Starting phenix.real_space_refine on Sun Jul 5 08:14:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1u_36804/07_2026/8k1u_36804.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1u_36804/07_2026/8k1u_36804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1u_36804/07_2026/8k1u_36804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1u_36804/07_2026/8k1u_36804.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1u_36804/07_2026/8k1u_36804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1u_36804/07_2026/8k1u_36804.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.081 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 24 5.49 5 S 118 5.16 5 Na 4 4.78 5 C 17450 2.51 5 N 4422 2.21 5 O 4942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26964 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "B" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "D" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "E" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1698 Classifications: {'peptide': 216} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 210} Chain: "F" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "G" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "H" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1698 Classifications: {'peptide': 216} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 210} Chain: "I" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "J" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "K" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "L" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Time building chain proxies: 5.57, per 1000 atoms: 0.21 Number of scatterers: 26964 At special positions: 0 Unit cell: (173.47, 133.63, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 118 16.00 P 24 15.00 Na 4 11.00 O 4942 8.00 N 4422 7.00 C 17450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6364 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 20 sheets defined 57.6% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 15 through 28 removed outlier: 3.598A pdb=" N SER A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG A 69 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 211 through 220 removed outlier: 3.645A pdb=" N LYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 28 removed outlier: 3.599A pdb=" N SER B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG B 69 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 123 through 138 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.646A pdb=" N LYS B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 28 removed outlier: 3.598A pdb=" N SER C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 45 Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG C 69 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'C' and resid 106 through 116 Processing helix chain 'C' and resid 123 through 138 Processing helix chain 'C' and resid 211 through 220 removed outlier: 3.644A pdb=" N LYS C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 28 removed outlier: 3.599A pdb=" N SER D 20 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 45 Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG D 69 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 95 Processing helix chain 'D' and resid 106 through 116 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'D' and resid 211 through 220 removed outlier: 3.645A pdb=" N LYS D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 28 removed outlier: 3.598A pdb=" N SER E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 45 Processing helix chain 'E' and resid 59 through 65 Processing helix chain 'E' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG E 69 " --> pdb=" O LEU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 95 Processing helix chain 'E' and resid 106 through 116 Processing helix chain 'E' and resid 123 through 138 Processing helix chain 'E' and resid 211 through 220 removed outlier: 3.645A pdb=" N LYS E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 28 removed outlier: 3.598A pdb=" N SER F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 45 Processing helix chain 'F' and resid 59 through 65 Processing helix chain 'F' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG F 69 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 95 Processing helix chain 'F' and resid 106 through 116 Processing helix chain 'F' and resid 123 through 138 Processing helix chain 'F' and resid 211 through 220 removed outlier: 3.645A pdb=" N LYS F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 28 removed outlier: 3.597A pdb=" N SER G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 45 Processing helix chain 'G' and resid 59 through 65 Processing helix chain 'G' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG G 69 " --> pdb=" O LEU G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 95 Processing helix chain 'G' and resid 106 through 116 Processing helix chain 'G' and resid 123 through 138 Processing helix chain 'G' and resid 211 through 220 removed outlier: 3.644A pdb=" N LYS G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 28 removed outlier: 3.598A pdb=" N SER H 20 " --> pdb=" O ARG H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 45 Processing helix chain 'H' and resid 59 through 65 Processing helix chain 'H' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG H 69 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 95 Processing helix chain 'H' and resid 106 through 116 Processing helix chain 'H' and resid 123 through 138 Processing helix chain 'H' and resid 211 through 220 removed outlier: 3.646A pdb=" N LYS H 215 " --> pdb=" O LYS H 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 37 removed outlier: 3.750A pdb=" N ILE I 28 " --> pdb=" O PHE I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 59 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 73 through 90 Processing helix chain 'I' and resid 90 through 103 removed outlier: 4.066A pdb=" N PHE I 94 " --> pdb=" O GLY I 90 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 removed outlier: 3.562A pdb=" N VAL I 114 " --> pdb=" O GLU I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 157 removed outlier: 3.553A pdb=" N VAL I 130 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE I 150 " --> pdb=" O LEU I 146 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG I 151 " --> pdb=" O ILE I 147 " (cutoff:3.500A) Proline residue: I 154 - end of helix Processing helix chain 'I' and resid 158 through 174 removed outlier: 3.531A pdb=" N LEU I 162 " --> pdb=" O TRP I 158 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 207 Processing helix chain 'I' and resid 208 through 218 Processing helix chain 'I' and resid 220 through 224 Processing helix chain 'I' and resid 225 through 250 Processing helix chain 'I' and resid 261 through 275 Processing helix chain 'I' and resid 285 through 289 removed outlier: 3.540A pdb=" N MET I 289 " --> pdb=" O PHE I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 303 removed outlier: 3.518A pdb=" N ILE I 303 " --> pdb=" O LEU I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 315 through 331 Processing helix chain 'I' and resid 344 through 373 Processing helix chain 'I' and resid 376 through 389 Processing helix chain 'I' and resid 397 through 401 Processing helix chain 'I' and resid 402 through 419 Processing helix chain 'I' and resid 419 through 428 removed outlier: 4.163A pdb=" N PHE I 427 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 37 removed outlier: 3.749A pdb=" N ILE J 28 " --> pdb=" O PHE J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 59 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 73 through 90 Processing helix chain 'J' and resid 90 through 103 removed outlier: 4.066A pdb=" N PHE J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 118 removed outlier: 3.563A pdb=" N VAL J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 157 removed outlier: 3.553A pdb=" N VAL J 130 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE J 150 " --> pdb=" O LEU J 146 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG J 151 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Proline residue: J 154 - end of helix Processing helix chain 'J' and resid 158 through 174 removed outlier: 3.532A pdb=" N LEU J 162 " --> pdb=" O TRP J 158 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 207 Processing helix chain 'J' and resid 208 through 218 Processing helix chain 'J' and resid 220 through 224 Processing helix chain 'J' and resid 225 through 250 Processing helix chain 'J' and resid 261 through 275 Processing helix chain 'J' and resid 285 through 289 removed outlier: 3.539A pdb=" N MET J 289 " --> pdb=" O PHE J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 303 removed outlier: 3.518A pdb=" N ILE J 303 " --> pdb=" O LEU J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 