230 GLU cc_start: 0.7748 (tp30) cc_final: 0.7469 (tp30) REVERT: P 14 ARG cc_start: 0.8271 (mtm110) cc_final: 0.8035 (mtp-110) REVERT: P 31 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8354 (tm-30) REVERT: P 241 ARG cc_start: 0.7934 (ttt180) cc_final: 0.7698 (ttt-90) REVERT: Q 142 TYR cc_start: 0.6669 (m-80) cc_final: 0.6446 (m-10) REVERT: Q 208 LYS cc_start: 0.8621 (tptp) cc_final: 0.8089 (mmtm) REVERT: R 141 HIS cc_start: 0.7500 (p-80) cc_final: 0.6939 (p-80) REVERT: R 142 TYR cc_start: 0.6171 (m-80) cc_final: 0.5926 (m-80) REVERT: R 198 ILE cc_start: 0.9146 (mm) cc_final: 0.8900 (tt) REVERT: R 208 LYS cc_start: 0.8868 (tptp) cc_final: 0.8565 (tppt) REVERT: R 229 ARG cc_start: 0.8025 (tpt90) cc_final: 0.7596 (tpp80) REVERT: R 274 ASP cc_start: 0.7895 (m-30) cc_final: 0.7633 (m-30) REVERT: S 51 TYR cc_start: 0.9114 (t80) cc_final: 0.8802 (t80) REVERT: S 187 MET cc_start: 0.9340 (mmp) cc_final: 0.8882 (mmm) REVERT: S 208 LYS cc_start: 0.8891 (tptp) cc_final: 0.8433 (mmtm) REVERT: S 215 SER cc_start: 0.8767 (t) cc_final: 0.8475 (p) REVERT: T 141 HIS cc_start: 0.7908 (p-80) cc_final: 0.7317 (p-80) REVERT: T 187 MET cc_start: 0.9410 (mmp) cc_final: 0.9055 (mmp) REVERT: T 195 LEU cc_start: 0.8780 (tt) cc_final: 0.8349 (mm) REVERT: T 229 ARG cc_start: 0.8106 (tpt90) cc_final: 0.7722 (tpp80) REVERT: T 249 LYS cc_start: 0.8703 (tttt) cc_final: 0.8469 (tttp) REVERT: T 250 LYS cc_start: 0.8808 (ttmt) cc_final: 0.8438 (ttpp) REVERT: U 229 ARG cc_start: 0.8074 (tpt90) cc_final: 0.7780 (tpp80) REVERT: V 195 LEU cc_start: 0.8746 (tt) cc_final: 0.8209 (mm) REVERT: V 208 LYS cc_start: 0.8859 (tptp) cc_final: 0.8465 (mmtp) REVERT: V 229 ARG cc_start: 0.8163 (tpt90) cc_final: 0.7576 (tpp80) outliers start: 0 outliers final: 0 residues processed: 1074 average time/residue: 0.3338 time to fit residues: 550.9038 Evaluate side-chains 660 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 523 optimal weight: 4.9990 chunk 497 optimal weight: 0.0570 chunk 414 optimal weight: 0.0770 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 0.9990 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN B 20 ASN B 184 GLN B 234 GLN C 184 GLN D 184 GLN E 184 GLN E 234 GLN F 184 GLN G 184 GLN H 184 GLN I 184 GLN I 234 GLN J 184 GLN K 184 GLN K 234 GLN L 184 GLN M 184 GLN N 184 GLN O 184 GLN P 184 GLN P 234 GLN Q 184 GLN Q 234 GLN R 184 GLN S 184 GLN T 184 GLN U 184 GLN V 184 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.161950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133836 restraints weight = 59245.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.136180 restraints weight = 42534.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.137381 restraints weight = 34920.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.138568 restraints weight = 31262.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139032 restraints weight = 28878.126| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 46882 Z= 0.149 Angle : 0.578 7.042 63690 Z= 0.312 Chirality : 0.039 0.133 7414 Planarity : 0.005 0.085 7898 Dihedral : 3.999 15.805 6270 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.95 % Allowed : 12.77 % Favored : 85.28 % 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: 1.72 (0.10), residues: 5786 helix: 2.02 (0.07), residues: 4532 sheet: None (None), residues: 0 loop : -2.32 (0.15), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 71 TYR 0.014 0.001 TYR J 142 PHE 0.018 0.002 PHE U 145 TRP 0.008 0.001 TRP G 221 HIS 0.004 0.001 HIS Q 141 Details of bonding type rmsd covalent geometry : bond 0.00302 (46838) covalent geometry : angle 0.57606 (63602) SS BOND : bond 0.00301 ( 44) SS BOND : angle 1.34061 ( 88) hydrogen bonds : bond 0.05623 ( 3543) hydrogen bonds : angle 4.05545 (10629) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 803 time to evaluate : 1.798 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 129 TYR cc_start: 0.9047 (t80) cc_final: 0.8534 (t80) REVERT: A 153 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7548 (ttp80) REVERT: A 154 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7766 (mm-30) REVERT: A 192 LEU cc_start: 0.9086 (tp) cc_final: 0.8847 (tt) REVERT: A 195 LEU cc_start: 0.8638 (tt) cc_final: 0.8306 (mm) REVERT: A 244 MET cc_start: 0.8014 (tpp) cc_final: 0.7609 (tpt) REVERT: B 14 ARG cc_start: 0.7399 (mtm110) cc_final: 0.6277 (ptm160) REVERT: B 104 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7525 (m-80) REVERT: B 195 LEU cc_start: 0.8544 (tt) cc_final: 0.8278 (mm) REVERT: C 14 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7772 (mtp-110) REVERT: C 104 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7718 (m-80) REVERT: C 129 TYR cc_start: 0.9073 (t80) cc_final: 0.8818 (t80) REVERT: C 187 MET cc_start: 0.9082 (mmp) cc_final: 0.8331 (mmm) REVERT: C 229 ARG cc_start: 0.8044 (tpt90) cc_final: 0.7837 (tpp80) REVERT: D 13 GLN cc_start: 0.8217 (tp40) cc_final: 0.7490 (tm-30) REVERT: D 31 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8276 (tm-30) REVERT: D 187 MET cc_start: 0.9167 (mmp) cc_final: 0.8758 (tpp) REVERT: D 237 GLU cc_start: 0.8268 (tm-30) cc_final: 0.8022 (tm-30) REVERT: E 104 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7034 (m-80) REVERT: E 187 MET cc_start: 0.9000 (mmp) cc_final: 0.8687 (mmm) REVERT: E 230 GLU cc_start: 0.8052 (tp30) cc_final: 0.7750 (tp30) REVERT: F 71 ARG cc_start: 0.7460 (mmm160) cc_final: 0.6219 (mmp-170) REVERT: F 141 HIS cc_start: 0.7602 (p-80) cc_final: 0.6979 (p-80) REVERT: F 192 LEU cc_start: 0.8811 (tp) cc_final: 0.8562 (tt) REVERT: F 195 LEU cc_start: 0.8632 (tt) cc_final: 0.8374 (mm) REVERT: F 208 LYS cc_start: 0.8695 (tptp) cc_final: 0.8349 (mmtm) REVERT: G 141 HIS cc_start: 0.7036 (p-80) cc_final: 0.6686 (p-80) REVERT: G 154 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7673 (mm-30) REVERT: G 187 MET cc_start: 0.9168 (mmp) cc_final: 0.8911 (mmm) REVERT: H 34 PHE cc_start: 0.8225 (t80) cc_final: 0.7958 (t80) REVERT: H 187 MET cc_start: 0.9134 (mmp) cc_final: 0.8932 (mmm) REVERT: H 195 LEU cc_start: 0.8663 (tt) cc_final: 0.8240 (mm) REVERT: H 208 LYS cc_start: 0.8817 (tptp) cc_final: 0.8333 (mmtp) REVERT: H 229 ARG cc_start: 0.7970 (tpt90) cc_final: 0.7761 (tpp80) REVERT: H 258 SER cc_start: 0.8360 (m) cc_final: 0.7948 (t) REVERT: I 208 LYS cc_start: 0.8966 (tptp) cc_final: 0.8486 (mmtm) REVERT: J 14 ARG cc_start: 0.8093 (mtm110) cc_final: 0.6853 (ptm160) REVERT: J 104 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: J 215 SER cc_start: 0.8945 (t) cc_final: 0.8476 (p) REVERT: J 244 MET cc_start: 0.8092 (tpp) cc_final: 0.7863 (tpt) REVERT: K 31 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8276 (tm-30) REVERT: K 104 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7275 (m-80) REVERT: K 188 LEU cc_start: 0.9361 (tp) cc_final: 0.9080 (tp) REVERT: K 258 SER cc_start: 0.7350 (m) cc_final: 0.7066 (t) REVERT: L 155 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7812 (tp30) REVERT: L 187 MET cc_start: 0.9166 (mmp) cc_final: 0.8917 (mmp) REVERT: L 195 LEU cc_start: 0.8735 (tt) cc_final: 0.8425 (mm) REVERT: L 208 LYS cc_start: 0.9012 (tptp) cc_final: 0.8541 (mmtm) REVERT: L 259 GLU cc_start: 0.7795 (mp0) cc_final: 0.7539 (mp0) REVERT: M 155 GLU cc_start: 0.8221 (tp30) cc_final: 0.8017 (tm-30) REVERT: M 187 MET cc_start: 0.9100 (mmp) cc_final: 0.8734 (mmp) REVERT: M 195 LEU cc_start: 0.8575 (tt) cc_final: 0.8334 (mm) REVERT: M 208 LYS cc_start: 0.8922 (tptp) cc_final: 0.8503 (mmtm) REVERT: N 195 LEU cc_start: 0.8674 (tt) cc_final: 0.8374 (mm) REVERT: N 258 SER cc_start: 0.8154 (m) cc_final: 0.7759 (t) REVERT: O 195 LEU cc_start: 0.8810 (tt) cc_final: 0.8310 (tp) REVERT: O 208 LYS cc_start: 0.8817 (tptp) cc_final: 0.8513 (mmtm) REVERT: P 31 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8243 (tm-30) REVERT: P 104 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: P 229 ARG cc_start: 0.7808 (tpt90) cc_final: 0.7578 (tpp80) REVERT: Q 187 MET cc_start: 0.9017 (mmp) cc_final: 0.8742 (mmm) REVERT: Q 208 LYS cc_start: 0.8622 (tptp) cc_final: 0.8195 (mmtm) REVERT: Q 244 MET cc_start: 0.8112 (tpp) cc_final: 0.7693 (tpt) REVERT: R 128 TYR cc_start: 0.8840 (m-10) cc_final: 0.8590 (m-10) REVERT: R 141 HIS cc_start: 0.7441 (p-80) cc_final: 0.7107 (p-80) REVERT: R 198 ILE cc_start: 0.9338 (mm) cc_final: 0.9078 (tt) REVERT: S 187 MET cc_start: 0.9308 (mmp) cc_final: 0.8838 (mmm) REVERT: S 195 LEU cc_start: 0.9037 (tt) cc_final: 0.8493 (mm) REVERT: S 208 LYS cc_start: 0.8846 (tptp) cc_final: 0.8521 (mmtm) REVERT: S 215 SER cc_start: 0.8686 (t) cc_final: 0.8485 (p) REVERT: T 104 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7515 (m-80) REVERT: T 141 HIS cc_start: 0.7814 (p-80) cc_final: 0.7346 (p-80) REVERT: T 187 MET cc_start: 0.9280 (mmp) cc_final: 0.8888 (mmp) REVERT: T 195 LEU cc_start: 0.8775 (tt) cc_final: 0.8435 (mm) REVERT: T 250 LYS cc_start: 0.8713 (ttmt) cc_final: 0.8488 (ttpp) REVERT: T 259 GLU cc_start: 0.7325 (mp0) cc_final: 0.7044 (mp0) REVERT: U 104 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: