Starting phenix.real_space_refine on Sat Mar 7 09:31:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ytk_10917/03_2026/6ytk_10917.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ytk_10917/03_2026/6ytk_10917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ytk_10917/03_2026/6ytk_10917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ytk_10917/03_2026/6ytk_10917.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ytk_10917/03_2026/6ytk_10917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ytk_10917/03_2026/6ytk_10917.map" } resolution = 4.07 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 400 5.16 5 C 26800 2.51 5 N 6980 2.21 5 O 7440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.04s 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: 41620 Number of models: 1 Model: "" Number of chains: 20 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 Time building chain proxies: 9.65, per 1000 atoms: 0.23 Number of scatterers: 41620 At special positions: 0 Unit cell: (132.66, 132.66, 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 400 16.00 O 7440 8.00 N 6980 7.00 C 26800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, 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=2.03 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=1.97 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 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: 3.43 Conformation dependent library (CDL) restraints added in 1.8 seconds 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10160 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 0 sheets defined 80.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.514A pdb=" N ILE A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 38 Processing helix chain 'A' and resid 48 through 70 removed outlier: 3.895A 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: 3.710A 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: 3.544A pdb=" N GLY A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 removed outlier: 3.692A 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 214 through 253 removed outlier: 3.564A pdb=" N HIS A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 removed outlier: 4.268A pdb=" N VAL A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 15 through 38 Processing helix chain 'B' and resid 48 through 70 removed outlier: 3.896A 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: 3.709A 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: 3.544A pdb=" N GLY B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 removed outlier: 3.693A 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 214 through 253 removed outlier: 3.563A pdb=" N HIS B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 277 removed outlier: 4.267A pdb=" N VAL B 277 " --> pdb=" O LYS B 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 15 through 38 Processing helix chain 'C' and resid 48 through 70 removed outlier: 3.895A 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: 3.709A 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: 3.544A pdb=" N GLY C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 133 removed outlier: 3.693A 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 214 through 253 removed outlier: 3.563A pdb=" N HIS C 218 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 277 removed outlier: 4.267A pdb=" N VAL C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 15 through 38 Processing helix chain 'D' and resid 48 through 70 removed outlier: 3.896A 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: 3.709A 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: 3.545A pdb=" N GLY D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 removed outlier: 3.692A 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 214 through 253 removed outlier: 3.563A pdb=" N HIS D 218 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 277 removed outlier: 4.268A pdb=" N VAL D 277 " --> pdb=" O LYS D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 15 through 38 Processing helix chain 'E' and resid 48 through 70 removed outlier: 3.896A 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: 3.708A 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: 3.544A pdb=" N GLY E 126 " --> pdb=" O THR E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 removed outlier: 3.692A 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 214 through 253 removed outlier: 3.563A pdb=" N HIS E 218 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 277 removed outlier: 4.268A pdb=" N VAL E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 15 through 38 Processing helix chain 'F' and resid 48 through 70 removed outlier: 3.895A 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: 3.709A 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: 3.544A pdb=" N GLY F 126 " --> pdb=" O THR F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 133 removed outlier: 3.692A 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 214 through 253 removed outlier: 3.563A pdb=" N HIS F 218 " --> pdb=" O THR F 214 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N CYS F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 277 removed outlier: 4.268A pdb=" N VAL F 277 " --> pdb=" O LYS F 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 15 through 38 Processing helix chain 'G' and resid 48 through 70 removed outlier: 3.896A 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: 3.709A 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: 3.545A pdb=" N GLY G 126 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 133 removed outlier: 3.694A 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 214 through 253 removed outlier: 3.563A pdb=" N HIS G 218 " --> pdb=" O THR G 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS G 219 " --> pdb=" O SER G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 277 removed outlier: 4.267A pdb=" N VAL G 277 " --> pdb=" O LYS G 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 15 through 38 Processing helix chain 'H' and resid 48 through 70 removed outlier: 3.896A 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: 3.709A 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: 3.545A pdb=" N GLY H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 133 removed outlier: 3.693A 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 214 through 253 removed outlier: 3.563A pdb=" N HIS H 218 " --> pdb=" O THR H 214 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N CYS H 219 " --> pdb=" O SER H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 277 removed outlier: 4.268A pdb=" N VAL H 277 " --> pdb=" O LYS H 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 15 through 38 Processing helix chain 'I' and resid 48 through 70 removed outlier: 3.896A 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: 3.709A 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: 3.546A pdb=" N GLY I 126 " --> pdb=" O THR I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 133 removed outlier: 3.692A 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 214 through 253 removed outlier: 3.563A pdb=" N HIS I 218 " --> pdb=" O THR I 214 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N CYS I 219 " --> pdb=" O SER I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 277 removed outlier: 4.268A pdb=" N VAL I 277 " --> pdb=" O LYS I 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 15 through 38 Processing helix chain 'J' and resid 48 through 70 removed outlier: 3.896A 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: 3.709A 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: 3.544A pdb=" N GLY J 126 " --> pdb=" O THR J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 removed outlier: 3.693A 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 214 through 253 removed outlier: 3.562A pdb=" N HIS J 218 " --> pdb=" O THR J 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS J 219 " --> pdb=" O SER J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 277 removed outlier: 4.267A pdb=" N VAL J 277 " --> pdb=" O LYS J 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 15 through 38 Processing helix chain 'K' and resid 48 through 70 removed outlier: 3.889A 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: 3.725A 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: 3.593A pdb=" N GLY K 126 " --> pdb=" O THR K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 133 removed outlier: 3.712A pdb=" N CYS K 131 " --> pdb=" O THR K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 159 removed outlier: 3.517A pdb=" N GLY K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 210 Processing helix chain 'K' and resid 214 through 253 removed outlier: 3.612A pdb=" N HIS K 218 " --> pdb=" O THR K 214 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS K 219 " --> pdb=" O SER K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 277 removed outlier: 4.328A pdb=" N VAL K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 15 through 38 Processing helix chain 'L' and resid 48 through 70 removed outlier: 3.890A 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: 3.725A 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: 3.593A pdb=" N GLY L 126 " --> pdb=" O THR L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.712A pdb=" N CYS L 131 " --> pdb=" O THR L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 159 removed outlier: 3.516A pdb=" N GLY L 159 " --> pdb=" O GLU L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 210 Processing helix chain 'L' and resid 214 through 253 removed outlier: 3.612A pdb=" N HIS L 218 " --> pdb=" O THR L 214 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N CYS L 219 " --> pdb=" O SER L 215 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 277 removed outlier: 4.327A pdb=" N VAL L 277 " --> pdb=" O LYS L 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 15 Processing helix chain 'M' and resid 15 through 38 Processing helix chain 'M' and resid 48 through 70 removed outlier: 3.890A 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: 3.725A 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: 3.594A pdb=" N GLY M 126 " --> pdb=" O THR M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 133 removed outlier: 3.711A pdb=" N CYS M 131 " --> pdb=" O THR M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 159 removed outlier: 3.517A pdb=" N GLY M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 210 Processing helix chain 'M' and resid 214 through 253 removed outlier: 3.613A pdb=" N HIS M 218 " --> pdb=" O THR M 214 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS M 219 " --> pdb=" O SER M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 