Starting phenix.real_space_refine on Sun Jul 5 08:13:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmh_38477/07_2026/8xmh_38477.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmh_38477/07_2026/8xmh_38477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xmh_38477/07_2026/8xmh_38477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmh_38477/07_2026/8xmh_38477.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xmh_38477/07_2026/8xmh_38477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmh_38477/07_2026/8xmh_38477.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.082 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 116 5.16 5 Na 4 4.78 5 C 17440 2.51 5 N 4420 2.21 5 O 4940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 26948 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: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} 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: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" 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: "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: 6.61, per 1000 atoms: 0.25 Number of scatterers: 26948 At special positions: 0 Unit cell: (135.29, 135.29, 169.32, 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 116 16.00 P 24 15.00 Na 4 11.00 O 4940 8.00 N 4420 7.00 C 17440 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: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6360 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 20 sheets defined 57.8% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 15 through 28 removed outlier: 3.646A 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 66 removed outlier: 3.629A pdb=" N LEU A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 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 221 removed outlier: 3.710A pdb=" N LYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 28 removed outlier: 3.645A 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 66 removed outlier: 3.628A pdb=" N LEU B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 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 221 removed outlier: 3.711A pdb=" N LYS B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 28 removed outlier: 3.645A 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 66 removed outlier: 3.629A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 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 221 removed outlier: 3.709A pdb=" N LYS C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 28 removed outlier: 3.645A 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 66 removed outlier: 3.629A pdb=" N LEU D 66 " --> pdb=" O GLU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 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 221 removed outlier: 3.710A pdb=" N LYS D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 28 removed outlier: 3.646A 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 66 removed outlier: 3.629A pdb=" N LEU E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 71 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 221 removed outlier: 3.710A pdb=" N LYS E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 28 removed outlier: 3.646A 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 66 removed outlier: 3.629A pdb=" N LEU F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 71 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 221 removed outlier: 3.710A pdb=" N LYS F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 28 removed outlier: 3.646A 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 66 removed outlier: 3.629A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 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 221 removed outlier: 3.710A pdb=" N LYS G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 28 removed outlier: 3.646A 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 66 removed outlier: 3.629A pdb=" N LEU H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 71 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 221 removed outlier: 3.710A pdb=" N LYS H 215 " --> pdb=" O LYS H 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 37 removed outlier: 3.528A pdb=" N LEU I 20 " --> pdb=" O PRO I 16 " (cutoff:3.500A) removed outlier: 3.749A 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: 4.040A pdb=" N PHE I 94 " --> pdb=" O GLY I 90 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 removed outlier: 3.552A pdb=" N LEU I 113 " --> pdb=" O LYS I 109 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL I 114 " --> pdb=" O GLU I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 157 removed outlier: 3.531A pdb=" N VAL I 130 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE I 150 " --> pdb=" O LEU I 146 " (cutoff:3.500A) removed outlier: 4.398A 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: 3.541A pdb=" N LEU I 162 " --> pdb=" O TRP I 158 " (cutoff:3.500A) removed outlier: 3.924A 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: 3.516A pdb=" N SER I 288 " --> pdb=" O ASP I 285 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET I 289 " --> pdb=" O PHE I 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 285 through 289' Processing helix chain 'I' and resid 290 through 303 removed outlier: 3.537A 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 removed outlier: 3.518A pdb=" N CYS I 407 " --> pdb=" O THR I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 428 removed outlier: 4.129A pdb=" N PHE I 427 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 37 removed outlier: 3.529A pdb=" N LEU J 20 " --> pdb=" O PRO J 16 " (cutoff:3.500A) removed outlier: 3.748A 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: 4.039A pdb=" N PHE J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 118 removed outlier: 3.551A pdb=" N LEU J 113 " --> pdb=" O LYS J 109 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 157 removed outlier: 3.532A pdb=" N VAL J 130 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE J 150 " --> pdb=" O LEU J 146 " (cutoff:3.500A) removed outlier: 4.396A 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: 3.542A pdb=" N LEU J 162 " --> pdb=" O TRP J 158 " (cutoff:3.500A) removed outlier: 3.923A 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: 3.516A pdb=" N SER J 288 " --> pdb=" O ASP J 285 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET J 289 " --> pdb=" O PHE J 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 285 through 289' Processing helix chain 'J' and resid 290 through 303 removed outlier: 3.638A pdb=" N LEU J 299 " --> pdb=" O VAL J 295 " (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 removed outlier: 3.519A pdb=" N CYS J 407 " --> pdb=" O THR J 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 419 through 428 removed outlier: 4.129A pdb=" N PHE J 427 " --> pdb=" O PHE J 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 37 removed outlier: 3.529A pdb=" N LEU K 20 " --> pdb=" O PRO K 16 " (cutoff:3.500A) removed outlier: 3.748A 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: 4.040A pdb=" N PHE K 94 " --> pdb=" O GLY K 90 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU K 97 " --> pdb=" O THR K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 removed outlier: 3.551A pdb=" N LEU K 113 " --> pdb=" O LYS K 109 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 157 removed