Starting phenix.real_space_refine on Mon Aug 25 08:36:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmh_38477/08_2025/8xmh_38477.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmh_38477/08_2025/8xmh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xmh_38477/08_2025/8xmh_38477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmh_38477/08_2025/8xmh_38477.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmh_38477/08_2025/8xmh_38477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmh_38477/08_2025/8xmh_38477.cif" } 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-2.0-5787/lib/python3.9/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, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.81, 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: 2.28 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.05 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: 6.01 Time building geometry restraints manager: 2.98 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.420 Find NCS groups from input model: 0.650 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:8.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 aren 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 covalent geometry : bond 0.00401 (27452) covalent geometry : angle 0.52895 (37260) hydrogen bonds : bond 0.25057 ( 1572) hydrogen bonds : angle 7.78521 ( 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 : 1.071 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: 0.7714 (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: 0.6812 time to fit residues: 677.6095 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 : 1.017 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4277 r_free = 0.4277 target = 0.196128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.157205 restraints weight = 28161.863| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.26 r_work: 0.3501 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 27452 Z= 0.192 Angle : 0.586 7.950 37260 Z= 0.312 Chirality : 0.045 0.259 4484 Planarity : 0.004 0.045 4576 Dihedral : 9.228 78.610 3914 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.64 % Allowed : 13.84 % Favored : 81.52 % 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 aren not related in a simple way. whole: 0.38 (0.13), residues: 3420 helix: 0.82 (0.11), residues: 1908 sheet: 0.26 (0.26), residues: 400 loop : -0.59 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 151 TYR 0.027 0.001 TYR F 107 PHE 0.044 0.002 PHE I 202 TRP 0.007 0.001 TRP J 181 HIS 0.007 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00451 (27452) covalent geometry : angle 0.58591 (37260) hydrogen bonds : bond 0.05237 ( 1572) hydrogen bonds : angle 4.74437 ( 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 645 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 510 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: A 85 SER cc_start: 0.8376 (t) cc_final: 0.8123 (m) REVERT: A 189 ILE cc_start: 0.6476 (OUTLIER) cc_final: 0.6176 (mt) REVERT: B 134 GLN cc_start: 0.8612 (mp10) cc_final: 0.8004 (mp10) REVERT: B 189 ILE cc_start: 0.5993 (OUTLIER) cc_final: 0.5635 (tp) REVERT: B 213 ASP cc_start: 0.6879 (m-30) cc_final: 0.6011 (t0) REVERT: C 128 MET cc_start: 0.8125 (mmm) cc_final: 0.7684 (mmp) REVERT: C 134 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8300 (mp10) REVERT: C 135 SER cc_start: 0.8836 (t) cc_final: 0.8560 (m) REVERT: D 23 LYS cc_start: 0.8602 (mttp) cc_final: 0.8394 (mttm) REVERT: D 95 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7748 (mt) REVERT: D 137 SER cc_start: 0.8240 (t) cc_final: 0.8036 (p) REVERT: D 152 SER cc_start: 0.8647 (OUTLIER) cc_final: 0.8340 (m) REVERT: E 85 SER cc_start: 0.8785 (t) cc_final: 0.8464 (t) REVERT: F 128 MET cc_start: 0.8488 (mmm) cc_final: 0.8153 (mmt) REVERT: F 134 GLN cc_start: 0.8319 (mm-40) cc_final: 0.8076 (mp10) REVERT: F 189 ILE cc_start: 0.5788 (OUTLIER) cc_final: 0.5432 (tp) REVERT: G 62 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8297 (mt-10) REVERT: G 128 MET cc_start: 0.8053 (mmm) cc_final: 0.7779 (mmp) REVERT: G 134 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8141 (mp10) REVERT: G 145 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6690 (tp) REVERT: H 39 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7881 (mm-30) REVERT: H 69 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7479 (mtm-85) REVERT: H 85 SER cc_start: 0.8672 (t) cc_final: 0.8398 (m) REVERT: H 95 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7705 (mt) REVERT: H 152 SER cc_start: 0.8638 (OUTLIER) cc_final: 0.8299 (m) REVERT: I 250 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8453 (tp30) REVERT: J 18 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8406 (mp10) REVERT: K 71 GLN cc_start: 0.7125 (mm-40) cc_final: 0.6087 (tp40) REVERT: K 244 LEU cc_start: 0.8133 (tp) cc_final: 0.7855 (mm) REVERT: K 352 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8365 (tp) REVERT: L 77 GLN cc_start: 0.7443 (mt0) cc_final: 0.7048 (mp10) REVERT: L 112 MET cc_start: 0.8573 (mtm) cc_final: 0.8347 (mtp) REVERT: L 352 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8368 (tp) outliers start: 135 outliers final: 30 