277 removed outlier: 4.328A pdb=" N VAL M 277 " --> pdb=" O LYS M 273 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 15 Processing helix chain 'N' and resid 15 through 39 removed outlier: 3.693A pdb=" N PHE N 39 " --> pdb=" O SER N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 70 removed outlier: 3.579A pdb=" N TYR N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) removed outlier: 3.712A 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: 3.716A 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: 3.533A pdb=" N LEU N 116 " --> pdb=" O VAL N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 133 removed outlier: 3.736A 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 277 removed outlier: 4.019A pdb=" N TRP N 272 " --> pdb=" O SER N 268 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS N 273 " --> pdb=" O CYS N 269 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL N 277 " --> pdb=" O LYS N 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 15 through 38 Processing helix chain 'O' and resid 48 through 70 removed outlier: 3.890A 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: 3.724A 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: 3.593A pdb=" N GLY O 126 " --> pdb=" O THR O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 133 removed outlier: 3.712A pdb=" N CYS O 131 " --> pdb=" O THR O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 159 removed outlier: 3.516A pdb=" N GLY O 159 " --> pdb=" O GLU O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 167 through 210 Processing helix chain 'O' and resid 214 through 253 removed outlier: 3.612A pdb=" N HIS O 218 " --> pdb=" O THR O 214 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS O 219 " --> pdb=" O SER O 215 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 277 removed outlier: 4.327A pdb=" N VAL O 277 " --> pdb=" O LYS O 273 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 15 Processing helix chain 'P' and resid 15 through 38 Processing helix chain 'P' and resid 48 through 70 removed outlier: 3.889A 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: 3.725A 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: 3.593A pdb=" N GLY P 126 " --> pdb=" O THR P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 133 removed outlier: 3.712A pdb=" N CYS P 131 " --> pdb=" O THR P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 159 removed outlier: 3.517A pdb=" N GLY P 159 " --> pdb=" O GLU P 155 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 210 Processing helix chain 'P' and resid 214 through 253 removed outlier: 3.612A pdb=" N HIS P 218 " --> pdb=" O THR P 214 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS P 219 " --> pdb=" O SER P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 277 removed outlier: 4.328A pdb=" N VAL P 277 " --> pdb=" O LYS P 273 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 15 Processing helix chain 'Q' and resid 15 through 38 Processing helix chain 'Q' and resid 48 through 70 removed outlier: 3.890A 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: 3.724A 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: 3.593A pdb=" N GLY Q 126 " --> pdb=" O THR Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 133 removed outlier: 3.712A pdb=" N CYS Q 131 " --> pdb=" O THR Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 159 removed outlier: 3.516A pdb=" N GLY Q 159 " --> pdb=" O GLU Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 210 Processing helix chain 'Q' and resid 214 through 253 removed outlier: 3.613A pdb=" N HIS Q 218 " --> pdb=" O THR Q 214 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N CYS Q 219 " --> pdb=" O SER Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 277 removed outlier: 4.328A pdb=" N VAL Q 277 " --> pdb=" O LYS Q 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 15 Processing helix chain 'R' and resid 15 through 38 Processing helix chain 'R' and resid 48 through 70 removed outlier: 3.889A 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: 3.724A 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: 3.592A pdb=" N GLY R 126 " --> pdb=" O THR R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 removed outlier: 3.711A pdb=" N CYS R 131 " --> pdb=" O THR R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 159 removed outlier: 3.516A pdb=" N GLY R 159 " --> pdb=" O GLU R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 210 Processing helix chain 'R' and resid 214 through 253 removed outlier: 3.612A pdb=" N HIS R 218 " --> pdb=" O THR R 214 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS R 219 " --> pdb=" O SER R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 277 removed outlier: 4.328A pdb=" N VAL R 277 " --> pdb=" O LYS R 273 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 15 Processing helix chain 'S' and resid 15 through 38 Processing helix chain 'S' and resid 48 through 70 removed outlier: 3.890A 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: 3.724A 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: 3.594A pdb=" N GLY S 126 " --> pdb=" O THR S 122 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 133 removed outlier: 3.712A pdb=" N CYS S 131 " --> pdb=" O THR S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 149 through 159 removed outlier: 3.516A pdb=" N GLY S 159 " --> pdb=" O GLU S 155 " (cutoff:3.500A) Processing helix chain 'S' and resid 167 through 210 Processing helix chain 'S' and resid 214 through 253 removed outlier: 3.613A pdb=" N HIS S 218 " --> pdb=" O THR S 214 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS S 219 " --> pdb=" O SER S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 270 through 277 removed outlier: 4.328A pdb=" N VAL S 277 " --> pdb=" O LYS S 273 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 15 Processing helix chain 'T' and resid 15 through 38 Processing helix chain 'T' and resid 48 through 70 removed outlier: 3.889A 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: 3.724A 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: 3.593A pdb=" N GLY T 126 " --> pdb=" O THR T 122 " (cutoff:3.500A) Processing helix chain 'T' and resid 126 through 133 removed outlier: 3.711A pdb=" N CYS T 131 " --> pdb=" O THR T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 149 through 159 removed outlier: 3.516A pdb=" N GLY T 159 " --> pdb=" O GLU T 155 " (cutoff:3.500A) Processing helix chain 'T' and resid 167 through 210 Processing helix chain 'T' and resid 214 through 253 removed outlier: 3.612A pdb=" N HIS T 218 " --> pdb=" O THR T 214 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS T 219 " --> pdb=" O SER T 215 " (cutoff:3.500A) Processing helix chain 'T' and resid 270 through 277 removed outlier: 4.328A pdb=" N VAL T 277 " --> pdb=" O LYS T 273 " (cutoff:3.500A) 3191 hydrogen bonds defined for protein. 9573 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: 7.31 Time building geometry restraints manager: 4.49 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: 13110 1.34 - 1.46: 8323 1.46 - 1.58: 20647 1.58 - 1.70: 0 1.70 - 1.82: 500 Bond restraints: 42580 Sorted by residual: bond pdb=" CA ILE A 255 " pdb=" CB ILE A 255 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.23e-02 6.61e+03 1.51e+00 bond pdb=" CA ILE H 255 " pdb=" CB ILE H 255 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.23e-02 6.61e+03 1.48e+00 bond pdb=" CA ILE G 255 " pdb=" CB ILE G 255 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.23e-02 6.61e+03 1.48e+00 bond pdb=" CA ILE E 255 " pdb=" CB ILE E 255 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.23e-02 6.61e+03 1.45e+00 bond pdb=" CA ILE C 255 " pdb=" CB ILE C 255 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.23e-02 6.61e+03 1.43e+00 ... (remaining 42575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 55344 1.30 - 2.60: 2107 2.60 - 3.90: 261 3.90 - 5.21: 68 5.21 - 6.51: 40 Bond angle restraints: 57820 Sorted by residual: angle pdb=" N ARG A 164 " pdb=" CA ARG A 164 " pdb=" C ARG A 164 " ideal model delta sigma weight residual 108.76 115.27 -6.51 1.69e+00 3.50e-01 1.48e+01 angle pdb=" N ARG C 164 " pdb=" CA ARG C 164 " pdb=" C ARG C 164 " ideal model delta sigma weight residual 108.76 115.27 -6.51 1.69e+00 3.50e-01 1.48e+01 angle pdb=" N ARG E 164 " pdb=" CA ARG E 164 " pdb=" C ARG E 164 " ideal model delta sigma weight residual 108.76 115.27 -6.51 1.69e+00 3.50e-01 1.48e+01 angle pdb=" N ARG J 164 " pdb=" CA ARG J 164 " pdb=" C ARG J 164 " ideal model delta sigma weight residual 108.76 115.26 -6.50 1.69e+00 3.50e-01 1.48e+01 angle pdb=" N ARG D 164 " pdb=" CA ARG D 164 " pdb=" C ARG D 164 " ideal model delta sigma weight residual 108.76 115.25 -6.49 1.69e+00 3.50e-01 1.48e+01 ... (remaining 57815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 23160 18.03 - 36.06: 1796 36.06 - 54.09: 366 54.09 - 72.12: 19 72.12 - 90.15: 99 Dihedral angle restraints: 25440 sinusoidal: 9820 harmonic: 15620 Sorted by residual: dihedral pdb=" CB CYS F 41 " pdb=" SG CYS F 41 " pdb=" SG CYS F 131 " pdb=" CB CYS F 131 " ideal model delta sinusoidal sigma weight residual -86.00 -176.15 90.15 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS J 41 " pdb=" SG CYS J 41 " pdb=" SG CYS J 131 " pdb=" CB CYS J 131 " ideal model delta sinusoidal sigma weight residual -86.00 -176.15 90.15 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS I 41 " pdb=" SG CYS I 41 " pdb=" SG CYS I 131 " pdb=" CB CYS I 131 " ideal model delta sinusoidal sigma weight residual -86.00 -176.14 90.14 1 1.00e+01 1.00e-02 9.62e+01 ... (remaining 25437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 5655 0.051 - 0.101: 915 0.101 - 0.152: 151 0.152 - 0.202: 0 0.202 - 0.253: 19 Chirality restraints: 6740 Sorted by residual: chirality pdb=" CA SER H 165 " pdb=" N SER H 165 " pdb=" C SER H 165 " pdb=" CB SER H 165 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA SER J 165 " pdb=" N SER J 165 " pdb=" C SER J 165 " pdb=" CB SER J 165 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA SER F 165 " pdb=" N SER F 165 " pdb=" C SER F 165 " pdb=" CB SER F 165 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 6737 not shown) Planarity restraints: 7180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 166 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO C 167 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 167 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 167 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 166 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO D 167 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 167 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 167 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 166 