331 Processing helix chain 'J' and resid 344 through 373 Processing helix chain 'J' and resid 376 through 389 Processing helix chain 'J' and resid 397 through 401 Processing helix chain 'J' and resid 402 through 419 Processing helix chain 'J' and resid 419 through 428 removed outlier: 4.163A pdb=" N PHE J 427 " --> pdb=" O PHE J 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 37 removed outlier: 3.749A pdb=" N ILE K 28 " --> pdb=" O PHE K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 59 Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 73 through 90 Processing helix chain 'K' and resid 90 through 103 removed outlier: 4.066A pdb=" N PHE K 94 " --> pdb=" O GLY K 90 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU K 97 " --> pdb=" O THR K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 removed outlier: 3.563A pdb=" N VAL K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 157 removed outlier: 3.553A pdb=" N VAL K 130 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE K 150 " --> pdb=" O LEU K 146 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG K 151 " --> pdb=" O ILE K 147 " (cutoff:3.500A) Proline residue: K 154 - end of helix Processing helix chain 'K' and resid 158 through 174 removed outlier: 3.532A pdb=" N LEU K 162 " --> pdb=" O TRP K 158 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 207 Processing helix chain 'K' and resid 208 through 218 Processing helix chain 'K' and resid 220 through 224 Processing helix chain 'K' and resid 225 through 250 Processing helix chain 'K' and resid 261 through 275 Processing helix chain 'K' and resid 285 through 289 removed outlier: 3.539A pdb=" N MET K 289 " --> pdb=" O PHE K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 303 removed outlier: 3.519A pdb=" N ILE K 303 " --> pdb=" O LEU K 299 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 331 Processing helix chain 'K' and resid 344 through 373 Processing helix chain 'K' and resid 376 through 389 Processing helix chain 'K' and resid 397 through 401 Processing helix chain 'K' and resid 402 through 419 Processing helix chain 'K' and resid 419 through 428 removed outlier: 4.163A pdb=" N PHE K 427 " --> pdb=" O PHE K 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 37 removed outlier: 3.749A pdb=" N ILE L 28 " --> pdb=" O PHE L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 59 Processing helix chain 'L' and resid 67 through 72 Processing helix chain 'L' and resid 73 through 90 Processing helix chain 'L' and resid 90 through 103 removed outlier: 4.066A pdb=" N PHE L 94 " --> pdb=" O GLY L 90 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 118 removed outlier: 3.562A pdb=" N VAL L 114 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 157 removed outlier: 3.553A pdb=" N VAL L 130 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE L 150 " --> pdb=" O LEU L 146 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG L 151 " --> pdb=" O ILE L 147 " (cutoff:3.500A) Proline residue: L 154 - end of helix Processing helix chain 'L' and resid 158 through 174 removed outlier: 3.532A pdb=" N LEU L 162 " --> pdb=" O TRP L 158 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 207 Processing helix chain 'L' and resid 208 through 218 Processing helix chain 'L' and resid 220 through 224 Processing helix chain 'L' and resid 225 through 250 Processing helix chain 'L' and resid 261 through 275 Processing helix chain 'L' and resid 285 through 289 removed outlier: 3.540A pdb=" N MET L 289 " --> pdb=" O PHE L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 290 through 303 removed outlier: 3.519A pdb=" N ILE L 303 " --> pdb=" O LEU L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 331 Processing helix chain 'L' and resid 344 through 373 Processing helix chain 'L' and resid 376 through 389 Processing helix chain 'L' and resid 397 through 401 Processing helix chain 'L' and resid 402 through 419 Processing helix chain 'L' and resid 419 through 428 removed outlier: 4.162A pdb=" N PHE L 427 " --> pdb=" O PHE L 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.600A pdb=" N TYR A 73 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 100 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 122 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 102 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 141 through 146 removed outlier: 6.260A pdb=" N VAL A 141 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU A 157 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A 143 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE A 183 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 206 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.599A pdb=" N TYR B 73 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 100 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE B 122 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 102 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 141 through 146 removed outlier: 6.260A pdb=" N VAL B 141 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU B 157 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN B 143 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE B 183 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 206 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.599A pdb=" N TYR C 73 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE C 100 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE C 122 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL C 102 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 141 through 146 removed outlier: 6.261A pdb=" N VAL C 141 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU C 157 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN C 143 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS C 204 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE C 183 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL C 206 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.599A pdb=" N TYR D 73 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE D 100 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE D 122 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL D 102 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 141 through 146 removed outlier: 6.260A pdb=" N VAL D 141 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU D 157 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN D 143 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS D 204 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE D 183 " --> pdb=" O CYS D 204 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL D 206 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 51 through 54 removed outlier: 3.600A pdb=" N TYR E 73 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE E 100 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE E 122 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL E 102 " --> pdb=" O ILE E 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 141 through 146 removed outlier: 6.260A pdb=" N VAL E 141 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU E 157 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN E 143 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS E 204 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE E 183 " --> pdb=" O CYS E 204 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL E 206 " --> pdb=" O LEU E 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.599A pdb=" N TYR F 73 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE F 100 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE F 122 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL F 102 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 141 through 146 removed outlier: 6.260A pdb=" N VAL F 141 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU F 157 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN F 143 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N CYS F 204 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE F 183 " --> pdb=" O CYS F 204 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL F 206 " --> pdb=" O LEU F 181 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.599A pdb=" N TYR G 73 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE G 100 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE G 122 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL G 102 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 141 through 146 removed outlier: 6.260A pdb=" N VAL G 141 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU G 157 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN G 143 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE G 183 " --> pdb=" O CYS G 204 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL G 206 " --> pdb=" O LEU G 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 51 through 54 removed outlier: 3.599A pdb=" N TYR H 73 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE H 100 " --> pdb=" O ARG H 120 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE H 122 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL H 102 " --> pdb=" O ILE H 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 141 through 146 removed outlier: 6.260A pdb=" N VAL H 141 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU H 157 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN H 143 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE H 183 " --> pdb=" O CYS H 204 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL H 206 " --> pdb=" O LEU H 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 336 through 338 removed outlier: 4.659A pdb=" N THR I 336 " --> pdb=" O ILE I 343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 336 through 338 removed outlier: 4.659A pdb=" N THR J 336 " --> pdb=" O ILE J 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 336 through 338 removed outlier: 4.659A pdb=" N THR K 336 " --> pdb=" O ILE K 343 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 336 through 338 removed outlier: 4.659A pdb=" N THR L 336 " --> pdb=" O ILE L 343 " (cutoff:3.500A) 1588 hydrogen bonds defined for protein. 