V 187 MET cc_start: 0.9176 (mmm) cc_final: 0.8458 (mmm) REVERT: V 195 LEU cc_start: 0.8762 (tt) cc_final: 0.8328 (mm) REVERT: V 202 VAL cc_start: 0.9138 (p) cc_final: 0.8883 (t) REVERT: V 208 LYS cc_start: 0.8816 (tptp) cc_final: 0.8524 (mmtp) REVERT: V 229 ARG cc_start: 0.8134 (tpt90) cc_final: 0.7692 (tpp80) outliers start: 99 outliers final: 74 residues processed: 850 average time/residue: 0.2754 time to fit residues: 385.8053 Evaluate side-chains 752 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 669 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 104 PHE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 258 SER Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 245 MET Chi-restraints excluded: chain S residue 205 CYS Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 153 ARG Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain U residue 104 PHE Chi-restraints excluded: chain U residue 153 ARG Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain V residue 205 CYS Chi-restraints excluded: chain V residue 245 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 233 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 404 optimal weight: 0.0470 chunk 139 optimal weight: 3.9990 chunk 323 optimal weight: 0.0770 chunk 232 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 431 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 411 optimal weight: 0.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 ASN G 20 ASN N 20 ASN Q 234 GLN S 20 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.157032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128257 restraints weight = 59285.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130622 restraints weight = 42566.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.131965 restraints weight = 34923.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.133014 restraints weight = 31121.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133479 restraints weight = 28901.395| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 46882 Z= 0.148 Angle : 0.535 7.897 63690 Z= 0.289 Chirality : 0.038 0.170 7414 Planarity : 0.005 0.059 7898 Dihedral : 3.919 16.640 6270 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.42 % Allowed : 15.92 % Favored : 81.66 % 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: 2.35 (0.11), residues: 5786 helix: 2.49 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.25 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 71 TYR 0.020 0.001 TYR C 51 PHE 0.033 0.001 PHE P 104 TRP 0.009 0.001 TRP G 221 HIS 0.002 0.000 HIS Q 181 Details of bonding type rmsd covalent geometry : bond 0.00322 (46838) covalent geometry : angle 0.53317 (63602) SS BOND : bond 0.00360 ( 44) SS BOND : angle 1.24355 ( 88) hydrogen bonds : bond 0.05349 ( 3543) hydrogen bonds : angle 3.83223 (10629) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 701 time to evaluate : 1.605 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 74 MET cc_start: 0.7817 (tmm) cc_final: 0.7616 (tmm) REVERT: A 129 TYR cc_start: 0.9133 (t80) cc_final: 0.8884 (t80) REVERT: A 153 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7617 (ttp80) REVERT: A 195 LEU cc_start: 0.8673 (tt) cc_final: 0.8339 (mm) REVERT: B 14 ARG cc_start: 0.7394 (mtm110) cc_final: 0.6335 (ptm160) REVERT: B 104 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: B 116 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7992 (tp) REVERT: B 195 LEU cc_start: 0.8613 (tt) cc_final: 0.8328 (mm) REVERT: B 244 MET cc_start: 0.8322 (tpp) cc_final: 0.8062 (tpt) REVERT: C 14 ARG cc_start: 0.8240 (mtm110) cc_final: 0.7978 (mtp-110) REVERT: C 74 MET cc_start: 0.8549 (tpp) cc_final: 0.8257 (tpp) REVERT: C 104 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: C 187 MET cc_start: 0.9049 (mmp) cc_final: 0.8404 (mmm) REVERT: C 191 ILE cc_start: 0.9169 (mt) cc_final: 0.8914 (mt) REVERT: D 13 GLN cc_start: 0.8143 (tp40) cc_final: 0.7380 (tm-30) REVERT: D 31 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8591 (tm-30) REVERT: D 175 ASP cc_start: 0.7883 (m-30) cc_final: 0.7526 (m-30) REVERT: D 187 MET cc_start: 0.9098 (mmp) cc_final: 0.8639 (tpp) REVERT: E 74 MET cc_start: 0.8089 (tpp) cc_final: 0.7725 (tpp) REVERT: E 187 MET cc_start: 0.9121 (mmp) cc_final: 0.8870 (mmm) REVERT: F 71 ARG cc_start: 0.7676 (mmm160) cc_final: 0.6311 (mmp-170) REVERT: F 141 HIS cc_start: 0.7524 (p-80) cc_final: 0.6963 (p-80) REVERT: F 192 LEU cc_start: 0.8751 (tp) cc_final: 0.8472 (tt) REVERT: F 195 LEU cc_start: 0.8726 (tt) cc_final: 0.8439 (mm) REVERT: F 237 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7779 (tm-30) REVERT: G 141 HIS cc_start: 0.7151 (p-80) cc_final: 0.6814 (p-80) REVERT: G 187 MET cc_start: 0.9106 (mmp) cc_final: 0.8866 (mmm) REVERT: H 34 PHE cc_start: 0.8240 (t80) cc_final: 0.8015 (t80) REVERT: H 187 MET cc_start: 0.9154 (mmp) cc_final: 0.8910 (mmm) REVERT: H 195 LEU cc_start: 0.8727 (tt) cc_final: 0.8237 (mm) REVERT: H 258 SER cc_start: 0.8283 (m) cc_final: 0.7958 (t) REVERT: I 208 LYS cc_start: 0.8958 (tptp) cc_final: 0.8447 (mmtm) REVERT: J 14 ARG cc_start: 0.8249 (mtm110) cc_final: 0.7174 (ptm160) REVERT: J 104 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7694 (m-80) REVERT: J 130 GLU cc_start: 0.8034 (pp20) cc_final: 0.7811 (tm-30) REVERT: J 155 GLU cc_start: 0.8127 (tp30) cc_final: 0.7832 (tm-30) REVERT: J 187 MET cc_start: 0.8887 (mmm) cc_final: 0.8464 (mmm) REVERT: J 215 SER cc_start: 0.8826 (t) cc_final: 0.8455 (p) REVERT: K 104 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: K 258 SER cc_start: 0.7269 (m) cc_final: 0.6918 (t) REVERT: L 141 HIS cc_start: 0.7511 (p-80) cc_final: 0.7271 (p-80) REVERT: L 195 LEU cc_start: 0.8767 (tt) cc_final: 0.8417 (mm) REVERT: L 208 LYS cc_start: 0.9036 (tptp) cc_final: 0.8502 (mmtm) REVERT: M 187 MET cc_start: 0.9068 (mmp) cc_final: 0.8807 (mmp) REVERT: M 195 LEU cc_start: 0.8584 (tt) cc_final: 0.8285 (mm) REVERT: M 208 LYS cc_start: 0.8917 (tptp) cc_final: 0.8425 (mmtm) REVERT: N 175 ASP cc_start: 0.7770 (m-30) cc_final: 0.7550 (m-30) REVERT: N 195 LEU cc_start: 0.8675 (tt) cc_final: 0.8384 (mm) REVERT: N 258 SER cc_start: 0.7988 (m) cc_final: 0.7622 (t) REVERT: O 195 LEU cc_start: 0.8807 (tt) cc_final: 0.8364 (mm) REVERT: O 208 LYS cc_start: 0.8899 (tptp) cc_final: 0.8551 (mmtm) REVERT: P 104 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: P 160 PHE cc_start: 0.7896 (m-80) cc_final: 0.7687 (m-80) REVERT: P 230 GLU cc_start: 0.7825 (tp30) cc_final: 0.7558 (tp30) REVERT: Q 187 MET cc_start: 0.9083 (mmp) cc_final: 0.8652 (mmm) REVERT: Q 208 LYS cc_start: 0.8774 (tptp) cc_final: 0.8291 (mmtm) REVERT: Q 244 MET cc_start: 0.8248 (tpp) cc_final: 0.7803 (tpt) REVERT: R 141 HIS cc_start: 0.7512 (p-80) cc_final: 0.7114 (p-80) REVERT: S 187 MET cc_start: 0.9254 (mmp) cc_final: 0.8968 (mmm) REVERT: S 195 LEU cc_start: 0.9083 (tt) cc_final: 0.8511 (mm) REVERT: S 208 LYS cc_start: 0.8876 (tptp) cc_final: 0.8556 (mmtm) REVERT: T 141 HIS cc_start: 0.7806 (p-80) cc_final: 0.7335 (p-80) REVERT: T 155 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7496 (tm-30) REVERT: T 187 MET cc_start: 0.9259 (mmp) cc_final: 0.8904 (mmp) REVERT: T 195 LEU cc_start: 0.8759 (tt) cc_final: 0.8384 (mm) REVERT: T 250 LYS cc_start: 0.8688 (ttmt) cc_final: 0.8325 (ttpp) REVERT: U 104 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7392 (m-80) REVERT: V 187 MET cc_start: 0.9160 (mmm) cc_final: 0.8353 (mmm) REVERT: V 195 LEU cc_start: 0.8739 (tt) cc_final: 0.8290 (mm) REVERT: V 208 LYS cc_start: 0.8866 (tptp) cc_final: 0.8486 (mmtp) REVERT: V 229 ARG cc_start: 0.8170 (tpt90) cc_final: 0.7694 (tpp80) REVERT: V 259 GLU cc_start: 0.7454 (mp0) cc_final: 0.7248 (mp0) outliers start: 123 outliers final: 100 residues processed: 770 average time/residue: 0.2683 time to fit residues: 342.7770 Evaluate side-chains 749 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 641 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 104 PHE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 258 SER Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 245 MET Chi-restraints excluded: chain S residue 205 CYS Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 153 ARG Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain U residue 104 PHE Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 153 ARG Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 205 CYS Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 245 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 113 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 355 optimal weight: 4.9990 chunk 336 optimal weight: 0.0050 chunk 454 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 524 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 566 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN C 20 ASN D 20 ASN E 20 ASN H 20 ASN I 20 ASN K 20 ASN K 234 GLN L 20 ASN M 20 ASN O 20 ASN Q 234 GLN R 20 ASN T 20 ASN U 20 ASN V 20 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122990 restraints weight = 59630.