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO F 167 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 167 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 167 " -0.028 5.00e-02 4.00e+02 ... (remaining 7177 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 48 2.46 - 3.07: 28771 3.07 - 3.68: 62109 3.68 - 4.29: 82937 4.29 - 4.90: 138161 Nonbonded interactions: 312026 Sorted by model distance: nonbonded pdb=" NH1 ARG N 182 " pdb=" OG SER O 40 " model vdw 1.844 3.120 nonbonded pdb=" OH TYR N 142 " pdb=" OE1 GLU N 176 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR R 142 " pdb=" OE1 GLU R 176 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR K 142 " pdb=" OE1 GLU K 176 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR L 142 " pdb=" OE1 GLU L 176 " model vdw 2.234 3.040 ... (remaining 312021 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: 0.07 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' } 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: 0.820 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: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 35.380 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.003 0.057 42620 Z= 0.151 Angle : 0.587 6.507 57900 Z= 0.354 Chirality : 0.039 0.253 6740 Planarity : 0.004 0.051 7180 Dihedral : 13.760 87.971 15160 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.11), residues: 5260 helix: 0.70 (0.07), residues: 3980 sheet: None (None), residues: 0 loop : -3.02 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 247 TYR 0.006 0.001 TYR N 51 PHE 0.012 0.001 PHE O 232 TRP 0.005 0.001 TRP N 221 HIS 0.003 0.001 HIS N 239 Details of bonding type rmsd covalent geometry : bond 0.00281 (42580) covalent geometry : angle 0.58293 (57820) SS BOND : bond 0.00933 ( 40) SS BOND : angle 1.98781 ( 80) hydrogen bonds : bond 0.12748 ( 3191) hydrogen bonds : angle 4.85849 ( 9573) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1232 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.6946 (m-40) cc_final: 0.6700 (m-40) REVERT: A 45 VAL cc_start: 0.8474 (m) cc_final: 0.7662 (p) REVERT: A 51 TYR cc_start: 0.9104 (t80) cc_final: 0.8705 (t80) REVERT: B 51 TYR cc_start: 0.8922 (t80) cc_final: 0.8680 (t80) REVERT: B 74 MET cc_start: 0.7655 (tmm) cc_final: 0.7190 (tmm) REVERT: B 129 TYR cc_start: 0.9053 (t80) cc_final: 0.8798 (t80) REVERT: B 182 ARG cc_start: 0.7517 (mtp-110) cc_final: 0.6977 (ttt-90) REVERT: B 270 GLN cc_start: 0.7448 (tp40) cc_final: 0.6933 (tm-30) REVERT: C 44 GLN cc_start: 0.8293 (mm-40) cc_final: 0.8052 (mm110) REVERT: C 51 TYR cc_start: 0.8949 (t80) cc_final: 0.8747 (t80) REVERT: C 104 PHE cc_start: 0.8562 (t80) cc_final: 0.8348 (t80) REVERT: C 117 THR cc_start: 0.8844 (t) cc_final: 0.8471 (m) REVERT: C 144 MET cc_start: 0.6812 (ptp) cc_final: 0.6424 (ptp) REVERT: C 234 GLN cc_start: 0.8374 (tt0) cc_final: 0.7831 (tm-30) REVERT: C 249 LYS cc_start: 0.8677 (tttt) cc_final: 0.8443 (ttmm) REVERT: C 270 GLN cc_start: 0.7899 (tp40) cc_final: 0.7320 (tm-30) REVERT: D 13 GLN cc_start: 0.7244 (tp40) cc_final: 0.6950 (tm-30) REVERT: D 51 TYR cc_start: 0.9185 (t80) cc_final: 0.8889 (t80) REVERT: D 135 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7237 (mt-10) REVERT: D 145 PHE cc_start: 0.7233 (m-80) cc_final: 0.6932 (m-80) REVERT: D 234 GLN cc_start: 0.8266 (tt0) cc_final: 0.7819 (tm-30) REVERT: D 244 MET cc_start: 0.8114 (tpt) cc_final: 0.7913 (tpp) REVERT: E 13 GLN cc_start: 0.7718 (tp40) cc_final: 0.7392 (tm-30) REVERT: E 44 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8112 (mm110) REVERT: E 129 TYR cc_start: 0.9221 (t80) cc_final: 0.8864 (t80) REVERT: E 187 MET cc_start: 0.9395 (mmp) cc_final: 0.9136 (mmp) REVERT: E 234 GLN cc_start: 0.8202 (tt0) cc_final: 0.7779 (tm-30) REVERT: E 270 GLN cc_start: 0.7633 (tp40) cc_final: 0.7407 (tm-30) REVERT: F 145 PHE cc_start: 0.7405 (m-80) cc_final: 0.7121 (m-80) REVERT: F 270 GLN cc_start: 0.7616 (tp40) cc_final: 0.7167 (tm-30) REVERT: G 117 THR cc_start: 0.8733 (t) cc_final: 0.8435 (m) REVERT: G 129 TYR cc_start: 0.9197 (t80) cc_final: 0.8896 (t80) REVERT: G 144 MET cc_start: 0.6582 (ptp) cc_final: 0.6179 (ptp) REVERT: G 270 GLN cc_start: 0.7591 (tp40) cc_final: 0.7380 (tm-30) REVERT: H 14 ARG cc_start: 0.6643 (mtm110) cc_final: 0.6376 (mmt180) REVERT: H 44 GLN cc_start: 0.8226 (mm-40) cc_final: 0.8001 (mm110) REVERT: H 117 THR cc_start: 0.8872 (t) cc_final: 0.8472 (m) REVERT: H 144 MET cc_start: 0.6689 (ptp) cc_final: 0.6306 (ptp) REVERT: H 234 GLN cc_start: 0.8367 (tt0) cc_final: 0.8046 (tt0) REVERT: H 249 LYS cc_start: 0.8629 (tttt) cc_final: 0.8422 (ttmm) REVERT: H 270 GLN cc_start: 0.7890 (tp40) cc_final: 0.7316 (tm-30) REVERT: I 13 GLN cc_start: 0.7245 (tp40) cc_final: 0.6909 (tm-30) REVERT: I 135 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7255 (mt-10) REVERT: I 144 MET cc_start: 0.7103 (ptp) cc_final: 0.6700 (ptm) REVERT: I 145 PHE cc_start: 0.7168 (m-80) cc_final: 0.6874 (m-80) REVERT: I 234 GLN cc_start: 0.8218 (tt0) cc_final: 0.7923 (tm-30) REVERT: I 244 MET cc_start: 0.8200 (tpt) cc_final: 0.7963 (tpp) REVERT: I 270 GLN cc_start: 0.7588 (tp40) cc_final: 0.7376 (tm-30) REVERT: J 13 GLN cc_start: 0.7690 (tp40) cc_final: 0.7395 (tm-30) REVERT: J 44 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8115 (mm110) REVERT: J 129 TYR cc_start: 0.9246 (t80) cc_final: 0.8881 (t80) REVERT: J 187 MET cc_start: 0.9364 (mmp) cc_final: 0.9073 (mmp) REVERT: J 234 GLN cc_start: 0.8219 (tt0) cc_final: 0.7797 (tm-30) REVERT: J 270 GLN cc_start: 0.7651 (tp40) cc_final: 0.7445 (tm-30) REVERT: K 51 TYR cc_start: 0.9231 (t80) cc_final: 0.9026 (t80) REVERT: K 117 THR cc_start: 0.8850 (t) cc_final: 0.8508 (m) REVERT: K 129 TYR cc_start: 0.9211 (t80) cc_final: 0.8938 (t80) REVERT: K 144 MET cc_start: 0.6551 (ptp) cc_final: 0.6269 (ptp) REVERT: K 215 SER cc_start: 0.8790 (t) cc_final: 0.8558 (p) REVERT: K 234 GLN cc_start: 0.8393 (tt0) cc_final: 0.7962 (tm-30) REVERT: K 270 GLN cc_start: 0.7587 (tp40) cc_final: 0.7008 (tm-30) REVERT: L 44 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7985 (mm110) REVERT: L 135 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7607 (mt-10) REVERT: L 144 MET cc_start: 0.6982 (ptp) cc_final: 0.6575 (ptp) REVERT: L 187 MET cc_start: 0.9361 (mmp) cc_final: 0.9110 (mmm) REVERT: L 234 GLN cc_start: 0.8331 (tt0) cc_final: 0.7760 (tm-30) REVERT: L 249 LYS cc_start: 0.8607 (tttt) cc_final: 0.8347 (ttmm) REVERT: L 270 GLN cc_start: 0.7489 (tp40) cc_final: 0.6837 (tm-30) REVERT: M 13 GLN cc_start: 0.7418 (tp40) cc_final: 0.7138 (tm-30) REVERT: M 51 TYR cc_start: 0.9248 (t80) cc_final: 0.8965 (t80) REVERT: M 135 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7367 (mt-10) REVERT: M 144 MET cc_start: 0.6766 (ptp) cc_final: 0.6203 (ptm) REVERT: M 234 GLN cc_start: 0.8244 (tt0) cc_final: 0.7937 (tm-30) REVERT: M 270 GLN cc_start: 0.7628 (tp40) cc_final: 0.7274 (tm-30) REVERT: N 234 GLN cc_start: 0.8070 (tt0) cc_final: 0.7773 (tt0) REVERT: O 15 ASN cc_start: 0.7444 (m-40) cc_final: 0.7210 (m110) REVERT: O 234 GLN cc_start: 0.8060 (tt0) cc_final: 0.7785 (tt0) REVERT: O 270 GLN cc_start: 0.7749 (tp40) cc_final: 0.7146 (tm-30) REVERT: P 51 TYR cc_start: 0.9226 (t80) cc_final: 0.9017 (t80) REVERT: P 117 THR cc_start: 0.8847 (t) cc_final: 0.8511 (m) REVERT: P 129 TYR cc_start: 0.9217 (t80) cc_final: 0.8956 (t80) REVERT: P 144 MET cc_start: 0.6522 (ptp) cc_final: 0.6272 (ptp) REVERT: P 234 GLN cc_start: 0.8426 (tt0) cc_final: 0.7967 (tm-30) REVERT: P 270 GLN cc_start: 0.7590 (tp40) cc_final: 0.7009 (tm-30) REVERT: Q 13 GLN cc_start: 0.7832 (tp40) cc_final: 0.7535 (tp40) REVERT: Q 14 ARG cc_start: 0.6674 (mtm110) cc_final: 0.6253 (mmt-90) REVERT: Q 44 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8043 (mm110) REVERT: Q 51 TYR cc_start: 0.9057 (t80) cc_final: 0.8809 (t80) REVERT: Q 234 GLN cc_start: 0.8289 (tt0) cc_final: 0.7796 (tm-30) REVERT: Q 249 LYS cc_start: 0.8611 (tttt) cc_final: 0.8310 (ttmm) REVERT: Q 270 GLN cc_start: 0.7445 (tp40) cc_final: 0.6630 (tm-30) REVERT: R 13 GLN cc_start: 0.7383 (tp40) cc_final: 0.7177 (tm-30) REVERT: R 51 TYR cc_start: 0.9262 (t80) cc_final: 0.9053 (t80) REVERT: R 234 GLN cc_start: 0.8353 (tt0) cc_final: 0.7960 (tm-30) REVERT: R 270 GLN cc_start: 0.7685 (tp40) cc_final: 0.7308 (tm-30) REVERT: S 13 GLN cc_start: 0.7772 (tp40) cc_final: 0.7477 (tm-30) REVERT: S 15 ASN cc_start: 0.7456 (m-40) cc_final: 0.7162 (m-40) REVERT: S 44 GLN cc_start: 0.8361 (mm-40) cc_final: 0.8131 (mm110) REVERT: S 51 TYR cc_start: 0.9152 (t80) cc_final: 0.8777 (t80) REVERT: S 129 TYR cc_start: 0.9214 (t80) cc_final: 0.8848 (t80) REVERT: S 153 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7563 (ttp-110) REVERT: S 234 GLN cc_start: 0.8311 (tt0) cc_final: 0.7799 (tm-30) REVERT: S 270 GLN cc_start: 0.7745 (tp40) cc_final: 0.7012 (tm-30) REVERT: T 15 ASN cc_start: 0.7408 (m-40) cc_final: 0.7192 (m110) REVERT: T 234 GLN cc_start: 0.8013 (tt0) cc_final: 0.7700 (tt0) REVERT: T 270 GLN cc_start: 0.7744 (tp40) cc_final: 0.7188 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1232 average time/residue: 0.2991 time to fit residues: 566.2334 Evaluate side-chains 729 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 729 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 394 optimal weight: 2.9990 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 0.1980 chunk 310 optimal weight: 0.5980 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 0.9980 chunk 223 optimal weight: 6.9990 chunk 516 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 184 GLN A 227 ASN B 20 ASN B 184 GLN B 224 HIS B 227 ASN C 20 ASN C 184 GLN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN D 20 ASN D 184 GLN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN E 20 ASN E 184 GLN E 227 ASN E 234 GLN F 20 ASN F 184 GLN F 217 GLN F 227 ASN G 20 ASN G 44 GLN G 184 GLN G 227 ASN H 20 ASN H 184 GLN ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 GLN I 20 ASN I 184 GLN I 227 ASN I 234 GLN J 20 ASN J 184 GLN ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 GLN K 15 ASN K 20 ASN K 44 GLN K 184 GLN K 234 GLN L 20 ASN L 184 GLN L 186 GLN L 234 GLN M 20 ASN M 184 GLN M 234 GLN N 20 ASN N 184 GLN ** N 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 GLN O 20 ASN O 184 GLN O 217 GLN O 226 GLN O 234 GLN P 15 ASN P 20 ASN P 44 GLN P 184 GLN P 234 GLN Q 20 ASN Q 184 GLN Q 186 GLN Q 234 GLN R 20 ASN R 184 GLN R 234 GLN S 20 ASN S 184 GLN S 234 GLN T 20 ASN T 184 GLN T 217 GLN T 226 GLN T 234 GLN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.142018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118555 restraints weight = 56696.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119417 restraints weight = 44392.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.119983 restraints weight = 39184.