4572 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: 4.48 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4874 1.33 - 1.45: 6501 1.45 - 1.57: 15853 1.57 - 1.69: 40 1.69 - 1.81: 200 Bond restraints: 27468 Sorted by residual: bond pdb=" CA VAL I 66 " pdb=" CB VAL I 66 " ideal model delta sigma weight residual 1.545 1.495 0.050 1.51e-02 4.39e+03 1.10e+01 bond pdb=" CA VAL L 66 " pdb=" CB VAL L 66 " ideal model delta sigma weight residual 1.545 1.496 0.049 1.51e-02 4.39e+03 1.07e+01 bond pdb=" CA VAL K 66 " pdb=" CB VAL K 66 " ideal model delta sigma weight residual 1.544 1.499 0.045 1.39e-02 5.18e+03 1.04e+01 bond pdb=" CA VAL K 65 " pdb=" CB VAL K 65 " ideal model delta sigma weight residual 1.540 1.498 0.041 1.37e-02 5.33e+03 8.99e+00 bond pdb=" C HIS H 185 " pdb=" N HIS H 186 " ideal model delta sigma weight residual 1.333 1.292 0.040 1.42e-02 4.96e+03 8.13e+00 ... (remaining 27463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 36809 1.68 - 3.37: 372 3.37 - 5.05: 45 5.05 - 6.74: 37 6.74 - 8.42: 17 Bond angle restraints: 37280 Sorted by residual: angle pdb=" O VAL J 65 " pdb=" C VAL J 65 " pdb=" N VAL J 66 " ideal model delta sigma weight residual 121.83 127.14 -5.31 1.03e+00 9.43e-01 2.66e+01 angle pdb=" CA VAL J 65 " pdb=" C VAL J 65 " pdb=" N VAL J 66 " ideal model delta sigma weight residual 117.28 111.87 5.41 1.16e+00 7.43e-01 2.17e+01 angle pdb=" N VAL K 65 " pdb=" CA VAL K 65 " pdb=" C VAL K 65 " ideal model delta sigma weight residual 111.00 106.05 4.95 1.09e+00 8.42e-01 2.06e+01 angle pdb=" C VAL K 66 " pdb=" CA VAL K 66 " pdb=" CB VAL K 66 " ideal model delta sigma weight residual 110.95 103.70 7.25 1.61e+00 3.86e-01 2.03e+01 angle pdb=" N HIS G 185 " pdb=" CA HIS G 185 " pdb=" C HIS G 185 " ideal model delta sigma weight residual 108.58 116.01 -7.43 1.82e+00 3.02e-01 1.67e+01 ... (remaining 37275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 15705 17.90 - 35.80: 551 35.80 - 53.70: 104 53.70 - 71.60: 52 71.60 - 89.50: 16 Dihedral angle restraints: 16428 sinusoidal: 6538 harmonic: 9890 Sorted by residual: dihedral pdb=" CA GLU A 201 " pdb=" C GLU A 201 " pdb=" N GLN A 202 " pdb=" CA GLN A 202 " ideal model delta harmonic sigma weight residual 180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLU D 201 " pdb=" C GLU D 201 " pdb=" N GLN D 202 " pdb=" CA GLN D 202 " ideal model delta harmonic sigma weight residual 180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLU F 201 " pdb=" C GLU F 201 " pdb=" N GLN F 202 " pdb=" CA GLN F 202 " ideal model delta harmonic sigma weight residual -180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 16425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3738 0.055 - 0.110: 650 0.110 - 0.164: 89 0.164 - 0.219: 6 0.219 - 0.274: 3 Chirality restraints: 4486 Sorted by residual: chirality pdb=" CA VAL K 66 " pdb=" N VAL K 66 " pdb=" C VAL K 66 " pdb=" CB VAL K 66 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA VAL J 66 " pdb=" N VAL J 66 " pdb=" C VAL J 66 " pdb=" CB VAL J 66 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA VAL K 65 " pdb=" N VAL K 65 " pdb=" C VAL K 65 " pdb=" CB VAL K 65 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 4483 not shown) Planarity restraints: 4578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA K 64 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C ALA K 64 " 0.028 2.00e-02 2.50e+03 pdb=" O ALA K 64 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL K 65 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L 15 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO L 16 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 16 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 16 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 15 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO J 16 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO J 16 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 16 " -0.023 5.00e-02 4.00e+02 ... (remaining 4575 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 9165 2.86 - 3.43: 28700 3.43 - 4.00: 51582 4.00 - 4.57: 72145 4.57 - 5.14: 106384 Nonbonded interactions: 267976 Sorted by model distance: nonbonded pdb=" OH TYR D 108 " pdb=" OE1 GLU E 60 " model vdw 2.294 3.040 nonbonded pdb=" O ILE J 418 " pdb=" OG1 THR J 422 " model vdw 2.301 3.040 nonbonded pdb=" O ILE I 418 " pdb=" OG1 THR I 422 " model vdw 2.301 3.040 nonbonded pdb=" O ILE K 418 " pdb=" OG1 THR K 422 " model vdw 2.301 3.040 nonbonded pdb=" O ILE L 418 " pdb=" OG1 THR L 422 " model vdw 2.301 3.040 ... (remaining 267971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 221) selection = (chain 'B' and resid 7 through 221) selection = (chain 'C' and resid 7 through 221) selection = (chain 'D' and resid 7 through 221) selection = (chain 'E' and resid 7 through 221) selection = (chain 'F' and resid 7 through 221) selection = (chain 'G' and resid 7 through 221) selection = (chain 'H' and resid 7 through 221) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.330 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.180 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.002 0.050 27468 Z= 0.124 Angle : 0.503 8.419 37280 Z= 0.276 Chirality : 0.042 0.274 4486 Planarity : 0.003 0.040 4578 Dihedral : 10.679 89.502 10064 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.51 % Allowed : 3.12 % Favored : 95.37 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: -1.57 (0.12), residues: 3422 helix: -1.28 (0.09), residues: 1836 sheet: 0.83 (0.27), residues: 400 loop : -1.03 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 220 TYR 0.005 0.001 TYR C 107 PHE 0.021 0.001 PHE L 202 TRP 0.002 0.001 TRP C 101 HIS 0.004 0.001 HIS E 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.12 (27468) covalent geometry : angle 0.50259 / 0.28 (37280) hydrogen bonds : bond 0.26662 / 18.11 ( 1588) hydrogen bonds : angle 7.47877 / 5.24 ( 4572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 843 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.7279 (mmm) cc_final: 0.7002 (mmp) REVERT: I 390 THR cc_start: 0.8141 (p) cc_final: 0.7890 (p) REVERT: L 390 THR cc_start: 0.8107 (p) cc_final: 0.7834 (p) outliers start: 44 outliers final: 6 residues processed: 869 average time/residue: 0.5574 time to fit residues: 569.7869 Evaluate side-chains 503 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 497 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain L residue 352 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 134 GLN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN G 134 GLN I 120 GLN I 253 ASN I 282 ASN J 155 GLN J 195 ASN J 253 ASN J 434 ASN K 18 GLN K 119 ASN K 120 GLN K 155 GLN K 253 ASN K 434 ASN L 85 GLN L 120 GLN L 253 ASN L 282 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.178453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.137671 restraints weight = 29814.646| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.57 r_work: 0.3290 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27468 Z= 0.178 Angle : 0.577 7.945 37280 Z= 0.307 Chirality : 0.045 0.245 4486 Planarity : 0.004 0.038 4578 Dihedral : 9.584 88.223 3915 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.23 % Allowed : 12.53 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.13), residues: 3422 helix: 0.88 (0.11), residues: 1912 sheet: 0.32 (0.26), residues: 404 loop : -0.80 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 340 TYR 0.018 0.001 TYR I 270 PHE 0.045 0.002 PHE J 202 TRP 0.003 0.001 TRP A 101 HIS 0.012 0.001 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (27468) covalent geometry : angle 0.57685 / 0.31 (37280) hydrogen bonds : bond 0.05084 / 3.45 ( 1588) hydrogen