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.125169 restraints weight = 43856.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.126339 restraints weight = 36440.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127320 restraints weight = 32842.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127936 restraints weight = 30500.206| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 46882 Z= 0.173 Angle : 0.545 6.956 63690 Z= 0.297 Chirality : 0.039 0.155 7414 Planarity : 0.005 0.049 7898 Dihedral : 3.955 16.517 6270 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.44 % Allowed : 16.94 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.11), residues: 5786 helix: 2.59 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.19 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 71 TYR 0.013 0.001 TYR O 129 PHE 0.018 0.002 PHE R 232 TRP 0.009 0.001 TRP M 221 HIS 0.004 0.001 HIS J 239 Details of bonding type rmsd covalent geometry : bond 0.00397 (46838) covalent geometry : angle 0.54362 (63602) SS BOND : bond 0.00252 ( 44) SS BOND : angle 1.30046 ( 88) hydrogen bonds : bond 0.05521 ( 3543) hydrogen bonds : angle 3.79288 (10629) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 700 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 TYR cc_start: 0.9095 (t80) cc_final: 0.8772 (t80) REVERT: A 153 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7636 (ttp80) REVERT: A 195 LEU cc_start: 0.8666 (tt) cc_final: 0.8302 (mm) REVERT: B 116 LEU cc_start: 0.8379 (tp) cc_final: 0.8107 (tp) REVERT: B 155 GLU cc_start: 0.7953 (tp30) cc_final: 0.7531 (tm-30) REVERT: B 195 LEU cc_start: 0.8750 (tt) cc_final: 0.8466 (mm) REVERT: B 244 MET cc_start: 0.8357 (tpp) cc_final: 0.8118 (tpt) REVERT: C 71 ARG cc_start: 0.8197 (mmm160) cc_final: 0.6636 (mmp-170) REVERT: C 187 MET cc_start: 0.8925 (mmp) cc_final: 0.8341 (mmm) REVERT: C 191 ILE cc_start: 0.9165 (mt) cc_final: 0.8917 (mt) REVERT: D 13 GLN cc_start: 0.7971 (tp40) cc_final: 0.7328 (tm-30) REVERT: D 175 ASP cc_start: 0.7735 (m-30) cc_final: 0.7390 (m-30) REVERT: D 187 MET cc_start: 0.9091 (mmp) cc_final: 0.8715 (tpp) REVERT: D 195 LEU cc_start: 0.8890 (tt) cc_final: 0.8443 (mm) REVERT: D 229 ARG cc_start: 0.7959 (tpp-160) cc_final: 0.7752 (tpp80) REVERT: D 231 LEU cc_start: 0.9094 (tp) cc_final: 0.8790 (mm) REVERT: E 31 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8332 (tm-30) REVERT: E 74 MET cc_start: 0.8018 (tpp) cc_final: 0.7692 (tpp) REVERT: E 175 ASP cc_start: 0.8205 (m-30) cc_final: 0.8003 (m-30) REVERT: E 187 MET cc_start: 0.9106 (mmp) cc_final: 0.8859 (mmm) REVERT: E 195 LEU cc_start: 0.8589 (tt) cc_final: 0.8232 (mm) REVERT: F 116 LEU cc_start: 0.8453 (tp) cc_final: 0.8081 (tp) REVERT: F 141 HIS cc_start: 0.7523 (p-80) cc_final: 0.6987 (p-80) REVERT: F 195 LEU cc_start: 0.8804 (tt) cc_final: 0.8368 (mm) REVERT: F 233 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7610 (tm-30) REVERT: F 237 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7812 (tm-30) REVERT: F 242 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.7950 (mm) REVERT: G 129 TYR cc_start: 0.9090 (t80) cc_final: 0.8605 (t80) REVERT: G 141 HIS cc_start: 0.7120 (p-80) cc_final: 0.6805 (p-80) REVERT: G 195 LEU cc_start: 0.8785 (tt) cc_final: 0.8308 (mm) REVERT: H 187 MET cc_start: 0.9026 (mmp) cc_final: 0.8805 (mmm) REVERT: H 195 LEU cc_start: 0.8828 (tt) cc_final: 0.8317 (mm) REVERT: H 258 SER cc_start: 0.8177 (m) cc_final: 0.7944 (t) REVERT: I 116 LEU cc_start: 0.8409 (tp) cc_final: 0.7977 (tp) REVERT: I 208 LYS cc_start: 0.8931 (tptp) cc_final: 0.8585 (mmtm) REVERT: I 242 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8569 (mt) REVERT: J 14 ARG cc_start: 0.8159 (mtm110) cc_final: 0.7133 (ptm160) REVERT: J 155 GLU cc_start: 0.8074 (tp30) cc_final: 0.7859 (tm-30) REVERT: J 187 MET cc_start: 0.8865 (mmm) cc_final: 0.8497 (mmm) REVERT: J 229 ARG cc_start: 0.8017 (tpt90) cc_final: 0.7742 (tpp80) REVERT: K 31 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8305 (tm-30) REVERT: K 104 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: K 155 GLU cc_start: 0.8012 (tp30) cc_final: 0.7758 (tp30) REVERT: K 258 SER cc_start: 0.7595 (m) cc_final: 0.7248 (t) REVERT: L 116 LEU cc_start: 0.8367 (tp) cc_final: 0.8003 (tp) REVERT: L 141 HIS cc_start: 0.7634 (p-80) cc_final: 0.7421 (p-80) REVERT: L 195 LEU cc_start: 0.8806 (tt) cc_final: 0.8455 (mm) REVERT: L 242 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.7919 (mm) REVERT: M 144 MET cc_start: 0.7758 (ptp) cc_final: 0.7488 (ptt) REVERT: M 187 MET cc_start: 0.8952 (mmp) cc_final: 0.8714 (mmp) REVERT: M 195 LEU cc_start: 0.8600 (tt) cc_final: 0.8311 (mm) REVERT: M 208 LYS cc_start: 0.8881 (tptp) cc_final: 0.8507 (mmtm) REVERT: N 175 ASP cc_start: 0.7736 (m-30) cc_final: 0.7496 (m-30) REVERT: N 195 LEU cc_start: 0.8634 (tt) cc_final: 0.8356 (mm) REVERT: N 258 SER cc_start: 0.7591 (m) cc_final: 0.7279 (t) REVERT: O 195 LEU cc_start: 0.8715 (tt) cc_final: 0.8276 (mm) REVERT: O 208 LYS cc_start: 0.8903 (tptp) cc_final: 0.8619 (mmtm) REVERT: P 74 MET cc_start: 0.8303 (tpp) cc_final: 0.7954 (tpp) REVERT: P 230 GLU cc_start: 0.7758 (tp30) cc_final: 0.7448 (tp30) REVERT: Q 74 MET cc_start: 0.8329 (tpp) cc_final: 0.7997 (tpp) REVERT: Q 104 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7511 (m-80) REVERT: Q 187 MET cc_start: 0.9007 (mmp) cc_final: 0.8455 (mmm) REVERT: Q 191 ILE cc_start: 0.9199 (mt) cc_final: 0.8963 (mt) REVERT: Q 208 LYS cc_start: 0.8885 (tptp) cc_final: 0.8381 (mmtm) REVERT: Q 244 MET cc_start: 0.8381 (tpp) cc_final: 0.7946 (tpt) REVERT: R 141 HIS cc_start: 0.7432 (p-80) cc_final: 0.7128 (p-80) REVERT: R 195 LEU cc_start: 0.8828 (tt) cc_final: 0.8455 (mm) REVERT: S 51 TYR cc_start: 0.9162 (t80) cc_final: 0.8776 (t80) REVERT: S 187 MET cc_start: 0.9101 (mmp) cc_final: 0.8806 (mmm) REVERT: S 195 LEU cc_start: 0.9065 (tt) cc_final: 0.8518 (mm) REVERT: T 141 HIS cc_start: 0.7766 (p-80) cc_final: 0.7325 (p-80) REVERT: T 187 MET cc_start: 0.9152 (mmp) cc_final: 0.8859 (mmp) REVERT: T 195 LEU cc_start: 0.8769 (tt) cc_final: 0.8391 (mm) REVERT: T 250 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8501 (ttpp) REVERT: U 104 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: V 187 MET cc_start: 0.8965 (mmm) cc_final: 0.8303 (mmm) REVERT: V 195 LEU cc_start: 0.8763 (tt) cc_final: 0.8298 (mm) REVERT: V 229 ARG cc_start: 0.8137 (tpt90) cc_final: 0.7763 (tpp80) outliers start: 175 outliers final: 129 residues processed: 840 average time/residue: 0.2565 time to fit residues: 360.4568 Evaluate side-chains 748 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 612 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 240 SER Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain P residue 36 SER Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 104 PHE Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain Q residue 258 SER Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 245 MET Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 205 CYS Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain U residue 104 PHE Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 153 ARG Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 205 CYS Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain V residue 245 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 255 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 286 optimal weight: 20.0000 chunk 401 optimal weight: 0.8980 chunk 571 optimal weight: 0.9980 chunk 542 optimal weight: 0.5980 chunk 347 optimal weight: 3.9990 chunk 412 optimal weight: 0.8980 chunk 291 optimal weight: 0.0470 chunk 499 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 20 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.159837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.131442 restraints weight = 58715.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133849 restraints weight = 41635.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135427 restraints weight = 34035.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136203 restraints weight = 30067.