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120353 restraints weight = 35841.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.120550 restraints weight = 33838.263| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 42620 Z= 0.145 Angle : 0.557 7.609 57900 Z= 0.293 Chirality : 0.040 0.136 6740 Planarity : 0.005 0.071 7180 Dihedral : 3.950 15.246 5700 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.19 % Allowed : 6.45 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.31 (0.12), residues: 5260 helix: 1.83 (0.08), residues: 4080 sheet: None (None), residues: 0 loop : -2.71 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 174 TYR 0.021 0.001 TYR H 51 PHE 0.016 0.001 PHE B 105 TRP 0.008 0.001 TRP M 75 HIS 0.006 0.001 HIS E 224 Details of bonding type rmsd covalent geometry : bond 0.00301 (42580) covalent geometry : angle 0.54932 (57820) SS BOND : bond 0.00188 ( 40) SS BOND : angle 2.51430 ( 80) hydrogen bonds : bond 0.05416 ( 3191) hydrogen bonds : angle 4.19492 ( 9573) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 966 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 45 VAL cc_start: 0.8446 (m) cc_final: 0.7956 (p) REVERT: A 51 TYR cc_start: 0.9204 (t80) cc_final: 0.8791 (t80) REVERT: A 142 TYR cc_start: 0.5833 (m-80) cc_final: 0.5488 (m-10) REVERT: B 15 ASN cc_start: 0.7409 (m-40) cc_final: 0.7163 (m-40) REVERT: B 19 ILE cc_start: 0.8068 (mm) cc_final: 0.7844 (tp) REVERT: B 51 TYR cc_start: 0.8997 (t80) cc_final: 0.8675 (t80) REVERT: B 61 LEU cc_start: 0.7771 (tt) cc_final: 0.6673 (mp) REVERT: B 182 ARG cc_start: 0.7583 (mtp-110) cc_final: 0.7125 (ttt-90) REVERT: B 208 LYS cc_start: 0.8212 (tppt) cc_final: 0.7935 (tptp) REVERT: C 105 PHE cc_start: 0.8556 (t80) cc_final: 0.8332 (t80) REVERT: C 117 THR cc_start: 0.8883 (t) cc_final: 0.8631 (m) REVERT: C 144 MET cc_start: 0.6588 (ptp) cc_final: 0.6079 (ptp) REVERT: C 187 MET cc_start: 0.9299 (mmm) cc_final: 0.9075 (mmm) REVERT: C 234 GLN cc_start: 0.8189 (tt0) cc_final: 0.7811 (tm-30) REVERT: D 45 VAL cc_start: 0.8559 (m) cc_final: 0.8149 (m) REVERT: D 135 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7112 (mt-10) REVERT: D 145 PHE cc_start: 0.7196 (m-80) cc_final: 0.6953 (m-80) REVERT: E 129 TYR cc_start: 0.9281 (t80) cc_final: 0.8954 (t80) REVERT: E 187 MET cc_start: 0.9391 (mmp) cc_final: 0.9083 (mmp) REVERT: E 208 LYS cc_start: 0.8350 (tppt) cc_final: 0.8081 (tmmt) REVERT: E 229 ARG cc_start: 0.7449 (tpp80) cc_final: 0.6801 (ttp-110) REVERT: E 234 GLN cc_start: 0.7911 (tt0) cc_final: 0.7646 (tm-30) REVERT: E 270 GLN cc_start: 0.7707 (tp40) cc_final: 0.7373 (tm-30) REVERT: F 45 VAL cc_start: 0.8417 (m) cc_final: 0.7599 (p) REVERT: F 51 TYR cc_start: 0.9208 (t80) cc_final: 0.8825 (t80) REVERT: F 142 TYR cc_start: 0.5708 (m-80) cc_final: 0.5265 (m-10) REVERT: F 145 PHE cc_start: 0.7478 (m-80) cc_final: 0.7120 (m-80) REVERT: F 187 MET cc_start: 0.9350 (mmm) cc_final: 0.8996 (mmm) REVERT: G 117 THR cc_start: 0.8946 (t) cc_final: 0.8649 (m) REVERT: G 129 TYR cc_start: 0.9285 (t80) cc_final: 0.8973 (t80) REVERT: G 187 MET cc_start: 0.9372 (mmp) cc_final: 0.9028 (mmt) REVERT: G 255 ILE cc_start: 0.9174 (mm) cc_final: 0.8957 (mm) REVERT: H 14 ARG cc_start: 0.6444 (mtm110) cc_final: 0.6100 (mmt-90) REVERT: H 74 MET cc_start: 0.8440 (tpp) cc_final: 0.8167 (tpp) REVERT: H 117 THR cc_start: 0.8955 (t) cc_final: 0.8643 (m) REVERT: H 128 TYR cc_start: 0.8585 (m-10) cc_final: 0.8383 (m-80) REVERT: H 144 MET cc_start: 0.6917 (ptp) cc_final: 0.6621 (ptp) REVERT: H 208 LYS cc_start: 0.8571 (tppt) cc_final: 0.8313 (tmmt) REVERT: H 233 GLU cc_start: 0.8362 (tp30) cc_final: 0.8155 (tp30) REVERT: I 45 VAL cc_start: 0.8584 (m) cc_final: 0.8203 (m) REVERT: I 51 TYR cc_start: 0.9222 (t80) cc_final: 0.8918 (t80) REVERT: I 135 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7165 (mt-10) REVERT: I 145 PHE cc_start: 0.7189 (m-80) cc_final: 0.6897 (m-80) REVERT: I 233 GLU cc_start: 0.8402 (tp30) cc_final: 0.8201 (tp30) REVERT: I 249 LYS cc_start: 0.8670 (tttp) cc_final: 0.8444 (ttmm) REVERT: I 270 GLN cc_start: 0.7852 (tp40) cc_final: 0.7519 (tm-30) REVERT: J 129 TYR cc_start: 0.9296 (t80) cc_final: 0.8958 (t80) REVERT: J 187 MET cc_start: 0.9365 (mmp) cc_final: 0.9063 (mmp) REVERT: J 208 LYS cc_start: 0.8349 (tppt) cc_final: 0.8107 (tmmt) REVERT: J 229 ARG cc_start: 0.7463 (tpp80) cc_final: 0.6805 (ttp-110) REVERT: J 234 GLN cc_start: 0.7857 (tt0) cc_final: 0.7629 (tm-30) REVERT: J 263 HIS cc_start: 0.7246 (m90) cc_final: 0.7028 (m90) REVERT: J 270 GLN cc_start: 0.7762 (tp40) cc_final: 0.7398 (tm-30) REVERT: K 129 TYR cc_start: 0.9285 (t80) cc_final: 0.8970 (t80) REVERT: K 208 LYS cc_start: 0.8325 (tppt) cc_final: 0.7935 (tptp) REVERT: K 229 ARG cc_start: 0.7827 (tpp80) cc_final: 0.6925 (ttp-110) REVERT: K 270 GLN cc_start: 0.7691 (tp40) cc_final: 0.7014 (tm-30) REVERT: L 14 ARG cc_start: 0.6469 (mtm110) cc_final: 0.6145 (mmt-90) REVERT: L 74 MET cc_start: 0.8431 (tpp) cc_final: 0.8109 (tpp) REVERT: L 174 ARG cc_start: 0.8864 (tmm-80) cc_final: 0.8107 (ttp-170) REVERT: L 234 GLN cc_start: 0.8173 (tt0) cc_final: 0.7835 (tm-30) REVERT: M 14 ARG cc_start: 0.6853 (mtm110) cc_final: 0.6612 (mmt-90) REVERT: M 45 VAL cc_start: 0.8650 (m) cc_final: 0.8340 (m) REVERT: M 153 ARG cc_start: 0.7844 (ttp-110) cc_final: 0.7486 (ttp-110) REVERT: M 187 MET cc_start: 0.9283 (mmm) cc_final: 0.9062 (mmm) REVERT: M 238 GLN cc_start: 0.7794 (tt0) cc_final: 0.7561 (tt0) REVERT: M 245 MET cc_start: 0.8499 (tpp) cc_final: 0.8250 (tpp) REVERT: M 270 GLN cc_start: 0.7775 (tp40) cc_final: 0.7301 (tm-30) REVERT: N 187 MET cc_start: 0.9254 (mmp) cc_final: 0.9030 (mmp) REVERT: N 234 GLN cc_start: 0.8041 (tt0) cc_final: 0.7680 (tm-30) REVERT: O 32 GLN cc_start: 0.7934 (tp40) cc_final: 0.7534 (mm-40) REVERT: O 142 TYR cc_start: 0.5911 (m-80) cc_final: 0.5624 (m-10) REVERT: O 245 MET cc_start: 0.8290 (tpp) cc_final: 0.8037 (tpp) REVERT: O 270 GLN cc_start: 0.7803 (tp40) cc_final: 0.7187 (tm-30) REVERT: P 129 TYR cc_start: 0.9297 (t80) cc_final: 0.8981 (t80) REVERT: P 208 LYS cc_start: 0.8342 (tppt) cc_final: 0.7857 (tptp) REVERT: P 229 ARG cc_start: 0.7872 (tpp80) cc_final: 0.6968 (ttp-110) REVERT: P 238 GLN cc_start: 0.7790 (tt0) cc_final: 0.7585 (tp40) REVERT: P 270 GLN cc_start: 0.7574 (tp40) cc_final: 0.7004 (tm-30) REVERT: Q 45 VAL cc_start: 0.8490 (m) cc_final: 0.8060 (p) REVERT: Q 74 MET cc_start: 0.8420 (tpp) cc_final: 0.8129 (tpp) REVERT: Q 117 THR cc_start: 0.8837 (t) cc_final: 0.8412 (m) REVERT: Q 155 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7262 (mt-10) REVERT: Q 234 GLN cc_start: 0.8220 (tt0) cc_final: 0.7843 (tm-30) REVERT: R 14 ARG cc_start: 0.6771 (mtm110) cc_final: 0.6561 (mmt-90) REVERT: R 141 HIS cc_start: 0.6052 (p-80) cc_final: 0.5082 (p-80) REVERT: R 153 ARG cc_start: 0.7905 (ttp-110) cc_final: 0.7561 (ttp-110) REVERT: R 229 ARG cc_start: 0.7525 (tpp80) cc_final: 0.6952 (ttp-110) REVERT: R 270 GLN cc_start: 0.7776 (tp40) cc_final: 0.7283 (tm-30) REVERT: S 51 TYR cc_start: 0.9079 (t80) cc_final: 0.8792 (t80) REVERT: S 129 TYR cc_start: 0.9276 (t80) cc_final: 0.8931 (t80) REVERT: S 229 ARG cc_start: 0.7820 (tpp80) cc_final: 0.7019 (ttp-110) REVERT: S 238 GLN cc_start: 0.7984 (tt0) cc_final: 0.7592 (tp40) REVERT: S 270 GLN cc_start: 0.7891 (tp40) cc_final: 0.7070 (tm-30) REVERT: T 32 GLN cc_start: 0.7950 (tp40) cc_final: 0.7533 (mm-40) REVERT: T 142 TYR cc_start: 0.5853 (m-80) cc_final: 0.5580 (m-10) REVERT: T 187 MET cc_start: 0.9358 (mmp) cc_final: 0.9118 (mmm) REVERT: T 270 GLN cc_start: 0.7823 (tp40) cc_final: 0.7214 (tm-30) outliers start: 9 outliers final: 0 residues processed: 966 average time/residue: 0.2489 time to fit residues: 394.5865 Evaluate side-chains 688 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 688 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 348 optimal weight: 0.6980 chunk 307 optimal weight: 2.9990 chunk 326 optimal weight: 0.5980 chunk 299 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 204 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 291 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 263 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN C 44 GLN C 227 ASN D 227 ASN H 15 ASN H 44 GLN H 227 ASN I 15 ASN J 227 ASN K 15 ASN K 238 GLN M 15 ASN N 227 ASN P 15 ASN Q 15 ASN R 15 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.144731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122146 restraints weight = 56341.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122270 restraints weight = 46853.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122511 restraints weight = 41597.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122707 restraints weight = 40693.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.122867 restraints weight = 38337.510| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 42620 Z= 0.127 Angle : 0.516 5.927 57900 Z= 0.272 Chirality : 0.039 0.138 6740 Planarity : 0.005 0.060 7180 Dihedral : 3.876 15.094 5700 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: 1.71 (0.12), residues: 5260 helix: 2.10 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.79 (0.16), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 103 TYR 0.017 0.001 TYR S 128 PHE 0.020 0.001 PHE L 232 TRP 0.005 0.001 TRP M 118 HIS 0.004 0.000 HIS E 224 Details of bonding type rmsd covalent geometry : bond 0.00257 (42580) covalent geometry : angle 0.50852 (57820) SS BOND : bond 0.00363 ( 40) SS BOND : angle 2.37103 ( 80) hydrogen bonds : bond 0.04894 ( 3191) hydrogen bonds : angle 3.93454 ( 9573) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 932 time to evaluate : 1.663 Fit side-chains revert: symmetry clash REVERT: A 45 VAL cc_start: 0.8555 (m) cc_final: 0.7900 (p) REVERT: A 142 TYR cc_start: 0.5659 (m-80) cc_final: 0.5392 (m-10) REVERT: A 144 MET cc_start: 0.6171 (ptp) cc_final: 0.5789 (ptm) REVERT: B 51 TYR cc_start: 0.9049 (t80) cc_final: 0.8788 (t80) REVERT: B 182 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.7219 (ttt-90) REVERT: B 208 LYS cc_start: 0.8290 (tppt) cc_final: 0.7981 (tptp) REVERT: B 228 GLU cc_start: 0.8025 (tt0) cc_final: 0.7739 (tt0) REVERT: C 234 GLN cc_start: 0.8048 (tt0) cc_final: 0.7775 (tm-30) REVERT: D 45 VAL cc_start: 0.8565 (m) cc_final: 0.8144 (m) REVERT: D 51 TYR cc_start: 0.9309 (t80) cc_final: 0.9103 (t80) REVERT: D 135 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7029 (mt-10) REVERT: D 145 PHE cc_start: 0.7247 (m-80) cc_final: 0.6922 (m-80) REVERT: D 187 MET cc_start: 0.9284 (mmm) cc_final: 0.9063 (mmm) REVERT: D 233 GLU cc_start: 0.8423 (tp30) cc_final: 0.8185 (tp30) REVERT: D 234 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7769 (tm-30) REVERT: E 129 TYR cc_start: 0.9242 (t80) cc_final: 