bonds : angle 4.69108 / 3.26 ( 4572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 514 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8743 (t) cc_final: 0.8452 (m) REVERT: A 95 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7593 (mt) REVERT: A 128 MET cc_start: 0.8744 (mmm) cc_final: 0.8142 (mmp) REVERT: B 155 GLU cc_start: 0.6921 (tt0) cc_final: 0.6273 (mt-10) REVERT: B 183 ILE cc_start: 0.7666 (mt) cc_final: 0.7137 (mp) REVERT: B 213 ASP cc_start: 0.7016 (m-30) cc_final: 0.6683 (m-30) REVERT: C 147 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7224 (mp) REVERT: C 155 GLU cc_start: 0.6912 (tt0) cc_final: 0.6246 (mt-10) REVERT: C 183 ILE cc_start: 0.7806 (mt) cc_final: 0.7294 (mp) REVERT: C 213 ASP cc_start: 0.6983 (m-30) cc_final: 0.6712 (m-30) REVERT: D 27 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7727 (mtm110) REVERT: D 72 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8269 (tt0) REVERT: D 181 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.5827 (mp) REVERT: E 86 THR cc_start: 0.8921 (t) cc_final: 0.8539 (m) REVERT: E 95 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7745 (mt) REVERT: E 222 MET cc_start: 0.6352 (ttm) cc_final: 0.6119 (ttp) REVERT: F 213 ASP cc_start: 0.7786 (m-30) cc_final: 0.7339 (p0) REVERT: G 111 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8283 (mtpt) REVERT: G 134 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: G 213 ASP cc_start: 0.7656 (m-30) cc_final: 0.7367 (p0) REVERT: H 86 THR cc_start: 0.8861 (t) cc_final: 0.8502 (m) REVERT: I 36 MET cc_start: 0.7613 (mmm) cc_final: 0.7359 (mmm) REVERT: I 97 LEU cc_start: 0.7652 (mt) cc_final: 0.7326 (mt) REVERT: I 106 ILE cc_start: 0.6997 (mm) cc_final: 0.6595 (tp) REVERT: I 217 LYS cc_start: 0.7578 (ptmt) cc_final: 0.7047 (mmtt) REVERT: I 222 LYS cc_start: 0.8541 (mmmt) cc_final: 0.7700 (ptmm) REVERT: I 400 GLU cc_start: 0.7944 (mp0) cc_final: 0.7533 (mp0) REVERT: J 91 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7305 (t80) REVERT: J 92 MET cc_start: 0.7801 (tpt) cc_final: 0.7536 (mmm) REVERT: J 104 LYS cc_start: 0.5516 (tttt) cc_final: 0.4936 (tttm) REVERT: K 91 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7212 (t80) REVERT: K 220 ARG cc_start: 0.7003 (mmt180) cc_final: 0.6611 (mmp80) REVERT: K 334 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7949 (pttp) REVERT: L 36 MET cc_start: 0.7709 (mmm) cc_final: 0.7478 (mmm) REVERT: L 86 ILE cc_start: 0.8271 (mp) cc_final: 0.7990 (mp) REVERT: L 97 LEU cc_start: 0.7665 (mt) cc_final: 0.7403 (mt) REVERT: L 216 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7450 (mmt) REVERT: L 217 LYS cc_start: 0.7599 (ptmt) cc_final: 0.7063 (mmtt) REVERT: L 222 LYS cc_start: 0.8621 (ptmm) cc_final: 0.8020 (mmmt) REVERT: L 344 LYS cc_start: 0.7551 (tttt) cc_final: 0.7324 (ptpp) REVERT: L 400 GLU cc_start: 0.7895 (mp0) cc_final: 0.7561 (mp0) outliers start: 94 outliers final: 29 residues processed: 581 average time/residue: 0.5187 time to fit residues: 356.0840 Evaluate side-chains 503 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 464 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 374 GLN Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 47 optimal weight: 0.4980 chunk 146 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 234 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN A 210 HIS B 105 GLN B 134 GLN C 105 GLN C 134 GLN D 38 ASN D 210 HIS G 38 ASN I 85 GLN I 239 ASN I 253 ASN J 119 ASN J 155 GLN J 434 ASN K 119 ASN K 434 ASN L 85 GLN L 253 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.175281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.134307 restraints weight = 29883.119| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.40 r_work: 0.3248 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 27468 Z= 0.198 Angle : 0.579 7.830 37280 Z= 0.306 Chirality : 0.045 0.253 4486 Planarity : 0.004 0.042 4578 Dihedral : 9.364 86.524 3912 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.98 % Allowed : 13.52 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.14), residues: 3422 helix: 1.42 (0.11), residues: 1880 sheet: 0.07 (0.26), residues: 404 loop : -0.96 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 436 TYR 0.013 0.001 TYR L 270 PHE 0.041 0.002 PHE J 202 TRP 0.005 0.001 TRP L 47 HIS 0.009 0.001 HIS F 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (27468) covalent geometry : angle 0.57939 / 0.31 (37280) hydrogen bonds : bond 0.04859 / 3.28 ( 1588) hydrogen bonds : angle 4.53008 / 3.15 ( 4572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 479 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8817 (mmm) cc_final: 0.8249 (mmp) REVERT: A 189 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7090 (tp) REVERT: B 155 GLU cc_start: 0.6798 (tt0) cc_final: 0.6188 (mt-10) REVERT: B 183 ILE cc_start: 0.7796 (mt) cc_final: 0.7308 (mp) REVERT: B 213 ASP cc_start: 0.6897 (m-30) cc_final: 0.6560 (m-30) REVERT: C 147 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7123 (mp) REVERT: C 155 GLU cc_start: 0.6810 (tt0) cc_final: 0.6332 (mt-10) REVERT: C 183 ILE cc_start: 0.7947 (mt) cc_final: 0.7470 (mp) REVERT: D 27 ARG cc_start: 0.7994 (mtm110) cc_final: 0.7773 (mtm110) REVERT: D 72 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8318 (tm-30) REVERT: D 85 SER cc_start: 0.8710 (t) cc_final: 0.8430 (m) REVERT: D 181 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.5846 (mp) REVERT: E 39 GLU cc_start: 0.7933 (mp0) cc_final: 0.7677 (mp0) REVERT: E 86 THR cc_start: 0.8937 (t) cc_final: 0.8521 (m) REVERT: E 213 ASP cc_start: 0.6684 (OUTLIER) cc_final: 0.6428 (t70) REVERT: F 93 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8014 (tmtt) REVERT: F 128 MET cc_start: 0.8703 (mmm) cc_final: 0.8379 (mmm) REVERT: F 138 ASP cc_start: 0.7669 (t0) cc_final: 0.7328 (m-30) REVERT: G 93 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8021 (tmtt) REVERT: G 111 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8313 (mtpt) REVERT: G 128 MET cc_start: 0.8725 (mmm) cc_final: 0.8385 (mmm) REVERT: G 134 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7677 (mp10) REVERT: G 138 ASP cc_start: 0.7651 (t0) cc_final: 0.7203 (m-30) REVERT: H 39 GLU cc_start: 0.7910 (mp0) cc_final: 0.7641 (mp0) REVERT: H 86 THR cc_start: 0.8908 (t) cc_final: 0.8511 (m) REVERT: H 139 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7135 (pm20) REVERT: H 213 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6535 (t70) REVERT: I 97 LEU cc_start: 0.7717 (mt) cc_final: 0.7357 (mt) REVERT: I 106 ILE cc_start: 0.7093 (mm) cc_final: 0.6783 (tp) REVERT: I 110 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7195 (mt-10) REVERT: I 217 LYS cc_start: 0.7562 (ptmt) cc_final: 0.7049 (mmtt) REVERT: I 222 LYS cc_start: 0.8483 (mmmt) cc_final: 0.7791 (ptpt) REVERT: J 91 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7306 (t80) REVERT: J 142 LEU cc_start: 0.7764 (tp) cc_final: 0.7540 (tp) REVERT: J 220 ARG cc_start: 0.7106 (mmt180) cc_final: 0.6745 (mmp80) REVERT: J 344 LYS cc_start: 0.7960 (tppt) cc_final: 0.7651 (tppt) REVERT: J 350 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8838 (tttm) REVERT: J 373 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6686 (mt-10) REVERT: K 91 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7181 (t80) REVERT: K 220 ARG cc_start: 0.7131 (mmt180) cc_final: 0.6768 (mmp80) REVERT: K 250 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8179 (mm-30) REVERT: K 289 MET cc_start: 0.8021 (mtm) cc_final: 0.7792 (mtt) REVERT: K 334 LYS cc_start: 0.8587 (mmtt) cc_final: 0.7994 (pttp) REVERT: L 97 LEU cc_start: 0.7781 (mt) cc_final: 0.7442 (mt) REVERT: L 110 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: L 155 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7546 (tt0) REVERT: L 217 LYS cc_start: 0.7589 (ptmt) cc_final: 0.7098 (mmtt) REVERT: L 400 GLU cc_start: 0.8041 (mp0) cc_final: 0.7743 (mp0) outliers start: 116 outliers final: 44 residues processed: 556 average time/residue: 0.5295 time to fit residues: 345.6224 Evaluate side-chains 514 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 452 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 350 LYS Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 83 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 310 optimal weight: 9.9990 chunk 326 optimal weight: 4.9990 chunk 311 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 202 optimal weight: 0.7980 chunk 305 optimal weight: 9.9990 chunk 247 optimal weight: 2.9990 chunk 59 optimal weight: 0.0470 chunk 232 optimal weight: 2.