outlier: 3.531A pdb=" N VAL K 130 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE K 150 " --> pdb=" O LEU K 146 " (cutoff:3.500A) removed outlier: 4.397A 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: 3.541A pdb=" N LEU K 162 " --> pdb=" O TRP K 158 " (cutoff:3.500A) removed outlier: 3.924A 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: 3.515A pdb=" N SER K 288 " --> pdb=" O ASP K 285 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET K 289 " --> pdb=" O PHE K 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 285 through 289' Processing helix chain 'K' and resid 290 through 303 removed outlier: 3.536A 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 removed outlier: 3.519A pdb=" N CYS K 407 " --> pdb=" O THR K 403 " (cutoff:3.500A) Processing helix chain 'K' and resid 419 through 428 removed outlier: 4.130A pdb=" N PHE K 427 " --> pdb=" O PHE K 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 37 removed outlier: 3.528A pdb=" N LEU L 20 " --> pdb=" O PRO L 16 " (cutoff:3.500A) removed outlier: 3.748A 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: 4.040A pdb=" N PHE L 94 " --> pdb=" O GLY L 90 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 118 removed outlier: 3.551A pdb=" N LEU L 113 " --> pdb=" O LYS L 109 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL L 114 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 157 removed outlier: 3.531A pdb=" N VAL L 130 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE L 150 " --> pdb=" O LEU L 146 " (cutoff:3.500A) removed outlier: 4.396A 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: 3.542A pdb=" N LEU L 162 " --> pdb=" O TRP L 158 " (cutoff:3.500A) removed outlier: 3.923A 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: 3.516A pdb=" N SER L 288 " --> pdb=" O ASP L 285 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET L 289 " --> pdb=" O PHE L 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 285 through 289' Processing helix chain 'L' and resid 290 through 303 removed outlier: 3.537A 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 removed outlier: 3.519A pdb=" N CYS L 407 " --> pdb=" O THR L 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 419 through 428 removed outlier: 4.130A 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: 3.588A pdb=" N TYR A 73 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 100 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE A 122 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.568A 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: 6.175A pdb=" N VAL A 141 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU A 157 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 143 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS A 204 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 182 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET A 208 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE A 180 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.587A pdb=" N TYR B 73 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 100 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE B 122 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.568A 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: 6.174A pdb=" N VAL B 141 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU B 157 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN B 143 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS B 204 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 182 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET B 208 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE B 180 " --> pdb=" O MET B 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.588A pdb=" N TYR C 73 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 100 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE C 122 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.568A 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: 6.175A pdb=" N VAL C 141 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU C 157 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN C 143 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS C 204 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA C 182 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET C 208 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE C 180 " --> pdb=" O MET C 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.588A pdb=" N TYR D 73 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 100 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE D 122 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.568A 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: 6.175A pdb=" N VAL D 141 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU D 157 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN D 143 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS D 204 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 182 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET D 208 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ILE D 180 " --> pdb=" O MET D 208 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 51 through 54 removed outlier: 3.588A pdb=" N TYR E 73 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE E 100 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE E 122 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.569A 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: 6.175A pdb=" N VAL E 141 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU E 157 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN E 143 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS E 204 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 182 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET E 208 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE E 180 " --> pdb=" O MET E 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.587A pdb=" N TYR F 73 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE F 100 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE F 122 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.568A 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: 6.175A pdb=" N VAL F 141 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU F 157 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN F 143 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS F 204 " --> pdb=" O LYS F 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA F 182 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET F 208 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE F 180 " --> pdb=" O MET F 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.588A pdb=" N TYR G 73 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE G 100 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE G 122 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.568A 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: 6.175A pdb=" N VAL G 141 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU G 157 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN G 143 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS G 204 " --> pdb=" O LYS G 184 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA G 182 " --> pdb=" O VAL G 206 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET G 208 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE G 180 " --> pdb=" O MET G 208 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 