0.8971 (t80) REVERT: E 153 ARG cc_start: 0.8327 (ttp-110) cc_final: 0.8019 (ttp-110) REVERT: E 187 MET cc_start: 0.9369 (mmp) cc_final: 0.9053 (mmp) REVERT: E 208 LYS cc_start: 0.8319 (tppt) cc_final: 0.8051 (tmmt) REVERT: E 229 ARG cc_start: 0.7311 (tpp80) cc_final: 0.6708 (ttp-110) REVERT: F 45 VAL cc_start: 0.8366 (m) cc_final: 0.7619 (p) REVERT: F 142 TYR cc_start: 0.5729 (m-80) cc_final: 0.5428 (m-10) REVERT: F 174 ARG cc_start: 0.8636 (tmm-80) cc_final: 0.8027 (ttp-170) REVERT: F 187 MET cc_start: 0.9264 (mmm) cc_final: 0.8929 (mmm) REVERT: G 117 THR cc_start: 0.8877 (t) cc_final: 0.8611 (m) REVERT: H 14 ARG cc_start: 0.6355 (mtm110) cc_final: 0.6151 (mmt-90) REVERT: H 144 MET cc_start: 0.6539 (ptp) cc_final: 0.6218 (ptp) REVERT: H 208 LYS cc_start: 0.8586 (tppt) cc_final: 0.8303 (tmmt) REVERT: I 45 VAL cc_start: 0.8611 (m) cc_final: 0.8259 (m) REVERT: I 135 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7108 (mt-10) REVERT: I 145 PHE cc_start: 0.7216 (m-80) cc_final: 0.6883 (m-80) REVERT: I 233 GLU cc_start: 0.8418 (tp30) cc_final: 0.8200 (tp30) REVERT: I 234 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7732 (tm-30) REVERT: I 245 MET cc_start: 0.8583 (tpp) cc_final: 0.8357 (tpp) REVERT: I 270 GLN cc_start: 0.7952 (tp40) cc_final: 0.7568 (tm-30) REVERT: J 187 MET cc_start: 0.9340 (mmp) cc_final: 0.9022 (mmp) REVERT: J 208 LYS cc_start: 0.8336 (tppt) cc_final: 0.8065 (tmmt) REVERT: J 229 ARG cc_start: 0.7317 (tpp80) cc_final: 0.6735 (ttp-110) REVERT: J 234 GLN cc_start: 0.7935 (tt0) cc_final: 0.7685 (tm-30) REVERT: K 129 TYR cc_start: 0.9277 (t80) cc_final: 0.8976 (t80) REVERT: K 187 MET cc_start: 0.9500 (mmp) cc_final: 0.9181 (mmp) REVERT: K 208 LYS cc_start: 0.8286 (tppt) cc_final: 0.7811 (tptp) REVERT: K 229 ARG cc_start: 0.7695 (tpp80) cc_final: 0.7039 (ttp-110) REVERT: K 270 GLN cc_start: 0.7585 (tp40) cc_final: 0.6949 (tm-30) REVERT: L 14 ARG cc_start: 0.6516 (mtm110) cc_final: 0.6226 (mmt-90) REVERT: L 45 VAL cc_start: 0.8772 (m) cc_final: 0.8454 (p) REVERT: L 117 THR cc_start: 0.8756 (t) cc_final: 0.8318 (m) REVERT: L 174 ARG cc_start: 0.8826 (tmm-80) cc_final: 0.8138 (ttp-170) REVERT: L 234 GLN cc_start: 0.8136 (tt0) cc_final: 0.7853 (tm-30) REVERT: M 45 VAL cc_start: 0.8593 (m) cc_final: 0.8140 (p) REVERT: M 141 HIS cc_start: 0.5745 (p-80) cc_final: 0.4802 (p-80) REVERT: M 154 GLU cc_start: 0.7714 (pp20) cc_final: 0.7485 (pp20) REVERT: M 270 GLN cc_start: 0.7801 (tp40) cc_final: 0.7494 (tp40) REVERT: N 234 GLN cc_start: 0.8050 (tt0) cc_final: 0.7670 (tm-30) REVERT: O 32 GLN cc_start: 0.7966 (tp40) cc_final: 0.7441 (mm-40) REVERT: O 142 TYR cc_start: 0.5775 (m-80) cc_final: 0.5568 (m-10) REVERT: O 245 MET cc_start: 0.8194 (tpp) cc_final: 0.7953 (tpp) REVERT: P 129 TYR cc_start: 0.9300 (t80) cc_final: 0.8995 (t80) REVERT: P 187 MET cc_start: 0.9498 (mmp) cc_final: 0.9240 (mmp) REVERT: P 208 LYS cc_start: 0.8277 (tppt) cc_final: 0.7808 (tptp) REVERT: P 229 ARG cc_start: 0.7613 (tpp80) cc_final: 0.7041 (ttp-110) REVERT: P 270 GLN cc_start: 0.7606 (tp40) cc_final: 0.7007 (tm-30) REVERT: Q 74 MET cc_start: 0.8549 (tpp) cc_final: 0.8242 (tpp) REVERT: Q 117 THR cc_start: 0.8761 (t) cc_final: 0.8338 (m) REVERT: Q 174 ARG cc_start: 0.8850 (tmm-80) cc_final: 0.8116 (ttp-170) REVERT: Q 234 GLN cc_start: 0.8203 (tt0) cc_final: 0.7919 (tm-30) REVERT: R 14 ARG cc_start: 0.6878 (mtm110) cc_final: 0.6567 (mmt-90) REVERT: R 45 VAL cc_start: 0.8677 (m) cc_final: 0.8221 (p) REVERT: R 141 HIS cc_start: 0.5702 (p-80) cc_final: 0.4778 (p-80) REVERT: R 154 GLU cc_start: 0.7680 (pp20) cc_final: 0.7432 (pp20) REVERT: R 174 ARG cc_start: 0.8558 (tmm-80) cc_final: 0.8036 (ttp-170) REVERT: R 229 ARG cc_start: 0.7123 (tpp80) cc_final: 0.6837 (ttp-110) REVERT: R 238 GLN cc_start: 0.7741 (tt0) cc_final: 0.7459 (tt0) REVERT: R 265 ARG cc_start: 0.7450 (ttt-90) cc_final: 0.7059 (ttp80) REVERT: R 270 GLN cc_start: 0.7811 (tp40) cc_final: 0.7454 (tp40) REVERT: S 45 VAL cc_start: 0.8404 (m) cc_final: 0.7993 (p) REVERT: S 129 TYR cc_start: 0.9220 (t80) cc_final: 0.8994 (t80) REVERT: S 229 ARG cc_start: 0.7597 (tpp80) cc_final: 0.6987 (ttp-110) REVERT: S 238 GLN cc_start: 0.7786 (tt0) cc_final: 0.7576 (tp40) REVERT: S 270 GLN cc_start: 0.7925 (tp40) cc_final: 0.7126 (tm-30) outliers start: 0 outliers final: 0 residues processed: 932 average time/residue: 0.2586 time to fit residues: 391.5761 Evaluate side-chains 637 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 637 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 226 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 410 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 405 optimal weight: 0.5980 chunk 460 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN C 15 ASN C 44 GLN ** K 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 226 GLN ** M 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115627 restraints weight = 56720.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.115866 restraints weight = 50552.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116014 restraints weight = 46682.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116059 restraints weight = 45761.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116077 restraints weight = 45641.503| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42620 Z= 0.127 Angle : 0.506 6.014 57900 Z= 0.265 Chirality : 0.038 0.137 6740 Planarity : 0.004 0.066 7180 Dihedral : 3.844 15.615 5700 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.01 (0.12), residues: 5260 helix: 2.30 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.62 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 265 TYR 0.009 0.001 TYR S 128 PHE 0.019 0.001 PHE T 232 TRP 0.005 0.001 TRP F 118 HIS 0.004 0.001 HIS S 224 Details of bonding type rmsd covalent geometry : bond 0.00259 (42580) covalent geometry : angle 0.50187 (57820) SS BOND : bond 0.00144 ( 40) SS BOND : angle 1.88628 ( 80) hydrogen bonds : bond 0.04734 ( 3191) hydrogen bonds : angle 3.83671 ( 9573) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 871 time to evaluate : 1.618 Fit side-chains revert: symmetry clash REVERT: A 45 VAL cc_start: 0.8519 (m) cc_final: 0.7792 (p) REVERT: A 142 TYR cc_start: 0.5586 (m-80) cc_final: 0.5324 (m-10) REVERT: B 51 TYR cc_start: 0.9075 (t80) cc_final: 0.8824 (t80) REVERT: B 105 PHE cc_start: 0.8595 (t80) cc_final: 0.8316 (t80) REVERT: B 208 LYS cc_start: 0.8382 (tppt) cc_final: 0.7947 (tptp) REVERT: C 233 GLU cc_start: 0.8310 (tp30) cc_final: 0.8100 (tp30) REVERT: D 45 VAL cc_start: 0.8480 (m) cc_final: 0.8065 (m) REVERT: D 51 TYR cc_start: 0.9297 (t80) cc_final: 0.9069 (t80) REVERT: D 135 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6969 (mt-10) REVERT: D 145 PHE cc_start: 0.7334 (m-80) cc_final: 0.6980 (m-80) REVERT: D 234 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7795 (tm-30) REVERT: E 45 VAL cc_start: 0.8306 (m) cc_final: 0.8013 (p) REVERT: E 208 LYS cc_start: 0.8312 (tppt) cc_final: 0.8076 (tmmt) REVERT: E 229 ARG cc_start: 0.7162 (tpp80) cc_final: 0.6883 (ttp-110) REVERT: E 244 MET cc_start: 0.7885 (tpp) cc_final: 0.7623 (tpp) REVERT: E 263 HIS cc_start: 0.7327 (m90) cc_final: 0.7063 (m90) REVERT: F 45 VAL cc_start: 0.8288 (m) cc_final: 0.7476 (p) REVERT: F 142 TYR cc_start: 0.5594 (m-80) cc_final: 0.5390 (m-10) REVERT: F 187 MET cc_start: 0.9242 (mmm) cc_final: 0.9006 (mmm) REVERT: G 117 THR cc_start: 0.8861 (t) cc_final: 0.8565 (m) REVERT: G 187 MET cc_start: 0.9388 (mmp) cc_final: 0.9143 (mmp) REVERT: I 45 VAL cc_start: 0.8580 (m) cc_final: 0.8240 (m) REVERT: I 135 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7074 (mt-10) REVERT: I 145 PHE cc_start: 0.7306 (m-80) cc_final: 0.6930 (m-80) REVERT: I 234 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7729 (tm-30) REVERT: J 45 VAL cc_start: 0.8273 (m) cc_final: 0.7991 (p) REVERT: J 187 MET cc_start: 0.9341 (mmp) cc_final: 0.9012 (mmp) REVERT: J 208 LYS cc_start: 0.8303 (tppt) cc_final: 0.8100 (tmmt) REVERT: J 229 ARG cc_start: 0.7219 (tpp80) cc_final: 0.6951 (ttp-110) REVERT: J 234 GLN cc_start: 0.7888 (tt0) cc_final: 0.7670 (tm-30) REVERT: J 244 MET cc_start: 0.7918 (tpp) cc_final: 0.7629 (tpp) REVERT: J 263 HIS cc_start: 0.7284 (m90) cc_final: 0.6878 (m90) REVERT: K 129 TYR cc_start: 0.9291 (t80) cc_final: 0.8976 (t80) REVERT: K 187 MET cc_start: 0.9419 (mmp) cc_final: 0.9152 (mmp) REVERT: K 208 LYS cc_start: 0.8340 (tppt) cc_final: 0.7834 (tptp) REVERT: K 229 ARG cc_start: 0.7575 (tpp80) cc_final: 0.7077 (ttp-110) REVERT: K 270 GLN cc_start: 0.7613 (tp40) cc_final: 0.7031 (tm-30) REVERT: L 45 VAL cc_start: 0.8708 (m) cc_final: 0.8432 (p) REVERT: L 117 THR cc_start: 0.8808 (t) cc_final: 0.8463 (m) REVERT: L 174 ARG cc_start: 0.8816 (tmm-80) cc_final: 0.8127 (ttp-170) REVERT: L 234 GLN cc_start: 0.8069 (tt0) cc_final: 0.7863 (tm-30) REVERT: M 45 VAL cc_start: 0.8601 (m) cc_final: 0.8205 (p) REVERT: M 154 GLU cc_start: 0.7673 (pp20) cc_final: 0.7448 (pp20) REVERT: M 270 GLN cc_start: 0.7758 (tp40) cc_final: 0.7436 (tp40) REVERT: N 234 GLN cc_start: 0.7964 (tt0) cc_final: 0.7724 (tm-30) REVERT: N 265 ARG cc_start: 0.6441 (ttt-90) cc_final: 0.6184 (tmm-80) REVERT: O 32 GLN cc_start: 0.7992 (tp40) cc_final: 0.7421 (mm-40) REVERT: O 142 TYR cc_start: 0.5621 (m-80) cc_final: 0.5372 (m-10) REVERT: O 187 MET cc_start: 0.9260 (mmm) cc_final: 0.9043 (mmm) REVERT: P 129 TYR cc_start: 0.9253 (t80) cc_final: 0.8980 (t80) REVERT: P 187 MET cc_start: 0.9423 (mmp) cc_final: 0.9164 (mmp) REVERT: P 208 LYS cc_start: 0.8334 (tppt) cc_final: 0.7842 (tptp) REVERT: P 229 ARG cc_start: 0.7559 (tpp80) cc_final: 0.7092 (ttp-110) REVERT: P 270 GLN cc_start: 0.7654 (tp40) cc_final: 0.7103 (tm-30) REVERT: Q 117 THR cc_start: 0.8816 (t) cc_final: 0.8448 (m) REVERT: Q 174 ARG cc_start: 0.8807 (tmm-80) cc_final: 0.8116 (ttp-170) REVERT: R 45 VAL cc_start: 0.8646 (m) cc_final: 0.8273 (p) REVERT: R 154 GLU cc_start: 0.7638 (pp20) cc_final: 0.7381 (pp20) REVERT: R 174 ARG cc_start: 0.8505 (tmm-80) cc_final: 0.7975 (ttp-170) REVERT: R 265 ARG cc_start: 0.7452 (ttt-90) cc_final: 0.7069 (ttp80) REVERT: R 270 GLN cc_start: 0.7805 (tp40) cc_final: 0.7487 (tp40) REVERT: S 129 TYR cc_start: 0.9185 (t80) cc_final: 0.8976 (t80) REVERT: S 154 GLU cc_start: 0.7720 (pp20) cc_final: 0.7412 (pp20) REVERT: S 229 ARG cc_start: 0.7509 (tpp80) cc_final: 0.7061 (ttp-110) REVERT: S 270 GLN cc_start: 0.7882 (tp40) cc_final: 0.7177 (tm-30) REVERT: T 45 VAL cc_start: 0.8479 (m) cc_final: 0.7982 (m) outliers start: 0 outliers final: 0 residues processed: 871 average time/residue: 0.2516 time to fit residues: 358.3174 Evaluate side-chains 614 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 614 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 119 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 361 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 451 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 334 optimal weight: 0.9980 chunk 511 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN C 44 GLN ** K 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 GLN ** M 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.154030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.127554 restraints weight = 57064.