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN B 134 GLN C 134 GLN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN I 85 GLN I 253 ASN J 119 ASN J 155 GLN J 434 ASN K 119 ASN K 434 ASN L 253 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.178187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.137548 restraints weight = 29756.998| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.36 r_work: 0.3309 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 27468 Z= 0.122 Angle : 0.498 7.512 37280 Z= 0.265 Chirality : 0.042 0.225 4486 Planarity : 0.003 0.039 4578 Dihedral : 8.901 86.424 3910 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.16 % Allowed : 15.41 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 1.10 (0.14), residues: 3422 helix: 1.82 (0.12), residues: 1892 sheet: 0.02 (0.26), residues: 416 loop : -0.88 (0.17), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 436 TYR 0.011 0.001 TYR B 107 PHE 0.035 0.001 PHE L 202 TRP 0.004 0.001 TRP L 47 HIS 0.007 0.001 HIS F 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (27468) covalent geometry : angle 0.49792 / 0.27 (37280) hydrogen bonds : bond 0.03744 / 2.53 ( 1588) hydrogen bonds : angle 4.22469 / 2.92 ( 4572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 482 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8053 (mm-30) REVERT: A 85 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.8258 (m) REVERT: A 128 MET cc_start: 0.8776 (mmm) cc_final: 0.8110 (mmp) REVERT: A 189 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6919 (tp) REVERT: B 134 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7671 (mp10) REVERT: B 155 GLU cc_start: 0.6717 (tt0) cc_final: 0.6156 (mt-10) REVERT: B 183 ILE cc_start: 0.7605 (mt) cc_final: 0.7091 (mp) REVERT: B 213 ASP cc_start: 0.6805 (m-30) cc_final: 0.6571 (m-30) REVERT: C 59 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7900 (mt-10) REVERT: C 134 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: C 147 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7142 (mp) REVERT: C 155 GLU cc_start: 0.6869 (tt0) cc_final: 0.6434 (mt-10) REVERT: C 183 ILE cc_start: 0.7831 (mt) cc_final: 0.7361 (mp) REVERT: D 85 SER cc_start: 0.8554 (t) cc_final: 0.8288 (m) REVERT: E 39 GLU cc_start: 0.7908 (mp0) cc_final: 0.7668 (mp0) REVERT: E 86 THR cc_start: 0.8743 (t) cc_final: 0.8529 (m) REVERT: E 139 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: E 213 ASP cc_start: 0.6815 (OUTLIER) cc_final: 0.6599 (t70) REVERT: F 128 MET cc_start: 0.8592 (mmm) cc_final: 0.8270 (mmm) REVERT: F 134 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7930 (mp10) REVERT: F 138 ASP cc_start: 0.7734 (t0) cc_final: 0.7385 (m-30) REVERT: G 111 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8266 (mtpt) REVERT: G 128 MET cc_start: 0.8610 (mmm) cc_final: 0.8320 (mmm) REVERT: G 134 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7976 (mp10) REVERT: G 138 ASP cc_start: 0.7640 (t0) cc_final: 0.7353 (m-30) REVERT: H 39 GLU cc_start: 0.7972 (mp0) cc_final: 0.7762 (mp0) REVERT: H 95 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7733 (mt) REVERT: H 139 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: H 213 ASP cc_start: 0.6774 (OUTLIER) cc_final: 0.6568 (t70) REVERT: I 36 MET cc_start: 0.7528 (mmm) cc_final: 0.7238 (mmt) REVERT: I 97 LEU cc_start: 0.7634 (mt) cc_final: 0.7309 (mt) REVERT: I 106 ILE cc_start: 0.7077 (mm) cc_final: 0.6645 (tp) REVERT: I 158 TRP cc_start: 0.7728 (m100) cc_final: 0.6976 (m-90) REVERT: I 217 LYS cc_start: 0.7445 (ptmt) cc_final: 0.6984 (mmtt) REVERT: I 222 LYS cc_start: 0.8452 (mmmt) cc_final: 0.7825 (ptpt) REVERT: J 91 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.7100 (t80) REVERT: J 92 MET cc_start: 0.7714 (tpt) cc_final: 0.7468 (mmm) REVERT: J 142 LEU cc_start: 0.7816 (tp) cc_final: 0.7606 (tp) REVERT: J 220 ARG cc_start: 0.7108 (mmt180) cc_final: 0.6763 (mmp80) REVERT: J 373 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6492 (mt-10) REVERT: K 220 ARG cc_start: 0.7146 (mmt180) cc_final: 0.6795 (mmp80) REVERT: K 334 LYS cc_start: 0.8579 (mmtt) cc_final: 0.7984 (pttp) REVERT: L 36 MET cc_start: 0.7620 (mmm) cc_final: 0.7338 (mmm) REVERT: L 97 LEU cc_start: 0.7728 (mt) cc_final: 0.7403 (mt) REVERT: L 155 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: L 217 LYS cc_start: 0.7488 (ptmt) cc_final: 0.7041 (mmtt) outliers start: 92 outliers final: 34 residues processed: 536 average time/residue: 0.5540 time to fit residues: 349.0277 Evaluate side-chains 499 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 448 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 142 optimal weight: 0.0980 chunk 291 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS B 134 GLN C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN I 85 GLN I 253 ASN J 119 ASN J 155 GLN J 434 ASN K 119 ASN K 434 ASN L 85 GLN L 253 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.174465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132727 restraints weight = 29713.666| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.41 r_work: 0.3238 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27468 Z= 0.183 Angle : 0.561 8.067 37280 Z= 0.295 Chirality : 0.044 0.268 4486 Planarity : 0.003 0.039 4578 Dihedral : 9.098 77.375 3910 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.81 % Allowed : 15.61 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.97 (0.14), residues: 3422 helix: 1.73 (0.12), residues: 1888 sheet: -0.08 (0.26), residues: 416 loop : -0.92 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 27 TYR 0.011 0.001 TYR F 73 PHE 0.037 0.002 PHE J 202 TRP 0.006 0.001 TRP L 47 HIS 0.005 0.001 HIS F 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (27468) covalent geometry : angle 0.56055 / 0.30 (37280) hydrogen bonds : bond 0.04367 / 2.95 ( 1588) hydrogen bonds : angle 4.36415 / 3.02 ( 4572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 455 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8020 (mm-30) REVERT: A 85 SER cc_start: 0.8626 (t) cc_final: 0.8300 (m) REVERT: A 128 MET cc_start: 0.8813 (mmm) cc_final: 0.8140 (mmp) REVERT: A 189 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7087 (tp) REVERT: B 155 GLU cc_start: 0.6750 (tt0) cc_final: 0.6117 (mt-10) REVERT: B 183 ILE cc_start: 0.7670 (mt) cc_final: 0.7173 (mp) REVERT: C 147 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6890 (mp) REVERT: C 155 GLU cc_start: 0.6771 (tt0) cc_final: 0.6264 (mt-10) REVERT: C 183 ILE cc_start: 0.7771 (mt) cc_final: 0.7272 (mp) REVERT: D 85 SER cc_start: 0.8688 (t) cc_final: 0.8339 (m) REVERT: E 39 GLU cc_start: 0.7844 (mp0) cc_final: 0.7522 (mp0) REVERT: E 59 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7886 (mt-10) REVERT: E 86 THR cc_start: 0.8837 (t) cc_final: 0.8467 (m) REVERT: E 95 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7681 (mt) REVERT: E 139 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7020 (pm20) REVERT: E 213 ASP cc_start: 0.6743 (OUTLIER) cc_final: 0.6539 (t70) REVERT: F 128 MET cc_start: 0.8570 (mmm) cc_final: 0.8197 (mmm) REVERT: F 134 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7831 (mp10) REVERT: F 138 ASP cc_start: 0.7605 (t0) cc_final: 0.7216 (m-30) REVERT: G 93 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.7898 (tmtt) REVERT: G 111 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8100 (mtpt) REVERT: G 128 MET cc_start: 0.8564 (mmm) cc_final: 0.8181 (mmm) REVERT: G 134 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: G 138 ASP cc_start: 0.7451 (t0) cc_final: 0.7165 (m-30) REVERT: H 95 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7657 (mt) REVERT: H 139 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: H 213 ASP cc_start: 0.6663 (OUTLIER) cc_final: 0.6463 (t70) REVERT: I 97 LEU cc_start: 0.7532 (mt) cc_final: 0.7241 (mt) REVERT: I 158 TRP cc_start: 0.7620 (m100) cc_final: 0.6842 (m-90) REVERT: I 217 LYS cc_start: 0.7412 (ptmt) cc_final: 0.6927 (mmtt) REVERT: I 222 LYS cc_start: 0.8480 (mmmt) cc_final: 0.7784 (ptpt) REVERT: J 91 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.7106 (t80) REVERT: J 109 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8152 (mmmm) REVERT: J 220 ARG cc_start: 0.6942 (mmt180) cc_final: 0.6581 (mmp80) REVERT: J 248 ILE cc_start: 0.9142 (mm) cc_final: 0.8930 (mt) REVERT: J 350 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8650 (tttm) REVERT: J 373 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6351 (mt-10) REVERT: K 71 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: K 109 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8100 (mmmm) REVERT: K 220 ARG cc_start: 0.7018 (mmt180) cc_final: 0.6505 (mmp80) REVERT: K 334 LYS cc_start: 0.8488 (mmtt) cc_final: 0.7848 (pttp) REVERT: K 373 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6601 (mt-10) REVERT: L 36 MET cc_start: 0.7669 (mmm) cc_final: 0.7324 (mmm) REVERT: L 97 LEU cc_start: 0.7666 (mt) cc_final: 0.7301 (mt) REVERT: L 155 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: L 217 LYS cc_start: 0.7418 (ptmt) cc_final: 0.6952 (mmtt) REVERT: L 222 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8240 (ptpt) REVERT: L 400 GLU cc_start: 0.8257 (mp0) cc_final: 0.8012 (mp0) outliers