residues processed: 596 average time/residue: 0.6272 time to fit residues: 439.7329 Evaluate side-chains 495 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 449 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER 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 102 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 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 39 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 193 THR 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 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: 0.8980 chunk 21 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 124 optimal weight: 30.0000 chunk 274 optimal weight: 0.0670 chunk 251 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 262 optimal weight: 6.9990 chunk 283 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 253 ASN K 261 HIS K 434 ASN L 115 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.197710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.159639 restraints weight = 28156.395| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.17 r_work: 0.3506 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27452 Z= 0.129 Angle : 0.515 7.266 37260 Z= 0.273 Chirality : 0.043 0.215 4484 Planarity : 0.003 0.040 4576 Dihedral : 8.772 79.743 3910 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.71 % Allowed : 15.59 % Favored : 80.70 % 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 aren not related in a simple way. whole: 1.08 (0.14), residues: 3420 helix: 1.67 (0.12), residues: 1920 sheet: 0.03 (0.26), residues: 400 loop : -0.68 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 27 TYR 0.023 0.001 TYR F 107 PHE 0.036 0.001 PHE J 202 TRP 0.006 0.001 TRP J 181 HIS 0.006 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00290 (27452) covalent geometry : angle 0.51541 (37260) hydrogen bonds : bond 0.04123 ( 1572) hydrogen bonds : angle 4.30531 ( 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 609 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 501 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8325 (t) cc_final: 0.8110 (m) REVERT: B 134 GLN cc_start: 0.8512 (mp10) cc_final: 0.7802 (mp10) REVERT: B 189 ILE cc_start: 0.5843 (OUTLIER) cc_final: 0.5630 (mt) REVERT: B 213 ASP cc_start: 0.6849 (m-30) cc_final: 0.5988 (t0) REVERT: C 128 MET cc_start: 0.8206 (mmm) cc_final: 0.7757 (mmp) REVERT: C 135 SER cc_start: 0.8696 (t) cc_final: 0.8460 (m) REVERT: D 85 SER cc_start: 0.8672 (t) cc_final: 0.8282 (m) REVERT: D 95 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7739 (mt) REVERT: D 137 SER cc_start: 0.8225 (t) cc_final: 0.7997 (p) REVERT: D 152 SER cc_start: 0.8665 (OUTLIER) cc_final: 0.8361 (m) REVERT: D 184 LYS cc_start: 0.7318 (ttpp) cc_final: 0.7075 (mtpp) REVERT: E 139 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6661 (tp30) REVERT: F 128 MET cc_start: 0.8493 (mmm) cc_final: 0.8202 (mmt) REVERT: F 134 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7995 (mp10) REVERT: F 189 ILE cc_start: 0.5809 (OUTLIER) cc_final: 0.5526 (tp) REVERT: G 128 MET cc_start: 0.8045 (mmm) cc_final: 0.7768 (mmp) REVERT: H 39 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: H 95 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7748 (mt) REVERT: H 152 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8391 (m) REVERT: I 222 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8011 (tttp) REVERT: K 25 PHE cc_start: 0.6628 (t80) cc_final: 0.6409 (t80) REVERT: K 71 GLN cc_start: 0.6923 (mm-40) cc_final: 0.5827 (tp40) REVERT: K 112 MET cc_start: 0.8621 (mtm) cc_final: 0.8408 (mtp) REVERT: K 213 PHE cc_start: 0.7537 (t80) cc_final: 0.7224 (t80) REVERT: L 77 GLN cc_start: 0.7379 (mt0) cc_final: 0.7055 (mp10) REVERT: L 112 MET cc_start: 0.8606 (mtm) cc_final: 0.8394 (mtp) REVERT: L 352 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8416 (tp) REVERT: L 374 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7327 (tp-100) outliers start: 108 outliers final: 42 residues processed: 566 average time/residue: 0.6222 time to fit residues: 415.0388 Evaluate side-chains 505 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 454 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 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 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 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 189 ILE Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 59 GLU 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 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 187 SER 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 65 VAL 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 J residue 371 ILE Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 92 MET Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain K residue 236 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 236 LEU 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: 6.9990 chunk 138 optimal weight: 0.9980 chunk 192 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 165 optimal weight: 0.0170 chunk 279 optimal weight: 3.9990 chunk 247 optimal weight: 0.0970 chunk 60 optimal weight: 0.3980 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 