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136922 restraints weight = 28043.518| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 46882 Z= 0.121 Angle : 0.507 6.915 63690 Z= 0.272 Chirality : 0.037 0.140 7414 Planarity : 0.004 0.057 7898 Dihedral : 3.894 16.224 6270 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.65 % Allowed : 19.74 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.11), residues: 5786 helix: 2.88 (0.07), residues: 4532 sheet: None (None), residues: 0 loop : -2.22 (0.15), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 71 TYR 0.013 0.001 TYR J 129 PHE 0.014 0.001 PHE E 232 TRP 0.010 0.001 TRP D 221 HIS 0.002 0.000 HIS H 141 Details of bonding type rmsd covalent geometry : bond 0.00239 (46838) covalent geometry : angle 0.50487 (63602) SS BOND : bond 0.00450 ( 44) SS BOND : angle 1.29781 ( 88) hydrogen bonds : bond 0.04562 ( 3543) hydrogen bonds : angle 3.58526 (10629) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 759 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 TYR cc_start: 0.9129 (t80) cc_final: 0.8767 (t80) REVERT: A 153 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7630 (ttp80) REVERT: A 188 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9201 (tp) REVERT: A 195 LEU cc_start: 0.8665 (tt) cc_final: 0.8299 (mm) REVERT: A 244 MET cc_start: 0.8017 (tpp) cc_final: 0.7664 (tpt) REVERT: B 116 LEU cc_start: 0.8330 (tp) cc_final: 0.8065 (tp) REVERT: B 155 GLU cc_start: 0.8100 (tp30) cc_final: 0.7642 (tm-30) REVERT: B 195 LEU cc_start: 0.8776 (tt) cc_final: 0.8481 (mm) REVERT: B 244 MET cc_start: 0.8304 (tpp) cc_final: 0.7968 (tpt) REVERT: C 14 ARG cc_start: 0.8058 (mtp-110) cc_final: 0.7834 (mtp-110) REVERT: C 71 ARG cc_start: 0.8260 (mmm160) cc_final: 0.6487 (mmp-170) REVERT: C 104 PHE cc_start: 0.7907 (m-80) cc_final: 0.7435 (m-10) REVERT: C 187 MET cc_start: 0.8955 (mmp) cc_final: 0.8217 (mmm) REVERT: C 191 ILE cc_start: 0.9128 (mt) cc_final: 0.8861 (mt) REVERT: D 13 GLN cc_start: 0.7912 (tp40) cc_final: 0.7295 (tm-30) REVERT: D 31 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8493 (tm-30) REVERT: D 187 MET cc_start: 0.9131 (mmp) cc_final: 0.8689 (tpp) REVERT: D 195 LEU cc_start: 0.8921 (tt) cc_final: 0.8483 (mm) REVERT: D 229 ARG cc_start: 0.7896 (tpp-160) cc_final: 0.7694 (tpp80) REVERT: D 231 LEU cc_start: 0.8932 (tp) cc_final: 0.8671 (mm) REVERT: E 31 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8246 (tm-30) REVERT: E 175 ASP cc_start: 0.8176 (m-30) cc_final: 0.7922 (m-30) REVERT: E 187 MET cc_start: 0.9138 (mmp) cc_final: 0.8861 (mmm) REVERT: E 195 LEU cc_start: 0.8627 (tt) cc_final: 0.8298 (mm) REVERT: F 116 LEU cc_start: 0.8342 (tp) cc_final: 0.7938 (tp) REVERT: F 141 HIS cc_start: 0.7500 (p-80) cc_final: 0.6955 (p-80) REVERT: F 195 LEU cc_start: 0.8777 (tt) cc_final: 0.8337 (mm) REVERT: F 250 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8536 (ttpp) REVERT: G 116 LEU cc_start: 0.8476 (tp) cc_final: 0.8216 (tp) REVERT: G 141 HIS cc_start: 0.7140 (p-80) cc_final: 0.6813 (p-80) REVERT: G 195 LEU cc_start: 0.8792 (tt) cc_final: 0.8288 (mm) REVERT: H 187 MET cc_start: 0.9054 (mmp) cc_final: 0.8766 (mmm) REVERT: H 195 LEU cc_start: 0.8812 (tt) cc_final: 0.8301 (mm) REVERT: I 116 LEU cc_start: 0.8236 (tp) cc_final: 0.7860 (tp) REVERT: I 208 LYS cc_start: 0.8967 (tptp) cc_final: 0.8524 (mmtm) REVERT: J 130 GLU cc_start: 0.8015 (pp20) cc_final: 0.7663 (tm-30) REVERT: J 155 GLU cc_start: 0.7999 (tp30) cc_final: 0.7769 (tm-30) REVERT: J 215 SER cc_start: 0.8764 (t) cc_final: 0.8520 (p) REVERT: J 229 ARG cc_start: 0.8003 (tpt90) cc_final: 0.7665 (tpp80) REVERT: K 31 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8482 (tm-30) REVERT: K 195 LEU cc_start: 0.8627 (tt) cc_final: 0.8276 (mm) REVERT: K 258 SER cc_start: 0.7353 (m) cc_final: 0.7080 (t) REVERT: L 116 LEU cc_start: 0.8276 (tp) cc_final: 0.7924 (tp) REVERT: L 141 HIS cc_start: 0.7500 (p-80) cc_final: 0.7282 (p-80) REVERT: L 144 MET cc_start: 0.7673 (ptm) cc_final: 0.7428 (ptt) REVERT: L 195 LEU cc_start: 0.8801 (tt) cc_final: 0.8432 (mm) REVERT: M 128 TYR cc_start: 0.9018 (m-10) cc_final: 0.8671 (m-10) REVERT: M 144 MET cc_start: 0.7769 (ptp) cc_final: 0.7510 (ptt) REVERT: M 187 MET cc_start: 0.9005 (mmp) cc_final: 0.8757 (mmp) REVERT: M 195 LEU cc_start: 0.8595 (tt) cc_final: 0.8282 (mm) REVERT: M 208 LYS cc_start: 0.8908 (tptp) cc_final: 0.8451 (mmtm) REVERT: N 128 TYR cc_start: 0.9017 (m-10) cc_final: 0.8786 (m-10) REVERT: N 195 LEU cc_start: 0.8640 (tt) cc_final: 0.8326 (mm) REVERT: N 258 SER cc_start: 0.7313 (m) cc_final: 0.7040 (t) REVERT: O 195 LEU cc_start: 0.8729 (tt) cc_final: 0.8278 (mm) REVERT: O 208 LYS cc_start: 0.8958 (tptp) cc_final: 0.8597 (mmtm) REVERT: O 242 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8530 (mt) REVERT: Q 187 MET cc_start: 0.9048 (mmp) cc_final: 0.8445 (mmm) REVERT: Q 208 LYS cc_start: 0.8926 (tptp) cc_final: 0.8315 (mmtm) REVERT: Q 242 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8236 (mm) REVERT: Q 244 MET cc_start: 0.8385 (tpp) cc_final: 0.8030 (tpt) REVERT: R 141 HIS cc_start: 0.7445 (p-80) cc_final: 0.7058 (p-80) REVERT: S 187 MET cc_start: 0.9179 (mmp) cc_final: 0.8842 (mmm) REVERT: S 195 LEU cc_start: 0.9041 (tt) cc_final: 0.8469 (mm) REVERT: T 141 HIS cc_start: 0.7751 (p-80) cc_final: 0.7325 (p-80) REVERT: T 195 LEU cc_start: 0.8762 (tt) cc_final: 0.8328 (mm) REVERT: T 242 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.7658 (mm) REVERT: T 250 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8437 (ttpp) REVERT: V 187 MET cc_start: 0.8960 (mmm) cc_final: 0.8356 (mmm) REVERT: V 195 LEU cc_start: 0.8759 (tt) cc_final: 0.8337 (mm) REVERT: V 229 ARG cc_start: 0.8079 (tpt90) cc_final: 0.7668 (tpp80) outliers start: 84 outliers final: 52 residues processed: 810 average time/residue: 0.2622 time to fit residues: 352.9001 Evaluate side-chains 728 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 671 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 245 MET Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 41 CYS Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 242 LEU Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain Q residue 258 SER Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain T residue 280 LEU Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 245 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 457 optimal weight: 3.9990 chunk 570 optimal weight: 0.9980 chunk 485 optimal weight: 2.9990 chunk 474 optimal weight: 1.9990 chunk 353 optimal weight: 7.9990 chunk 561 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 502 optimal weight: 0.7980 chunk 392 optimal weight: 0.9990 chunk 468 optimal weight: 0.0010 chunk 445 optimal weight: 4.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.131413 restraints weight = 58747.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133644 restraints weight = 43432.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.134808 restraints weight = 36029.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135928 restraints weight = 32425.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136285 restraints weight = 30106.485| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 46882 Z= 0.123 Angle : 0.518 12.290 63690 Z= 0.276 Chirality : 0.037 0.133 7414 Planarity : 0.004 0.048 7898 Dihedral : 3.801 16.016 6270 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.66 % Allowed : 20.05 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.11), residues: 5786 helix: 2.94 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.29 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 71 TYR 0.013 0.001 TYR M 129 PHE 0.016 0.001 PHE D 145 TRP 0.008 0.001 TRP D 221 HIS 0.002 0.000 HIS H 141 Details of bonding type rmsd covalent geometry : bond 0.00256 (46838) covalent geometry : angle 0.51603 (63602) SS BOND : bond 0.00264 ( 44) SS BOND : angle 1.45171 ( 88) hydrogen bonds : bond 0.04510 ( 3543) hydrogen bonds : angle 3.52877 (10629) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 719 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 TYR cc_start: 0.9101 (t80) cc_final: 0.8612 (t80) REVERT: A 176 GLU cc_start: 0.7731 (tp30) cc_final: 0.7475 (tm-30) REVERT: A 195 LEU cc_start: 0.8720 (tt) cc_final: 0.8317 (mm) REVERT: A 242 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.7935 (mm) REVERT: B 116 LEU cc_start: 0.8393 (tp) cc_final: 0.8110 (tp) REVERT: B 155 GLU cc_start: 0.8072 (tp30) cc_final: 0.7559 (tm-30) REVERT: B 195 LEU cc_start: 0.8731 (tt) cc_final: 0.8420 (mm) REVERT: B 244 MET cc_start: 0.8302 (tpp) cc_final: 0.7955 (tpt) REVERT: C 71 ARG cc_start: 0.8331 (mmm160) cc_final: 0.6534 (mmp-170) REVERT: C 104 PHE cc_start: 0.7808 (m-80) cc_final: 0.7442 (m-80) REVERT: C 187 MET cc_start: 0.8952 (mmp) cc_final: 0.8228 (mmm) REVERT: C 191 ILE cc_start: 0.9129 (mt) cc_final: 0.8867 (mt) REVERT: D 13 GLN cc_start: 0.7896 (tp40) cc_final: 0.7332 (tm-30) REVERT: D 31 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8350 (tm-30) REVERT: D 195 LEU cc_start: 0.8846 (tt) cc_final: 0.8439 (mm) REVERT: D 231 LEU cc_start: 0.8941 (tp) cc_final: 0.8660 (mm) REVERT: E 31 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8210 (tm-30) REVERT: E 187 MET cc_start: 0.9145 (mmp) cc_final: 0.8881 (mmm) REVERT: E 195 LEU cc_start: 0.8586 (tt) cc_final: 0.8270 (mm) REVERT: E 237 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7767 (tm-30) REVERT: F 116 LEU cc_start: 0.8416 (tp) cc_final: 0.7937 (tp) REVERT: F 141 HIS cc_start: 0.7468 (p-80) cc_final: 0.6946 (p-80) REVERT: F 195 LEU cc_start: 0.8778 (tt) cc_final: 0.8316 (mm) REVERT: F 242 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.7811 (mm) REVERT: F 250 LYS cc_start: 0.8889 (ttmt) cc_final: 0.8524 (ttpp) REVERT: G 116 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8209 (tp) REVERT: G 141 HIS cc_start: 0.7171 (p-80) cc_final: 0.6832 (p-80) REVERT: G 195 LEU cc_start: 0.8787 (tt) cc_final: 0.8307 (mm) REVERT: H 187 MET cc_start: 0.9102 (mmp) cc_final: 0.8893 (mmm) REVERT: H 195 LEU cc_start: 0.8814 (tt) cc_final: 0.8357 (mm) REVERT: I 116 LEU cc_start: 0.8270 (tp) cc_final: 0.7922 (tp) REVERT: I 208 LYS cc_start: 0.8988 (tptp) cc_final: 0.8474 (mmtm) REVERT: I 242 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8463 (mt) REVERT: I 250 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8323 (tttm) REVERT: J 130 GLU cc_start: 0.8018 (pp20) cc_final: 0.7633 (tm-30) REVERT: J 155 GLU cc_start: 0.7959 (tp30) cc_final: 0.7736 (tm-30) REVERT: J 187 MET cc_start: 0.8969 (mmm) cc_final: 0.8613 (mmm) REVERT: J 229 ARG cc_start: 0.7904 (tpt90) cc_final: 0.7566 (tpp80) REVERT: K 19 ILE cc_start: 0.9035 (mm) cc_final: 0.8724 (mt) REVERT: K 31 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8457 (tm-30) REVERT: K 195 LEU cc_start: 0.8614 (tt) cc_final: 0.8292 (mm) REVERT: K 258 SER cc_start: 0.7292 (m) cc_final: 0.6987 (t) REVERT: L 116 LEU cc_start: 0.8304 (tp) cc_final: 0.7932 (tp) REVERT: L 195 LEU cc_start: 0.8849 (tt) cc_final: 0.8465 (mm) REVERT: L 250 LYS cc_start: 0.8795 (ttmt) cc_final: 0.8292 (tttm) REVERT: M 144 MET cc_start: 0.7820 (ptp) cc_final: 0.7582 (ptt) REVERT: M 187 MET cc_start: 0.8993 (mmp) cc_final: 0.8763 (mmp) REVERT: M 195 LEU cc_start: 0.8600 (tt) cc_final: 0.8297 (mm) REVERT: M 208 LYS cc_start: 0.8908 (tptp) cc_final: 0.8449 (mmtm) REVERT: N 128 TYR cc_start: 0.9015 (m-10) cc_final: 0.8780 (m-10) REVERT: N 195 LEU cc_start: 0.8631 (tt) cc_final: 0.8341 (mm) REVERT: N 258 SER cc_start: 0.7239 (m) cc_final: 0.6952 (t) REVERT: O 195 LEU cc_start: 0.8655 (tt) cc_final: 0.8253 (mm) REVERT: O 208 LYS cc_start: 0.8954 (tptp) cc_final: 0.8601 (mmtm) REVERT: O 242 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8034 (mm) REVERT: P 195 LEU cc_start: 0.8667 (tt) cc_final: 0.8381 (mm) REVERT: Q 104 PHE cc_start: 0.7888 (m-80) cc_final: 0.7580 (m-10) REVERT: Q 187 MET cc_start: 0.9053 (mmp) cc_final: 0.8420 (mmm) REVERT: Q 208 LYS cc_start: 0.8927 (tptp) cc_final: 0.8683 (tppt) REVERT: Q 242 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8255 (mm) REVERT: Q 244 MET cc_start: 0.8412 (tpp) cc_final: 0.8035 (tpt) REVERT: R 141 HIS cc_start: 0.7463 (p-80) cc_final: 0.7056 (p-80) REVERT: S 187 MET cc_start: 0.9175 (mmp) cc_final: 0.8862 (mmm) REVERT: S 195 LEU cc_start: 0.9049 (tt) cc_final: 0.8485 (mm) REVERT: T 141 HIS cc_start: 0.7778 (p-80) cc_final: 0.7324 (p-80) REVERT: T 187 MET cc_start: 0.9148 (mmm) cc_final: 0.8841 (mmp) REVERT: T 195 LEU cc_start: 0.8760 (tt) cc_final: 0.8353 (mm) REVERT: T 242 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.7693 (mm) REVERT: T 250 LYS cc_start: 0.8776 (ttmt) cc_final: 0.8451 (ttpp) REVERT: V 187 MET cc_start: 0.8964 (mmm) cc_final: 0.8307 (mmm) REVERT: V 195 LEU cc_start: 0.8737 (tt) cc_final: 0.8337 (mm) REVERT: V 229 ARG cc_start: 0.7990 (tpt90) cc_final: 0.7570 (tpp80) outliers start: 135 outliers final: 106 residues processed: 803 average time/residue: 0.2609 time to fit residues: 350.5719 Evaluate side-chains 774 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 661 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 245 MET Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 280 LEU Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 187 MET Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 242 LEU Chi-restraints excluded: chain Q residue 245 MET Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain Q residue 258 SER Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 205 CYS Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 153 ARG Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 245 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 327 optimal weight: 2.9990 chunk 322 optimal weight: 0.8980 chunk 324 optimal weight: 10.0000 chunk 374 optimal weight: 0.8980 chunk 325 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 398 optimal weight: 8.9990 chunk 547 optimal weight: 7.9990 chunk 358 optimal weight: 0.9980 chunk 402 optimal weight: 0.0270 chunk 552 optimal weight: 0.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.161203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.132838 restraints weight = 58618.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.135224 restraints weight = 42126.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136768 restraints weight = 34543.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.137333 restraints weight = 30574.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.137920 restraints weight = 28874.345| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 46882 Z= 0.118 Angle : 0.516 10.639 63690 Z= 0.274 Chirality : 0.037 0.187 7414 Planarity : 0.004 0.047 7898 Dihedral : 3.745 15.813 6270 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.22 % Allowed : 20.78 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.11), residues: 5786 helix: 3.02 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.30 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 229 TYR 0.012 0.001 TYR Q 129 PHE 0.012 0.001 PHE Q 104 TRP 0.009 0.001 TRP D 221 HIS 0.002 0.000 HIS L 141 Details of bonding type rmsd covalent geometry : bond 0.00239 (46838) covalent geometry : angle 0.51406 (63602) SS BOND : bond 0.00272 ( 44) SS BOND : angle 1.37526 ( 88) hydrogen bonds : bond 0.04183 ( 3543) hydrogen bonds : angle 3.45455 (10629) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 726 time to evaluate : 1.749 Fit side-chains revert: symmetry clash REVERT: A 53 SER cc_start: 0.9045 (t) cc_final: 0.8691 (t) REVERT: A 129 TYR cc_start: 0.9114 (t80) cc_final: 0.8603 (t80) REVERT: A 195 LEU cc_start: 0.8687 (tt) cc_final: 0.8324 (mm) REVERT: A 242 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7774 (mm) REVERT: B 116 LEU cc_start: 0.8389 (tp) cc_final: 0.8094 (tp) REVERT: B 155 GLU cc_start: 0.8065 (tp30) cc_final: 0.7627 (tm-30) REVERT: B 195 LEU cc_start: 0.8721 (tt) cc_final: 0.8418 (mm) REVERT: B 244 MET cc_start: 0.8294 (tpp) cc_final: 0.7940 (tpt) REVERT: C 14 ARG cc_start: 0.7966 (mtp-110) cc_final: 0.7679 (mtp-110) REVERT: C 71 ARG cc_start: 0.8318 (mmm160) cc_final: 0.6430 (mmp-170) REVERT: C 104 PHE cc_start: 0.7704 (m-80) cc_final: 0.7388 (m-80) REVERT: C 187 MET cc_start: 0.8960 (mmp) cc_final: 0.8231 (mmm) REVERT: C 191 ILE cc_start: 0.9122 (mt) cc_final: 0.8864 (mt) REVERT: D 13 GLN cc_start: 0.7908 (tp40) cc_final: 0.7290 (tm-30) REVERT: D 31 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8415 (tm-30) REVERT: D 195 LEU cc_start: 0.8747 (tt) cc_final: 0.8415 (mm) REVERT: D 231 LEU cc_start: 0.8918 (tp) cc_final: 0.8686 (mm) REVERT: E 31 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8230 (tm-30) REVERT: E 187 MET cc_start: 0.9157 (mmp) cc_final: 0.8837 (mmm) REVERT: E 195 LEU cc_start: 0.8610 (tt) cc_final: 0.8314 (mm) REVERT: F 116 LEU cc_start: 0.8364 (tp) cc_final: 0.7882 (tp) REVERT: F 141 HIS cc_start: 0.7444 (p-80) cc_final: 0.6888 (p-80) REVERT: F 195 LEU cc_start: 0.8758 (tt) cc_final: 0.8315 (mm) REVERT: F 242 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.7797 (mm) REVERT: F 250 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8529 (ttpp) REVERT: G 116 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8127 (tp) REVERT: G 141 HIS cc_start: 0.7168 (p-80) cc_final: 0.6783 (p-80) REVERT: G 144 MET cc_start: 0.6932 (ptt) cc_final: 0.6694 (ptt) REVERT: G 195 LEU cc_start: 0.8780 (tt) cc_final: 0.8296 (mm) REVERT: G 258 SER cc_start: 0.7839 (m) cc_final: 0.7627 (t) REVERT: H 187 MET cc_start: 0.9046 (mmp) cc_final: 0.8788 (mmm) REVERT: H 195 LEU cc_start: 0.8813 (tt) cc_final: 0.8397 (mm) REVERT: I 116 LEU cc_start: 0.8232 (tp) cc_final: 0.7921 (tp) REVERT: I 208 LYS cc_start: 0.8993 (tptp) cc_final: 0.8453 (mmtm) REVERT: I 250 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8317 (tttm) REVERT: J 130 GLU cc_start: 0.7995 (pp20) cc_final: 0.7755 (tm-30) REVERT: J 155 GLU cc_start: 0.7952 (tp30) cc_final: 0.7634 (tm-30) REVERT: J 187 MET cc_start: 0.8962 (mmm) cc_final: 0.8593 (mmm) REVERT: J 229 ARG cc_start: 0.7846 (tpt90) cc_final: 0.7508 (tpp80) REVERT: K 19 ILE cc_start: 0.9017 (mm) cc_final: 0.8705 (mt) REVERT: K 31 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8346 (tm-30) REVERT: K 195 LEU cc_start: 0.8615 (tt) cc_final: 0.8301 (mm) REVERT: L 116 LEU cc_start: 0.8262 (tp) cc_final: 0.7910 (tp) REVERT: L 195 LEU cc_start: 0.8843 (tt) cc_final: 0.8467 (mm) REVERT: L 242 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.7870 (mm) REVERT: L 250 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8285 (tttm) REVERT: M 144 MET cc_start: 0.7837 (ptp) cc_final: 0.7560 (ptt) REVERT: M 187 MET cc_start: 0.9011 (mmp) cc_final: 0.8772 (mmp) REVERT: M 195 LEU cc_start: 0.8616 (tt) cc_final: 0.8241 (mm) REVERT: M 208 LYS cc_start: 0.8921 (tptp) cc_final: 0.8421 (mmtm) REVERT: N 195 LEU cc_start: 0.8628 (tt) cc_final: 0.8335 (mm) REVERT: N 258 SER cc_start: 0.7316 (m) cc_final: 0.7068 (t) REVERT: O 53 SER cc_start: 0.9149 (t) cc_final: 0.8777 (t) REVERT: O 195 LEU cc_start: 0.8708 (tt) cc_final: 0.8304 (mm) REVERT: O 208 LYS cc_start: 0.8923 (tptp) cc_final: 0.8525 (mmtm) REVERT: O 242 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8046 (mm) REVERT: P 116 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8181 (tp) REVERT: P 160 PHE cc_start: 0.7931 (m-80) cc_final: 0.7638 (t80) REVERT: P 195 LEU cc_start: 0.8590 (tt) cc_final: 0.8208 (mm) REVERT: Q 104 PHE cc_start: 0.7918 (m-80) cc_final: 0.7624 (m-80) REVERT: Q 187 MET cc_start: 0.9049 (mmp) cc_final: 0.8430 (mmm) REVERT: Q 208 LYS cc_start: 0.8894 (tptp) cc_final: 0.8631 (tppt) REVERT: Q 242 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8197 (mm) REVERT: Q 244 MET cc_start: 0.8426 (tpp) cc_final: 0.8027 (tpt) REVERT: R 141 HIS cc_start: 0.7451 (p-80) cc_final: 0.7043 (p-80) REVERT: S 187 MET cc_start: 0.9185 (mmp) cc_final: 0.8801 (mmm) REVERT: S 195 LEU cc_start: 0.9001 (tt) cc_final: 0.8409 (mm) REVERT: S 237 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7618 (tm-30) REVERT: T 141 HIS cc_start: 0.7751 (p-80) cc_final: 0.7265 (p-80) REVERT: T 187 MET cc_start: 0.9160 (mmm) cc_final: 0.8793 (mmp) REVERT: T 195 LEU cc_start: 0.8758 (tt) cc_final: 0.8285 (mm) REVERT: T 237 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7696 (tm-30) REVERT: T 242 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.7747 (mm) REVERT: T 250 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8467 (ttpp) REVERT: U 187 MET cc_start: 0.9069 (mmm) cc_final: 0.8756 (mmm) REVERT: U 195 LEU cc_start: 0.8752 (tt) cc_final: 0.8305 (mm) REVERT: V 187 MET cc_start: 0.9062 (mmm) cc_final: 0.8606 (mmm) REVERT: V 195 LEU cc_start: 0.8731 (tt) cc_final: 0.8337 (mm) REVERT: V 229 ARG cc_start: 0.7857 (tpt90) cc_final: 0.7488 (tpp80) outliers start: 113 outliers final: 89 residues processed: 794 average time/residue: 0.2552 time to fit residues: 338.9666 Evaluate side-chains 782 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 685 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 131 CYS Chi-restraints excluded: chain M residue 245 MET Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 131 CYS Chi-restraints excluded: chain O residue 187 MET Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 242 LEU Chi-restraints excluded: chain Q residue 245 MET Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 245 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 103 optimal weight: 6.9990 chunk 431 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 321 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 358 optimal weight: 0.9980 chunk 399 optimal weight: 3.9990 chunk 403 optimal weight: 3.9990 chunk 373 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN I 32 GLN O 227 ASN U 227 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.151833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.123093 restraints weight = 59272.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125263 restraints weight = 43615.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126398 restraints weight = 36254.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127476 restraints weight = 32650.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127895 restraints weight = 30439.297| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 46882 Z= 0.173 Angle : 0.573 10.086 63690 Z= 0.306 Chirality : 0.039 0.222 7414 Planarity : 0.004 0.048 7898 Dihedral : 3.782 16.104 6270 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.89 % Allowed : 20.50 % Favored : 76.60 % 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: 2.81 (0.11), residues: 5786 helix: 2.83 (0.07), residues: 4576 sheet: None (None), residues: 0 loop : -2.28 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 174 TYR 0.014 0.001 TYR P 128 PHE 0.017 0.002 PHE Q 232 TRP 0.011 0.001 TRP Q 190 HIS 0.003 0.001 HIS S 181 Details of bonding type rmsd covalent geometry : bond 0.00402 (46838) covalent geometry : angle 0.56978 (63602) SS BOND : bond 0.00261 ( 44) SS BOND : angle 1.76437 ( 88) hydrogen bonds : bond 0.05177 ( 3543) hydrogen bonds : angle 3.60200 (10629) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 693 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7796 (tp30) cc_final: 0.7471 (tm-30) REVERT: A 195 LEU cc_start: 0.8750 (tt) cc_final: 0.8342 (mm) REVERT: A 242 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.7929 (mm) REVERT: B 116 LEU cc_start: 0.8460 (tp) cc_final: 0.8160 (tp) REVERT: B 155 GLU cc_start: 0.8087 (tp30) cc_final: 0.7689 (tm-30) REVERT: B 195 LEU cc_start: 0.8751 (tt) cc_final: 0.8433 (mm) REVERT: B 244 MET cc_start: 0.8307 (tpp) cc_final: 0.7935 (tpt) REVERT: C 14 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7610 (mtm-85) REVERT: C 104 PHE cc_start: 0.7641 (m-80) cc_final: 0.7437 (m-80) REVERT: C 116 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8223 (tp) REVERT: C 187 MET cc_start: 0.8927 (mmp) cc_final: 0.8244 (mmm) REVERT: C 191 ILE cc_start: 0.9186 (mt) cc_final: 0.8949 (mt) REVERT: D 13 GLN cc_start: 0.8120 (tp40) cc_final: 0.7334 (tm-30) REVERT: D 31 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8416 (tm-30) REVERT: D 116 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8390 (tp) REVERT: D 195 LEU cc_start: 0.8769 (tt) cc_final: 0.8412 (mm) REVERT: E 31 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8409 (tm-30) REVERT: E 187 MET cc_start: 0.9185 (mmp) cc_final: 0.8903 (mmm) REVERT: E 195 LEU cc_start: 0.8616 (tt) cc_final: 0.8261 (mm) REVERT: F 116 LEU cc_start: 0.8496 (tp) cc_final: 0.7951 (tp) REVERT: F 141 HIS cc_start: 0.7487 (p-80) cc_final: 0.6996 (p-80) REVERT: F 195 LEU cc_start: 0.8819 (tt) cc_final: 0.8324 (mm) REVERT: F 242 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.7899 (mm) REVERT: F 250 LYS cc_start: 0.8963 (ttmt) cc_final: 0.8649 (ttpp) REVERT: G 116 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8327 (tp) REVERT: G 141 HIS cc_start: 0.7147 (p-80) cc_final: 0.6864 (p-80) REVERT: G 144 MET cc_start: 0.7162 (ptt) cc_final: 0.6957 (ptt) REVERT: G 176 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7782 (tm-30) REVERT: G 195 LEU cc_start: 0.8804 (tt) cc_final: 0.8317 (mm) REVERT: H 187 MET cc_start: 0.9063 (mmp) cc_final: 0.8843 (mmm) REVERT: H 195 LEU cc_start: 0.8810 (tt) cc_final: 0.8386 (mm) REVERT: I 116 LEU cc_start: 0.8371 (tp) cc_final: 0.8007 (tp) REVERT: I 208 LYS cc_start: 0.8971 (tptp) cc_final: 0.8504 (mmtm) REVERT: I 242 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8536 (mt) REVERT: I 250 LYS cc_start: 0.8963 (ttmt) cc_final: 0.8399 (tttm) REVERT: J 130 GLU cc_start: 0.7594 (pp20) cc_final: 0.7242 (tm-30) REVERT: J 155 GLU cc_start: 0.7945 (tp30) cc_final: 0.7707 (tm-30) REVERT: J 187 MET cc_start: 0.8994 (mmm) cc_final: 0.8722 (mmm) REVERT: J 229 ARG cc_start: 0.7955 (tpt90) cc_final: 0.7569 (tpp80) REVERT: K 19 ILE cc_start: 0.9032 (mm) cc_final: 0.8747 (mt) REVERT: K 195 LEU cc_start: 0.8652 (tt) cc_final: 0.8379 (mm) REVERT: L 116 LEU cc_start: 0.8436 (tp) cc_final: 0.8022 (tp) REVERT: L 195 LEU cc_start: 0.8858 (tt) cc_final: 0.8485 (mm) REVERT: L 242 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.7879 (mm) REVERT: L 250 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8442 (tttm) REVERT: M 195 LEU cc_start: 0.8604 (tt) cc_final: 0.8294 (mm) REVERT: M 208 LYS cc_start: 0.8902 (tptp) cc_final: 0.8447 (mmtm) REVERT: M 229 ARG cc_start: 0.8030 (tpt90) cc_final: 0.7684 (tpp80) REVERT: N 175 ASP cc_start: 0.7690 (m-30) cc_final: 0.7478 (m-30) REVERT: N 195 LEU cc_start: 0.8615 (tt) cc_final: 0.8339 (mm) REVERT: N 258 SER cc_start: 0.7278 (m) cc_final: 0.7052 (t) REVERT: O 195 LEU cc_start: 0.8679 (tt) cc_final: 0.8282 (mm) REVERT: O 208 LYS cc_start: 0.8905 (tptp) cc_final: 0.8567 (mmtm) REVERT: O 242 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8164 (mm) REVERT: P 116 LEU cc_start: 0.8553 (tp) cc_final: 0.8248 (tp) REVERT: P 160 PHE cc_start: 0.8006 (m-80) cc_final: 0.7640 (t80) REVERT: Q 104 PHE cc_start: 0.7730 (m-80) cc_final: 0.7509 (m-80) REVERT: Q 187 MET cc_start: 0.8940 (mmp) cc_final: 0.8438 (mmm) REVERT: Q 208 LYS cc_start: 0.8886 (tptp) cc_final: 0.8658 (tppt) REVERT: Q 242 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8607 (mm) REVERT: Q 244 MET cc_start: 0.8461 (tpp) cc_final: 0.8067 (tpt) REVERT: R 141 HIS cc_start: 0.7461 (p-80) cc_final: 0.7026 (p-80) REVERT: S 51 TYR cc_start: 0.9086 (t80) cc_final: 0.8852 (t80) REVERT: S 187 MET cc_start: 0.9132 (mmp) cc_final: 0.8821 (mmm) REVERT: S 195 LEU cc_start: 0.9024 (tt) cc_final: 0.8442 (mm) REVERT: T 141 HIS cc_start: 0.7756 (p-80) cc_final: 0.7313 (p-80) REVERT: T 187 MET cc_start: 0.9198 (mmm) cc_final: 0.8706 (mmp) REVERT: T 195 LEU cc_start: 0.8784 (tt) cc_final: 0.8267 (mm) REVERT: T 242 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.7822 (mm) REVERT: T 250 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8570 (ttpp) REVERT: U 187 MET cc_start: 0.9022 (mmm) cc_final: 0.8661 (mmm) REVERT: V 187 MET cc_start: 0.8967 (mmm) cc_final: 