Starting phenix.real_space_refine on Mon Aug 25 08:37:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1u_36804/08_2025/8k1u_36804.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1u_36804/08_2025/8k1u_36804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k1u_36804/08_2025/8k1u_36804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1u_36804/08_2025/8k1u_36804.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k1u_36804/08_2025/8k1u_36804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1u_36804/08_2025/8k1u_36804.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 24 5.49 5 S 118 5.16 5 Na 4 4.78 5 C 17450 2.51 5 N 4422 2.21 5 O 4942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 26964 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "B" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "D" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "E" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1698 Classifications: {'peptide': 216} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 210} Chain: "F" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "G" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "H" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1698 Classifications: {'peptide': 216} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 210} Chain: "I" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "J" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "K" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "L" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 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: 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: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 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: 5.28, per 1000 atoms: 0.20 Number of scatterers: 26964 At special positions: 0 Unit cell: (173.47, 133.63, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 118 16.00 P 24 15.00 Na 4 11.00 O 4942 8.00 N 4422 7.00 C 17450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6364 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 20 sheets defined 57.6% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 15 through 28 removed outlier: 3.598A pdb=" N SER A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG A 69 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 211 through 220 removed outlier: 3.645A pdb=" N LYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 28 removed outlier: 3.599A pdb=" N SER B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG B 69 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 123 through 138 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.646A pdb=" N LYS B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 28 removed outlier: 3.598A pdb=" N SER C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 45 Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG C 69 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'C' and resid 106 through 116 Processing helix chain 'C' and resid 123 through 138 Processing helix chain 'C' and resid 211 through 220 removed outlier: 3.644A pdb=" N LYS C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 28 removed outlier: 3.599A pdb=" N SER D 20 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 45 Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG D 69 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 95 Processing helix chain 'D' and resid 106 through 116 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'D' and resid 211 through 220 removed outlier: 3.645A pdb=" N LYS D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 28 removed outlier: 3.598A pdb=" N SER E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 45 Processing helix chain 'E' and resid 59 through 65 Processing helix chain 'E' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG E 69 " --> pdb=" O LEU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 95 Processing helix chain 'E' and resid 106 through 116 Processing helix chain 'E' and resid 123 through 138 Processing helix chain 'E' and resid 211 through 220 removed outlier: 3.645A pdb=" N LYS E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 28 removed outlier: 3.598A pdb=" N SER F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 45 Processing helix chain 'F' and resid 59 through 65 Processing helix chain 'F' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG F 69 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 95 Processing helix chain 'F' and resid 106 through 116 Processing helix chain 'F' and resid 123 through 138 Processing helix chain 'F' and resid 211 through 220 removed outlier: 3.645A pdb=" N LYS F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 28 removed outlier: 3.597A pdb=" N SER G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 45 Processing helix chain 'G' and resid 59 through 65 Processing helix chain 'G' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG G 69 " --> pdb=" O LEU G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 95 Processing helix chain 'G' and resid 106 through 116 Processing helix chain 'G' and resid 123 through 138 Processing helix chain 'G' and resid 211 through 220 removed outlier: 3.644A pdb=" N LYS G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 28 removed outlier: 3.598A pdb=" N SER H 20 " --> pdb=" O ARG H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 45 Processing helix chain 'H' and resid 59 through 65 Processing helix chain 'H' and resid 66 through 71 removed outlier: 6.145A pdb=" N ARG H 69 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 95 Processing helix chain 'H' and resid 106 through 116 Processing helix chain 'H' and resid 123 through 138 Processing helix chain 'H' and resid 211 through 220 removed outlier: 3.646A pdb=" N LYS H 215 " --> pdb=" O LYS H 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 37 removed outlier: 3.750A pdb=" N ILE I 28 " --> pdb=" O PHE I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 59 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 73 through 90 Processing helix chain 'I' and resid 90 through 103 removed outlier: 4.066A pdb=" N PHE I 94 " --> pdb=" O GLY I 90 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 removed outlier: 3.562A pdb=" N VAL I 114 " --> pdb=" O GLU I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 157 removed outlier: 3.553A pdb=" N VAL I 130 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE I 150 " --> pdb=" O LEU I 146 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG I 151 " --> pdb=" O ILE I 147 " (cutoff:3.500A) Proline residue: I 154 - end of helix Processing helix chain 'I' and resid 158 through 174 removed outlier: 3.531A pdb=" N LEU I 162 " --> pdb=" O TRP I 158 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 207 Processing helix chain 'I' and resid 208 through 218 Processing helix chain 'I' and resid 220 through 224 Processing helix chain 'I' and resid 225 through 250 Processing helix chain 'I' and resid 261 through 275 Processing helix chain 'I' and resid 285 through 289 removed outlier: 3.540A pdb=" N MET I 289 " --> pdb=" O PHE I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 303 removed outlier: 3.518A pdb=" N ILE I 303 " --> pdb=" O LEU I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 315 through 331 Processing helix chain 'I' and resid 344 through 373 Processing helix chain 'I' and resid 376 through 389 Processing helix chain 'I' and resid 397 through 401 Processing helix chain 'I' and resid 402 through 419 Processing helix chain 'I' and resid 419 through 428 removed outlier: 4.163A pdb=" N PHE I 427 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 37 removed outlier: 3.749A pdb=" N ILE J 28 " --> pdb=" O PHE J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 59 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 73 through 90 Processing helix chain 'J' and resid 90 through 103 removed outlier: 4.066A pdb=" N PHE J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 118 removed outlier: 3.563A pdb=" N VAL J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 157 removed outlier: 3.553A pdb=" N VAL J 130 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE J 150 " --> pdb=" O LEU J 146 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG J 151 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Proline residue: J 154 - end of helix Processing helix chain 'J' and resid 158 through 174 removed outlier: 3.532A pdb=" N LEU J 162 " --> pdb=" O TRP J 158 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 