8 GLN D 70 ASN D 134 GLN E 134 GLN H 81 ASN K 115 GLN K 253 ASN K 261 HIS L 155 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.199678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.162217 restraints weight = 27944.172| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.15 r_work: 0.3533 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27452 Z= 0.104 Angle : 0.477 7.270 37260 Z= 0.255 Chirality : 0.041 0.198 4484 Planarity : 0.003 0.042 4576 Dihedral : 8.447 77.942 3908 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.92 % Allowed : 17.10 % Favored : 79.98 % 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 aren not related in a simple way. whole: 1.47 (0.14), residues: 3420 helix: 2.10 (0.12), residues: 1916 sheet: -0.07 (0.26), residues: 400 loop : -0.62 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 27 TYR 0.024 0.001 TYR F 107 PHE 0.033 0.001 PHE I 202 TRP 0.005 0.001 TRP L 181 HIS 0.008 0.001 HIS G 185 Details of bonding type rmsd covalent geometry : bond 0.00221 (27452) covalent geometry : angle 0.47685 (37260) hydrogen bonds : bond 0.03503 ( 1572) hydrogen bonds : angle 4.08003 ( 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 570 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 485 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7673 (tt) REVERT: B 213 ASP cc_start: 0.6794 (m-30) cc_final: 0.6020 (t0) REVERT: C 128 MET cc_start: 0.8112 (mmm) cc_final: 0.7674 (mmp) REVERT: C 134 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8181 (mp10) REVERT: D 95 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7691 (mt) REVERT: D 137 SER cc_start: 0.8194 (t) cc_final: 0.7965 (p) REVERT: D 152 SER cc_start: 0.8778 (p) cc_final: 0.8566 (m) REVERT: F 59 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7839 (mm-30) REVERT: F 128 MET cc_start: 0.8489 (mmm) cc_final: 0.8176 (mmt) REVERT: F 189 ILE cc_start: 0.6066 (OUTLIER) cc_final: 0.5776 (tp) REVERT: G 62 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8340 (mt-10) REVERT: G 128 MET cc_start: 0.8028 (mmm) cc_final: 0.7709 (mmp) REVERT: H 39 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7877 (mm-30) REVERT: H 95 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7628 (mt) REVERT: I 222 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8058 (tttp) REVERT: J 222 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8026 (tttp) REVERT: K 25 PHE cc_start: 0.6572 (t80) cc_final: 0.6365 (t80) REVERT: K 71 GLN cc_start: 0.7101 (mm-40) cc_final: 0.6064 (tp40) REVERT: K 77 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7085 (mt0) REVERT: K 213 PHE cc_start: 0.7587 (t80) cc_final: 0.7284 (t80) REVERT: L 213 PHE cc_start: 0.7501 (t80) cc_final: 0.7204 (t80) outliers start: 85 outliers final: 39 residues processed: 534 average time/residue: 0.6282 time to fit residues: 394.4066 Evaluate side-chains 490 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 442 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER 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 C residue 58 THR Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 146 ASP 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 E residue 47 SER Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 102 VAL 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 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 I residue 28 ILE Chi-restraints excluded: chain I residue 36 MET Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 93 THR 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 J residue 39 ILE Chi-restraints excluded: chain J residue 140 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 K residue 77 GLN 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 314 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 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: 0.0040 chunk 26 optimal weight: 1.9990 chunk 242 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 247 optimal weight: 0.3980 chunk 328 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 336 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 8 GLN D 70 ASN D 81 ASN D 134 GLN E 134 GLN F 134 GLN H 70 ASN H 81 ASN I 253 ASN J 71 GLN K 253 ASN K 272 GLN L 77 GLN L 115 GLN L 155 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.199222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.162043 restraints weight = 27918.919| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.12 r_work: 0.3555 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27452 Z= 0.107 Angle : 0.482 7.199 37260 Z= 0.256 Chirality : 0.042 0.196 4484 Planarity : 0.003 0.044 4576 Dihedral : 8.373 77.982 3904 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.54 % Allowed : 16.83 % Favored : 79.64 % 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 aren not related in a simple way. whole: 1.59 (0.14), residues: 3420 helix: 2.21 (0.12), residues: 1924 sheet: -0.12 (0.25), residues: 400 loop : -0.56 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 341 TYR 0.022 0.001 TYR F 107 PHE 0.031 0.001 PHE I 202 TRP 0.006 0.001 TRP L 181 HIS 0.006 0.001 HIS G 185 Details of bonding type rmsd covalent geometry : bond 0.00234 (27452) covalent geometry : angle 0.48194 (37260) hydrogen bonds : bond 0.03475 ( 1572) hydrogen bonds : angle 4.02251 ( 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 565 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 462 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.7855 (tt) cc_final: 0.7649 (pp) REVERT: B 213 ASP cc_start: 0.6836 (m-30) cc_final: 0.6027 (t0) REVERT: C 128 MET cc_start: 0.8104 (mmm) cc_final: 0.7702 (mmp) REVERT: C 134 GLN cc_start: 0.8354 (tp40) cc_final: 0.8125 (mp10) REVERT: C 208 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7695 (ttm) REVERT: D 95 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7663 (mt) REVERT: D 137 SER cc_start: 0.8161 (t) cc_final: 0.7885 (p) REVERT: D 152 SER cc_start: 0.8631 (p) cc_final: 0.8399 (m) REVERT: F 59 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7809 (mm-30) REVERT: F 128 MET cc_start: 0.8450 (mmm) cc_final: 0.8152 (mmt) REVERT: F 134 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8151 (mp10) REVERT: F 189 ILE cc_start: 0.5884 (OUTLIER) cc_final: 0.5629 (tp) REVERT: G 62 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8307 (mt-10) REVERT: G 128 MET cc_start: 0.8014 (mmm) cc_final: 0.7678 (mmp) REVERT: H 95 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7678 (mt) REVERT: I 222 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8035 (tttp) REVERT: J 135 LEU cc_start: 0.8551 (mm) cc_final: 0.8236 (mm) REVERT: J 222 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8043 (tttp) REVERT: K 213 PHE cc_start: 0.7520 (t80) cc_final: 0.7201 (t80) REVERT: L 77 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: L 213 PHE cc_start: 0.7465 (t80) cc_final: 0.7150 (t80) REVERT: L 352 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8481 (tp) outliers start: 103 outliers final: 53 residues processed: 531 average time/residue: 0.6316 time to fit residues: 393.8429 Evaluate side-chains 495 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 433 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 141 VAL 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 137 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 208 MET 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 102 VAL 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 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 I residue 39 ILE 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 426 SER Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 140 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 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 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 74 VAL Chi-restraints excluded: chain L residue 77 GLN 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 352 LEU 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: 1.9990 chunk 250 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 317 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 142 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 8 GLN D 70 ASN D 81 ASN D 134 GLN E 134 GLN F 134 GLN H 70 ASN H 81 ASN K 85 GLN K 115 GLN K 253 ASN L 155 GLN L 272 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.196510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.157584 restraints weight = 27996.755| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.21 r_work: 0.3514 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27452 Z= 0.150 Angle : 0.523 7.592 37260 Z= 0.276 Chirality : 0.043 0.226 4484 Planarity : 0.003 0.045 4576 Dihedral : 8.707 80.493 3904 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.74 % Allowed : 16.62 % Favored : 79.64 % 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 aren not related in a simple way. whole: 1.47 (0.14), residues: 3420 helix: 2.09 (0.12), residues: 1928 sheet: -0.16 (0.25), residues: 400 loop : -0.60 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 436 TYR 0.023 0.001 TYR F 107 PHE 0.033 0.001 PHE I 202 TRP 0.009 0.001 TRP L 181 HIS 0.005 0.001 HIS G 185 Details of bonding type rmsd covalent geometry : bond 0.00355 (27452) covalent geometry : angle 0.52333 (37260) hydrogen bonds : bond 0.03979 ( 1572) hydrogen bonds : angle 4.13490 ( 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 572 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 463 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.7788 (tt) cc_final: 0.7548 (pp) REVERT: B 213 ASP cc_start: 0.6837 (m-30) cc_final: 0.6009 (t0) REVERT: C 128 MET cc_start: 0.8185 (mmm) cc_final: 0.7717 (mmp) REVERT: C 134 GLN cc_start: 0.8440 (tp40) cc_final: 0.8173 (mp10) REVERT: D 95 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7773 (mt) REVERT: D 137 SER cc_start: 0.8208 (t) cc_final: 0.7946 (p) REVERT: D 152 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8340 (m) REVERT: F 59 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7818 (mm-30) REVERT: F 128 MET cc_start: 0.8480 (mmm) cc_final: 0.8166 (mmt) REVERT: F 189 ILE cc_start: 0.5809 (OUTLIER) cc_final: 0.5565 (tp) REVERT: G 62 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8327 (mt-10) REVERT: G 128 MET cc_start: 0.8116 (mmm) cc_final: 0.7784 (mmp) REVERT: H 95 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7747 (mt) REVERT: I 222 