51 through 54 removed outlier: 3.588A pdb=" N TYR H 73 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE H 100 " --> pdb=" O ARG H 120 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE H 122 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.569A 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: 6.175A pdb=" N VAL H 141 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU H 157 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN H 143 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS H 204 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA H 182 " --> pdb=" O VAL H 206 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET H 208 " --> pdb=" O ILE H 180 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE H 180 " --> pdb=" O MET H 208 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 336 through 338 removed outlier: 4.695A 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: 4.695A 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: 4.694A 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: 4.694A pdb=" N THR L 336 " --> pdb=" O ILE L 343 " (cutoff:3.500A) 1572 hydrogen bonds defined for protein. 4560 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: 5.56 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4315 1.29 - 1.42: 6694 1.42 - 1.55: 16188 1.55 - 1.68: 59 1.68 - 1.81: 196 Bond restraints: 27452 Sorted by residual: bond pdb=" CA LEU J 299 " pdb=" C LEU J 299 " ideal model delta sigma weight residual 1.524 1.430 0.093 1.29e-02 6.01e+03 5.25e+01 bond pdb=" C LEU I 298 " pdb=" O LEU I 298 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.19e-02 7.06e+03 4.39e+01 bond pdb=" C LEU E 87 " pdb=" O LEU E 87 " ideal model delta sigma weight residual 1.237 1.169 0.068 1.19e-02 7.06e+03 3.24e+01 bond pdb=" C LEU A 87 " pdb=" O LEU A 87 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.26e-02 6.30e+03 2.99e+01 bond pdb=" CA LEU D 87 " pdb=" C LEU D 87 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.35e-02 5.49e+03 2.66e+01 ... (remaining 27447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 36683 1.63 - 3.26: 452 3.26 - 4.89: 84 4.89 - 6.52: 20 6.52 - 8.15: 21 Bond angle restraints: 37260 Sorted by residual: angle pdb=" N LEU J 299 " pdb=" CA LEU J 299 " pdb=" C LEU J 299 " ideal model delta sigma weight residual 111.36 105.52 5.84 1.09e+00 8.42e-01 2.87e+01 angle pdb=" O THR I 297 " pdb=" C THR I 297 " pdb=" N LEU I 298 " ideal model delta sigma weight residual 122.27 116.17 6.10 1.23e+00 6.61e-01 2.46e+01 angle pdb=" CA THR I 297 " pdb=" C THR I 297 " pdb=" N LEU I 298 " ideal model delta sigma weight residual 117.72 123.94 -6.22 1.31e+00 5.83e-01 2.25e+01 angle pdb=" N THR L 275 " pdb=" CA THR L 275 " pdb=" C THR L 275 " ideal model delta sigma weight residual 109.81 116.83 -7.02 2.21e+00 2.05e-01 1.01e+01 angle pdb=" N THR J 275 " pdb=" CA THR J 275 " pdb=" C THR J 275 " ideal model delta sigma weight residual 109.81 116.82 -7.01 2.21e+00 2.05e-01 1.01e+01 ... (remaining 37255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 15437 15.76 - 31.51: 752 31.51 - 47.27: 135 47.27 - 63.03: 60 63.03 - 78.79: 32 Dihedral angle restraints: 16416 sinusoidal: 6532 harmonic: 9884 Sorted by residual: dihedral pdb=" CA GLU B 201 " pdb=" C GLU B 201 " pdb=" N GLN B 202 " pdb=" CA GLN B 202 " ideal model delta harmonic sigma weight residual -180.00 -163.34 -16.66 0 5.00e+00 4.00e-02 1.11e+01 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 -163.35 -16.65 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA GLU G 201 " pdb=" C GLU G 201 " pdb=" N GLN G 202 " pdb=" CA GLN G 202 " ideal model delta harmonic sigma weight residual -180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 16413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3124 0.040 - 0.080: 1019 0.080 - 0.121: 291 0.121 - 0.161: 44 0.161 - 0.201: 6 Chirality restraints: 4484 Sorted by residual: chirality pdb=" CA THR K 275 " pdb=" N THR K 275 " pdb=" C THR K 275 " pdb=" CB THR K 275 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA THR J 275 " pdb=" N THR J 275 " pdb=" C THR J 275 " pdb=" CB THR J 275 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CA THR I 275 " pdb=" N THR I 275 " pdb=" C THR I 275 " pdb=" CB THR I 275 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 4481 not shown) Planarity restraints: 4576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 298 " -0.009 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C LEU I 298 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU I 298 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU I 299 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR J 15 " -0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO J 16 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO J 16 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO J 16 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR L 15 " 0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO L 16 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO L 16 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 16 " 0.023 5.00e-02 4.00e+02 ... (remaining 4573 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 9213 2.86 - 3.43: 28452 3.43 - 4.00: 50971 4.00 - 4.57: 72756 4.57 - 5.14: 106687 Nonbonded interactions: 268079 Sorted by model distance: nonbonded pdb=" OE1 GLU A 60 " pdb=" OH TYR H 108 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR D 108 " pdb=" OE1 GLU E 60 " model vdw 2.293 3.040 nonbonded pdb=" OE1 GLU D 60 " pdb=" OH TYR E 108 " model vdw 2.317 3.040 nonbonded pdb=" O ASN K 195 " pdb=" OG1 THR K 199 " model vdw 2.330 3.040 nonbonded pdb=" O ASN J 195 " pdb=" OG1 THR J 199 " model vdw 2.330 3.040 ... (remaining 268074 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: 0.01 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: 5.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.460 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 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:8.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 0.004 0.093 27452 Z= 0.217 Angle : 0.529 8.148 37260 Z= 0.285 Chirality : 0.043 0.201 4484 Planarity : 0.004 0.042 4576 Dihedral : 10.948 78.787 10056 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.55 % Allowed : 4.09 % Favored : 94.37 % 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: -1.68 (0.12), residues: 3420 helix: -1.51 (0.08), residues: 1852 sheet: 0.79 (0.27), residues: 416 loop : -0.81 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 111 TYR 0.006 0.001 TYR F 108 PHE 0.025 0.001 PHE I 202 TRP 0.004 0.001 TRP J 181 HIS 0.003 0.001 HIS K 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.22 (27452) covalent geometry : angle 0.52895 / 0.28 (37260) hydrogen bonds : bond 0.25057 / 17.02 ( 1572) hydrogen bonds : angle 7.78521 / 5.42 ( 4560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 831 time to evaluate : 1.104 Fit side-chains REVERT: F 128 MET cc_start: 0.7541 (mmm) cc_final: 0.7290 (mmt) REVERT: G 41 LYS cc_start: 0.8352 (mmtp) cc_final: 0.7977 (mmtt) REVERT: J 407 CYS cc_start: 0.7767 (m) cc_final: 0.7499 (m) REVERT: K 213 PHE cc_start: 0.7658 (t80) cc_final: 0.7315 (t80) REVERT: L 74 VAL cc_start: 0.7713 (t) cc_final: 0.7354 (p) REVERT: L 213 PHE cc_start: 0.7575 (t80) cc_final: 0.7267 (t80) outliers start: 45 outliers final: 5 residues processed: 857 average time/residue: 0.6013 time to