207 Processing helix chain 'J' and resid 208 through 218 Processing helix chain 'J' and resid 220 through 224 Processing helix chain 'J' and resid 225 through 250 Processing helix chain 'J' and resid 261 through 275 Processing helix chain 'J' and resid 285 through 289 removed outlier: 3.539A pdb=" N MET J 289 " --> pdb=" O PHE J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 303 removed outlier: 3.518A pdb=" N ILE J 303 " --> pdb=" O LEU J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 331 Processing helix chain 'J' and resid 344 through 373 Processing helix chain 'J' and resid 376 through 389 Processing helix chain 'J' and resid 397 through 401 Processing helix chain 'J' and resid 402 through 419 Processing helix chain 'J' and resid 419 through 428 removed outlier: 4.163A pdb=" N PHE J 427 " --> pdb=" O PHE J 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 37 removed outlier: 3.749A pdb=" N ILE K 28 " --> pdb=" O PHE K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 59 Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 73 through 90 Processing helix chain 'K' and resid 90 through 103 removed outlier: 4.066A pdb=" N PHE K 94 " --> pdb=" O GLY K 90 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU K 97 " --> pdb=" O THR K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 removed outlier: 3.563A pdb=" N VAL K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 157 removed outlier: 3.553A pdb=" N VAL K 130 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE K 150 " --> pdb=" O LEU K 146 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG K 151 " --> pdb=" O ILE K 147 " (cutoff:3.500A) Proline residue: K 154 - end of helix Processing helix chain 'K' and resid 158 through 174 removed outlier: 3.532A pdb=" N LEU K 162 " --> pdb=" O TRP K 158 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 207 Processing helix chain 'K' and resid 208 through 218 Processing helix chain 'K' and resid 220 through 224 Processing helix chain 'K' and resid 225 through 250 Processing helix chain 'K' and resid 261 through 275 Processing helix chain 'K' and resid 285 through 289 removed outlier: 3.539A pdb=" N MET K 289 " --> pdb=" O PHE K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 303 removed outlier: 3.519A pdb=" N ILE K 303 " --> pdb=" O LEU K 299 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 331 Processing helix chain 'K' and resid 344 through 373 Processing helix chain 'K' and resid 376 through 389 Processing helix chain 'K' and resid 397 through 401 Processing helix chain 'K' and resid 402 through 419 Processing helix chain 'K' and resid 419 through 428 removed outlier: 4.163A pdb=" N PHE K 427 " --> pdb=" O PHE K 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 37 removed outlier: 3.749A pdb=" N ILE L 28 " --> pdb=" O PHE L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 59 Processing helix chain 'L' and resid 67 through 72 Processing helix chain 'L' and resid 73 through 90 Processing helix chain 'L' and resid 90 through 103 removed outlier: 4.066A pdb=" N PHE L 94 " --> pdb=" O GLY L 90 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 118 removed outlier: 3.562A pdb=" N VAL L 114 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 157 removed outlier: 3.553A pdb=" N VAL L 130 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE L 150 " --> pdb=" O LEU L 146 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG L 151 " --> pdb=" O ILE L 147 " (cutoff:3.500A) Proline residue: L 154 - end of helix Processing helix chain 'L' and resid 158 through 174 removed outlier: 3.532A pdb=" N LEU L 162 " --> pdb=" O TRP L 158 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 207 Processing helix chain 'L' and resid 208 through 218 Processing helix chain 'L' and resid 220 through 224 Processing helix chain 'L' and resid 225 through 250 Processing helix chain 'L' and resid 261 through 275 Processing helix chain 'L' and resid 285 through 289 removed outlier: 3.540A pdb=" N MET L 289 " --> pdb=" O PHE L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 290 through 303 removed outlier: 3.519A pdb=" N ILE L 303 " --> pdb=" O LEU L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 331 Processing helix chain 'L' and resid 344 through 373 Processing helix chain 'L' and resid 376 through 389 Processing helix chain 'L' and resid 397 through 401 Processing helix chain 'L' and resid 402 through 419 Processing helix chain 'L' and resid 419 through 428 removed outlier: 4.162A pdb=" N PHE L 427 " --> pdb=" O PHE L 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.600A pdb=" N TYR A 73 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 100 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 122 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 102 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 141 through 146 removed outlier: 6.260A pdb=" N VAL A 141 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU A 157 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A 143 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS A 204 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE A 183 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 206 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.599A pdb=" N TYR B 73 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 100 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE B 122 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 102 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 141 through 146 removed outlier: 6.260A pdb=" N VAL B 141 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU B 157 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN B 143 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE B 183 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 206 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.599A pdb=" N TYR C 73 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE C 100 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE C 122 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL C 102 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 141 through 146 removed outlier: 6.261A pdb=" N VAL C 141 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU C 157 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN C 143 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS C 204 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE C 183 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL C 206 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.599A pdb=" N TYR D 73 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE D 100 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE D 122 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL D 102 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 141 through 146 removed outlier: 6.260A pdb=" N VAL D 141 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU D 157 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN D 143 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS D 204 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE D 183 " --> pdb=" O CYS D 204 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL D 206 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 51 through 54 removed outlier: 3.600A pdb=" N TYR E 73 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE E 100 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE E 122 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL E 102 " --> pdb=" O ILE E 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 141 through 146 removed outlier: 6.260A pdb=" N VAL E 141 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU E 157 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN E 143 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS E 204 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE E 183 " --> pdb=" O CYS E 204 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL E 206 " --> pdb=" O LEU E 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.599A pdb=" N TYR F 73 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE F 100 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE F 122 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL F 102 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 141 through 146 removed outlier: 6.260A pdb=" N VAL F 141 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU F 157 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN F 143 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N CYS F 204 