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129073 restraints weight = 43520.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.130477 restraints weight = 37125.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131114 restraints weight = 33352.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.131696 restraints weight = 31267.533| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42620 Z= 0.135 Angle : 0.531 6.404 57900 Z= 0.277 Chirality : 0.039 0.161 6740 Planarity : 0.004 0.061 7180 Dihedral : 3.865 15.497 5700 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: 2.11 (0.12), residues: 5260 helix: 2.38 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.63 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 229 TYR 0.010 0.001 TYR E 129 PHE 0.029 0.002 PHE S 68 TRP 0.004 0.001 TRP G 118 HIS 0.004 0.001 HIS Q 141 Details of bonding type rmsd covalent geometry : bond 0.00288 (42580) covalent geometry : angle 0.52411 (57820) SS BOND : bond 0.00256 ( 40) SS BOND : angle 2.38275 ( 80) hydrogen bonds : bond 0.04852 ( 3191) hydrogen bonds : angle 3.82379 ( 9573) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 861 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: A 45 VAL cc_start: 0.8508 (m) cc_final: 0.7794 (p) REVERT: A 142 TYR cc_start: 0.5680 (m-80) cc_final: 0.5476 (m-10) REVERT: B 32 GLN cc_start: 0.8340 (tm-30) cc_final: 0.8097 (tm-30) REVERT: B 51 TYR cc_start: 0.9135 (t80) cc_final: 0.8928 (t80) REVERT: D 45 VAL cc_start: 0.8565 (m) cc_final: 0.8110 (m) REVERT: D 51 TYR cc_start: 0.9322 (t80) cc_final: 0.9078 (t80) REVERT: D 135 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7172 (mt-10) REVERT: D 145 PHE cc_start: 0.7273 (m-80) cc_final: 0.6810 (m-80) REVERT: D 234 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7545 (tm-30) REVERT: D 245 MET cc_start: 0.8474 (tpp) cc_final: 0.8240 (tpp) REVERT: E 45 VAL cc_start: 0.8415 (m) cc_final: 0.8037 (p) REVERT: E 208 LYS cc_start: 0.8318 (tppt) cc_final: 0.7993 (tmmt) REVERT: E 229 ARG cc_start: 0.7233 (tpp80) cc_final: 0.6863 (ttp-110) REVERT: E 244 MET cc_start: 0.7831 (tpp) cc_final: 0.7597 (tpp) REVERT: E 263 HIS cc_start: 0.7334 (m90) cc_final: 0.6996 (m90) REVERT: F 45 VAL cc_start: 0.8332 (m) cc_final: 0.7501 (p) REVERT: F 142 TYR cc_start: 0.5683 (m-80) cc_final: 0.5470 (m-10) REVERT: F 187 MET cc_start: 0.9242 (mmm) cc_final: 0.8952 (mmm) REVERT: G 117 THR cc_start: 0.8951 (t) cc_final: 0.8628 (m) REVERT: G 187 MET cc_start: 0.9408 (mmp) cc_final: 0.9170 (mmp) REVERT: H 51 TYR cc_start: 0.9233 (t80) cc_final: 0.8946 (t80) REVERT: H 144 MET cc_start: 0.5814 (ptp) cc_final: 0.4631 (ptp) REVERT: I 45 VAL cc_start: 0.8629 (m) cc_final: 0.8274 (m) REVERT: I 135 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7207 (mt-10) REVERT: I 145 PHE cc_start: 0.7200 (m-80) cc_final: 0.6732 (m-80) REVERT: I 187 MET cc_start: 0.9284 (mmm) cc_final: 0.9040 (mmm) REVERT: I 234 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7610 (tm-30) REVERT: J 45 VAL cc_start: 0.8452 (m) cc_final: 0.8079 (p) REVERT: J 187 MET cc_start: 0.9341 (mmp) cc_final: 0.9007 (mmp) REVERT: J 208 LYS cc_start: 0.8292 (tppt) cc_final: 0.7997 (tmmt) REVERT: J 229 ARG cc_start: 0.7255 (tpp80) cc_final: 0.6863 (ttp-110) REVERT: J 234 GLN cc_start: 0.7938 (tt0) cc_final: 0.7672 (tm-30) REVERT: J 263 HIS cc_start: 0.7287 (m90) cc_final: 0.6813 (m90) REVERT: K 187 MET cc_start: 0.9444 (mmp) cc_final: 0.9193 (mmp) REVERT: K 229 ARG cc_start: 0.7536 (tpp80) cc_final: 0.6983 (ttp-110) REVERT: K 270 GLN cc_start: 0.7722 (tp40) cc_final: 0.7101 (tm-30) REVERT: L 45 VAL cc_start: 0.8719 (m) cc_final: 0.8384 (p) REVERT: L 174 ARG cc_start: 0.8863 (tmm-80) cc_final: 0.8152 (ttp-170) REVERT: L 234 GLN cc_start: 0.8145 (tt0) cc_final: 0.7797 (tm-30) REVERT: M 45 VAL cc_start: 0.8515 (m) cc_final: 0.8149 (p) REVERT: M 270 GLN cc_start: 0.7870 (tp40) cc_final: 0.7348 (tm-30) REVERT: N 234 GLN cc_start: 0.8050 (tt0) cc_final: 0.7686 (tm-30) REVERT: N 265 ARG cc_start: 0.6782 (ttt-90) cc_final: 0.6485 (tmm-80) REVERT: O 32 GLN cc_start: 0.8089 (tp40) cc_final: 0.7477 (mm-40) REVERT: O 144 MET cc_start: 0.6518 (ptm) cc_final: 0.6273 (ptm) REVERT: O 187 MET cc_start: 0.9313 (mmm) cc_final: 0.8830 (mmm) REVERT: P 187 MET cc_start: 0.9422 (mmp) cc_final: 0.9207 (mmp) REVERT: P 229 ARG cc_start: 0.7545 (tpp80) cc_final: 0.6972 (ttp-110) REVERT: P 270 GLN cc_start: 0.7744 (tp40) cc_final: 0.7147 (tm-30) REVERT: Q 45 VAL cc_start: 0.8702 (m) cc_final: 0.8482 (p) REVERT: Q 154 GLU cc_start: 0.7800 (pp20) cc_final: 0.7495 (pp20) REVERT: Q 174 ARG cc_start: 0.8841 (tmm-80) cc_final: 0.8134 (ttp-170) REVERT: R 45 VAL cc_start: 0.8682 (m) cc_final: 0.8298 (p) REVERT: S 129 TYR cc_start: 0.9241 (t80) cc_final: 0.8996 (t80) REVERT: S 229 ARG cc_start: 0.7582 (tpp80) cc_final: 0.7074 (ttp-110) REVERT: S 234 GLN cc_start: 0.8209 (tt0) cc_final: 0.7639 (tm-30) REVERT: S 270 GLN cc_start: 0.7901 (tp40) cc_final: 0.7195 (tm-30) REVERT: T 45 VAL cc_start: 0.8454 (m) cc_final: 0.8057 (m) REVERT: T 144 MET cc_start: 0.6251 (ptm) cc_final: 0.5976 (ptm) outliers start: 0 outliers final: 0 residues processed: 861 average time/residue: 0.2445 time to fit residues: 341.7355 Evaluate side-chains 601 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 601 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 212 optimal weight: 7.9990 chunk 278 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 475 optimal weight: 8.9990 chunk 230 optimal weight: 4.9990 chunk 351 optimal weight: 7.9990 chunk 255 optimal weight: 0.8980 chunk 516 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 332 optimal weight: 1.9990 chunk 406 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN C 15 ASN ** P 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.154191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128139 restraints weight = 57079.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.130044 restraints weight = 42110.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.130940 restraints weight = 33973.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.132086 restraints weight = 31074.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.132142 restraints weight = 29273.647| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 42620 Z= 0.154 Angle : 0.552 6.976 57900 Z= 0.287 Chirality : 0.040 0.158 6740 Planarity : 0.004 0.057 7180 Dihedral : 3.915 16.536 5700 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 2.14 (0.12), residues: 5260 helix: 2.40 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.60 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 153 TYR 0.010 0.001 TYR E 129 PHE 0.021 0.002 PHE T 232 TRP 0.007 0.001 TRP J 272 HIS 0.004 0.001 HIS G 239 Details of bonding type rmsd covalent geometry : bond 0.00345 (42580) covalent geometry : angle 0.54819 (57820) SS BOND : bond 0.00116 ( 40) SS BOND : angle 1.81490 ( 80) hydrogen bonds : bond 0.05118 ( 3191) hydrogen bonds : angle 3.86839 ( 9573) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 820 time to evaluate : 1.603 Fit side-chains revert: symmetry clash REVERT: A 45 VAL cc_start: 0.8416 (m) cc_final: 0.7741 (p) REVERT: A 142 TYR cc_start: 0.5810 (m-80) cc_final: 0.5604 (m-10) REVERT: B 51 TYR cc_start: 0.9201 (t80) cc_final: 0.8998 (t80) REVERT: B 265 ARG cc_start: 0.7008 (ttt90) cc_final: 0.6776 (ttp80) REVERT: D 45 VAL cc_start: 0.8529 (m) cc_final: 0.7864 (p) REVERT: D 51 TYR cc_start: 0.9341 (t80) cc_final: 0.9080 (t80) REVERT: D 145 PHE cc_start: 0.7541 (m-80) cc_final: 0.6981 (m-80) REVERT: D 234 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7659 (tm-30) REVERT: E 208 LYS cc_start: 0.8346 (tppt) cc_final: 0.8028 (tmmt) REVERT: E 229 ARG cc_start: 0.7279 (tpp80) cc_final: 0.6910 (ttp-110) REVERT: E 244 MET cc_start: 0.7852 (tpp) cc_final: 0.7646 (tpp) REVERT: E 263 HIS cc_start: 0.7384 (m90) cc_final: 0.6996 (m90) REVERT: F 45 VAL cc_start: 0.8223 (m) cc_final: 0.7531 (p) REVERT: F 142 TYR cc_start: 0.5731 (m-80) cc_final: 0.5526 (m-10) REVERT: F 187 MET cc_start: 0.9211 (mmm) cc_final: 0.9011 (mmm) REVERT: G 117 THR cc_start: 0.8866 (t) cc_final: 0.8522 (m) REVERT: H 51 TYR cc_start: 0.9224 (t80) cc_final: 0.8922 (t80) REVERT: I 45 VAL cc_start: 0.8603 (m) cc_final: 0.8027 (p) REVERT: I 145 PHE cc_start: 0.7542 (m-80) cc_final: 0.6986 (m-80) REVERT: I 187 MET cc_start: 0.9278 (mmm) cc_final: 0.9044 (mmm) REVERT: I 234 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7612 (tm-30) REVERT: J 187 MET cc_start: 0.9340 (mmp) cc_final: 0.9072 (mmp) REVERT: J 208 LYS cc_start: 0.8332 (tppt) cc_final: 0.8035 (tmmt) REVERT: J 229 ARG cc_start: 0.7273 (tpp80) cc_final: 0.6888 (ttp-110) REVERT: J 234 GLN cc_start: 0.7966 (tt0) cc_final: 0.7670 (tm-30) REVERT: J 263 HIS cc_start: 0.7346 (m90) cc_final: 0.6805 (m90) REVERT: K 117 THR cc_start: 0.8990 (t) cc_final: 0.8559 (m) REVERT: K 144 MET cc_start: 0.5414 (ptt) cc_final: 0.5120 (ptt) REVERT: K 229 ARG cc_start: 0.7549 (tpp80) cc_final: 0.7013 (ttp-110) REVERT: K 270 GLN cc_start: 0.7803 (tp40) cc_final: 0.7199 (tm-30) REVERT: L 45 VAL cc_start: 0.8723 (m) cc_final: 0.8486 (p) REVERT: L 154 GLU cc_start: 0.7742 (pp20) cc_final: 0.7488 (pp20) REVERT: L 174 ARG cc_start: 0.8899 (tmm-80) cc_final: 0.8157 (ttp-170) REVERT: L 234 GLN cc_start: 0.8136 (tt0) cc_final: 0.7849 (tm-30) REVERT: M 45 VAL cc_start: 0.8634 (m) cc_final: 0.8226 (p) REVERT: M 270 GLN cc_start: 0.7956 (tp40) cc_final: 0.7674 (tp40) REVERT: N 234 GLN cc_start: 0.8004 (tt0) cc_final: 0.7571 (tm-30) REVERT: N 263 HIS cc_start: 0.7339 (m90) cc_final: 0.7098 (m90) REVERT: O 32 GLN cc_start: 0.8162 (tp40) cc_final: 0.7536 (mm-40) REVERT: O 144 MET cc_start: 0.6479 (ptm) cc_final: 0.6218 (ptm) REVERT: O 187 MET cc_start: 0.9258 (mmm) cc_final: 0.8921 (mmm) REVERT: P 117 THR cc_start: 0.8978 (t) cc_final: 0.8543 (m) REVERT: P 229 ARG cc_start: 0.7550 (tpp80) cc_final: 0.7001 (ttp-110) REVERT: Q 174 ARG cc_start: 0.8860 (tmm-80) cc_final: 0.8132 (ttp-170) REVERT: R 45 VAL cc_start: 0.8680 (m) cc_final: 0.8253 (p) REVERT: R 154 GLU cc_start: 0.7666 (pp20) cc_final: 0.7409 (pp20) REVERT: R 234 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7778 (tm-30) REVERT: S 129 TYR cc_start: 0.9213 (t80) cc_final: 0.8953 (t80) REVERT: S 229 ARG cc_start: 0.7628 (tpp80) cc_final: 0.7094 (ttp-110) REVERT: S 234 GLN cc_start: 0.8213 (tt0) cc_final: 0.7619 (tm-30) REVERT: S 270 GLN cc_start: 0.7930 (tp40) cc_final: 0.7458 (tm-30) REVERT: T 45 VAL cc_start: 0.8431 (m) cc_final: 0.8107 (m) REVERT: T 144 MET cc_start: 0.6498 (ptm) cc_final: 0.6295 (ptm) outliers start: 0 outliers final: 0 residues processed: 820 average time/residue: 0.2441 time to fit residues: 328.7947 Evaluate side-chains 599 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 599 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 121 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 211 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 419 optimal weight: 0.2980 chunk 336 optimal weight: 0.0020 chunk 238 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 400 optimal weight: 1.