0.8365 (mmm) REVERT: V 195 LEU cc_start: 0.8752 (tt) cc_final: 0.8362 (mm) REVERT: V 229 ARG cc_start: 0.8014 (tpt90) cc_final: 0.7734 (tpp80) outliers start: 147 outliers final: 126 residues processed: 802 average time/residue: 0.2448 time to fit residues: 329.4472 Evaluate side-chains 782 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 646 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 240 SER Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 245 MET Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 131 CYS Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 242 LEU Chi-restraints excluded: chain Q residue 245 MET Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 205 CYS Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 153 ARG Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain T residue 280 LEU Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 205 CYS Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain V residue 245 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 466 optimal weight: 0.0670 chunk 99 optimal weight: 0.9990 chunk 428 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 520 optimal weight: 20.0000 chunk 546 optimal weight: 20.0000 chunk 374 optimal weight: 2.9990 chunk 481 optimal weight: 3.9990 chunk 493 optimal weight: 6.9990 chunk 312 optimal weight: 20.0000 chunk 397 optimal weight: 4.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 ASN E 227 ASN J 227 ASN M 227 ASN S 227 ASN T 227 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.117613 restraints weight = 58964.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.120118 restraints weight = 40208.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121673 restraints weight = 31863.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122483 restraints weight = 27740.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123185 restraints weight = 25629.260| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 46882 Z= 0.182 Angle : 0.586 9.863 63690 Z= 0.312 Chirality : 0.039 0.256 7414 Planarity : 0.004 0.053 7898 Dihedral : 3.884 16.588 6270 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.87 % Allowed : 20.96 % Favored : 76.17 % 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: 2.71 (0.11), residues: 5786 helix: 2.76 (0.07), residues: 4576 sheet: None (None), residues: 0 loop : -2.32 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 174 TYR 0.013 0.001 TYR J 129 PHE 0.015 0.001 PHE C 232 TRP 0.011 0.001 TRP Q 190 HIS 0.004 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00423 (46838) covalent geometry : angle 0.58373 (63602) SS BOND : bond 0.00297 ( 44) SS BOND : angle 1.63196 ( 88) hydrogen bonds : bond 0.05266 ( 3543) hydrogen bonds : angle 3.62878 (10629) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 691 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.8779 (tt) cc_final: 0.8322 (mm) REVERT: A 242 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8064 (mm) REVERT: B 116 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8198 (tp) REVERT: B 195 LEU cc_start: 0.8780 (tt) cc_final: 0.8432 (mm) REVERT: B 244 MET cc_start: 0.8260 (tpp) cc_final: 0.7853 (tpt) REVERT: C 14 ARG cc_start: 0.7810 (mtp-110) cc_final: 0.7599 (mtm-85) REVERT: C 31 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8487 (tm-30) REVERT: C 187 MET cc_start: 0.8896 (mmp) cc_final: 0.8255 (mmm) REVERT: C 191 ILE cc_start: 0.9238 (mt) cc_final: 0.8945 (mt) REVERT: D 13 GLN cc_start: 0.8142 (tp40) cc_final: 0.7159 (tm-30) REVERT: D 19 ILE cc_start: 0.8941 (mm) cc_final: 0.8709 (mt) REVERT: D 141 HIS cc_start: 0.6901 (p-80) cc_final: 0.6531 (p-80) REVERT: D 155 GLU cc_start: 0.8193 (tp30) cc_final: 0.7965 (tm-30) REVERT: D 195 LEU cc_start: 0.8750 (tt) cc_final: 0.8408 (mm) REVERT: E 187 MET cc_start: 0.9132 (mmp) cc_final: 0.8811 (mmm) REVERT: E 195 LEU cc_start: 0.8646 (tt) cc_final: 0.8240 (mm) REVERT: E 208 LYS cc_start: 0.8827 (tppt) cc_final: 0.8379 (mmtm) REVERT: E 237 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7688 (tm-30) REVERT: F 116 LEU cc_start: 0.8532 (tp) cc_final: 0.7969 (tp) REVERT: F 141 HIS cc_start: 0.7533 (p-80) cc_final: 0.7046 (p-80) REVERT: F 195 LEU cc_start: 0.8810 (tt) cc_final: 0.8336 (mm) REVERT: F 242 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.7927 (mm) REVERT: F 250 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8671 (ttpp) REVERT: G 116 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8207 (tp) REVERT: G 141 HIS cc_start: 0.7124 (p-80) cc_final: 0.6875 (p-80) REVERT: G 144 MET cc_start: 0.7271 (ptt) cc_final: 0.7071 (ptt) REVERT: G 176 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7745 (tm-30) REVERT: G 195 LEU cc_start: 0.8859 (tt) cc_final: 0.8398 (mm) REVERT: H 195 LEU cc_start: 0.8827 (tt) cc_final: 0.8423 (mm) REVERT: H 237 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7537 (tm-30) REVERT: I 31 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8152 (tm-30) REVERT: I 116 LEU cc_start: 0.8375 (tp) cc_final: 0.8000 (tp) REVERT: I 208 LYS cc_start: 0.8981 (tptp) cc_final: 0.8672 (mmtm) REVERT: I 242 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8489 (mt) REVERT: I 250 LYS cc_start: 0.9008 (ttmt) cc_final: 0.8493 (tttm) REVERT: J 128 TYR cc_start: 0.8869 (m-10) cc_final: 0.8496 (m-10) REVERT: J 130 GLU cc_start: 0.7674 (pp20) cc_final: 0.7315 (tm-30) REVERT: J 187 MET cc_start: 0.8986 (mmm) cc_final: 0.8726 (mmm) REVERT: J 227 ASN cc_start: 0.7693 (OUTLIER) cc_final: 0.7295 (m110) REVERT: J 229 ARG cc_start: 0.7968 (tpt90) cc_final: 0.7539 (tpp80) REVERT: K 19 ILE cc_start: 0.9044 (mm) cc_final: 0.8772 (mt) REVERT: K 31 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8444 (tm-30) REVERT: K 195 LEU cc_start: 0.8643 (tt) cc_final: 0.8393 (mm) REVERT: L 116 LEU cc_start: 0.8386 (tp) cc_final: 0.7948 (tp) REVERT: L 195 LEU cc_start: 0.8881 (tt) cc_final: 0.8499 (mm) REVERT: L 242 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8310 (mt) REVERT: M 144 MET cc_start: 0.7923 (ptt) cc_final: 0.7708 (ptt) REVERT: M 195 LEU cc_start: 0.8619 (tt) cc_final: 0.8266 (mm) REVERT: M 208 LYS cc_start: 0.8905 (tptp) cc_final: 0.8447 (mmtm) REVERT: M 229 ARG cc_start: 0.8054 (tpt90) cc_final: 0.7799 (tpp80) REVERT: N 31 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8392 (tm-30) REVERT: N 195 LEU cc_start: 0.8638 (tt) cc_final: 0.8337 (mm) REVERT: N 258 SER cc_start: 0.7347 (m) cc_final: 0.6988 (t) REVERT: O 195 LEU cc_start: 0.8689 (tt) cc_final: 0.8277 (mm) REVERT: O 208 LYS cc_start: 0.8893 (tptp) cc_final: 0.8577 (mmtm) REVERT: O 242 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8078 (mm) REVERT: P 74 MET cc_start: 0.8311 (tpp) cc_final: 0.7840 (tpp) REVERT: Q 96 GLU cc_start: 0.7609 (pt0) cc_final: 0.7400 (pt0) REVERT: Q 187 MET cc_start: 0.8979 (mmp) cc_final: 0.8440 (mmm) REVERT: Q 242 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8310 (mm) REVERT: Q 244 MET cc_start: 0.8447 (tpp) cc_final: 0.8120 (tpt) REVERT: R 141 HIS cc_start: 0.7284 (p-80) cc_final: 0.6929 (p-80) REVERT: S 51 TYR cc_start: 0.9105 (t80) cc_final: 0.8903 (t80) REVERT: S 187 MET cc_start: 0.9007 (mmp) cc_final: 0.8730 (mmm) REVERT: S 195 LEU cc_start: 0.9071 (tt) cc_final: 0.8468 (mm) REVERT: S 227 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7704 (m110) REVERT: T 141 HIS cc_start: 0.7809 (p-80) cc_final: 0.7405 (p-80) REVERT: T 187 MET cc_start: 0.9177 (mmm) cc_final: 0.8751 (mmp) REVERT: T 195 LEU cc_start: 0.8788 (tt) cc_final: 0.8274 (mm) REVERT: T 242 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.7847 (mm) REVERT: T 250 LYS cc_start: 0.8861 (ttmt) cc_final: 0.8561 (ttpp) REVERT: U 195 LEU cc_start: 0.8835 (tt) cc_final: 0.8411 (mm) REVERT: V 187 MET cc_start: 0.8965 (mmm) cc_final: 0.8390 (mmm) REVERT: V 195 LEU cc_start: 0.8759 (tt) cc_final: 0.8353 (mm) REVERT: V 229 ARG cc_start: 0.8013 (tpt90) cc_final: 0.7740 (tpp80) outliers start: 146 outliers final: 125 residues processed: 804 average time/residue: 0.2361 time to fit residues: 318.0981 Evaluate side-chains 795 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 659 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 227 ASN Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 245 MET Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 131 CYS Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 245 MET Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 131 CYS Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 242 LEU Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 205 CYS Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 227 ASN Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain T residue 280 LEU Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 205 CYS Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain V residue 245 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 100 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 448 optimal weight: 2.9990 chunk 128 optimal weight: 0.0770 chunk 455 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 550 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 225 optimal weight: 0.8980 chunk 164 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.158978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130688 restraints weight = 58582.