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE F 183 " --> pdb=" O CYS F 204 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL F 206 " --> pdb=" O LEU F 181 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.599A pdb=" N TYR G 73 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE G 100 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE G 122 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL G 102 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 141 through 146 removed outlier: 6.260A pdb=" N VAL G 141 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU G 157 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN G 143 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE G 183 " --> pdb=" O CYS G 204 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL G 206 " --> pdb=" O LEU G 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 51 through 54 removed outlier: 3.599A pdb=" N TYR H 73 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE H 100 " --> pdb=" O ARG H 120 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE H 122 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL H 102 " --> pdb=" O ILE H 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 141 through 146 removed outlier: 6.260A pdb=" N VAL H 141 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU H 157 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN H 143 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE H 183 " --> pdb=" O CYS H 204 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL H 206 " --> pdb=" O LEU H 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 336 through 338 removed outlier: 4.659A pdb=" N THR I 336 " --> pdb=" O ILE I 343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 336 through 338 removed outlier: 4.659A pdb=" N THR J 336 " --> pdb=" O ILE J 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 336 through 338 removed outlier: 4.659A pdb=" N THR K 336 " --> pdb=" O ILE K 343 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 336 through 338 removed outlier: 4.659A pdb=" N THR L 336 " --> pdb=" O ILE L 343 " (cutoff:3.500A) 1588 hydrogen bonds defined for protein. 4572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.15 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4874 1.33 - 1.45: 6501 1.45 - 1.57: 15853 1.57 - 1.69: 40 1.69 - 1.81: 200 Bond restraints: 27468 Sorted by residual: bond pdb=" CA VAL I 66 " pdb=" CB VAL I 66 " ideal model delta sigma weight residual 1.545 1.495 0.050 1.51e-02 4.39e+03 1.10e+01 bond pdb=" CA VAL L 66 " pdb=" CB VAL L 66 " ideal model delta sigma weight residual 1.545 1.496 0.049 1.51e-02 4.39e+03 1.07e+01 bond pdb=" CA VAL K 66 " pdb=" CB VAL K 66 " ideal model delta sigma weight residual 1.544 1.499 0.045 1.39e-02 5.18e+03 1.04e+01 bond pdb=" CA VAL K 65 " pdb=" CB VAL K 65 " ideal model delta sigma weight residual 1.540 1.498 0.041 1.37e-02 5.33e+03 8.99e+00 bond pdb=" C HIS H 185 " pdb=" N HIS H 186 " ideal model delta sigma weight residual 1.333 1.292 0.040 1.42e-02 4.96e+03 8.13e+00 ... (remaining 27463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 36809 1.68 - 3.37: 372 3.37 - 5.05: 45 5.05 - 6.74: 37 6.74 - 8.42: 17 Bond angle restraints: 37280 Sorted by residual: angle pdb=" O VAL J 65 " pdb=" C VAL J 65 " pdb=" N VAL J 66 " ideal model delta sigma weight residual 121.83 127.14 -5.31 1.03e+00 9.43e-01 2.66e+01 angle pdb=" CA VAL J 65 " pdb=" C VAL J 65 " pdb=" N VAL J 66 " ideal model delta sigma weight residual 117.28 111.87 5.41 1.16e+00 7.43e-01 2.17e+01 angle pdb=" N VAL K 65 " pdb=" CA VAL K 65 " pdb=" C VAL K 65 " ideal model delta sigma weight residual 111.00 106.05 4.95 1.09e+00 8.42e-01 2.06e+01 angle pdb=" C VAL K 66 " pdb=" CA VAL K 66 " pdb=" CB VAL K 66 " ideal model delta sigma weight residual 110.95 103.70 7.25 1.61e+00 3.86e-01 2.03e+01 angle pdb=" N HIS G 185 " pdb=" CA HIS G 185 " pdb=" C HIS G 185 " ideal model delta sigma weight residual 108.58 116.01 -7.43 1.82e+00 3.02e-01 1.67e+01 ... (remaining 37275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 15705 17.90 - 35.80: 551 35.80 - 53.70: 104 53.70 - 71.60: 52 71.60 - 89.50: 16 Dihedral angle restraints: 16428 sinusoidal: 6538 harmonic: 9890 Sorted by residual: dihedral pdb=" CA GLU A 201 " pdb=" C GLU A 201 " pdb=" N GLN A 202 " pdb=" CA GLN A 202 " ideal model delta harmonic sigma weight residual 180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLU D 201 " pdb=" C GLU D 201 " pdb=" N GLN D 202 " pdb=" CA GLN D 202 " ideal model delta harmonic sigma weight residual 180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLU F 201 " pdb=" C GLU F 201 " pdb=" N GLN F 202 " pdb=" CA GLN F 202 " ideal model delta harmonic sigma weight residual -180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 16425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3738 0.055 - 0.110: 650 0.110 - 0.164: 89 0.164 - 0.219: 6 0.219 - 0.274: 3 Chirality restraints: 4486 Sorted by residual: chirality pdb=" CA VAL K 66 " pdb=" N VAL K 66 " pdb=" C VAL K 66 " pdb=" CB VAL K 66 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA VAL J 66 " pdb=" N VAL J 66 " pdb=" C VAL J 66 " pdb=" CB VAL J 66 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA VAL K 65 " pdb=" N VAL K 65 " pdb=" C VAL K 65 " pdb=" CB VAL K 65 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 4483 not shown) Planarity restraints: 4578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA K 64 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C ALA K 64 " 0.028 2.00e-02 2.50e+03 pdb=" O ALA K 64 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL K 65 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L 15 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO L 16 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 16 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 16 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 15 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO J 16 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO J 16 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 16 " -0.023 5.00e-02 4.00e+02 ... (remaining 4575 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 9165 2.86 - 3.43: 28700 3.43 - 4.00: 51582 4.00 - 4.57: 72145 4.57 - 5.14: 106384 Nonbonded interactions: 267976 Sorted by model distance: nonbonded pdb=" OH TYR D 108 " pdb=" OE1 GLU E 60 " model vdw 2.294 3.040 nonbonded pdb=" O ILE J 418 " pdb=" OG1 THR J 422 " model vdw 2.301 3.040 nonbonded pdb=" O ILE I 418 " pdb=" OG1 THR I 422 " model vdw 2.301 3.040 nonbonded pdb=" O ILE K 418 " pdb=" OG1 THR K 422 " model vdw 2.301 3.040 nonbonded pdb=" O ILE L 418 " pdb=" OG1 THR L 422 " model vdw 2.301 3.040 ... (remaining 267971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 221) selection = (chain 'B' and resid 7 through 221) selection = (chain 'C' and resid 7 through 221) selection = (chain 'D' and resid 7 through 221) selection = (chain 'E' and resid 7 through 221) selection = (chain 'F' and resid 7 through 221) selection = (chain 'G' and resid 7 through 221) selection = (chain 'H' and resid 7 through 221) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.200 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 27468 Z= 0.124 Angle : 0.503 8.419 37280 Z= 0.276 Chirality : 0.042 0.274 4486 Planarity : 0.003 0.040 4578 Dihedral : 10.679 89.502 10064 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.51 % Allowed : 3.12 % Favored : 95.37 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.12), residues: 3422 helix: -1.28 (0.09), residues: 1836 sheet: 0.83 (0.27), residues: 400 loop : -1.03 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 220 TYR 0.005 0.001 TYR C 107 PHE 0.021 0.001 PHE L 202 TRP 0.002 0.001 TRP C 101 HIS 0.004 0.001 HIS E 185 Details of bonding type rmsd covalent geometry : bond 0.00210 (27468) covalent geometry : angle 0.50259 (37280) hydrogen bonds : bond 0.26662 ( 1588) hydrogen bonds : angle 7.47877 ( 4572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 843 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.7279 (mmm) cc_final: 0.7002 (mmp) REVERT: I 390 THR cc_start: 0.8141 (p) cc_final: 0.7890 (p) REVERT: L 390 THR cc_start: 0.8107 (p) cc_final: 0.7834 (p) outliers start: 44 outliers final: 6 residues processed: 869 average time/residue: 0.5483 time to fit residues: 558.1618 Evaluate side-chains 503 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 497 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain L residue 352 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS C 81 ASN C 134 GLN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN G 134 GLN I 85 GLN I 120 GLN I 253 ASN I 282 ASN J 155 GLN J 195 ASN J 253 ASN J 434 ASN K 18 GLN K 119 ASN K 120 GLN K 155 GLN K 253 ASN K 434 ASN L 85 GLN L 120 GLN L 253 ASN L 282 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.178318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136947 restraints weight = 29754.553| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.36 r_work: 0.3290 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27468 Z= 0.181 Angle : 0.582 7.987 37280 Z= 0.309 Chirality : 0.045 0.229 4486 Planarity : 0.004 0.038 4578 Dihedral : 9.323 86.039 3915 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.40 % Allowed : 12.22 % Favored : 84.39 % 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: 0.30 (0.13), residues: 3422 helix: 0.87 (0.11), residues: 1912 sheet: 0.30 (0.26), residues: 404 loop : -0.90 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 340 TYR 0.019 0.001 TYR I 270 PHE 0.045 0.002 PHE J 202 TRP 0.003 0.001 TRP D 101 HIS 0.012 0.001 HIS G 185 Details of bonding type rmsd covalent geometry : bond 0.00418 (27468) covalent geometry : angle 0.58190 (37280) hydrogen bonds : bond 0.04877 ( 1588) hydrogen bonds : angle 4.67156 ( 4572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 525 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7420 (ttm-80) REVERT: A 85 SER cc_start: 0.8693 (t) cc_final: 0.8370 (m) REVERT: A 95 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7506 (mt) REVERT: A 128 MET cc_start: 0.8687 (mmm) cc_final: 0.8037 (mmp) REVERT: B 155 GLU cc_start: 0.6757 (tt0) cc_final: 0.6086 (mt-10) REVERT: B 183 ILE cc_start: 0.7543 (mt) cc_final: 0.7040 (mp) REVERT: B 213 ASP cc_start: 0.6929 (m-30) cc_final: 0.6596 (m-30) REVERT: C 147 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7149 (mp) REVERT: C 155 GLU cc_start: 0.6777 (tt0) cc_final: 0.6104 (mt-10) REVERT: C 183 ILE cc_start: 0.7733 (mt) cc_final: 0.7207 (mp) REVERT: C 213 ASP cc_start: 0.6958 (m-30) cc_final: 0.6692 (m-30) REVERT: D 27 ARG cc_start: 0.7907 (mtm110) cc_final: 0.7679 (mtm110) REVERT: D 72 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: D 181 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.5674 (mp) REVERT: E 86 THR cc_start: 0.8902 (t) cc_final: 0.8523 (m) REVERT: E 95 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7644 (mt) REVERT: E 222 MET cc_start: 0.6289 (ttm) cc_final: 0.6047 (ttp) REVERT: F 213 ASP cc_start: 0.7787 (m-30) cc_final: 0.7295 (p0) REVERT: G 111 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8157 (mtpt) REVERT: G 134 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7871 (mp10) REVERT: G 213 ASP cc_start: 0.7627 (m-30) cc_final: 0.7308 (p0) REVERT: H 86 THR cc_start: 0.8835 (t) cc_final: 0.8476 (m) REVERT: I 36 MET cc_start: 0.7609 (mmm) cc_final: 0.7371 (mmm) REVERT: I 97 LEU cc_start: 0.7593 (mt) cc_final: 0.7253 (mt) REVERT: I 106 ILE cc_start: 0.6909 (mm) cc_final: 0.6498 (tp) REVERT: I 217 LYS cc_start: 0.7498 (ptmt) cc_final: 0.6949 (mmtt) REVERT: I 222 LYS cc_start: 0.8542 (mmmt) cc_final: 0.7662 (ptmm) REVERT: I 344 LYS cc_start: 0.7445 (tttt) cc_final: 0.7236 (ptpp) REVERT: I 400 GLU cc_start: 0.7919 (mp0) cc_final: 0.7539 (mp0) REVERT: I 418 ILE cc_start: 0.8231 (tp) cc_final: 0.7986 (pt) REVERT: J 91 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7157 (t80) REVERT: J 92 MET cc_start: 0.7693 (tpt) cc_final: 0.7454 (mmm) REVERT: K 91 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7106 (t80) REVERT: K 220 ARG cc_start: 0.6847 (mmt180) cc_final: 0.6443 (mmp80) REVERT: K 334 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7894 (pttp) REVERT: L 36 MET cc_start: 0.7620 (mmm) cc_final: 0.7334 (mmm) REVERT: L 86 ILE cc_start: 0.8113 (mp) cc_final: 0.7840 (mp) REVERT: L 97 LEU cc_start: 0.7603 (mt) cc_final: 0.7321 (mt) REVERT: L 217 LYS cc_start: 0.7519 (ptmt) cc_final: 0.6961 (mmtt) REVERT: L 222 LYS cc_start: 0.8609 (ptmm) cc_final: 0.7969 (mmmt) REVERT: L 344 LYS cc_start: 0.7450 (tttt) cc_final: 0.7194 (ptpp) REVERT: L 400 GLU cc_start: 0.7868 (mp0) cc_final: 0.7605 (mp0) REVERT: L 418 ILE cc_start: 0.8221 (tp) cc_final: 0.7986 (pt) outliers start: 99 outliers final: 30 residues processed: 592 average time/residue: 0.6106 time to fit residues: 423.9909 Evaluate side-chains 510 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 471 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 374 GLN Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 47 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 259 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 263 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 210 HIS B 105 GLN B 134 GLN C 134 GLN D 210 HIS I 85 GLN I 239 ASN I 253 ASN J 119 ASN J 434 ASN K 119 ASN K 434 ASN L 85 GLN L 253 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.173991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132048 restraints weight = 29655.781| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.39 r_work: 0.3242 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 27468 Z= 0.226 Angle : 0.605 8.011 37280 Z= 0.319 Chirality : 0.046 0.263 4486 Planarity : 0.004 0.042 4578 Dihedral : 9.305 79.332 3912 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.19 % Allowed : 13.42 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.13), residues: 3422 helix: 1.30 (0.11), residues: 1880 sheet: 0.06 (0.26), residues: 404 loop : -1.12 (0.16), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 436 TYR 0.014 0.002 TYR I 270 PHE 0.043 0.002 PHE J 202 TRP 0.005 0.001 TRP I 158 HIS 0.008 0.001 HIS F 185 Details of bonding type rmsd covalent geometry : bond 0.00544 (27468) covalent geometry : angle 0.60518 (37280) hydrogen bonds : bond 0.05094 ( 1588) hydrogen bonds : angle 4.59815 ( 4572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 483 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7473 (ttm-80) REVERT: A 95 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7642 (mt) REVERT: A 128 MET cc_start: 0.8786 (mmm) cc_final: 0.8169 (mmp) REVERT: A 189 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7140 (tp) REVERT: B 155 GLU cc_start: 0.6672 (tt0) cc_final: 0.6033 (mt-10) REVERT: B 183 ILE cc_start: 0.7758 (mt) cc_final: 0.7230 (mp) REVERT: B 213 ASP cc_start: 0.6890 (m-30) cc_final: 0.6522 (m-30) REVERT: C 147 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7026 (mp) REVERT: C 155 GLU cc_start: 0.6776 (tt0) cc_final: 0.6245 (mt-10) REVERT: C 183 ILE cc_start: 0.7895 (mt) cc_final: 0.7389 (mp) REVERT: C 213 ASP cc_start: 0.6834 (m-30) cc_final: 0.6606 (m-30) REVERT: D 27 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7713 (mtm110) REVERT: D 72 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: D 85 SER cc_start: 0.8717 (t) cc_final: 0.8408 (m) REVERT: D 181 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.5712 (mp) REVERT: E 39 GLU cc_start: 0.7917 (mp0) cc_final: 0.7630 (mp0) REVERT: E 86 THR cc_start: 0.8946 (t) cc_final: 0.8470 (m) REVERT: E 134 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7692 (mp10) REVERT: E 213 ASP cc_start: 0.6650 (OUTLIER) cc_final: 0.6392 (t70) REVERT: F 128 MET cc_start: 0.8649 (mmm) cc_final: 0.8290 (mmm) REVERT: F 134 GLN cc_start: 0.7928 (mm110) cc_final: 0.7720 (mp10) REVERT: F 138 ASP cc_start: 0.7693 (t0) cc_final: 0.7302 (m-30) REVERT: G 69 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.8172 (ttm-80) REVERT: G 93 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.7991 (tmtt) REVERT: G 111 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8193 (mtpt) REVERT: G 128 MET cc_start: 0.8661 (mmm) cc_final: 0.8293 (mmm) REVERT: G 134 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7665 (mp10) REVERT: G 138 ASP cc_start: 0.7624 (t0) cc_final: 0.7164 (m-30) REVERT: H 39 GLU cc_start: 0.7873 (mp0) cc_final: 0.7559 (mp0) REVERT: H 72 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7757 (tp30) REVERT: H 134 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7809 (mp10) REVERT: H 139 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7125 (pm20) REVERT: H 213 ASP cc_start: 0.6746 (OUTLIER) cc_final: 0.6520 (t70) REVERT: I 36 MET cc_start: 0.7626 (mmm) cc_final: 0.7290 (mmm) REVERT: I 97 LEU cc_start: 0.7655 (mt) cc_final: 0.7279 (mt) REVERT: I 106 ILE cc_start: 0.7094 (mm) cc_final: 0.6808 (tp) REVERT: I 110 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7071 (mt-10) REVERT: I 158 TRP cc_start: 0.7664 (m100) cc_final: 0.6872 (m-90) REVERT: I 217 LYS cc_start: 0.7489 (ptmt) cc_final: 0.6975 (mmtt) REVERT: I 222 LYS cc_start: 0.8514 (mmmt) cc_final: 0.7775 (ptpt) REVERT: J 91 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7298 (t80) REVERT: J 220 ARG cc_start: 0.6987 (mmt180) cc_final: 0.6595 (mmp80) REVERT: J 344 LYS cc_start: 0.7885 (tppt) cc_final: 0.7582 (tppt) REVERT: K 91 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7168 (t80) REVERT: K 220 ARG cc_start: 0.7048 (mmt180) cc_final: 0.6668 (mmp80) REVERT: K 250 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8230 (mm-30) REVERT: K 334 LYS cc_start: 0.8558 (mmtt) cc_final: 0.7945 (pttp) REVERT: L 36 MET cc_start: 0.7608 (mmm) cc_final: 0.7275 (mmm) REVERT: L 97 LEU cc_start: 0.7717 (mt) cc_final: 0.7347 (mt) REVERT: L 110 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7154 (mt-10) REVERT: L 155 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: L 217 LYS cc_start: 0.7509 (ptmt) cc_final: 0.7015 (mmtt) REVERT: L 418 ILE cc_start: 0.8301 (tp) cc_final: 0.7984 (pt) outliers start: 122 outliers final: 48 residues processed: 563 average time/residue: 0.5552 time to fit residues: 365.0223 Evaluate side-chains 515 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 447 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 134 GLN Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 83 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 310 optimal weight: 9.9990 chunk 326 optimal weight: 2.9990 chunk 311 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 305 optimal weight: 8.9990 chunk 247 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 232 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN G 134 GLN I 85 GLN I 253 ASN J 77 GLN J 119 ASN J 434 ASN K 119 ASN K 434 ASN L 85 GLN L 253 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.172889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130444 restraints weight = 29742.229| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.44 r_work: 0.3221 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 27468 Z= 0.230 Angle : 0.605 8.309 37280 Z= 0.317 Chirality : 0.046 0.277 4486 Planarity : 0.004 0.048 4578 Dihedral : 9.211 77.495 3910 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.15 % Allowed : 15.00 % Favored : 80.85 % 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: 0.52 (0.14), residues: 3422 helix: 1.33 (0.11), residues: 1888 sheet: -0.07 (0.25), residues: 416 loop : -1.17 (0.16), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 436 TYR 0.013 0.002 TYR E 45 PHE 0.041 0.002 PHE J 202 TRP 0.006 0.001 TRP I 158 HIS 0.006 0.001 HIS F 185 Details of bonding type rmsd covalent geometry : bond 0.00557 (27468) covalent geometry : angle 0.60464 (37280) hydrogen bonds : bond 0.04874 ( 1588) hydrogen bonds : angle 4.56184 ( 4572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 444 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7754 (ttp80) cc_final: 0.7499 (ttm-80) REVERT: A 85 SER cc_start: 0.8783 (t) cc_final: 0.8462 (m) REVERT: A 128 MET cc_start: 0.8871 (mmm) cc_final: 0.8215 (mmp) REVERT: A 189 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7216 (tp) REVERT: B 155 GLU cc_start: 0.6679 (tt0) cc_final: 0.6090 (mt-10) REVERT: B 183 ILE cc_start: 0.7828 (mt) cc_final: 0.7334 (mp) REVERT: C 147 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6991 (mp) REVERT: C 155 GLU cc_start: 0.6779 (tt0) cc_final: 0.6262 (mt-10) REVERT: C 183 ILE cc_start: 0.7954 (mt) cc_final: 0.7415 (mp) REVERT: D 27 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7725 (mtm110) REVERT: D 72 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8262 (tm-30) REVERT: D 85 SER cc_start: 0.8786 (t) cc_final: 0.8444 (m) REVERT: E 39 GLU cc_start: 0.7939 (mp0) cc_final: 0.7631 (mp0) REVERT: E 86 THR cc_start: 0.8905 (t) cc_final: 0.8480 (m) REVERT: E 134 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7695 (mp10) REVERT: E 139 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7056 (pm20) REVERT: E 213 ASP cc_start: 0.6744 (OUTLIER) cc_final: 0.6522 (t70) REVERT: F 93 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.7878 (tmtt) REVERT: F 128 MET cc_start: 0.8637 (mmm) cc_final: 0.8270 (mmm) REVERT: F 134 GLN cc_start: 0.7950 (mm110) cc_final: 0.7724 (mp10) REVERT: F 138 ASP cc_start: 0.7720 (t0) cc_final: 0.7324 (m-30) REVERT: G 69 ARG cc_start: 0.8453 (mtm-85) cc_final: 0.8197 (ttm-80) REVERT: G 111 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8171 (mtpt) REVERT: G 128 MET cc_start: 0.8653 (mmm) cc_final: 0.8269 (mmm) REVERT: G 134 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7951 (mp10) REVERT: G 138 ASP cc_start: 0.7551 (t0) cc_final: 0.7269 (m-30) REVERT: H 39 GLU cc_start: 0.7964 (mp0) cc_final: 0.7627 (mp0) REVERT: H 72 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7827 (tp30) REVERT: H 86 THR cc_start: 0.8938 (t) cc_final: 0.8483 (m) REVERT: H 134 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: H 139 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6999 (pm20) REVERT: H 213 ASP cc_start: 0.6736 (OUTLIER) cc_final: 0.6518 (t70) REVERT: I 29 ILE cc_start: 0.7968 (mm) cc_final: 0.7705 (mt) REVERT: I 97 LEU cc_start: 0.7531 (mt) cc_final: 0.7169 (mt) REVERT: I 106 ILE cc_start: 0.7181 (mm) cc_final: 0.6889 (tp) REVERT: I 110 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: I 158 TRP cc_start: 0.7646 (m100) cc_final: 0.6877 (m-90) REVERT: I 217 LYS cc_start: 0.7571 (ptmt) cc_final: 0.7010 (mmtt) REVERT: I 222 LYS cc_start: 0.8527 (mmmt) cc_final: 0.7791 (ptpt) REVERT: I 418 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7957 (pt) REVERT: J 91 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7183 (t80) REVERT: J 220 ARG cc_start: 0.7061 (mmt180) cc_final: 0.6697 (mmp80) REVERT: J 350 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8752 (tttm) REVERT: K 71 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: K 91 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7139 (t80) REVERT: K 220 ARG cc_start: 0.7123 (mmt180) cc_final: 0.6630 (mmp80) REVERT: K 250 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8269 (mm-30) REVERT: K 334 LYS cc_start: 0.8530 (mmtt) cc_final: 0.7896 (pttp) REVERT: K 373 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6705 (mt-10) REVERT: L 29 ILE cc_start: 0.7945 (mm) cc_final: 0.7683 (mt) REVERT: L 97 LEU cc_start: 0.7707 (mt) cc_final: 0.7337 (mt) REVERT: L 110 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: L 155 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: L 217 LYS cc_start: 0.7577 (ptmt) cc_final: 0.7029 (mmtt) REVERT: L 222 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8255 (ptpt) REVERT: L 418 ILE cc_start: 0.8262 (tp) cc_final: 0.7929 (pt) outliers start: 121 outliers final: 58 residues processed: 526 average time/residue: 0.5785 time to fit residues: 357.4469 Evaluate side-chains 512 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 431 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 134 GLN Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 418 ILE Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 350 LYS Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 127 optimal weight: 0.0980 chunk 98 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 291 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 210 HIS B 105 GLN B 134 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN I 253 ASN J 119 ASN J 434 ASN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 ASN K 434 ASN L 253 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.175845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.133948 restraints weight = 29597.466| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.48 r_work: 0.3250 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 27468 Z= 0.131 Angle : 0.510 7.503 37280 Z= 0.271 Chirality : 0.043 0.217 4486 Planarity : 0.003 0.042 4578 Dihedral : 8.734 83.376 3910 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.67 % Allowed : 15.79 % Favored : 80.54 % 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: 0.93 (0.14), residues: 3422 helix: 1.74 (0.12), residues: 1896 sheet: -0.08 (0.25), residues: 416 loop : -1.06 (0.16), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 27 TYR 0.011 0.001 TYR E 108 PHE 0.033 0.001 PHE J 202 TRP 0.004 0.001 TRP J 267 HIS 0.006 0.001 HIS G 185 Details of bonding type rmsd covalent geometry : bond 0.00297 (27468) covalent geometry : angle 0.50986 (37280) hydrogen bonds : bond 0.03888 ( 1588) hydrogen bonds : angle 4.27889 ( 