fit residues: 601.9054 Evaluate side-chains 491 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 486 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain K 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: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A 140 ASN B 70 ASN C 134 GLN D 70 ASN D 81 ASN D 134 GLN E 30 HIS E 134 GLN F 134 GLN H 70 ASN H 81 ASN H 134 GLN I 120 GLN I 253 ASN I 282 ASN I 432 GLN J 253 ASN J 282 ASN K 155 GLN K 195 ASN K 253 ASN K 261 HIS K 432 GLN L 77 GLN L 253 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.196303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.158382 restraints weight = 28178.917| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.20 r_work: 0.3500 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27452 Z= 0.190 Angle : 0.588 7.979 37260 Z= 0.312 Chirality : 0.045 0.261 4484 Planarity : 0.004 0.045 4576 Dihedral : 9.469 80.006 3914 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.64 % Allowed : 13.80 % Favored : 81.56 % 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: 0.42 (0.13), residues: 3420 helix: 0.82 (0.11), residues: 1908 sheet: 0.25 (0.26), residues: 400 loop : -0.49 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 151 TYR 0.029 0.001 TYR F 107 PHE 0.044 0.002 PHE I 202 TRP 0.007 0.001 TRP J 181 HIS 0.008 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (27452) covalent geometry : angle 0.58755 / 0.31 (37260) hydrogen bonds : bond 0.05081 / 3.44 ( 1572) hydrogen bonds : angle 4.74529 / 3.31 ( 4560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 509 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 85 SER cc_start: 0.8387 (t) cc_final: 0.8132 (m) REVERT: A 145 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7560 (tt) REVERT: A 189 ILE cc_start: 0.6508 (OUTLIER) cc_final: 0.6185 (mt) REVERT: B 134 GLN cc_start: 0.8606 (mp10) cc_final: 0.7998 (mp10) REVERT: B 189 ILE cc_start: 0.5938 (OUTLIER) cc_final: 0.5603 (tp) REVERT: B 213 ASP cc_start: 0.6913 (m-30) cc_final: 0.6012 (t0) REVERT: C 128 MET cc_start: 0.8093 (mmm) cc_final: 0.7663 (mmp) REVERT: C 134 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8281 (mp10) REVERT: C 135 SER cc_start: 0.8836 (t) cc_final: 0.8561 (m) REVERT: D 23 LYS cc_start: 0.8599 (mttp) cc_final: 0.8399 (mttm) REVERT: D 95 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7768 (mt) REVERT: D 152 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8368 (m) REVERT: E 85 SER cc_start: 0.8801 (t) cc_final: 0.8472 (t) REVERT: F 128 MET cc_start: 0.8522 (mmm) cc_final: 0.8184 (mmt) REVERT: F 134 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8111 (mp10) REVERT: F 189 ILE cc_start: 0.5742 (OUTLIER) cc_final: 0.5402 (tp) REVERT: G 62 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8332 (mt-10) REVERT: G 128 MET cc_start: 0.8047 (mmm) cc_final: 0.7773 (mmp) REVERT: G 134 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8178 (mp10) REVERT: G 145 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6730 (tp) REVERT: H 39 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7850 (mm-30) REVERT: H 69 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7334 (mtm-85) REVERT: H 85 SER cc_start: 0.8695 (t) cc_final: 0.8418 (m) REVERT: H 95 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7742 (mt) REVERT: H 152 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8335 (m) REVERT: I 250 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8436 (tp30) REVERT: J 18 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8413 (mp10) REVERT: K 71 GLN cc_start: 0.7113 (mm-40) cc_final: 0.6081 (tp40) REVERT: K 112 MET cc_start: 0.8611 (mtm) cc_final: 0.8404 (mtp) REVERT: K 244 LEU cc_start: 0.8147 (tp) cc_final: 0.7878 (mm) REVERT: K 352 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8417 (tp) REVERT: L 77 GLN cc_start: 0.7447 (mt0) cc_final: 0.7060 (mp10) REVERT: L 112 MET cc_start: 0.8589 (mtm) cc_final: 0.8370 (mtp) REVERT: L 216 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.6381 (mmp) REVERT: L 352 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8377 (tp) outliers start: 135 outliers final: 29 residues processed: 596 average time/residue: 0.5510 time to fit residues: 389.3226 Evaluate side-chains 502 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 455 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 36 MET Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 289 MET Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 371 ILE Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 6.9990 chunk 246 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 274 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 chunk 283 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 70 ASN D 81 ASN D 134 GLN E 134 GLN H 70 ASN H 81 ASN H 134 GLN H 210 HIS J 432 GLN K 115 GLN K 261 HIS K 434 ASN L 115 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.195819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.155789 restraints weight = 28121.966| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.36 r_work: 0.3495 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27452 Z= 0.175 Angle : 0.559 7.897 37260 Z= 0.294 Chirality : 0.044 0.259 4484 Planarity : 0.004 0.045 4576 Dihedral : 9.298 80.499 3910 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.05 % Allowed : 15.62 % Favored : 80.32 % 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: 0.94 (0.14), residues: 3420 helix: 1.49 (0.11), residues: 1920 sheet: -0.00 (0.26), residues: 400 loop : -0.62 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 27 TYR 0.018 0.001 TYR F 107 PHE 0.037 0.002 PHE J 202 TRP 0.007 0.001 TRP J 181 HIS 0.006 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (27452) covalent geometry : angle 0.55871 / 0.29 (37260) hydrogen bonds : bond 0.04615 / 3.13 ( 1572) hydrogen bonds : angle 4.44701 / 3.10 ( 4560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 477 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8369 (t) cc_final: 0.8140 (m) REVERT: A 145 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7540 (tt) REVERT: B 134 GLN cc_start: 0.8524 (mp10) cc_final: 0.7776 (mp10) REVERT: B 189 ILE cc_start: 0.5903 (OUTLIER) cc_final: 0.5602 (tp) REVERT: B 213 ASP cc_start: 0.6835 (m-30) cc_final: 0.5975 (t0) REVERT: C 128 MET cc_start: 0.8191 (mmm) cc_final: 0.7732 (mmp) REVERT: C 135 SER cc_start: 0.8802 (t) cc_final: 0.8555 (m) REVERT: D 85 SER cc_start: 0.8719 (t) cc_final: 0.8331 (m) REVERT: D 95 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7795 (mt) REVERT: D 152 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8363 (m) REVERT: D 184 LYS cc_start: 0.7339 (ttpp) cc_final: 0.7066 (mtpp) REVERT: E 139 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6677 (tp30) REVERT: F 128 MET cc_start: 0.8427 (mmm) cc_final: 0.8135 (mmt) REVERT: F 189 ILE cc_start: 0.5864 (OUTLIER) cc_final: 0.5568 (tp) REVERT: G 62 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: G 128 MET cc_start: 0.8030 (mmm) cc_final: 0.7763 (mmp) REVERT: G 145 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6709 (tp) REVERT: H 39 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: H 69 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7732 (mtm-85) REVERT: H 85 SER cc_start: 0.8699 (t) cc_final: 0.8457 (m) REVERT: H 95 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7787 (mt) REVERT: H 152 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8417 (m) REVERT: J 18 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8371 (mp10) REVERT: J 110 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: J 250 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8393 (tp30) REVERT: K 25 PHE cc_start: 0.6710 (t80) cc_final: 0.6500 (t80) REVERT: K 71 GLN cc_start: 0.7024 (mm-40) cc_final: 0.5902 (tp40) REVERT: K 112 MET cc_start: 0.8622 (mtm) cc_final: 0.8402 (mtp) REVERT: K 213 PHE cc_start: 0.7475 (t80) cc_final: 0.7173 (t80) REVERT: K 352 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8354 (tp) REVERT: L 77 GLN cc_start: 0.7429 (mt0) cc_final: 0.7073 (mp10) REVERT: L 112 MET cc_start: 0.8570 (mtm) cc_final: 0.8342 (mtp) REVERT: L 170 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8206 (mp) REVERT: L 213 PHE cc_start: 0.7443 (t80) cc_final: 0.7144 (t80) REVERT: L 352 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8366 (tp) outliers start: 118 outliers final: 50 residues processed: 552 average time/residue: 0.5596 time to fit residues: 364.8651 Evaluate side-chains 516 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 450 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 157 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 F residue 102 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 170 ILE Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 98 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 165 optimal weight: 50.0000 chunk 279 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 chunk 60 optimal weight: 0.0370 chunk 116 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN B 8 GLN D 70 ASN D 134 GLN E 134 GLN ** J 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN K 261 HIS L 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.197534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.159893 restraints weight = 27940.936| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.12 r_work: 0.3534 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27452 Z= 0.119 Angle : 0.501 7.388 37260 Z= 0.266 Chirality : 0.042 0.231 4484 Planarity : 0.003 0.045 4576 Dihedral : 8.970 78.158 3910 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.61 % Allowed : 16.38 % Favored : 80.01 % 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: 1.34 (0.14), residues: 3420 helix: 1.93 (0.12), residues: 1916 sheet: -0.10 (0.26), residues: 400 loop : -0.54 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 436 TYR 0.019 0.001 TYR F 107 PHE 0.034 0.001 PHE I 202 TRP 0.005 0.001 TRP I 181 HIS 0.005 0.001 HIS K 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (27452) covalent geometry : angle 0.50073 / 0.27 (37260) hydrogen bonds : bond 0.03763 / 2.55 ( 1572) hydrogen bonds : angle 4.20272 / 2.94 ( 4560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 475 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7593 (tt) REVERT: B 181 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6990 (mp) REVERT: B 213 ASP cc_start: 0.6820 (m-30) cc_final: 0.6000 (t0) REVERT: C 128 MET cc_start: 0.8094 (mmm) cc_final: 0.7643 (mmp) REVERT: C 134 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8121 (mp10) REVERT: C 135 SER cc_start: 0.8775 (t) cc_final: 0.8550 (m) REVERT: D 85 SER cc_start: 0.8604 (t) cc_final: 0.8283 (m) REVERT: D 95 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7723 (mt) REVERT: D 152 SER cc_start: 0.8697 (p) cc_final: 0.8471 (m) REVERT: F 59 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7872 (mm-30) REVERT: F 128 MET cc_start: 0.8409 (mmm) cc_final: 0.8112 (mmt) REVERT: F 134 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7859 (mp10) REVERT: F 189 ILE cc_start: 0.5996 (OUTLIER) cc_final: 0.5702 (tp) REVERT: G 128 MET cc_start: 0.7967 (mmm) cc_final: 0.7705 (mmp) REVERT: G 145 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6604 (tp) REVERT: H 39 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: H 95 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7669 (mt) REVERT: H 184 LYS cc_start: 0.7465 (mtpp) cc_final: 0.7189 (mtpt) REVERT: I 222 LYS cc_start: 0.8435 (mmtt) cc_final: 0.8038 (tttp) REVERT: J 222 LYS cc_start: 0.8468 (mmtt) cc_final: 0.8031 (tttp) REVERT: J 291 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: K 25 PHE cc_start: 0.6574 (t80) cc_final: 0.6362 (t80) REVERT: K 71 GLN cc_start: 0.7080 (mm-40) cc_final: 0.6019 (tp40) REVERT: K 213 PHE cc_start: 0.7500 (t80) cc_final: 0.7181 (t80) REVERT: L 213 PHE cc_start: 0.7449 (t80) cc_final: 0.7138 (t80) outliers start: 105 outliers final: 44 residues processed: 538 average time/residue: 0.5456 time to fit residues: 347.4902 Evaluate side-chains 489 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 434 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 36 MET Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 291 GLU Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 92 MET Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 371 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 183 optimal weight: 4.9990 chunk 330 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 242 optimal weight: 0.6980 chunk 170 optimal weight: 0.4980 chunk 247 optimal weight: 0.0980 chunk 328 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 336 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN D 70 ASN D 134 GLN E 134 GLN H 70 ASN K 253 ASN L 115 GLN L 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.197759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.159639 restraints weight = 27879.161| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.14 r_work: 0.3549 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27452 Z= 0.121 Angle : 0.497 7.283 37260 Z= 0.264 Chirality : 0.042 0.228 4484 Planarity : 0.003 0.045 4576 Dihedral : 8.858 78.741 3906 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.54 % Allowed : 16.76 % Favored : 79.70 % 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: 1.51 (0.14), residues: 3420 helix: 2.11 (0.12), residues: 1916 sheet: -0.15 (0.26), residues: 400 loop : -0.50 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 436 TYR 0.012 0.001 TYR F 107 PHE 0.033 0.001 PHE I 202 TRP 0.006 0.001 TRP L 181 HIS 0.008 0.001 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (27452) covalent geometry : angle 0.49720 / 0.26 (37260) hydrogen bonds : bond 0.03679 / 2.50 ( 1572) hydrogen bonds : angle 4.13147 / 2.88 ( 4560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 471 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7626 (tt) REVERT: B 213 ASP cc_start: 0.6820 (m-30) cc_final: 0.6009 (t0) REVERT: C 128 MET cc_start: 0.8059 (mmm) cc_final: 0.7586 (mmp) REVERT: C 134 GLN cc_start: 0.8405 (tp40) cc_final: 0.8144 (mp10) REVERT: C 135 SER cc_start: 0.8750 (t) cc_final: 0.8527 (m) REVERT: D 95 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7737 (mt) REVERT: D 152 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.8472 (m) REVERT: F 40 GLU cc_start: 0.8106 (pt0) cc_final: 0.7877 (pp20) REVERT: F 59 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7824 (mm-30) REVERT: F 128 MET cc_start: 0.8420 (mmm) cc_final: 0.8127 (mmt) REVERT: F 134 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: F 189 ILE cc_start: 0.5919 (OUTLIER) cc_final: 0.5646 (tp) REVERT: G 62 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8330 (mt-10) REVERT: G 128 MET cc_start: 0.7996 (mmm) cc_final: 0.7692 (mmp) REVERT: H 39 