start: 111 outliers final: 48 residues processed: 531 average time/residue: 0.5898 time to fit residues: 369.0717 Evaluate side-chains 511 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 442 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 350 LYS Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 228 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 chunk 143 optimal weight: 0.0370 chunk 112 optimal weight: 4.9990 chunk 336 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS B 134 GLN C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN I 253 ASN J 119 ASN J 434 ASN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 ASN K 434 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.175632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.134323 restraints weight = 29743.220| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.50 r_work: 0.3265 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 27468 Z= 0.144 Angle : 0.524 7.595 37280 Z= 0.277 Chirality : 0.043 0.253 4486 Planarity : 0.003 0.039 4578 Dihedral : 8.912 83.433 3910 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.91 % Allowed : 16.03 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 1.06 (0.14), residues: 3422 helix: 1.82 (0.12), residues: 1900 sheet: -0.14 (0.25), residues: 416 loop : -0.93 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 27 TYR 0.010 0.001 TYR E 108 PHE 0.034 0.001 PHE J 202 TRP 0.008 0.001 TRP I 181 HIS 0.007 0.001 HIS F 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (27468) covalent geometry : angle 0.52380 / 0.28 (37280) hydrogen bonds : bond 0.03937 / 2.66 ( 1588) hydrogen bonds : angle 4.24791 / 2.94 ( 4572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 454 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8343 (mt) REVERT: A 85 SER cc_start: 0.8554 (t) cc_final: 0.8233 (m) REVERT: A 128 MET cc_start: 0.8767 (mmm) cc_final: 0.8098 (mmp) REVERT: A 189 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.7058 (tp) REVERT: B 155 GLU cc_start: 0.6766 (tt0) cc_final: 0.6152 (mt-10) REVERT: B 183 ILE cc_start: 0.7657 (mt) cc_final: 0.7159 (mp) REVERT: C 59 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: C 147 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6831 (mp) REVERT: C 155 GLU cc_start: 0.6765 (tt0) cc_final: 0.6264 (mt-10) REVERT: C 183 ILE cc_start: 0.7723 (mt) cc_final: 0.7213 (mp) REVERT: D 128 MET cc_start: 0.8775 (mmm) cc_final: 0.8545 (mmm) REVERT: E 39 GLU cc_start: 0.7825 (mp0) cc_final: 0.7507 (mp0) REVERT: E 86 THR cc_start: 0.8832 (t) cc_final: 0.8453 (m) REVERT: E 95 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7640 (mt) REVERT: E 115 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8195 (mttp) REVERT: E 139 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7024 (pm20) REVERT: E 213 ASP cc_start: 0.6754 (OUTLIER) cc_final: 0.6541 (t70) REVERT: F 128 MET cc_start: 0.8564 (mmm) cc_final: 0.8182 (mmm) REVERT: F 134 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7789 (mp10) REVERT: F 138 ASP cc_start: 0.7605 (t0) cc_final: 0.7210 (m-30) REVERT: G 111 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8089 (mtpt) REVERT: G 128 MET cc_start: 0.8571 (mmm) cc_final: 0.8166 (mmm) REVERT: G 138 ASP cc_start: 0.7465 (t0) cc_final: 0.7162 (m-30) REVERT: H 39 GLU cc_start: 0.7913 (mp0) cc_final: 0.7628 (mp0) REVERT: H 95 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7618 (mt) REVERT: H 139 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: H 213 ASP cc_start: 0.6720 (OUTLIER) cc_final: 0.6518 (t70) REVERT: I 97 LEU cc_start: 0.7476 (mt) cc_final: 0.7044 (mt) REVERT: I 158 TRP cc_start: 0.7612 (m100) cc_final: 0.6849 (m-90) REVERT: I 217 LYS cc_start: 0.7361 (ptmt) cc_final: 0.6882 (mmtt) REVERT: I 222 LYS cc_start: 0.8472 (mmmt) cc_final: 0.7780 (ptpt) REVERT: J 91 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7040 (t80) REVERT: J 109 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8086 (mmmm) REVERT: J 220 ARG cc_start: 0.6912 (mmt180) cc_final: 0.6554 (mmp80) REVERT: J 248 ILE cc_start: 0.9115 (mm) cc_final: 0.8912 (mt) REVERT: J 373 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6291 (mt-10) REVERT: K 71 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.6836 (tm-30) REVERT: K 104 LYS cc_start: 0.5649 (tttt) cc_final: 0.5428 (tttp) REVERT: K 109 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8041 (mmmm) REVERT: K 220 ARG cc_start: 0.6942 (mmt180) cc_final: 0.6424 (mmp80) REVERT: K 334 LYS cc_start: 0.8505 (mmtt) cc_final: 0.7840 (pttp) REVERT: K 373 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6431 (mt-10) REVERT: L 97 LEU cc_start: 0.7494 (mt) cc_final: 0.7127 (mt) REVERT: L 155 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: L 217 LYS cc_start: 0.7395 (ptmt) cc_final: 0.6923 (mmtt) REVERT: L 222 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8239 (ptpt) REVERT: L 400 GLU cc_start: 0.8277 (mp0) cc_final: 0.8050 (mp0) outliers start: 114 outliers final: 54 residues processed: 533 average time/residue: 0.5993 time to fit residues: 376.3692 Evaluate side-chains 513 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 439 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 95 optimal weight: 1.9990 chunk 249 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 201 optimal weight: 0.9990 chunk 283 optimal weight: 9.9990 chunk 336 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 300 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS B 105 GLN B 134 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN I 85 GLN I 253 ASN J 119 ASN J 434 ASN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 ASN K 434 ASN L 85 GLN L 253 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.174640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.133073 restraints weight = 29762.560| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.42 r_work: 0.3249 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 27468 Z= 0.168 Angle : 0.551 7.789 37280 Z= 0.290 Chirality : 0.044 0.258 4486 Planarity : 0.003 0.044 4578 Dihedral : 8.926 78.190 3910 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.81 % Allowed : 16.61 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.98 (0.14), residues: 3422 helix: 1.77 (0.12), residues: 1896 sheet: -0.17 (0.25), residues: 416 loop : -0.95 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 331 TYR 0.009 0.001 TYR H 45 PHE 0.035 0.002 PHE J 202 TRP 0.010 0.001 TRP I 181 HIS 0.006 0.001 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (27468) covalent geometry : angle 0.55114 / 0.29 (37280) hydrogen bonds : bond 0.04187 / 2.82 ( 1588) hydrogen bonds : angle 4.30142 / 2.98 ( 4572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 452 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8358 (mt) REVERT: A 85 SER cc_start: 0.8599 (t) cc_final: 0.8274 (m) REVERT: A 128 MET cc_start: 0.8792 (mmm) cc_final: 0.8121 (mmp) REVERT: A 189 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7134 (tp) REVERT: B 155 GLU cc_start: 0.6752 (tt0) cc_final: 0.6117 (mt-10) REVERT: B 169 ASP cc_start: 0.6920 (t0) cc_final: 0.6692 (m-30) REVERT: B 183 ILE cc_start: 0.7739 (mt) cc_final: 0.7256 (mp) REVERT: C 147 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6820 (mp) REVERT: C 155 GLU cc_start: 0.6800 (tt0) cc_final: 0.6291 (mt-10) REVERT: C 183 ILE cc_start: 0.7772 (mt) cc_final: 0.7257 (mp) REVERT: D 85 SER cc_start: 0.8673 (t) cc_final: 0.8323 (m) REVERT: E 39 GLU cc_start: 0.7855 (mp0) cc_final: 0.7538 (mp0) REVERT: E 59 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7954 (mt-10) REVERT: E 86 THR cc_start: 0.8877 (t) cc_final: 0.8392 (m) REVERT: E 95 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7658 (mt) REVERT: E 139 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7041 (pm20) REVERT: E 213 ASP cc_start: 0.6778 (OUTLIER) cc_final: 0.6575 (t70) REVERT: F 128 MET cc_start: 0.8562 (mmm) cc_final: 0.8180 (mmm) REVERT: F 134 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7843 (mp10) REVERT: F 138 ASP cc_start: 0.7647 (t0) cc_final: 0.7246 (m-30) REVERT: F 146 ASP cc_start: 0.7059 (m-30) cc_final: 0.6736 (p0) REVERT: G 111 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8107 (mtpt) REVERT: G 128 MET cc_start: 0.8572 (mmm) cc_final: 0.8183 (mmm) REVERT: G 134 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: G 138 ASP cc_start: 0.7439 (t0) cc_final: 0.7208 (m-30) REVERT: G 146 ASP cc_start: 0.7126 (m-30) cc_final: 0.6785 (p0) REVERT: H 59 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7768 (mt-10) REVERT: H 95 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7657 (mt) REVERT: H 139 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6971 (pm20) REVERT: I 71 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7225 (tp40) REVERT: I 97 LEU cc_start: 0.7570 (mt) cc_final: 0.7235 (mt) REVERT: I 142 LEU cc_start: 0.7049 (tp) cc_final: 0.6817 (mm) REVERT: I 158 TRP cc_start: 0.7630 (m100) cc_final: 0.6881 (m-90) REVERT: I 217 LYS cc_start: 0.7448 (ptmt) cc_final: 0.6932 (mmtt) REVERT: I 222 LYS cc_start: 0.8478 (mmmt) cc_final: 0.7794 (ptpt) REVERT: J 91 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7144 (t80) REVERT: J 109 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8091 (mmmm) REVERT: J 220 ARG cc_start: 0.6977 (mmt180) cc_final: 0.6482 (mmp80) REVERT: J 248 ILE cc_start: 0.9113 (mm) cc_final: 0.8895 (mt) REVERT: J 350 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8650 (tttm) REVERT: J 373 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6281 (mt-10) REVERT: K 71 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.6892 (tm-30) REVERT: K 91 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.6968 (t80) REVERT: K 109 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8092 (mmmm) REVERT: K 220 ARG cc_start: 0.7041 (mmt180) cc_final: 0.6550 (mmp80) REVERT: K 334 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7868 (pttp) REVERT: K 373 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6431 (mt-10) REVERT: L 97 LEU cc_start: 0.7490 (mt) cc_final: 0.7129 (mt) REVERT: L 155 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: L 217 LYS cc_start: 0.7434 (ptmt) cc_final: 0.6949 (mmtt) REVERT: L 222 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8267 (ptpt) REVERT: L 400 GLU cc_start: 0.8320 (mp0) cc_final: 0.8075 (mp0) outliers start: 111 outliers final: 61 residues processed: 529 average time/residue: 0.5517 time to fit residues: 343.4719 Evaluate side-chains 518 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 436 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 344 LYS Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 350 LYS Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 283 optimal weight: 10.0000 chunk 339 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 301 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 270 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS B 134 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS G 30 HIS G 134 GLN I 253 ASN J 434 ASN K 77 GLN K 434 ASN L 85 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.170151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128574 restraints weight = 29807.067| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.32 r_work: 0.3195 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 27468 Z= 0.341 Angle : 0.717 9.013 37280 Z= 0.372 Chirality : 0.051 0.335 4486 Planarity : 0.004 0.049 4578 Dihedral : 9.599 86.361 3910 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.36 % Allowed : 16.33 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.37 (0.14), residues: 3422 helix: 1.20 (0.11), residues: 1888 sheet: -0.17 (0.26), residues: 412 loop : -1.18 (0.16), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 436 TYR 0.020 0.002 TYR H 45 PHE 0.044 0.002 PHE J 202 TRP 0.012 0.002 TRP L 181 HIS 0.007 0.002 HIS L 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00835 / 0.34 (27468) covalent geometry : angle 0.71715 / 0.37 (37280) hydrogen bonds : bond 0.05601 / 3.77 ( 1588) hydrogen bonds : angle 4.72786 / 3.29 ( 4572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 415 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8347 (mt) REVERT: A 189 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7283 (tp) REVERT: B 155 GLU cc_start: 0.6943 (tt0) cc_final: 0.6186 (mt-10) REVERT: B 183 ILE cc_start: 0.8072 (mt) cc_final: 0.7557 (mp) REVERT: B 208 MET cc_start: 0.8317 (ttp) cc_final: 0.8110 (ttm) REVERT: C 59 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: C 155 GLU cc_start: 0.6982 (tt0) cc_final: 0.6385 (mt-10) REVERT: C 183 ILE cc_start: 0.8078 (mt) cc_final: 0.7561 (mp) REVERT: E 39 GLU cc_start: 0.8027 (mp0) cc_final: 0.7688 (mp0) REVERT: E 139 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7073 (pm20) REVERT: E 222 MET cc_start: 0.7186 (ttp) cc_final: 0.6878 (ptm) REVERT: F 134 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7995 (mp10) REVERT: F 138 ASP cc_start: 0.7674 (t0) cc_final: 0.7400 (m-30) REVERT: G 111 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8177 (mtpt) REVERT: G 134 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7949 (mp10) REVERT: G 138 ASP cc_start: 0.7495 (t0) cc_final: 0.7228 (m-30) REVERT: G 146 ASP cc_start: 0.7065 (m-30) cc_final: 0.6701 (p0) REVERT: H 59 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7854 (mt-10) REVERT: H 139 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7062 (pm20) REVERT: I 71 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7335 (tp40) REVERT: I 92 MET cc_start: 0.6216 (mmt) cc_final: 0.5704 (tpp) REVERT: I 97 LEU cc_start: 0.7631 (mt) cc_final: 0.7219 (mt) REVERT: I 135 LEU cc_start: 0.6859 (mm) cc_final: 0.6579 (pp) REVERT: I 158 TRP cc_start: 0.7632 (m100) cc_final: 0.6814 (m-90) REVERT: I 217 LYS cc_start: 0.7620 (ptmt) cc_final: 0.7025 (mmtt) REVERT: J 91 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7500 (t80) REVERT: J 109 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8268 (mmmm) REVERT: J 220 ARG cc_start: 0.7164 (mmt180) cc_final: 0.6708 (mmp80) REVERT: K 71 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7055 (tm-30) REVERT: K 91 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7310 (t80) REVERT: K 109 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8236 (mmmm) REVERT: K 220 ARG cc_start: 0.7170 (mmt180) cc_final: 0.6721 (mmp80) REVERT: K 334 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7881 (pttp) REVERT: L 71 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7317 (tp40) REVERT: L 92 MET cc_start: 0.6187 (mmt) cc_final: 0.5702 (tpp) REVERT: L 217 LYS cc_start: 0.7613 (ptmt) cc_final: 0.7014 (mmtt) REVERT: L 222 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8306 (ptpt) REVERT: L 344 LYS cc_start: 0.7609 (tttt) cc_final: 0.7284 (ptpp) outliers start: 127 outliers final: 71 residues processed: 509 average time/residue: 0.5714 time to fit residues: 343.7109 Evaluate side-chains 487 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 402 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 191 optimal weight: 0.8980 chunk 123 optimal weight: 0.0470 chunk 55 optimal weight: 3.9990 chunk 312 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 314 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS B 105 GLN B 134 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS G 134 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 ASN J 434 ASN K 119 ASN K 434 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.175863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134742 restraints weight = 29908.359| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.45 r_work: 0.3260 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27468 Z= 0.120 Angle : 0.525 7.650 37280 Z= 0.277 Chirality : 0.043 0.237 4486 Planarity : 0.003 0.043 4578 Dihedral : 8.785 79.812 3910 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.61 % Allowed : 18.05 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.87 (0.14), residues: 3422 helix: 1.71 (0.12), residues: 1902 sheet: -0.28 (0.27), residues: 370 loop : -1.04 (0.16), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 27 TYR 0.012 0.001 TYR H 108 PHE 0.033 0.001 PHE L 202 TRP 0.012 0.001 TRP L 181 HIS 0.005 0.001 HIS L 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (27468) covalent geometry : angle 0.52524 / 0.28 (37280) hydrogen bonds : bond 0.03751 / 2.54 ( 1588) hydrogen bonds : angle 4.27210 / 2.96 ( 4572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 437 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8354 (mt) REVERT: A 72 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: A 85 SER cc_start: 0.8502 (t) cc_final: 0.8203 (m) REVERT: A 128 MET cc_start: 0.8616 (mmm) cc_final: 0.8079 (mmp) REVERT: A 189 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7270 (tp) REVERT: B 155 GLU cc_start: 0.6685 (tt0) cc_final: 0.6046 (mt-10) REVERT: B 169 ASP cc_start: 0.6931 (t0) cc_final: 0.6673 (m-30) REVERT: B 183 ILE cc_start: 0.7840 (mt) cc_final: 0.7361 (mp) REVERT: C 59 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: C 155 GLU cc_start: 0.6767 (tt0) cc_final: 0.6205 (mt-10) REVERT: C 183 ILE cc_start: 0.7868 (mt) cc_final: 0.7384 (mp) REVERT: D 85 SER cc_start: 0.8571 (t) cc_final: 0.8240 (m) REVERT: E 39 GLU cc_start: 0.7876 (mp0) cc_final: 0.7544 (mp0) REVERT: E 59 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7829 (mt-10) REVERT: E 86 THR cc_start: 0.8814 (t) cc_final: 0.8431 (m) REVERT: E 139 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: F 128 MET cc_start: 0.8531 (mmm) cc_final: 0.8149 (mmm) REVERT: F 134 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: F 138 ASP cc_start: 0.7562 (t0) cc_final: 0.7204 (m-30) REVERT: F 146 ASP cc_start: 0.7092 (m-30) cc_final: 