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN C 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.155200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.129116 restraints weight = 56929.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130939 restraints weight = 42260.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.131793 restraints weight = 34272.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.132385 restraints weight = 32342.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.132531 restraints weight = 30738.105| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 42620 Z= 0.121 Angle : 0.525 7.405 57900 Z= 0.270 Chirality : 0.038 0.168 6740 Planarity : 0.004 0.052 7180 Dihedral : 3.874 16.851 5700 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 2.39 (0.12), residues: 5260 helix: 2.57 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.50 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 153 TYR 0.010 0.001 TYR E 129 PHE 0.020 0.001 PHE T 232 TRP 0.007 0.001 TRP B 272 HIS 0.004 0.001 HIS L 141 Details of bonding type rmsd covalent geometry : bond 0.00243 (42580) covalent geometry : angle 0.52103 (57820) SS BOND : bond 0.00197 ( 40) SS BOND : angle 1.77403 ( 80) hydrogen bonds : bond 0.04611 ( 3191) hydrogen bonds : angle 3.71844 ( 9573) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 866 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 45 VAL cc_start: 0.8386 (m) cc_final: 0.7665 (p) REVERT: A 245 MET cc_start: 0.8496 (tpp) cc_final: 0.8277 (tpp) REVERT: B 51 TYR cc_start: 0.9126 (t80) cc_final: 0.8912 (t80) REVERT: B 105 PHE cc_start: 0.8796 (t80) cc_final: 0.8370 (t80) REVERT: B 153 ARG cc_start: 0.8098 (ttp-110) cc_final: 0.7898 (ttp80) REVERT: B 187 MET cc_start: 0.9059 (mmp) cc_final: 0.8783 (mmp) REVERT: B 265 ARG cc_start: 0.7002 (ttt90) cc_final: 0.6715 (tmm-80) REVERT: C 233 GLU cc_start: 0.8263 (tp30) cc_final: 0.7991 (tp30) REVERT: D 13 GLN cc_start: 0.7416 (tp40) cc_final: 0.7160 (tp-100) REVERT: D 45 VAL cc_start: 0.8328 (m) cc_final: 0.7974 (p) REVERT: D 145 PHE cc_start: 0.7470 (m-80) cc_final: 0.6883 (m-80) REVERT: D 270 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7575 (tm-30) REVERT: E 45 VAL cc_start: 0.8451 (t) cc_final: 0.8249 (t) REVERT: E 208 LYS cc_start: 0.8441 (tppt) cc_final: 0.8116 (tmmt) REVERT: E 244 MET cc_start: 0.7820 (tpp) cc_final: 0.7216 (tpp) REVERT: E 263 HIS cc_start: 0.7327 (m90) cc_final: 0.6962 (m-70) REVERT: F 45 VAL cc_start: 0.8240 (m) cc_final: 0.7504 (p) REVERT: G 129 TYR cc_start: 0.9283 (t80) cc_final: 0.9029 (t80) REVERT: G 187 MET cc_start: 0.9239 (mmp) cc_final: 0.9033 (mmm) REVERT: H 45 VAL cc_start: 0.8392 (p) cc_final: 0.7893 (p) REVERT: H 51 TYR cc_start: 0.9210 (t80) cc_final: 0.8896 (t80) REVERT: I 45 VAL cc_start: 0.8459 (m) cc_final: 0.8134 (p) REVERT: I 145 PHE cc_start: 0.7567 (m-80) cc_final: 0.6994 (m-80) REVERT: I 245 MET cc_start: 0.8446 (tpp) cc_final: 0.8172 (tpp) REVERT: I 270 GLN cc_start: 0.7946 (tp40) cc_final: 0.7708 (tm-30) REVERT: J 45 VAL cc_start: 0.8500 (t) cc_final: 0.8292 (t) REVERT: J 187 MET cc_start: 0.9299 (mmp) cc_final: 0.9035 (mmp) REVERT: J 208 LYS cc_start: 0.8412 (tppt) cc_final: 0.8130 (tmmt) REVERT: J 229 ARG cc_start: 0.7118 (tpp80) cc_final: 0.6760 (ttp-110) REVERT: J 234 GLN cc_start: 0.7930 (tt0) cc_final: 0.7588 (tm-30) REVERT: J 263 HIS cc_start: 0.7296 (m90) cc_final: 0.6743 (m90) REVERT: K 129 TYR cc_start: 0.9288 (t80) cc_final: 0.9026 (t80) REVERT: K 144 MET cc_start: 0.5400 (ptt) cc_final: 0.5001 (ptt) REVERT: K 174 ARG cc_start: 0.8617 (tmm-80) cc_final: 0.8045 (ttp-170) REVERT: K 229 ARG cc_start: 0.7459 (tpp80) cc_final: 0.6986 (ttp-110) REVERT: L 45 VAL cc_start: 0.8624 (m) cc_final: 0.8415 (p) REVERT: L 154 GLU cc_start: 0.7754 (pp20) cc_final: 0.7510 (pp20) REVERT: L 174 ARG cc_start: 0.8858 (tmm-80) cc_final: 0.8154 (ttp-170) REVERT: M 45 VAL cc_start: 0.8559 (m) cc_final: 0.8108 (p) REVERT: N 234 GLN cc_start: 0.8119 (tt0) cc_final: 0.7632 (tm-30) REVERT: N 263 HIS cc_start: 0.7351 (m90) cc_final: 0.6966 (m90) REVERT: O 187 MET cc_start: 0.9237 (mmm) cc_final: 0.8836 (mmm) REVERT: P 129 TYR cc_start: 0.9308 (t80) cc_final: 0.9031 (t80) REVERT: P 174 ARG cc_start: 0.8621 (tmm-80) cc_final: 0.8104 (ttp-170) REVERT: P 229 ARG cc_start: 0.7487 (tpp80) cc_final: 0.7027 (ttp-110) REVERT: Q 45 VAL cc_start: 0.8584 (m) cc_final: 0.8298 (p) REVERT: Q 154 GLU cc_start: 0.7859 (pp20) cc_final: 0.7587 (pp20) REVERT: Q 174 ARG cc_start: 0.8816 (tmm-80) cc_final: 0.8128 (ttp-170) REVERT: R 45 VAL cc_start: 0.8538 (m) cc_final: 0.8149 (p) REVERT: R 154 GLU cc_start: 0.7740 (pp20) cc_final: 0.7516 (pp20) REVERT: R 238 GLN cc_start: 0.7825 (tt0) cc_final: 0.7574 (tp40) REVERT: R 270 GLN cc_start: 0.7847 (tp40) cc_final: 0.7613 (tp40) REVERT: S 229 ARG cc_start: 0.7534 (tpp80) cc_final: 0.7065 (ttp-110) REVERT: S 234 GLN cc_start: 0.8128 (tt0) cc_final: 0.7536 (tm-30) REVERT: S 270 GLN cc_start: 0.7843 (tp40) cc_final: 0.7261 (tm-30) REVERT: T 245 MET cc_start: 0.8473 (tpp) cc_final: 0.8229 (tpp) outliers start: 0 outliers final: 0 residues processed: 866 average time/residue: 0.2440 time to fit residues: 344.0732 Evaluate side-chains 609 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 609 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 455 optimal weight: 8.9990 chunk 272 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 463 optimal weight: 3.9990 chunk 343 optimal weight: 0.0170 chunk 11 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 316 optimal weight: 0.3980 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN L 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128179 restraints weight = 57230.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130396 restraints weight = 42435.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131066 restraints weight = 33760.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.132072 restraints weight = 31305.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132126 restraints weight = 29699.278| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 42620 Z= 0.129 Angle : 0.540 7.490 57900 Z= 0.276 Chirality : 0.039 0.155 6740 Planarity : 0.004 0.051 7180 Dihedral : 3.855 16.665 5700 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: 2.41 (0.12), residues: 5260 helix: 2.58 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.48 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 265 TYR 0.017 0.001 TYR M 81 PHE 0.021 0.001 PHE T 232 TRP 0.006 0.001 TRP G 272 HIS 0.004 0.001 HIS Q 141 Details of bonding type rmsd covalent geometry : bond 0.00274 (42580) covalent geometry : angle 0.53676 (57820) SS BOND : bond 0.00110 ( 40) SS BOND : angle 1.71569 ( 80) hydrogen bonds : bond 0.04674 ( 3191) hydrogen bonds : angle 3.72730 ( 9573) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 802 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: A 45 VAL cc_start: 0.8307 (m) cc_final: 0.7662 (p) REVERT: A 187 MET cc_start: 0.9024 (mmm) cc_final: 0.8696 (mmm) REVERT: A 229 ARG cc_start: 0.7271 (ttm110) cc_final: 0.7033 (ttp-110) REVERT: A 245 MET cc_start: 0.8494 (tpp) cc_final: 0.8148 (tpp) REVERT: B 15 ASN cc_start: 0.7638 (m-40) cc_final: 0.7096 (m110) REVERT: B 51 TYR cc_start: 0.9167 (t80) cc_final: 0.8964 (t80) REVERT: B 187 MET cc_start: 0.9023 (mmp) cc_final: 0.8762 (mmp) REVERT: B 230 GLU cc_start: 0.7353 (tp30) cc_final: 0.7061 (tp30) REVERT: D 45 VAL cc_start: 0.8517 (m) cc_final: 0.8066 (p) REVERT: D 145 PHE cc_start: 0.7355 (m-80) cc_final: 0.6806 (m-80) REVERT: D 154 GLU cc_start: 0.7639 (pp20) cc_final: 0.7382 (pp20) REVERT: E 208 LYS cc_start: 0.8446 (tppt) cc_final: 0.8105 (tmmt) REVERT: E 244 MET cc_start: 0.7827 (tpp) cc_final: 0.7233 (tpp) REVERT: E 263 HIS cc_start: 0.7396 (m90) cc_final: 0.6858 (m90) REVERT: F 45 VAL cc_start: 0.8161 (m) cc_final: 0.7541 (p) REVERT: G 129 TYR cc_start: 0.9316 (t80) cc_final: 0.9025 (t80) REVERT: G 144 MET cc_start: 0.5212 (ptt) cc_final: 0.4911 (ptt) REVERT: I 45 VAL cc_start: 0.8585 (m) cc_final: 0.8171 (p) REVERT: I 145 PHE cc_start: 0.7467 (m-80) cc_final: 0.6946 (m-80) REVERT: I 154 GLU cc_start: 0.7593 (pp20) cc_final: 0.7360 (pp20) REVERT: I 245 MET cc_start: 0.8435 (tpp) cc_final: 0.8084 (tpp) REVERT: J 187 MET cc_start: 0.9274 (mmp) cc_final: 0.9013 (mmp) REVERT: J 208 LYS cc_start: 0.8438 (tppt) cc_final: 0.8133 (tmmt) REVERT: J 263 HIS cc_start: 0.7365 (m90) cc_final: 0.6712 (m90) REVERT: K 129 TYR cc_start: 0.9280 (t80) cc_final: 0.9046 (t80) REVERT: K 144 MET cc_start: 0.5302 (ptt) cc_final: 0.5069 (ptt) REVERT: K 229 ARG cc_start: 0.7372 (tpp80) cc_final: 0.6981 (ttp-110) REVERT: L 154 GLU cc_start: 0.7751 (pp20) cc_final: 0.7516 (pp20) REVERT: L 174 ARG cc_start: 0.8852 (tmm-80) cc_final: 0.8126 (ttp-170) REVERT: M 45 VAL cc_start: 0.8533 (m) cc_final: 0.8136 (p) REVERT: M 154 GLU cc_start: 0.7750 (pp20) cc_final: 0.7536 (pp20) REVERT: N 234 GLN cc_start: 0.8136 (tt0) cc_final: 0.7616 (tm-30) REVERT: N 263 HIS cc_start: 0.7433 (m90) cc_final: 0.7084 (m90) REVERT: O 187 MET cc_start: 0.9239 (mmm) cc_final: 0.8929 (mmm) REVERT: O 245 MET cc_start: 0.8506 (tpp) cc_final: 0.8304 (tpp) REVERT: P 129 TYR cc_start: 0.9338 (t80) cc_final: 0.9051 (t80) REVERT: P 229 ARG cc_start: 0.7460 (tpp80) cc_final: 0.7031 (ttp-110) REVERT: Q 174 ARG cc_start: 0.8829 (tmm-80) cc_final: 0.8141 (ttp-170) REVERT: R 45 VAL cc_start: 0.8573 (m) cc_final: 0.8142 (p) REVERT: R 154 GLU cc_start: 0.7768 (pp20) cc_final: 0.7528 (pp20) REVERT: R 234 GLN cc_start: 0.8279 (tt0) cc_final: 0.8011 (tm-30) REVERT: S 229 ARG cc_start: 0.7544 (tpp80) cc_final: 0.7238 (ttp-110) REVERT: S 263 HIS cc_start: 0.7358 (m90) cc_final: 0.6740 (m90) outliers start: 0 outliers final: 0 residues processed: 802 average time/residue: 0.2444 time to fit residues: 322.2875 Evaluate side-chains 580 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 281 optimal weight: 2.9990 chunk 406 optimal weight: 10.0000 chunk 278 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 404 optimal weight: 2.9990 chunk 457 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 300 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN C 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127790 restraints weight = 57319.