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: H 95 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7688 (mt) REVERT: I 222 LYS cc_start: 0.8389 (mmtt) cc_final: 0.8032 (tttp) REVERT: J 222 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8032 (tttp) REVERT: K 71 GLN cc_start: 0.7115 (mm-40) cc_final: 0.6244 (tm-30) REVERT: K 86 ILE cc_start: 0.8220 (mt) cc_final: 0.7899 (mm) REVERT: K 213 PHE cc_start: 0.7503 (t80) cc_final: 0.7192 (t80) REVERT: L 213 PHE cc_start: 0.7467 (t80) cc_final: 0.7160 (t80) REVERT: L 344 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7339 (mmpt) outliers start: 103 outliers final: 53 residues processed: 544 average time/residue: 0.5840 time to fit residues: 375.0488 Evaluate side-chains 512 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 449 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 92 MET Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 3 optimal weight: 3.9990 chunk 297 optimal weight: 0.8980 chunk 250 optimal weight: 0.7980 chunk 87 optimal weight: 0.0170 chunk 151 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 317 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN B 8 GLN D 70 ASN E 134 GLN F 51 HIS H 70 ASN H 81 ASN K 115 GLN K 253 ASN L 155 GLN L 272 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.198329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.160690 restraints weight = 27978.031| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.13 r_work: 0.3550 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27452 Z= 0.112 Angle : 0.492 7.290 37260 Z= 0.260 Chirality : 0.042 0.220 4484 Planarity : 0.003 0.045 4576 Dihedral : 8.735 77.505 3906 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.54 % Allowed : 17.07 % Favored : 79.40 % 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: 1.60 (0.14), residues: 3420 helix: 2.18 (0.12), residues: 1928 sheet: -0.16 (0.26), residues: 400 loop : -0.47 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 341 TYR 0.021 0.001 TYR F 107 PHE 0.032 0.001 PHE I 202 TRP 0.009 0.001 TRP L 181 HIS 0.007 0.001 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (27452) covalent geometry : angle 0.49158 / 0.26 (37260) hydrogen bonds : bond 0.03525 / 2.39 ( 1572) hydrogen bonds : angle 4.04954 / 2.83 ( 4560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 459 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7638 (tt) REVERT: B 213 ASP cc_start: 0.6840 (m-30) cc_final: 0.6027 (t0) REVERT: C 128 MET cc_start: 0.8061 (mmm) cc_final: 0.7579 (mmp) REVERT: C 134 GLN cc_start: 0.8373 (tp40) cc_final: 0.8140 (mp10) REVERT: C 135 SER cc_start: 0.8760 (t) cc_final: 0.8540 (m) REVERT: D 95 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7714 (mt) REVERT: D 152 SER cc_start: 0.8657 (p) cc_final: 0.8440 (m) REVERT: F 59 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7804 (mm-30) REVERT: F 128 MET cc_start: 0.8468 (mmm) cc_final: 0.8145 (mmt) REVERT: F 134 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: F 189 ILE cc_start: 0.5911 (OUTLIER) cc_final: 0.5658 (tp) REVERT: F 213 ASP cc_start: 0.6979 (m-30) cc_final: 0.6168 (t0) REVERT: G 62 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8351 (mt-10) REVERT: G 128 MET cc_start: 0.8037 (mmm) cc_final: 0.7713 (mmp) REVERT: G 145 ILE cc_start: 0.7646 (tt) cc_final: 0.7380 (tp) REVERT: H 95 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7723 (mt) REVERT: H 145 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7719 (pt) REVERT: H 184 LYS cc_start: 0.7458 (mtpp) cc_final: 0.7203 (mtpt) REVERT: I 222 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8062 (tttp) REVERT: J 18 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8289 (mp10) REVERT: J 222 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8045 (tttp) REVERT: K 71 GLN cc_start: 0.7153 (mm-40) cc_final: 0.6035 (tp40) REVERT: K 86 ILE cc_start: 0.8231 (mt) cc_final: 0.7926 (mm) REVERT: K 155 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7499 (tt0) REVERT: K 213 PHE cc_start: 0.7485 (t80) cc_final: 0.7166 (t80) REVERT: L 213 PHE cc_start: 0.7466 (t80) cc_final: 0.7172 (t80) REVERT: L 344 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7362 (mmpt) REVERT: L 352 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8466 (tp) outliers start: 103 outliers final: 49 residues processed: 528 average time/residue: 0.5895 time to fit residues: 367.1600 Evaluate side-chains 498 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 438 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 289 MET Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 129 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 306 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 321 optimal weight: 6.9990 chunk 270 optimal weight: 7.9990 chunk 322 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN C 30 HIS D 70 ASN D 81 ASN E 134 GLN H 70 ASN I 253 ASN J 71 GLN J 253 ASN K 115 GLN K 253 ASN K 272 GLN L 115 GLN L 155 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.196182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.158433 restraints weight = 27882.918| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.16 r_work: 0.3498 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27452 Z= 0.146 Angle : 0.523 8.762 37260 Z= 0.276 Chirality : 0.043 0.239 4484 Planarity : 0.003 0.046 4576 Dihedral : 8.948 79.284 3906 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.47 % Allowed : 17.27 % Favored : 79.26 % 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: 1.50 (0.14), residues: 3420 helix: 2.08 (0.12), residues: 1928 sheet: -0.17 (0.25), residues: 400 loop : -0.49 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 436 TYR 0.017 0.001 TYR F 107 PHE 0.033 0.001 PHE I 202 TRP 0.012 0.001 TRP L 181 HIS 0.006 0.001 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (27452) covalent geometry : angle 0.52295 / 0.28 (37260) hydrogen bonds : bond 0.03913 / 2.66 ( 1572) hydrogen bonds : angle 4.13531 / 2.89 ( 4560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 458 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.6910 (m-30) cc_final: 0.6058 (t0) REVERT: C 128 MET cc_start: 0.8217 (mmm) cc_final: 0.7751 (mmp) REVERT: C 134 GLN cc_start: 0.8432 (tp40) cc_final: 0.8172 (mp10) REVERT: C 135 SER cc_start: 0.8731 (t) cc_final: 0.8518 (m) REVERT: C 156 LEU cc_start: 0.8200 (mt) cc_final: 0.7990 (mm) REVERT: D 95 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7802 (mt) REVERT: D 152 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8467 (m) REVERT: E 134 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7842 (mp-120) REVERT: F 59 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: F 128 MET cc_start: 0.8534 (mmm) cc_final: 0.8195 (mmt) REVERT: F 134 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: F 189 ILE cc_start: 0.5928 (OUTLIER) cc_final: 0.5629 (tp) REVERT: F 213 ASP cc_start: 0.7014 (m-30) cc_final: 0.6191 (t0) REVERT: G 62 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: G 128 MET cc_start: 0.8185 (mmm) cc_final: 0.7845 (mmp) REVERT: G 145 ILE cc_start: 0.7735 (tt) cc_final: 0.7485 (tp) REVERT: H 59 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7630 (pm20) REVERT: H 95 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7757 (mt) REVERT: H 145 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7892 (pt) REVERT: H 184 LYS cc_start: 0.7477 (mtpp) cc_final: 0.7228 (mtpt) REVERT: H 208 