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8045 (tttp) REVERT: J 18 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8256 (mp10) REVERT: J 222 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8043 (tttp) REVERT: K 71 GLN cc_start: 0.7048 (mm-40) cc_final: 0.6162 (tm-30) REVERT: K 86 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7850 (mm) REVERT: K 213 PHE cc_start: 0.7445 (t80) cc_final: 0.7127 (t80) REVERT: L 77 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: L 213 PHE cc_start: 0.7420 (t80) cc_final: 0.7118 (t80) REVERT: L 344 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7337 (mmpt) REVERT: L 352 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8465 (tp) outliers start: 109 outliers final: 58 residues processed: 532 average time/residue: 0.6280 time to fit residues: 392.7453 Evaluate side-chains 508 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 439 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 47 SER 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 141 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 69 ARG 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 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 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 I residue 24 PHE Chi-restraints excluded: chain I residue 39 ILE 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 123 ILE Chi-restraints excluded: chain J residue 140 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 J residue 394 THR Chi-restraints excluded: chain K residue 86 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 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 74 VAL Chi-restraints excluded: chain L residue 77 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 129 optimal weight: 0.0670 chunk 76 optimal weight: 3.9990 chunk 118 optimal weight: 0.4980 chunk 306 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 321 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 322 optimal weight: 0.8980 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN D 70 ASN E 134 GLN F 134 GLN G 30 HIS H 70 ASN H 81 ASN K 85 GLN K 253 ASN L 77 GLN L 115 GLN L 155 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.196723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.158144 restraints weight = 27830.331| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.12 r_work: 0.3518 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27452 Z= 0.148 Angle : 0.528 7.379 37260 Z= 0.277 Chirality : 0.043 0.223 4484 Planarity : 0.003 0.045 4576 Dihedral : 8.747 80.178 3904 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.43 % Allowed : 17.51 % Favored : 79.05 % 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 aren not related in a simple way. whole: 1.44 (0.14), residues: 3420 helix: 2.07 (0.12), residues: 1928 sheet: -0.16 (0.25), residues: 400 loop : -0.62 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 27 TYR 0.021 0.001 TYR F 107 PHE 0.033 0.001 PHE I 202 TRP 0.013 0.001 TRP L 181 HIS 0.007 0.001 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.00350 (27452) covalent geometry : angle 0.52811 (37260) hydrogen bonds : bond 0.03958 ( 1572) hydrogen bonds : angle 4.13750 ( 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 548 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 448 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.7875 (tt) cc_final: 0.7671 (pp) REVERT: B 213 ASP cc_start: 0.6894 (m-30) cc_final: 0.6054 (t0) REVERT: C 128 MET cc_start: 0.8156 (mmm) cc_final: 0.7664 (mmp) REVERT: C 134 GLN cc_start: 0.8469 (tp40) cc_final: 0.8169 (mp10) REVERT: D 95 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7774 (mt) REVERT: D 137 SER cc_start: 0.8201 (t) cc_final: 0.7949 (p) REVERT: D 152 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8427 (m) REVERT: E 134 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7802 (mp-120) REVERT: F 59 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7823 (mm-30) REVERT: F 128 MET cc_start: 0.8485 (mmm) cc_final: 0.8177 (mmt) REVERT: F 189 ILE cc_start: 0.5953 (OUTLIER) cc_final: 0.5646 (tp) REVERT: F 213 ASP cc_start: 0.6999 (m-30) cc_final: 0.6180 (t0) REVERT: G 62 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: G 128 MET cc_start: 0.8096 (mmm) cc_final: 0.7775 (mmp) REVERT: G 145 ILE cc_start: 0.7778 (tt) cc_final: 0.7453 (tp) REVERT: H 59 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7547 (pm20) REVERT: H 95 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7732 (mt) REVERT: H 208 MET cc_start: 0.8030 (ptm) cc_final: 0.7706 (ptt) REVERT: I 222 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8077 (tttp) REVERT: J 18 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8248 (mp10) REVERT: J 135 LEU cc_start: 0.8604 (mm) cc_final: 0.8260 (mm) REVERT: J 222 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8058 (tttp) REVERT: K 71 GLN cc_start: 0.7186 (mm-40) cc_final: 0.6253 (tm-30) REVERT: K 86 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7919 (mm) REVERT: K 213 PHE cc_start: 0.7506 (t80) cc_final: 0.7198 (t80) REVERT: L 36 MET cc_start: 0.7278 (mmm) cc_final: 0.6942 (mmp) REVERT: L 77 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7270 (mp10) REVERT: L 213 PHE cc_start: 0.7430 (t80) cc_final: 0.7124 (t80) REVERT: L 344 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7330 (mmpt) REVERT: L 352 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8389 (tp) outliers start: 100 outliers final: 60 residues processed: 516 average time/residue: 0.6403 time to fit residues: 387.5271 Evaluate side-chains 504 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 432 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 47 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 137 SER 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 135 SER Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 208 MET 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 181 LEU 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 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 18 GLN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 193 THR 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 J residue 394 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 91 PHE 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 236 LEU 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 77 GLN 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: 0.5980 chunk 18 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 278 optimal weight: 0.0170 chunk 229 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN D 70 ASN E 134 GLN F 134 GLN H 70 ASN K 115 GLN K 155 GLN K 253 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.198242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.160256 restraints weight = 28040.877| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.14 r_work: 0.3549 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27452 Z= 0.108 Angle : 0.490 7.166 37260 Z= 0.260 Chirality : 0.042 0.191 4484 Planarity : 0.003 0.043 4576 Dihedral : 8.473 78.011 3904 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.92 % Allowed : 18.30 % Favored : 78.78 % 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 aren not related in a simple way. whole: 1.61 (0.14), residues: 3420 helix: 2.24 (0.12), residues: 1924 sheet: -0.20 (0.25), residues: 400 loop : -0.55 (0.18), residues: 1096 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 0.031 0.001 PHE I 202 TRP 0.015 0.001 TRP L 181 HIS 0.005 0.001 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.00234 (27452) covalent geometry : angle 0.48991 (37260) hydrogen bonds : bond 0.03485 ( 1572) hydrogen bonds : angle 4.03343 ( 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 532 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 447 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.6879 (m-30) cc_final: 0.6068 (t0) REVERT: C 128 MET cc_start: 0.8098 (mmm) cc_final: 0.7601 (mmp) REVERT: C 134 GLN cc_start: 0.8415 (tp40) cc_final: 0.8131 (mp10) REVERT: D 95 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7686 (mt) REVERT: D 137 SER cc_start: 0.8158 (t) cc_final: 0.7878 (p) REVERT: D 152 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8425 (m) REVERT: F 59 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7810 (mm-30) REVERT: F 128 MET cc_start: 0.8451 (mmm) cc_final: 0.8153 (mmt) REVERT: F 189 ILE cc_start: 0.5917 (OUTLIER) cc_final: 0.5660 (tp) REVERT: F 213 ASP cc_start: 0.6975 (m-30) cc_final: 0.6174 (t0) REVERT: G 62 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8346 (mt-10) REVERT: G 128 MET cc_start: 0.8017 (mmm) cc_final: 0.7680 (mmp) REVERT: G 145 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7485 (tp) REVERT: H 95 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7684 (mt) REVERT: H 208 MET cc_start: 0.7984 (ptm) cc_final: 0.7606 (ptt) REVERT: I 92 MET cc_start: 0.7145 (mmt) cc_final: 0.6900 (tpt) REVERT: I 222 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8075 (tttp) REVERT: J 18 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8253 (mp10) REVERT: J 222 LYS cc_start: 0.8452 (mmtt) cc_final: 0.8042 (tttp) REVERT: K 71 GLN cc_start: 0.7124 (mm-40) cc_final: 0.6213 (tm-30) REVERT: K 213 PHE cc_start: 0.7463 (t80) cc_final: 0.7150 (t80) REVERT: L 36 MET cc_start: 0.7218 (mmm) cc_final: 0.6935 (mmp) REVERT: L 71 GLN cc_start: 0.6829 (mm-40) cc_final: 0.5782 (tm-30) REVERT: L 213 PHE cc_start: 0.7396 (t80) cc_final: 0.7099 (t80) REVERT: L 344 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7458 (mmpt) REVERT: L 352 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8416 (tp) outliers start: 85 outliers final: 49 residues processed: 504 average time/residue: 0.6291 time to fit residues: 372.7819 Evaluate side-chains 488 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 429 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 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 141 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 69 ARG 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 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 G residue 145 ILE Chi-restraints excluded: chain G residue 181 LEU 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 152 SER Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 39 ILE 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 352 LEU 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 