0.6639 (p0) REVERT: G 59 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7388 (mm-30) REVERT: G 111 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8086 (mtpt) REVERT: G 128 MET cc_start: 0.8511 (mmm) cc_final: 0.8124 (mmm) REVERT: G 138 ASP cc_start: 0.7317 (t0) cc_final: 0.7054 (m-30) REVERT: H 59 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7717 (mt-10) REVERT: H 139 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: I 71 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7314 (tp40) REVERT: I 97 LEU cc_start: 0.7452 (mt) cc_final: 0.7103 (mt) REVERT: I 142 LEU cc_start: 0.7053 (tp) cc_final: 0.6753 (mm) REVERT: I 158 TRP cc_start: 0.7570 (m100) cc_final: 0.6848 (m-90) REVERT: I 217 LYS cc_start: 0.7423 (ptmt) cc_final: 0.6887 (mmtt) REVERT: I 222 LYS cc_start: 0.8550 (mmmt) cc_final: 0.7813 (ptpt) REVERT: J 46 SER cc_start: 0.7553 (OUTLIER) cc_final: 0.7162 (t) REVERT: J 91 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7045 (t80) REVERT: J 109 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8077 (mmmm) REVERT: J 220 ARG cc_start: 0.7073 (mmt180) cc_final: 0.6580 (mmp80) REVERT: J 373 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6269 (mt-10) REVERT: K 46 SER cc_start: 0.7595 (OUTLIER) cc_final: 0.7166 (t) REVERT: K 71 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: K 109 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7969 (mmmm) REVERT: K 220 ARG cc_start: 0.7096 (mmt180) cc_final: 0.6604 (mmp80) REVERT: K 334 LYS cc_start: 0.8490 (mmtt) cc_final: 0.7842 (pttp) REVERT: L 71 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7286 (tp40) REVERT: L 142 LEU cc_start: 0.7075 (tp) cc_final: 0.6773 (mm) REVERT: L 155 GLN cc_start: 0.7851 (tt0) cc_final: 0.7579 (tt0) REVERT: L 217 LYS cc_start: 0.7433 (ptmt) cc_final: 0.6923 (mmtt) REVERT: L 222 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8268 (ptpt) outliers start: 76 outliers final: 41 residues processed: 489 average time/residue: 0.5359 time to fit residues: 308.3312 Evaluate side-chains 476 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 419 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 238 optimal weight: 6.9990 chunk 231 optimal weight: 0.4980 chunk 61 optimal weight: 20.0000 chunk 321 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 249 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN A 210 HIS B 134 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS G 134 GLN I 85 GLN I 253 ASN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN J 119 ASN J 434 ASN K 85 GLN K 119 ASN K 434 ASN L 253 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.175304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133134 restraints weight = 29504.637| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.36 r_work: 0.3270 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 27468 Z= 0.162 Angle : 0.557 7.952 37280 Z= 0.293 Chirality : 0.044 0.227 4486 Planarity : 0.003 0.043 4578 Dihedral : 8.852 78.027 3910 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.51 % Allowed : 18.39 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.88 (0.14), residues: 3422 helix: 1.72 (0.12), residues: 1902 sheet: -0.32 (0.27), residues: 380 loop : -1.03 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 27 TYR 0.010 0.001 TYR H 108 PHE 0.034 0.002 PHE J 202 TRP 0.016 0.001 TRP L 181 HIS 0.006 0.001 HIS L 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (27468) covalent geometry : angle 0.55682 / 0.29 (37280) hydrogen bonds : bond 0.04139 / 2.80 ( 1588) hydrogen bonds : angle 4.31330 / 2.98 ( 4572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 428 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8385 (mt) REVERT: A 72 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8187 (mt-10) REVERT: A 85 SER cc_start: 0.8654 (t) cc_final: 0.8392 (m) REVERT: A 128 MET cc_start: 0.8699 (mmm) cc_final: 0.8195 (mmp) REVERT: A 189 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7242 (tp) REVERT: B 155 GLU cc_start: 0.6924 (tt0) cc_final: 0.6324 (mt-10) REVERT: B 183 ILE cc_start: 0.7972 (mt) cc_final: 0.7468 (mp) REVERT: B 208 MET cc_start: 0.8312 (ttp) cc_final: 0.8056 (ttm) REVERT: C 59 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7837 (mt-10) REVERT: C 155 GLU cc_start: 0.7017 (tt0) cc_final: 0.6502 (mt-10) REVERT: C 183 ILE cc_start: 0.7996 (mt) cc_final: 0.7498 (mp) REVERT: C 208 MET cc_start: 0.8323 (ttp) cc_final: 0.8028 (ttm) REVERT: D 27 ARG cc_start: 0.7898 (mtm110) cc_final: 0.7686 (ttm-80) REVERT: D 85 SER cc_start: 0.8724 (t) cc_final: 0.8429 (m) REVERT: E 39 GLU cc_start: 0.7948 (mp0) cc_final: 0.7670 (mp0) REVERT: E 86 THR cc_start: 0.8909 (t) cc_final: 0.8427 (m) REVERT: E 139 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7151 (pm20) REVERT: F 128 MET cc_start: 0.8684 (mmm) cc_final: 0.8339 (mmm) REVERT: F 134 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7973 (mp10) REVERT: F 138 ASP cc_start: 0.7814 (t0) cc_final: 0.7467 (m-30) REVERT: F 146 ASP cc_start: 0.7016 (m-30) cc_final: 0.6687 (p0) REVERT: F 157 LEU cc_start: 0.7535 (tt) cc_final: 0.7261 (tp) REVERT: G 111 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8307 (mtpt) REVERT: G 128 MET cc_start: 0.8693 (mmm) cc_final: 0.8360 (mmm) REVERT: G 134 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: G 138 ASP cc_start: 0.7713 (t0) cc_final: 0.7456 (m-30) REVERT: G 146 ASP cc_start: 0.6973 (m-30) cc_final: 0.6679 (p0) REVERT: H 59 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7766 (mt-10) REVERT: H 139 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7073 (pm20) REVERT: I 71 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7495 (tp40) REVERT: I 92 MET cc_start: 0.5827 (mmt) cc_final: 0.5345 (tpp) REVERT: I 97 LEU cc_start: 0.7613 (mt) cc_final: 0.7214 (mt) REVERT: I 142 LEU cc_start: 0.7178 (tp) cc_final: 0.6914 (mm) REVERT: I 158 TRP cc_start: 0.7651 (m100) cc_final: 0.6947 (m-90) REVERT: I 217 LYS cc_start: 0.7634 (ptmt) cc_final: 0.7084 (mmtt) REVERT: I 222 LYS cc_start: 0.8540 (mmmt) cc_final: 0.7851 (ptpt) REVERT: J 91 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7248 (t80) REVERT: J 109 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8213 (mmmm) REVERT: J 220 ARG cc_start: 0.7252 (mmt180) cc_final: 0.6777 (mmp80) REVERT: J 373 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6360 (mt-10) REVERT: K 71 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: K 109 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8161 (mmmm) REVERT: K 220 ARG cc_start: 0.7301 (mmt180) cc_final: 0.6844 (mmp80) REVERT: K 334 LYS cc_start: 0.8531 (mmtt) cc_final: 0.7956 (pttp) REVERT: L 71 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7435 (tp40) REVERT: L 92 MET cc_start: 0.5869 (mmt) cc_final: 0.5305 (tpp) REVERT: L 142 LEU cc_start: 0.7235 (tp) cc_final: 0.6947 (mm) REVERT: L 155 GLN cc_start: 0.7941 (tt0) cc_final: 0.7698 (tt0) REVERT: L 217 LYS cc_start: 0.7618 (ptmt) cc_final: 0.7123 (mmtt) REVERT: L 222 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8247 (ptpt) outliers start: 73 outliers final: 44 residues processed: 485 average time/residue: 0.6173 time to fit residues: 351.0050 Evaluate side-chains 479 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 421 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 99 optimal weight: 0.9990 chunk 24 optimal weight: 0.0870 chunk 258 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 259 optimal weight: 2.9990 chunk 291 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 269 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS B 83 GLN B 134 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS G 134 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN J 119 ASN J 434 ASN K 85 GLN K 119 ASN K 434 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.177983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.136415 restraints weight = 29415.732| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.40 r_work: 0.3308 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27468 Z= 0.114 Angle : 0.514 7.524 37280 Z= 0.271 Chirality : 0.043 0.202 4486 Planarity : 0.003 0.040 4578 Dihedral : 8.517 78.880 3910 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.13 % Allowed : 18.84 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 1.12 (0.14), residues: 3422 helix: 1.93 (0.12), residues: 1914 sheet: -0.38 (0.26), residues: 380 loop : -0.92 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 27 TYR 0.009 0.001 TYR B 107 PHE 0.033 0.001 PHE I 202 TRP 0.015 0.001 TRP L 181 HIS 0.005 0.001 HIS L 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (27468) covalent geometry : angle 0.51421 / 0.27 (37280) hydrogen bonds : bond 0.03551 / 2.41 ( 1588) hydrogen bonds : angle 4.15600 / 2.87 ( 4572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10714.77 seconds wall clock time: 198 minutes 47.09 seconds (11927.09 seconds total)