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7698 (ptt) REVERT: I 222 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8090 (tttp) REVERT: J 18 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8282 (mp10) REVERT: J 119 ASN cc_start: 0.8433 (t0) cc_final: 0.8118 (t0) REVERT: J 222 LYS cc_start: 0.8484 (mmtt) cc_final: 0.8059 (tttp) REVERT: K 71 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6024 (tp40) REVERT: K 86 ILE cc_start: 0.8270 (mt) cc_final: 0.7975 (mm) REVERT: K 155 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7648 (tt0) REVERT: K 213 PHE cc_start: 0.7518 (t80) cc_final: 0.7200 (t80) REVERT: L 36 MET cc_start: 0.7257 (mmm) cc_final: 0.6898 (mmp) REVERT: L 213 PHE cc_start: 0.7471 (t80) cc_final: 0.7162 (t80) REVERT: L 344 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7336 (mmpt) REVERT: L 352 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8461 (tp) outliers start: 101 outliers final: 58 residues processed: 519 average time/residue: 0.5845 time to fit residues: 358.6928 Evaluate side-chains 513 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 442 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain H residue 208 MET Chi-restraints excluded: chain I residue 24 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 181 TRP Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 371 ILE Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 290 optimal weight: 0.4980 chunk 18 optimal weight: 30.0000 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 278 optimal weight: 0.4980 chunk 229 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN B 8 GLN D 70 ASN E 134 GLN ** H 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN K 253 ASN L 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.197234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.159923 restraints weight = 28042.022| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.12 r_work: 0.3536 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27452 Z= 0.118 Angle : 0.501 9.808 37260 Z= 0.265 Chirality : 0.042 0.221 4484 Planarity : 0.003 0.046 4576 Dihedral : 8.793 77.470 3906 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.12 % Allowed : 17.89 % Favored : 78.98 % 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: 1.60 (0.14), residues: 3420 helix: 2.18 (0.12), residues: 1924 sheet: -0.16 (0.25), residues: 400 loop : -0.46 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 27 TYR 0.021 0.001 TYR F 107 PHE 0.032 0.001 PHE I 202 TRP 0.016 0.001 TRP L 181 HIS 0.005 0.001 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (27452) covalent geometry : angle 0.50116 / 0.26 (37260) hydrogen bonds : bond 0.03609 / 2.45 ( 1572) hydrogen bonds : angle 4.07147 / 2.85 ( 4560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 451 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.6884 (m-30) cc_final: 0.6069 (t0) REVERT: C 128 MET cc_start: 0.8118 (mmm) cc_final: 0.7618 (mmp) REVERT: C 134 GLN cc_start: 0.8416 (tp40) cc_final: 0.8148 (mp10) REVERT: C 135 SER cc_start: 0.8746 (t) cc_final: 0.8540 (m) REVERT: C 156 LEU cc_start: 0.8187 (mt) cc_final: 0.7954 (mm) REVERT: D 95 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7746 (mt) REVERT: D 152 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8434 (m) REVERT: E 134 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7848 (mp-120) REVERT: F 59 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7815 (mm-30) REVERT: F 128 MET cc_start: 0.8476 (mmm) cc_final: 0.8149 (mmt) REVERT: F 134 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: F 189 ILE cc_start: 0.5937 (OUTLIER) cc_final: 0.5652 (tp) REVERT: F 213 ASP cc_start: 0.6986 (m-30) cc_final: 0.6172 (t0) REVERT: G 62 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8336 (mt-10) REVERT: G 128 MET cc_start: 0.8038 (mmm) cc_final: 0.7714 (mmp) REVERT: G 145 ILE cc_start: 0.7741 (tt) cc_final: 0.7456 (tp) REVERT: H 59 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7568 (pm20) REVERT: H 95 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7720 (mt) REVERT: H 145 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7882 (pt) REVERT: H 184 LYS cc_start: 0.7454 (mtpp) cc_final: 0.7208 (mtpt) REVERT: H 208 MET cc_start: 0.7995 (ptm) cc_final: 0.7654 (ptt) REVERT: I 222 LYS cc_start: 0.8481 (mmtt) cc_final: 0.8080 (tttp) REVERT: J 18 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8270 (mp10) REVERT: J 135 LEU cc_start: 0.8529 (mm) cc_final: 0.8176 (mm) REVERT: J 222 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8040 (tttp) REVERT: K 71 GLN cc_start: 0.7187 (mm-40) cc_final: 0.6003 (tp40) REVERT: K 86 ILE cc_start: 0.8239 (mt) cc_final: 0.7942 (mm) REVERT: K 155 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7706 (tt0) REVERT: K 213 PHE cc_start: 0.7463 (t80) cc_final: 0.7153 (t80) REVERT: L 36 MET cc_start: 0.7249 (mmm) cc_final: 0.6914 (mmp) REVERT: L 213 PHE cc_start: 0.7439 (t80) cc_final: 0.7136 (t80) REVERT: L 344 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7378 (mmpt) REVERT: L 352 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8410 (tp) outliers start: 91 outliers final: 54 residues processed: 511 average time/residue: 0.5849 time to fit residues: 353.1561 Evaluate side-chains 505 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 439 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 24 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 289 MET Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 92 MET Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 227 optimal weight: 4.9990 chunk 289 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 316 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 210 optimal weight: 0.0670 chunk 39 optimal weight: 0.9980 chunk 198 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN D 70 ASN E 134 GLN H 70 ASN K 115 GLN K 253 ASN L 115 GLN L 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.197990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.160974 restraints weight = 27956.199| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.12 r_work: 0.3538 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27452 Z= 0.111 Angle : 0.495 10.187 37260 Z= 0.261 Chirality : 0.042 0.215 4484 Planarity : 0.003 0.045 4576 Dihedral : 8.687 77.378 3906 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.68 % Allowed : 18.37 % Favored : 78.95 % 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: 1.66 (0.14), residues: 3420 helix: 2.24 (0.12), residues: 1924 sheet: -0.16 (0.25), residues: 400 loop : -0.45 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 436 TYR 0.016 0.001 TYR F 107 PHE 0.031 0.001 PHE I 202 TRP 0.018 0.001 TRP L 181 HIS 0.005 0.001 HIS L 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (27452) covalent geometry : angle 0.49488 / 0.26 (37260) hydrogen bonds : bond 0.03499 / 2.38 ( 1572) hydrogen bonds : angle 4.02503 / 2.82 ( 4560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 455 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 GLN cc_start: 0.8528 (mp10) cc_final: 0.7901 (mp10) REVERT: B 213 ASP cc_start: 0.6899 (m-30) cc_final: 0.6138 (t0) REVERT: C 128 MET cc_start: 0.8136 (mmm) cc_final: 0.7633 (mmp) REVERT: C 134 GLN cc_start: 0.8426 (tp40) cc_final: 0.8176 (mp10) REVERT: C 156 LEU cc_start: 0.8196 (mt) cc_final: 0.7916 (mm) REVERT: C 215 LYS cc_start: 0.7402 (mmtt) cc_final: 0.7155 (mmtp) REVERT: D 95 