4572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 457 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7781 (ttp80) cc_final: 0.7493 (ttp-110) REVERT: A 72 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: A 85 SER cc_start: 0.8564 (t) cc_final: 0.8248 (m) REVERT: A 128 MET cc_start: 0.8771 (mmm) cc_final: 0.8130 (mmp) REVERT: A 189 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7108 (tp) REVERT: B 155 GLU cc_start: 0.6645 (tt0) cc_final: 0.6036 (mt-10) REVERT: B 183 ILE cc_start: 0.7730 (mt) cc_final: 0.7240 (mp) REVERT: C 147 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6949 (mp) REVERT: C 155 GLU cc_start: 0.6699 (tt0) cc_final: 0.6203 (mt-10) REVERT: C 183 ILE cc_start: 0.7835 (mt) cc_final: 0.7353 (mp) REVERT: D 27 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7418 (ttp-110) REVERT: D 85 SER cc_start: 0.8593 (t) cc_final: 0.8261 (m) REVERT: D 128 MET cc_start: 0.8778 (mmm) cc_final: 0.8576 (mmm) REVERT: E 39 GLU cc_start: 0.7843 (mp0) cc_final: 0.7528 (mp0) REVERT: E 86 THR cc_start: 0.8756 (t) cc_final: 0.8478 (m) REVERT: E 95 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7610 (mt) REVERT: E 139 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7034 (pm20) REVERT: E 213 ASP cc_start: 0.6697 (OUTLIER) cc_final: 0.6495 (t70) REVERT: F 128 MET cc_start: 0.8507 (mmm) cc_final: 0.8137 (mmm) REVERT: F 137 SER cc_start: 0.8638 (OUTLIER) cc_final: 0.8365 (p) REVERT: F 138 ASP cc_start: 0.7718 (t0) cc_final: 0.7298 (m-30) REVERT: G 69 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.8139 (ttm-80) REVERT: G 93 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.7879 (tmtt) REVERT: G 111 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8091 (mtpt) REVERT: G 128 MET cc_start: 0.8591 (mmm) cc_final: 0.8197 (mmm) REVERT: G 138 ASP cc_start: 0.7420 (t0) cc_final: 0.7149 (m-30) REVERT: H 72 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7744 (tp30) REVERT: H 86 THR cc_start: 0.8779 (t) cc_final: 0.8491 (m) REVERT: H 139 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: H 213 ASP cc_start: 0.6732 (OUTLIER) cc_final: 0.6524 (t70) REVERT: I 97 LEU cc_start: 0.7519 (mt) cc_final: 0.7209 (mt) REVERT: I 106 ILE cc_start: 0.7052 (mm) cc_final: 0.6787 (tp) REVERT: I 158 TRP cc_start: 0.7635 (m100) cc_final: 0.6881 (m-90) REVERT: I 217 LYS cc_start: 0.7388 (ptmt) cc_final: 0.6907 (mmtt) REVERT: I 222 LYS cc_start: 0.8501 (mmmt) cc_final: 0.7787 (ptpt) REVERT: I 400 GLU cc_start: 0.8283 (mp0) cc_final: 0.8057 (mp0) REVERT: I 418 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7845 (pt) REVERT: J 41 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7589 (p) REVERT: J 71 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.6922 (tm-30) REVERT: J 91 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7032 (t80) REVERT: J 220 ARG cc_start: 0.6958 (mmt180) cc_final: 0.6607 (mmp80) REVERT: J 352 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8020 (tt) REVERT: J 373 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6308 (mt-10) REVERT: K 71 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.6879 (tm-30) REVERT: K 220 ARG cc_start: 0.6981 (mmt180) cc_final: 0.6487 (mmp80) REVERT: K 334 LYS cc_start: 0.8487 (mmtt) cc_final: 0.7850 (pttp) REVERT: L 29 ILE cc_start: 0.7830 (mm) cc_final: 0.7567 (mt) REVERT: L 97 LEU cc_start: 0.7589 (mt) cc_final: 0.7255 (mt) REVERT: L 155 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: L 217 LYS cc_start: 0.7410 (ptmt) cc_final: 0.6922 (mmtt) REVERT: L 400 GLU cc_start: 0.8265 (mp0) cc_final: 0.8029 (mp0) REVERT: L 418 ILE cc_start: 0.8223 (tp) cc_final: 0.7830 (pt) outliers start: 107 outliers final: 43 residues processed: 527 average time/residue: 0.5700 time to fit residues: 353.1060 Evaluate side-chains 498 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 435 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 418 ILE Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 228 optimal weight: 6.9990 chunk 198 optimal weight: 0.5980 chunk 143 optimal weight: 0.4980 chunk 112 optimal weight: 5.9990 chunk 336 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 78 optimal weight: 9.9990 chunk 201 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS B 83 GLN B 134 GLN C 105 GLN C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN I 85 GLN I 253 ASN J 119 ASN J 434 ASN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 ASN K 434 ASN L 85 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.177531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.135623 restraints weight = 29695.296| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.40 r_work: 0.3294 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 27468 Z= 0.109 Angle : 0.489 7.532 37280 Z= 0.259 Chirality : 0.042 0.200 4486 Planarity : 0.003 0.042 4578 Dihedral : 8.414 80.825 3910 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.53 % Allowed : 16.75 % Favored : 79.72 % 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: 1.16 (0.14), residues: 3422 helix: 1.95 (0.12), residues: 1904 sheet: -0.12 (0.25), residues: 416 loop : -0.97 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 27 TYR 0.010 0.001 TYR F 107 PHE 0.031 0.001 PHE L 202 TRP 0.007 0.001 TRP I 181 HIS 0.007 0.001 HIS F 185 Details of bonding type rmsd covalent geometry : bond 0.00236 (27468) covalent geometry : angle 0.48922 (37280) hydrogen bonds : bond 0.03504 ( 1588) hydrogen bonds : angle 4.12860 ( 4572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 456 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7839 (ttp80) cc_final: 0.7622 (ttp-110) REVERT: A 72 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8012 (mt-10) REVERT: A 85 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.8109 (m) REVERT: A 128 MET cc_start: 0.8697 (mmm) cc_final: 0.8036 (mmp) REVERT: A 189 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.7081 (tp) REVERT: B 155 GLU cc_start: 0.6639 (tt0) cc_final: 0.6034 (mt-10) REVERT: B 183 ILE cc_start: 0.7559 (mt) cc_final: 0.7046 (mp) REVERT: C 59 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: C 147 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6912 (mp) REVERT: C 155 GLU cc_start: 0.6617 (tt0) cc_final: 0.6201 (mt-10) REVERT: C 183 ILE cc_start: 0.7699 (mt) cc_final: 0.7154 (mp) REVERT: D 85 SER cc_start: 0.8467 (t) cc_final: 0.8154 (m) REVERT: E 39 GLU cc_start: 0.7824 (mp0) cc_final: 0.7587 (mp0) REVERT: E 95 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7580 (mt) REVERT: E 115 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8007 (mttt) REVERT: E 139 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7006 (pm20) REVERT: E 213 ASP cc_start: 0.6753 (OUTLIER) cc_final: 0.6547 (t70) REVERT: F 128 MET cc_start: 0.8488 (mmm) cc_final: 0.8144 (mmm) REVERT: F 134 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: F 138 ASP cc_start: 0.7713 (t0) cc_final: 0.7343 (m-30) REVERT: G 69 ARG cc_start: 0.8345 (mtm-85) cc_final: 0.8072 (ttm-80) REVERT: G 111 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8053 (mtpt) REVERT: G 128 MET cc_start: 0.8523 (mmm) cc_final: 0.8165 (mmm) REVERT: G 134 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: G 138 ASP cc_start: 0.7392 (t0) cc_final: 0.7166 (m-30) REVERT: H 59 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7600 (mt-10) REVERT: H 72 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7749 (tp30) REVERT: H 86 THR cc_start: 0.8783 (t) cc_final: 0.8472 (m) REVERT: H 139 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: I 97 LEU cc_start: 0.7530 (mt) cc_final: 0.7153 (mt) REVERT: I 106 ILE cc_start: 0.7041 (mm) cc_final: 0.6805 (tp) REVERT: I 158 TRP cc_start: 0.7575 (m100) cc_final: 0.6894 (m-90) REVERT: I 217 LYS cc_start: 0.7358 (ptmt) cc_final: 0.6889 (mmtt) REVERT: I 222 LYS cc_start: 0.8483 (mmmt) cc_final: 0.7821 (ptpt) REVERT: J 41 THR cc_start: 0.7754 (OUTLIER) cc_final: 0.7548 (p) REVERT: J 46 SER cc_start: 0.7557 (OUTLIER) cc_final: 0.7193 (t) REVERT: J 71 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: J 91 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7034 (t80) REVERT: J 92 MET cc_start: 0.7479 (tpt) cc_final: 0.7266 (mmm) REVERT: J 220 ARG cc_start: 0.6937 (mmt180) cc_final: 0.6593 (mmp80) REVERT: J 352 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7985 (tt) REVERT: K 46 SER cc_start: 0.7582 (OUTLIER) cc_final: 0.7219 (t) REVERT: K 71 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: K 220 ARG cc_start: 0.6976 (mmt180) cc_final: 0.6632 (mmp80) REVERT: K 334 