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.129900 restraints weight = 42295.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131000 restraints weight = 33944.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.131401 restraints weight = 30786.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.131572 restraints weight = 29765.154| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 42620 Z= 0.133 Angle : 0.555 8.000 57900 Z= 0.285 Chirality : 0.039 0.174 6740 Planarity : 0.004 0.050 7180 Dihedral : 3.861 16.507 5700 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: 2.43 (0.12), residues: 5260 helix: 2.59 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.45 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 153 TYR 0.015 0.001 TYR M 81 PHE 0.020 0.001 PHE Q 232 TRP 0.005 0.001 TRP M 272 HIS 0.004 0.001 HIS L 141 Details of bonding type rmsd covalent geometry : bond 0.00288 (42580) covalent geometry : angle 0.54980 (57820) SS BOND : bond 0.00267 ( 40) SS BOND : angle 2.04679 ( 80) hydrogen bonds : bond 0.04712 ( 3191) hydrogen bonds : angle 3.74565 ( 9573) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 798 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.8358 (m) cc_final: 0.7671 (p) REVERT: A 187 MET cc_start: 0.9122 (mmm) cc_final: 0.8712 (mmm) REVERT: B 51 TYR cc_start: 0.9191 (t80) cc_final: 0.8970 (t80) REVERT: B 187 MET cc_start: 0.9129 (mmp) cc_final: 0.8828 (mmp) REVERT: B 229 ARG cc_start: 0.7860 (tpp80) cc_final: 0.7032 (ttp-110) REVERT: C 144 MET cc_start: 0.5063 (ptt) cc_final: 0.4579 (ttp) REVERT: D 45 VAL cc_start: 0.8490 (m) cc_final: 0.8095 (p) REVERT: D 51 TYR cc_start: 0.9259 (t80) cc_final: 0.8951 (t80) REVERT: D 145 PHE cc_start: 0.7302 (m-80) cc_final: 0.6696 (m-80) REVERT: D 154 GLU cc_start: 0.7725 (pp20) cc_final: 0.7505 (pp20) REVERT: E 208 LYS cc_start: 0.8442 (tppt) cc_final: 0.8079 (tmmt) REVERT: E 244 MET cc_start: 0.7840 (tpp) cc_final: 0.7601 (tpp) REVERT: E 263 HIS cc_start: 0.7487 (m90) cc_final: 0.6916 (m90) REVERT: F 45 VAL cc_start: 0.8196 (m) cc_final: 0.7542 (p) REVERT: G 129 TYR cc_start: 0.9274 (t80) cc_final: 0.9048 (t80) REVERT: G 144 MET cc_start: 0.5555 (ptt) cc_final: 0.5345 (ptt) REVERT: H 51 TYR cc_start: 0.9233 (t80) cc_final: 0.8844 (t80) REVERT: H 270 GLN cc_start: 0.8104 (tp40) cc_final: 0.7757 (tm-30) REVERT: I 45 VAL cc_start: 0.8569 (m) cc_final: 0.8144 (p) REVERT: I 145 PHE cc_start: 0.7419 (m-80) cc_final: 0.6881 (m-80) REVERT: I 154 GLU cc_start: 0.7678 (pp20) cc_final: 0.7461 (pp20) REVERT: J 187 MET cc_start: 0.9321 (mmp) cc_final: 0.9068 (mmp) REVERT: J 208 LYS cc_start: 0.8438 (tppt) cc_final: 0.8095 (tmmt) REVERT: J 263 HIS cc_start: 0.7408 (m90) cc_final: 0.6745 (m90) REVERT: K 129 TYR cc_start: 0.9297 (t80) cc_final: 0.9066 (t80) REVERT: K 144 MET cc_start: 0.5478 (ptt) cc_final: 0.5194 (ptt) REVERT: K 229 ARG cc_start: 0.7379 (tpp80) cc_final: 0.6958 (ttp-110) REVERT: L 174 ARG cc_start: 0.8873 (tmm-80) cc_final: 0.8135 (ttp-170) REVERT: M 45 VAL cc_start: 0.8547 (m) cc_final: 0.8161 (p) REVERT: M 144 MET cc_start: 0.4478 (ptt) cc_final: 0.4105 (ptt) REVERT: M 154 GLU cc_start: 0.7765 (pp20) cc_final: 0.7556 (pp20) REVERT: M 270 GLN cc_start: 0.7930 (tp40) cc_final: 0.7588 (tm-30) REVERT: N 234 GLN cc_start: 0.8147 (tt0) cc_final: 0.7621 (tm-30) REVERT: N 263 HIS cc_start: 0.7343 (m90) cc_final: 0.6749 (m90) REVERT: O 187 MET cc_start: 0.9226 (mmm) cc_final: 0.8741 (mmm) REVERT: O 245 MET cc_start: 0.8459 (tpp) cc_final: 0.8185 (tpp) REVERT: P 129 TYR cc_start: 0.9315 (t80) cc_final: 0.9071 (t80) REVERT: P 144 MET cc_start: 0.4863 (ptt) cc_final: 0.4341 (ttp) REVERT: P 229 ARG cc_start: 0.7391 (tpp80) cc_final: 0.6924 (ttp-110) REVERT: Q 174 ARG cc_start: 0.8844 (tmm-80) cc_final: 0.8142 (ttp-170) REVERT: R 45 VAL cc_start: 0.8519 (m) cc_final: 0.8104 (p) REVERT: R 154 GLU cc_start: 0.7781 (pp20) cc_final: 0.7519 (pp20) REVERT: R 234 GLN cc_start: 0.8201 (tt0) cc_final: 0.7873 (tm-30) REVERT: S 229 ARG cc_start: 0.7704 (tpp80) cc_final: 0.7320 (ttp-110) REVERT: S 234 GLN cc_start: 0.8156 (tt0) cc_final: 0.7562 (tm-30) REVERT: S 263 HIS cc_start: 0.7353 (m90) cc_final: 0.6735 (m90) REVERT: T 45 VAL cc_start: 0.8519 (m) cc_final: 0.7925 (p) REVERT: T 154 GLU cc_start: 0.7634 (pp20) cc_final: 0.7335 (pp20) outliers start: 0 outliers final: 0 residues processed: 798 average time/residue: 0.2428 time to fit residues: 322.5823 Evaluate side-chains 584 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 584 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 342 optimal weight: 0.9990 chunk 174 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 422 optimal weight: 4.9990 chunk 325 optimal weight: 7.9990 chunk 470 optimal weight: 4.9990 chunk 273 optimal weight: 7.9990 chunk 134 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.135304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.110317 restraints weight = 60334.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.111104 restraints weight = 52106.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111550 restraints weight = 46302.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.112190 restraints weight = 43990.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.112362 restraints weight = 42706.922| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 42620 Z= 0.191 Angle : 0.624 8.427 57900 Z= 0.325 Chirality : 0.042 0.178 6740 Planarity : 0.005 0.051 7180 Dihedral : 3.977 16.669 5700 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.12), residues: 5260 helix: 2.37 (0.08), residues: 4180 sheet: None (None), residues: 0 loop : -2.35 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 153 TYR 0.018 0.002 TYR R 51 PHE 0.024 0.002 PHE K 160 TRP 0.015 0.001 TRP N 272 HIS 0.006 0.001 HIS M 224 Details of bonding type rmsd covalent geometry : bond 0.00439 (42580) covalent geometry : angle 0.61890 (57820) SS BOND : bond 0.00132 ( 40) SS BOND : angle 2.17373 ( 80) hydrogen bonds : bond 0.05574 ( 3191) hydrogen bonds : angle 3.99270 ( 9573) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 763 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.8279 (m) cc_final: 0.7933 (p) REVERT: B 187 MET cc_start: 0.9194 (mmp) cc_final: 0.8855 (mmp) REVERT: B 229 ARG cc_start: 0.7821 (tpp80) cc_final: 0.6965 (ttp-110) REVERT: B 234 GLN cc_start: 0.8322 (tm-30) cc_final: 0.8075 (tm-30) REVERT: C 144 MET cc_start: 0.5015 (ptt) cc_final: 0.4558 (ttp) REVERT: D 45 VAL cc_start: 0.8457 (m) cc_final: 0.7995 (p) REVERT: D 51 TYR cc_start: 0.9272 (t80) cc_final: 0.8933 (t80) REVERT: E 263 HIS cc_start: 0.7601 (m90) cc_final: 0.6912 (m90) REVERT: G 144 MET cc_start: 0.5570 (ptt) cc_final: 0.5347 (ptt) REVERT: H 51 TYR cc_start: 0.9268 (t80) cc_final: 0.8897 (t80) REVERT: H 270 GLN cc_start: 0.7919 (tp40) cc_final: 0.7637 (tm-30) REVERT: I 45 VAL cc_start: 0.8499 (m) cc_final: 0.8099 (p) REVERT: I 145 PHE cc_start: 0.7363 (m-80) cc_final: 0.6789 (m-80) REVERT: I 154 GLU cc_start: 0.7668 (pp20) cc_final: 0.7443 (pp20) REVERT: I 245 MET cc_start: 0.8412 (tpp) cc_final: 0.8146 (tpp) REVERT: J 187 MET cc_start: 0.9310 (mmp) cc_final: 0.9067 (mmp) REVERT: J 263 HIS cc_start: 0.7512 (m90) cc_final: 0.6603 (m90) REVERT: K 117 THR cc_start: 0.8986 (t) cc_final: 0.8685 (m) REVERT: K 229 ARG cc_start: 0.7596 (tpp80) cc_final: 0.7134 (ttp-110) REVERT: M 45 VAL cc_start: 0.8487 (m) cc_final: 0.8104 (p) REVERT: M 144 MET cc_start: 0.4695 (ptt) cc_final: 0.4062 (ptt) REVERT: N 234 GLN cc_start: 0.8057 (tt0) cc_final: 0.7558 (tm-30) REVERT: N 263 HIS cc_start: 0.7309 (m90) cc_final: 0.6585 (m90) REVERT: O 45 VAL cc_start: 0.8402 (m) cc_final: 0.7865 (p) REVERT: O 154 GLU cc_start: 0.7766 (pp20) cc_final: 0.7489 (pp20) REVERT: O 187 MET cc_start: 0.9212 (mmm) cc_final: 0.8986 (mmm) REVERT: O 208 LYS cc_start: 0.8357 (tppt) cc_final: 0.8119 (tppt) REVERT: O 245 MET cc_start: 0.8577 (tpp) cc_final: 0.8304 (tpp) REVERT: P 51 TYR cc_start: 0.9395 (t80) cc_final: 0.9157 (t80) REVERT: P 117 THR cc_start: 0.8979 (t) cc_final: 0.8686 (m) REVERT: P 144 MET cc_start: 0.5035 (ptt) cc_final: 0.4447 (ttp) REVERT: P 229 ARG cc_start: 0.7526 (tpp80) cc_final: 0.7047 (ttp-110) REVERT: R 45 VAL cc_start: 0.8537 (m) cc_final: 0.8086 (p) REVERT: S 155 GLU cc_start: 0.8096 (tt0) cc_final: 0.7794 (tp30) REVERT: S 229 ARG cc_start: 0.7721 (tpp80) cc_final: 0.7341 (ttm110) REVERT: S 234 GLN cc_start: 0.8182 (tt0) cc_final: 0.7667 (tm-30) REVERT: S 263 HIS cc_start: 0.7401 (m90) cc_final: 0.6823 (m90) REVERT: T 45 VAL cc_start: 0.8386 (m) cc_final: 0.7927 (p) REVERT: T 154 GLU cc_start: 0.7641 (pp20) cc_final: 0.7392 (pp20) outliers start: 0 outliers final: 0 residues processed: 763 average time/residue: 0.2531 time to fit residues: 320.7219 Evaluate side-chains 579 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 579 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 479 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 470 optimal weight: 1.9990 chunk 386 optimal weight: 2.9990 chunk 415 optimal weight: 7.9990 chunk 334 optimal weight: 0.8980 chunk 427 optimal weight: 10.0000 chunk 498 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.153508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.127740 restraints weight = 56710.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.129466 restraints weight = 41671.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.130913 restraints weight = 34530.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.131866 restraints weight = 30460.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.132118 restraints weight = 28152.954| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 42620 Z= 0.130 Angle : 0.562 8.153 57900 Z= 0.288 Chirality : 0.039 0.150 6740 Planarity : 0.004 0.050 7180 Dihedral : 3.921 16.622 5700 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 2.41 (0.12), residues: 5260 helix: 2.54 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.31 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 153 TYR 0.022 0.001 TYR I 51 PHE 0.020 0.001 PHE Q 232 TRP 0.006 0.001 TRP O 190 HIS 0.005 0.001 HIS M 224 Details of bonding type rmsd covalent geometry : bond 0.00273 (42580) covalent geometry : angle 0.55770 (57820) SS BOND : bond 0.00198 ( 40) SS BOND : angle 1.97400 ( 80) hydrogen bonds : bond 0.04910 ( 3191) hydrogen bonds : angle 3.79444 ( 9573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7156.01 seconds wall clock time: 124 minutes 44.70 seconds (7484.70 seconds total)