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7702 (mt) REVERT: D 152 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8455 (m) REVERT: D 184 LYS cc_start: 0.7233 (ttpp) cc_final: 0.6781 (ptmt) REVERT: E 139 GLU cc_start: 0.7416 (pm20) cc_final: 0.7216 (pm20) REVERT: F 59 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7832 (mm-30) REVERT: F 128 MET cc_start: 0.8495 (mmm) cc_final: 0.8174 (mmt) REVERT: F 134 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7934 (mp10) REVERT: F 189 ILE cc_start: 0.5947 (OUTLIER) cc_final: 0.5676 (tp) REVERT: F 213 ASP cc_start: 0.6920 (m-30) cc_final: 0.6090 (t0) REVERT: G 62 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8353 (mt-10) REVERT: G 128 MET cc_start: 0.8093 (mmm) cc_final: 0.7755 (mmp) REVERT: H 95 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7696 (mt) REVERT: H 184 LYS cc_start: 0.7436 (mtpp) cc_final: 0.7216 (mtpt) REVERT: H 208 MET cc_start: 0.8006 (ptm) cc_final: 0.7646 (ptt) REVERT: I 222 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8090 (tttp) REVERT: J 18 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8305 (mp10) REVERT: J 135 LEU cc_start: 0.8521 (mm) cc_final: 0.8166 (mm) REVERT: J 222 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8049 (tttp) REVERT: K 71 GLN cc_start: 0.7199 (mm-40) cc_final: 0.5999 (tp40) REVERT: K 86 ILE cc_start: 0.8256 (mt) cc_final: 0.7978 (mm) REVERT: K 213 PHE cc_start: 0.7490 (t80) cc_final: 0.7182 (t80) REVERT: L 36 MET cc_start: 0.7251 (mmm) cc_final: 0.6924 (mmp) REVERT: L 213 PHE cc_start: 0.7479 (t80) cc_final: 0.7171 (t80) REVERT: L 344 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7387 (mmpt) REVERT: L 352 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8468 (tp) outliers start: 78 outliers final: 46 residues processed: 510 average time/residue: 0.5828 time to fit residues: 351.8507 Evaluate side-chains 497 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 441 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 24 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 248 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 279 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 81 optimal weight: 0.0060 chunk 207 optimal weight: 0.8980 chunk 178 optimal weight: 0.0470 chunk 232 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.5494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN D 70 ASN E 134 GLN H 70 ASN H 81 ASN K 253 ASN L 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.198735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.160889 restraints weight = 28023.606| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.25 r_work: 0.3539 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27452 Z= 0.106 Angle : 0.493 10.024 37260 Z= 0.260 Chirality : 0.042 0.212 4484 Planarity : 0.003 0.044 4576 Dihedral : 8.570 76.938 3906 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.37 % Allowed : 19.30 % Favored : 78.33 % 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: 1.68 (0.14), residues: 3420 helix: 2.30 (0.12), residues: 1924 sheet: -0.32 (0.24), residues: 416 loop : -0.45 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 436 TYR 0.018 0.001 TYR F 107 PHE 0.031 0.001 PHE J 202 TRP 0.022 0.001 TRP L 181 HIS 0.006 0.001 HIS L 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (27452) covalent geometry : angle 0.49323 / 0.26 (37260) hydrogen bonds : bond 0.03391 / 2.31 ( 1572) hydrogen bonds : angle 3.99256 / 2.80 ( 4560) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 460 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.6947 (m-30) cc_final: 0.6200 (t0) REVERT: C 128 MET cc_start: 0.8110 (mmm) cc_final: 0.7708 (mmp) REVERT: C 134 GLN cc_start: 0.8399 (tp40) cc_final: 0.8136 (mp10) REVERT: C 215 LYS cc_start: 0.7373 (mmtt) cc_final: 0.7083 (mmtp) REVERT: D 95 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7660 (mt) REVERT: D 152 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8431 (m) REVERT: D 184 LYS cc_start: 0.7137 (ttpp) cc_final: 0.6747 (ptmt) REVERT: F 128 MET cc_start: 0.8505 (mmm) cc_final: 0.8183 (mmt) REVERT: F 134 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7920 (mp10) REVERT: F 189 ILE cc_start: 0.5886 (OUTLIER) cc_final: 0.5636 (tp) REVERT: F 213 ASP cc_start: 0.6943 (m-30) cc_final: 0.6108 (t0) REVERT: G 27 ARG cc_start: 0.8484 (ttp80) cc_final: 0.8221 (ttp80) REVERT: G 62 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8378 (mt-10) REVERT: G 128 MET cc_start: 0.8027 (mmm) cc_final: 0.7688 (mmp) REVERT: H 95 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7624 (mt) REVERT: H 184 LYS cc_start: 0.7375 (mtpp) cc_final: 0.7151 (mtpt) REVERT: H 208 MET cc_start: 0.7983 (ptm) cc_final: 0.7658 (ptt) REVERT: I 92 MET cc_start: 0.6957 (mmt) cc_final: 0.6754 (tpt) REVERT: I 222 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8081 (tttp) REVERT: J 18 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8292 (mp10) REVERT: J 222 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8042 (tttp) REVERT: K 71 GLN cc_start: 0.7149 (mm-40) cc_final: 0.5931 (tp40) REVERT: K 86 ILE cc_start: 0.8194 (mt) cc_final: 0.7936 (mm) REVERT: K 213 PHE cc_start: 0.7439 (t80) cc_final: 0.7120 (t80) REVERT: L 36 MET cc_start: 0.7247 (mmm) cc_final: 0.6913 (mmp) REVERT: L 213 PHE cc_start: 0.7420 (t80) cc_final: 0.7120 (t80) REVERT: L 344 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7356 (mmtt) REVERT: L 352 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8469 (tp) outliers start: 69 outliers final: 43 residues processed: 509 average time/residue: 0.5807 time to fit residues: 349.9058 Evaluate side-chains 494 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 442 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 24 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 137 SER Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 289 MET Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 202 optimal weight: 4.9990 chunk 163 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 325 optimal weight: 1.9990 chunk 240 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 221 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN B 8 GLN D 70 ASN ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN K 115 GLN K 253 ASN L 115 GLN L 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.194875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.156522 restraints weight = 27725.652| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.07 r_work: 0.3508 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27452 Z= 0.177 Angle : 0.560 9.895 37260 Z= 0.293 Chirality : 0.044 0.256 4484 Planarity : 0.003 0.047 4576 Dihedral : 9.093 80.601 3906 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 2.51 % Allowed : 19.54 % Favored : 77.95 % 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: 1.43 (0.14), residues: 3420 helix: 2.06 (0.12), residues: 1920 sheet: -0.31 (0.25), residues: 416 loop : -0.53 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 436 TYR 0.017 0.001 TYR F 107 PHE 0.034 0.002 PHE J 202 TRP 0.026 0.001 TRP L 181 HIS 0.010 0.001 HIS L 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (27452) covalent geometry : angle 0.55993 / 0.29 (37260) hydrogen bonds : bond 0.04200 / 2.86 ( 1572) hydrogen bonds : angle 4.21337 / 2.96 ( 4560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9440.74 seconds wall clock time: 177 minutes 22.12 seconds (10642.12 seconds total)