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133000 restraints weight = 42468.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134301 restraints weight = 35102.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135356 restraints weight = 31363.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.135785 restraints weight = 29189.930| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 46882 Z= 0.128 Angle : 0.560 10.890 63690 Z= 0.295 Chirality : 0.037 0.241 7414 Planarity : 0.004 0.049 7898 Dihedral : 3.856 16.613 6270 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.89 % Allowed : 21.92 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.11), residues: 5786 helix: 2.98 (0.07), residues: 4576 sheet: None (None), residues: 0 loop : -2.29 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 174 TYR 0.014 0.001 TYR O 129 PHE 0.014 0.001 PHE S 232 TRP 0.010 0.001 TRP H 221 HIS 0.003 0.000 HIS S 141 Details of bonding type rmsd covalent geometry : bond 0.00268 (46838) covalent geometry : angle 0.55767 (63602) SS BOND : bond 0.00133 ( 44) SS BOND : angle 1.34446 ( 88) hydrogen bonds : bond 0.04532 ( 3543) hydrogen bonds : angle 3.47025 (10629) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 709 time to evaluate : 1.718 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7653 (tp30) cc_final: 0.7366 (tm-30) REVERT: A 195 LEU cc_start: 0.8684 (tt) cc_final: 0.8270 (mm) REVERT: A 237 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7643 (tm-30) REVERT: A 242 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.7935 (mm) REVERT: B 116 LEU cc_start: 0.8417 (tp) cc_final: 0.8177 (tp) REVERT: B 195 LEU cc_start: 0.8709 (tt) cc_final: 0.8437 (mm) REVERT: B 244 MET cc_start: 0.8249 (tpp) cc_final: 0.7873 (tpt) REVERT: C 14 ARG cc_start: 0.7774 (mtp-110) cc_final: 0.7544 (mtm-85) REVERT: C 31 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8499 (tm-30) REVERT: C 105 PHE cc_start: 0.8627 (t80) cc_final: 0.8175 (t80) REVERT: C 116 LEU cc_start: 0.8464 (tp) cc_final: 0.8109 (tp) REVERT: C 187 MET cc_start: 0.8857 (mmp) cc_final: 0.8208 (mmm) REVERT: C 191 ILE cc_start: 0.9154 (mt) cc_final: 0.8946 (mt) REVERT: D 13 GLN cc_start: 0.8106 (tp40) cc_final: 0.7161 (tm-30) REVERT: D 19 ILE cc_start: 0.8908 (mm) cc_final: 0.8658 (mt) REVERT: D 31 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8405 (tm-30) REVERT: D 155 GLU cc_start: 0.8079 (tp30) cc_final: 0.7822 (tm-30) REVERT: D 195 LEU cc_start: 0.8616 (tt) cc_final: 0.8305 (mm) REVERT: E 31 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8359 (tm-30) REVERT: E 187 MET cc_start: 0.9093 (mmp) cc_final: 0.8781 (mmm) REVERT: E 195 LEU cc_start: 0.8673 (tt) cc_final: 0.8324 (mm) REVERT: E 208 LYS cc_start: 0.8820 (tppt) cc_final: 0.8255 (mmtm) REVERT: F 116 LEU cc_start: 0.8454 (tp) cc_final: 0.7924 (tp) REVERT: F 141 HIS cc_start: 0.7472 (p-80) cc_final: 0.6947 (p-80) REVERT: F 195 LEU cc_start: 0.8756 (tt) cc_final: 0.8270 (mm) REVERT: F 233 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7616 (tm-30) REVERT: F 250 LYS cc_start: 0.8918 (ttmt) cc_final: 0.8600 (ttpp) REVERT: G 116 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8144 (tp) REVERT: G 141 HIS cc_start: 0.7077 (p-80) cc_final: 0.6774 (p-80) REVERT: G 144 MET cc_start: 0.7120 (ptt) cc_final: 0.6877 (ptt) REVERT: H 187 MET cc_start: 0.8793 (mmm) cc_final: 0.8405 (mmm) REVERT: H 195 LEU cc_start: 0.8746 (tt) cc_final: 0.8399 (mm) REVERT: H 237 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7511 (tm-30) REVERT: I 31 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8354 (tm-30) REVERT: I 116 LEU cc_start: 0.8282 (tp) cc_final: 0.7978 (tp) REVERT: I 141 HIS cc_start: 0.7354 (p90) cc_final: 0.6963 (p-80) REVERT: I 208 LYS cc_start: 0.8952 (tptp) cc_final: 0.8562 (mmtm) REVERT: I 242 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8524 (mt) REVERT: I 250 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8459 (tttm) REVERT: J 128 TYR cc_start: 0.8788 (m-10) cc_final: 0.8555 (m-10) REVERT: J 130 GLU cc_start: 0.7509 (pp20) cc_final: 0.7245 (tm-30) REVERT: J 187 MET cc_start: 0.8974 (mmm) cc_final: 0.8616 (mmm) REVERT: J 229 ARG cc_start: 0.7881 (tpt90) cc_final: 0.7487 (tpp80) REVERT: J 244 MET cc_start: 0.8173 (tpp) cc_final: 0.7904 (tpt) REVERT: K 19 ILE cc_start: 0.8993 (mm) cc_final: 0.8785 (mt) REVERT: K 31 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8170 (tm-30) REVERT: L 31 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8193 (tm-30) REVERT: L 116 LEU cc_start: 0.8315 (tp) cc_final: 0.7995 (tp) REVERT: L 195 LEU cc_start: 0.8836 (tt) cc_final: 0.8497 (mm) REVERT: L 237 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7789 (tm-30) REVERT: L 242 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8418 (mt) REVERT: M 144 MET cc_start: 0.7881 (ptt) cc_final: 0.7669 (ptt) REVERT: M 195 LEU cc_start: 0.8614 (tt) cc_final: 0.8219 (mm) REVERT: M 208 LYS cc_start: 0.8873 (tptp) cc_final: 0.8460 (mmtm) REVERT: M 229 ARG cc_start: 0.7944 (tpt90) cc_final: 0.7621 (tpp80) REVERT: N 31 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8197 (tm-30) REVERT: N 195 LEU cc_start: 0.8599 (tt) cc_final: 0.8361 (mm) REVERT: O 195 LEU cc_start: 0.8672 (tt) cc_final: 0.8293 (mm) REVERT: O 208 LYS cc_start: 0.8871 (tptp) cc_final: 0.8572 (mmtm) REVERT: O 242 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8059 (mm) REVERT: P 74 MET cc_start: 0.8270 (tpp) cc_final: 0.7921 (tpp) REVERT: P 280 LEU cc_start: 0.7106 (mt) cc_final: 0.6661 (mt) REVERT: Q 187 MET cc_start: 0.8956 (mmp) cc_final: 0.8351 (mmm) REVERT: Q 242 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8252 (mm) REVERT: Q 244 MET cc_start: 0.8432 (tpp) cc_final: 0.8036 (tpt) REVERT: R 141 HIS cc_start: 0.7253 (p-80) cc_final: 0.6893 (p-80) REVERT: S 187 MET cc_start: 0.9084 (mmp) cc_final: 0.8788 (mmm) REVERT: S 195 LEU cc_start: 0.9005 (tt) cc_final: 0.8464 (mm) REVERT: T 141 HIS cc_start: 0.7743 (p-80) cc_final: 0.7343 (p-80) REVERT: T 187 MET cc_start: 0.9146 (mmm) cc_final: 0.8624 (mmp) REVERT: T 195 LEU cc_start: 0.8745 (tt) cc_final: 0.8181 (mm) REVERT: T 237 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7576 (tm-30) REVERT: T 250 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8539 (ttpp) REVERT: U 195 LEU cc_start: 0.8788 (tt) cc_final: 0.8385 (mm) REVERT: V 187 MET cc_start: 0.9024 (mmm) cc_final: 0.8545 (mmm) REVERT: V 195 LEU cc_start: 0.8728 (tt) cc_final: 0.8371 (mm) outliers start: 96 outliers final: 83 residues processed: 768 average time/residue: 0.2379 time to fit residues: 305.0486 Evaluate side-chains 763 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 674 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 240 SER Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 131 CYS Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 245 MET Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 131 CYS Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 242 LEU Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 205 CYS Chi-restraints excluded: chain V residue 245 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 496 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 519 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 220 optimal weight: 8.9990 chunk 468 optimal weight: 20.0000 chunk 161 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 404 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130987 restraints weight = 58345.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.133354 restraints weight = 41908.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.134933 restraints weight = 34364.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.135673 restraints weight = 30405.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.136312 restraints weight = 28431.556| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 46882 Z= 0.130 Angle : 0.555 10.543 63690 Z= 0.293 Chirality : 0.037 0.248 7414 Planarity : 0.004 0.047 7898 Dihedral : 3.788 16.993 6270 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.26 % Allowed : 21.86 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.11), residues: 5786 helix: 3.00 (0.07), residues: 4576 sheet: None (None), residues: 0 loop : -2.30 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 174 TYR 0.013 0.001 TYR A 129 PHE 0.014 0.001 PHE V 232 TRP 0.008 0.001 TRP J 221 HIS 0.004 0.000 HIS S 141 Details of bonding type rmsd covalent geometry : bond 0.00284 (46838) covalent geometry : angle 0.55274 (63602) SS BOND : bond 0.00212 ( 44) SS BOND : angle 1.46967 ( 88) hydrogen bonds : bond 0.04506 ( 3543) hydrogen bonds : angle 3.46584 (10629) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7728.43 seconds wall clock time: 134 minutes 56.61 seconds (8096.61 seconds total)