140 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 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 74 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 227 optimal weight: 0.0970 chunk 289 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 316 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN D 70 ASN D 81 ASN E 134 GLN F 134 GLN H 70 ASN I 253 ASN K 155 GLN K 253 ASN L 115 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.195978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.159315 restraints weight = 27960.455| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.08 r_work: 0.3484 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3702 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= 0.158 Angle : 0.538 9.361 37260 Z= 0.283 Chirality : 0.043 0.225 4484 Planarity : 0.003 0.046 4576 Dihedral : 8.732 80.433 3904 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.85 % Allowed : 18.68 % Favored : 78.47 % 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 aren not related in a simple way. whole: 1.46 (0.14), residues: 3420 helix: 2.11 (0.12), residues: 1920 sheet: -0.17 (0.25), residues: 400 loop : -0.62 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 341 TYR 0.020 0.001 TYR F 107 PHE 0.033 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 covalent geometry : bond 0.00375 (27452) covalent geometry : angle 0.53789 (37260) hydrogen bonds : bond 0.03977 ( 1572) hydrogen bonds : angle 4.12985 ( 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 520 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 437 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.6837 (m-30) cc_final: 0.6131 (t0) REVERT: C 128 MET cc_start: 0.8225 (mmm) cc_final: 0.7738 (mmp) REVERT: C 134 GLN cc_start: 0.8454 (tp40) cc_final: 0.8229 (mp10) REVERT: D 95 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7772 (mt) REVERT: D 137 SER cc_start: 0.8216 (t) cc_final: 0.7943 (p) REVERT: D 152 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8487 (m) REVERT: D 184 LYS cc_start: 0.7286 (ttpp) cc_final: 0.6822 (ptmt) REVERT: F 59 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: F 128 MET cc_start: 0.8515 (mmm) cc_final: 0.8211 (mmt) REVERT: F 189 ILE cc_start: 0.6035 (OUTLIER) cc_final: 0.5740 (tp) REVERT: F 213 ASP cc_start: 0.6999 (m-30) cc_final: 0.6200 (t0) REVERT: G 62 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8445 (mt-10) REVERT: G 128 MET cc_start: 0.8182 (mmm) cc_final: 0.7845 (mmp) REVERT: G 145 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7620 (tp) REVERT: H 95 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7756 (mt) REVERT: H 184 LYS cc_start: 0.7520 (mtpt) cc_final: 0.7247 (mtmm) REVERT: H 208 MET cc_start: 0.8032 (ptm) cc_final: 0.7706 (ptt) REVERT: I 222 LYS cc_start: 0.8511 (mmtt) cc_final: 0.8090 (tttp) REVERT: J 18 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8251 (mp10) REVERT: J 222 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8076 (tttp) REVERT: K 71 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6233 (tm-30) REVERT: K 213 PHE cc_start: 0.7532 (t80) cc_final: 0.7214 (t80) REVERT: L 36 MET cc_start: 0.7240 (mmm) cc_final: 0.6919 (mmp) REVERT: L 213 PHE cc_start: 0.7461 (t80) cc_final: 0.7148 (t80) REVERT: L 344 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7339 (mmtt) REVERT: L 352 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8412 (tp) outliers start: 83 outliers final: 55 residues processed: 496 average time/residue: 0.6295 time to fit residues: 367.1297 Evaluate side-chains 490 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 425 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 C residue 47 SER 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 141 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 69 ARG 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 G residue 145 ILE Chi-restraints excluded: chain G residue 181 LEU 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 152 SER Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 39 ILE 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 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 140 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 193 THR 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 J residue 394 THR Chi-restraints excluded: chain K residue 106 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 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: 0.9990 chunk 44 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 178 optimal weight: 0.0770 chunk 232 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 60 optimal weight: 0.0570 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN C 134 GLN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN E 134 GLN H 70 ASN K 115 GLN K 155 GLN K 253 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.198367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.160646 restraints weight = 28016.977| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.18 r_work: 0.3550 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3777 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= 0.109 Angle : 0.498 9.218 37260 Z= 0.262 Chirality : 0.042 0.197 4484 Planarity : 0.003 0.045 4576 Dihedral : 8.411 77.491 3904 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.34 % Allowed : 19.06 % Favored : 78.61 % 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 aren not related in a simple way. whole: 1.64 (0.14), residues: 3420 helix: 2.27 (0.12), residues: 1924 sheet: -0.16 (0.25), residues: 400 loop : -0.56 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 27 TYR 0.020 0.001 TYR F 107 PHE 0.030 0.001 PHE I 202 TRP 0.018 0.001 TRP L 181 HIS 0.006 0.001 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.00239 (27452) covalent geometry : angle 0.49787 (37260) hydrogen bonds : bond 0.03468 ( 1572) hydrogen bonds : angle 4.01221 ( 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 519 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 451 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.6919 (m-30) cc_final: 0.6175 (t0) REVERT: C 128 MET cc_start: 0.8085 (mmm) cc_final: 0.7580 (mmp) REVERT: C 134 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: D 95 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7676 (mt) REVERT: D 137 SER cc_start: 0.8148 (t) cc_final: 0.7891 (p) REVERT: D 152 SER cc_start: 0.8654 (OUTLIER) cc_final: 0.8430 (m) REVERT: D 184 LYS cc_start: 0.7199 (ttpp) cc_final: 0.6786 (ptmt) REVERT: F 59 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: F 128 MET cc_start: 0.8465 (mmm) cc_final: 0.8159 (mmt) REVERT: F 189 ILE cc_start: 0.5911 (OUTLIER) cc_final: 0.5652 (tp) REVERT: F 213 ASP cc_start: 0.6963 (m-30) cc_final: 0.6118 (t0) REVERT: G 62 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: G 128 MET cc_start: 0.7980 (mmm) cc_final: 0.7657 (mmp) REVERT: G 145 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7630 (tp) REVERT: H 95 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7679 (mt) REVERT: H 208 MET cc_start: 0.7975 (ptm) cc_final: 0.7604 (ptt) REVERT: I 222 LYS cc_start: 0.8449 (mmtt) cc_final: 0.8079 (tttp) REVERT: J 18 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8257 (mp10) REVERT: J 92 MET cc_start: 0.7242 (mmt) cc_final: 0.6977 (tpt) REVERT: J 222 LYS cc_start: 0.8426 (mmtt) cc_final: 0.8058 (tttp) REVERT: K 71 GLN cc_start: 0.7182 (mm-40) cc_final: 0.6226 (tm-30) REVERT: K 213 PHE cc_start: 0.7491 (t80) cc_final: 0.7180 (t80) REVERT: L 36 MET cc_start: 0.7218 (mmm) cc_final: 0.6945 (mmp) REVERT: L 71 GLN cc_start: 0.6860 (mm-40) cc_final: 0.5901 (tm-30) REVERT: L 213 PHE cc_start: 0.7429 (t80) cc_final: 0.7127 (t80) REVERT: L 344 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7378 (mmpt) REVERT: L 352 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8400 (tp) outliers start: 68 outliers final: 45 residues processed: 500 average time/residue: 0.6406 time to fit residues: 375.4986 Evaluate side-chains 487 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 431 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 141 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 134 GLN 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 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 69 ARG 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 F residue 208 MET 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 181 LEU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL 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 123 ILE 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 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 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 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 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: 0.9980 chunk 61 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 163 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 325 optimal weight: 1.9990 chunk 240 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 221 optimal weight: 0.0020 chunk 91 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN D 70 ASN D 81 ASN E 134 GLN F 134 GLN H 70 ASN H 81 ASN K 155 GLN K 253 ASN L 115 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.197102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.158658 restraints weight = 27790.347| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.25 r_work: 0.3528 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27452 Z= 0.127 Angle : 0.519 10.257 37260 Z= 0.272 Chirality : 0.043 0.204 4484 Planarity : 0.003 0.044 4576 Dihedral : 8.526 79.496 3904 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.23 % Allowed : 19.47 % Favored : 78.30 % 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 aren not related in a simple way. whole: 1.58 (0.14), residues: 3420 helix: 2.22 (0.12), residues: 1924 sheet: -0.16 (0.25), residues: 400 loop : -0.58 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 27 TYR 0.020 0.001 TYR F 107 PHE 0.031 0.001 PHE I 202 TRP 0.025 0.001 TRP L 181 HIS 0.007 0.001 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.00293 (27452) covalent geometry : angle 0.51886 (37260) hydrogen bonds : bond 0.03703 ( 1572) hydrogen bonds : angle 4.04800 ( 4560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10197.30 seconds wall clock time: 174 minutes 53.17 seconds (10493.17 seconds total)