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7865 (pttp) REVERT: L 97 LEU cc_start: 0.7518 (mt) cc_final: 0.7186 (mt) REVERT: L 155 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: L 217 LYS cc_start: 0.7388 (ptmt) cc_final: 0.6925 (mmtt) outliers start: 103 outliers final: 33 residues processed: 523 average time/residue: 0.6162 time to fit residues: 378.0102 Evaluate side-chains 482 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 427 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 95 optimal weight: 0.0770 chunk 249 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 201 optimal weight: 0.7980 chunk 283 optimal weight: 8.9990 chunk 336 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS B 134 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN H 83 GLN J 119 ASN J 434 ASN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 ASN K 434 ASN L 85 GLN L 253 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.134154 restraints weight = 29487.784| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.43 r_work: 0.3259 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 27468 Z= 0.150 Angle : 0.529 7.813 37280 Z= 0.279 Chirality : 0.044 0.294 4486 Planarity : 0.003 0.045 4578 Dihedral : 8.606 74.485 3910 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.71 % Allowed : 16.88 % Favored : 79.41 % 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: 1.09 (0.14), residues: 3422 helix: 1.88 (0.12), residues: 1904 sheet: -0.14 (0.25), residues: 416 loop : -0.98 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 27 TYR 0.010 0.001 TYR F 73 PHE 0.034 0.002 PHE K 202 TRP 0.008 0.001 TRP I 181 HIS 0.005 0.001 HIS F 185 Details of bonding type rmsd covalent geometry : bond 0.00351 (27468) covalent geometry : angle 0.52919 (37280) hydrogen bonds : bond 0.03952 ( 1588) hydrogen bonds : angle 4.21532 ( 4572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 439 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7647 (ttm-80) REVERT: A 66 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8393 (mt) REVERT: A 72 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: A 85 SER cc_start: 0.8607 (t) cc_final: 0.8335 (m) REVERT: A 128 MET cc_start: 0.8780 (mmm) cc_final: 0.8162 (mmp) REVERT: A 189 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7101 (tp) REVERT: B 155 GLU cc_start: 0.6808 (tt0) cc_final: 0.6192 (mt-10) REVERT: B 183 ILE cc_start: 0.7714 (mt) cc_final: 0.7235 (mp) REVERT: C 59 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: C 147 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6893 (mp) REVERT: C 155 GLU cc_start: 0.6893 (tt0) cc_final: 0.6429 (mt-10) REVERT: C 183 ILE cc_start: 0.7795 (mt) cc_final: 0.7286 (mp) REVERT: D 27 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7739 (mtm110) REVERT: D 85 SER cc_start: 0.8648 (t) cc_final: 0.8369 (m) REVERT: D 128 MET cc_start: 0.8752 (mmm) cc_final: 0.8548 (mmm) REVERT: E 39 GLU cc_start: 0.7894 (mp0) cc_final: 0.7610 (mp0) REVERT: E 95 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7741 (mt) REVERT: E 139 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7087 (pm20) REVERT: E 213 ASP cc_start: 0.6844 (OUTLIER) cc_final: 0.6604 (t70) REVERT: F 128 MET cc_start: 0.8651 (mmm) cc_final: 0.8324 (mmm) REVERT: F 134 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: F 138 ASP cc_start: 0.7836 (t0) cc_final: 0.7439 (m-30) REVERT: F 146 ASP cc_start: 0.7008 (m-30) cc_final: 0.6747 (p0) REVERT: G 111 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8293 (mtpt) REVERT: G 128 MET cc_start: 0.8678 (mmm) cc_final: 0.8337 (mmm) REVERT: G 134 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7875 (mp10) REVERT: G 138 ASP cc_start: 0.7531 (t0) cc_final: 0.7291 (m-30) REVERT: H 72 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7831 (tp30) REVERT: H 86 THR cc_start: 0.8882 (t) cc_final: 0.8423 (m) REVERT: H 139 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7032 (pm20) REVERT: I 71 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7296 (tp40) REVERT: I 97 LEU cc_start: 0.7593 (mt) cc_final: 0.7252 (mt) REVERT: I 106 ILE cc_start: 0.7216 (mm) cc_final: 0.6981 (tp) REVERT: I 158 TRP cc_start: 0.7680 (m100) cc_final: 0.6996 (m-90) REVERT: I 217 LYS cc_start: 0.7483 (ptmt) cc_final: 0.6998 (mmtt) REVERT: I 222 LYS cc_start: 0.8467 (mmmt) cc_final: 0.7829 (ptpt) REVERT: I 289 MET cc_start: 0.8415 (mmt) cc_final: 0.8208 (mmt) REVERT: I 418 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7936 (pt) REVERT: J 71 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: J 91 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7196 (t80) REVERT: J 220 ARG cc_start: 0.7163 (mmt180) cc_final: 0.6655 (mmp80) REVERT: J 373 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6190 (mm-30) REVERT: K 71 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: K 220 ARG cc_start: 0.7183 (mmt180) cc_final: 0.6693 (mmp80) REVERT: K 334 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7953 (pttp) REVERT: L 71 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7253 (tp40) REVERT: L 97 LEU cc_start: 0.7591 (mt) cc_final: 0.7238 (mt) REVERT: L 142 LEU cc_start: 0.7193 (tp) cc_final: 0.6905 (mm) REVERT: L 155 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: L 217 LYS cc_start: 0.7527 (ptmt) cc_final: 0.7047 (mmtt) REVERT: L 222 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8252 (ptpt) REVERT: L 418 ILE cc_start: 0.8243 (tp) cc_final: 0.7929 (pt) outliers start: 108 outliers final: 49 residues processed: 513 average time/residue: 0.6185 time to fit residues: 373.3255 Evaluate side-chains 499 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 429 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 418 ILE Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain K residue 249 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 283 optimal weight: 10.0000 chunk 339 optimal weight: 0.9980 chunk 288 optimal weight: 0.6980 chunk 259 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS B 134 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS G 134 GLN J 119 ASN J 434 ASN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 434 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.172296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.129805 restraints weight = 29831.125| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.37 r_work: 0.3215 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 27468 Z= 0.244 Angle : 0.630 8.470 37280 Z= 0.328 Chirality : 0.047 0.323 4486 Planarity : 0.004 0.049 4578 Dihedral : 9.142 78.114 3910 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.91 % Allowed : 17.02 % Favored : 79.07 % 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: 0.69 (0.14), residues: 3422 helix: 1.53 (0.12), residues: 1896 sheet: -0.16 (0.25), residues: 416 loop : -1.13 (0.16), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 331 TYR 0.013 0.002 TYR E 45 PHE 0.039 0.002 PHE K 202 TRP 0.011 0.001 TRP I 181 HIS 0.007 0.001 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.00590 (27468) covalent geometry : angle 0.63018 (37280) hydrogen bonds : bond 0.04903 ( 1588) hydrogen bonds : angle 4.51436 ( 4572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 422 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7764 (ttp80) cc_final: 0.7482 (ttm-80) REVERT: A 66 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8335 (mt) REVERT: A 72 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: A 85 SER cc_start: 0.8742 (t) cc_final: 0.8407 (m) REVERT: A 189 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7212 (tp) REVERT: B 155 GLU cc_start: 0.6790 (tt0) cc_final: 0.6110 (mt-10) REVERT: B 183 ILE cc_start: 0.7876 (mt) cc_final: 0.7387 (mp) REVERT: C 59 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: C 147 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6985 (mp) REVERT: C 155 GLU cc_start: 0.6797 (tt0) cc_final: 0.6257 (mt-10) REVERT: C 183 ILE cc_start: 0.7963 (mt) cc_final: 0.7453 (mp) REVERT: D 27 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7765 (mtm110) REVERT: E 39 GLU cc_start: 0.7914 (mp0) cc_final: 0.7579 (mp0) REVERT: E 139 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6986 (pm20) REVERT: F 128 MET cc_start: 0.8619 (mmm) cc_final: 0.8224 (mmm) REVERT: F 134 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7838 (mp10) REVERT: F 138 ASP cc_start: 0.7811 (t0) cc_final: 0.7324 (m-30) REVERT: G 111 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8155 (mtpt) REVERT: G 128 MET cc_start: 0.8665 (mmm) cc_final: 0.8249 (mmm) REVERT: G 134 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7965 (mp10) REVERT: G 138 ASP cc_start: 0.7680 (t0) cc_final: 0.7399 (m-30) REVERT: H 59 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7706 (mt-10) REVERT: H 72 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7849 (tp30) REVERT: H 139 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7073 (pm20) REVERT: I 71 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7303 (tp40) REVERT: I 92 MET cc_start: 0.6059 (mmt) cc_final: 0.5501 (tpp) REVERT: I 97 LEU cc_start: 0.7544 (mt) cc_final: 0.7176 (mt) REVERT: I 142 LEU cc_start: 0.7134 (tp) cc_final: 0.6823 (mm) REVERT: I 158 TRP cc_start: 0.7618 (m100) cc_final: 0.6836 (m-90) REVERT: I 217 LYS cc_start: 0.7502 (ptmt) cc_final: 0.6915 (mmtt) REVERT: I 418 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7881 (pt) REVERT: J 71 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.6850 (tm-30) REVERT: J 91 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7258 (t80) REVERT: J 220 ARG cc_start: 0.7086 (mmt180) cc_final: 0.6592 (mmp80) REVERT: J 373 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6238 (mm-30) REVERT: K 71 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7055 (tm-30) REVERT: K 91 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7121 (t80) REVERT: K 220 ARG cc_start: 0.7127 (mmt180) cc_final: 0.6645 (mmp80) REVERT: K 334 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7884 (pttp) REVERT: K 373 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6419 (mm-30) REVERT: L 71 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7300 (tp40) REVERT: L 92 MET cc_start: 0.6082 (mmt) cc_final: 0.5532 (tpp) REVERT: L 97 LEU cc_start: 0.7390 (mt) cc_final: 0.7018 (mt) REVERT: L 142 LEU cc_start: 0.7098 (tp) cc_final: 0.6781 (mm) REVERT: L 155 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: L 217 LYS cc_start: 0.7533 (ptmt) cc_final: 0.6948 (mmtt) REVERT: L 222 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8296 (ptpt) REVERT: L 418 ILE cc_start: 0.8145 (tp) cc_final: 0.7860 (pt) outliers start: 114 outliers final: 61 residues processed: 503 average time/residue: 0.6150 time to fit residues: 365.1685 Evaluate side-chains 497 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 415 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 418 ILE Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 257 LEU Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 191 optimal weight: 0.8980 chunk 123 optimal weight: 0.2980 chunk 55 optimal weight: 3.9990 chunk 312 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 328 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 314 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS B 134 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS I 155 GLN J 119 ASN J 434 ASN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 ASN K 434 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.180832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.146813 restraints weight = 29564.900| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.20 r_work: 0.3371 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27468 Z= 0.116 Angle : 0.509 7.533 37280 Z= 0.269 Chirality : 0.043 0.232 4486 Planarity : 0.003 0.042 4578 Dihedral : 8.462 75.918 3910 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.92 % Allowed : 18.46 % Favored : 78.62 % 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: 1.04 (0.14), residues: 3422 helix: 1.86 (0.12), residues: 1910 sheet: -0.25 (0.27), residues: 380 loop : -1.00 (0.16), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 27 TYR 0.011 0.001 TYR H 108 PHE 0.031 0.001 PHE I 202 TRP 0.011 0.001 TRP I 181 HIS 0.005 0.001 HIS F 185 Details of bonding type rmsd covalent geometry : bond 0.00254 (27468) covalent geometry : angle 0.50923 (37280) hydrogen bonds : bond 0.03602 ( 1588) hydrogen bonds : angle 4.18174 ( 4572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 444 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8473 (mt) REVERT: A 72 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8246 (mt-10) REVERT: A 128 MET cc_start: 0.8634 (mmm) cc_final: 0.8225 (mmp) REVERT: A 145 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7922 (tt) REVERT: A 155 GLU cc_start: 0.7636 (tt0) cc_final: 0.7110 (mt-10) REVERT: A 189 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7057 (tp) REVERT: B 155 GLU cc_start: 0.7253 (tt0) cc_final: 0.6796 (mt-10) REVERT: B 183 ILE cc_start: 0.7989 (mt) cc_final: 0.7524 (mp) REVERT: C 59 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: C 147 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7288 (mt) REVERT: C 155 GLU cc_start: 0.7223 (tt0) cc_final: 0.6802 (mt-10) REVERT: C 183 ILE cc_start: 0.8138 (mt) cc_final: 0.7680 (mp) REVERT: E 139 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: F 134 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8087 (mp10) REVERT: F 138 ASP cc_start: 0.8110 (t0) cc_final: 0.7794 (m-30) REVERT: F 146 ASP cc_start: 0.7012 (m-30) cc_final: 0.6747 (p0) REVERT: G 157 LEU cc_start: 0.7576 (tt) cc_final: 0.7291 (tp) REVERT: H 59 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7868 (mt-10) REVERT: H 86 THR cc_start: 0.8778 (t) cc_final: 0.8444 (m) REVERT: H 95 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7906 (mt) REVERT: H 139 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7255 (pm20) REVERT: I 71 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7711 (tp40) REVERT: I 97 LEU cc_start: 0.7834 (mt) cc_final: 0.7526 (mt) REVERT: I 158 TRP cc_start: 0.7779 (m100) cc_final: 0.7199 (m-90) REVERT: I 217 LYS cc_start: 0.7729 (ptmt) cc_final: 0.7361 (mmtt) REVERT: I 222 LYS cc_start: 0.8465 (mmmt) cc_final: 0.7966 (ptpt) REVERT: J 46 SER cc_start: 0.7869 (OUTLIER) cc_final: 0.7640 (t) REVERT: J 71 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: J 91 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7365 (t80) REVERT: J 92 MET cc_start: 0.7939 (tpt) cc_final: 0.7694 (mmm) REVERT: J 104 LYS cc_start: 0.6223 (tttt) cc_final: 0.5982 (tttp) REVERT: J 220 ARG cc_start: 0.7676 (mmt180) cc_final: 0.7265 (mmp80) REVERT: K 46 SER cc_start: 0.7817 (OUTLIER) cc_final: 0.7584 (t) REVERT: K 71 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: K 220 ARG cc_start: 0.7708 (mmt180) cc_final: 0.7302 (mmp80) REVERT: K 334 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8236 (pttp) REVERT: K 373 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6497 (mm-30) REVERT: L 71 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7665 (tp40) REVERT: L 97 LEU cc_start: 0.7718 (mt) cc_final: 0.7415 (mt) REVERT: L 155 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: L 181 TRP cc_start: 0.8274 (m-90) cc_final: 0.7942 (p90) REVERT: L 217 LYS cc_start: 0.7734 (ptmt) cc_final: 0.7370 (mmtt) REVERT: L 222 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8217 (ptpt) outliers start: 85 outliers final: 42 residues processed: 503 average time/residue: 0.6215 time to fit residues: 367.4636 Evaluate side-chains 491 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 430 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 207 ILE Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 172 VAL 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 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 249 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 238 optimal weight: 0.9990 chunk 231 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 165 optimal weight: 0.4980 chunk 249 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS B 134 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS G 134 GLN I 155 GLN J 85 GLN J 119 ASN J 434 ASN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 119 ASN K 434 ASN L 253 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.180481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147089 restraints weight = 29484.059| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.29 r_work: 0.3357 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27468 Z= 0.123 Angle : 0.523 7.745 37280 Z= 0.275 Chirality : 0.043 0.226 4486 Planarity : 0.003 0.044 4578 Dihedral : 8.406 74.863 3910 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.75 % Allowed : 19.08 % Favored : 78.17 % 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: 1.17 (0.14), residues: 3422 helix: 1.94 (0.12), residues: 1922 sheet: -0.23 (0.27), residues: 380 loop : -0.91 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 436 TYR 0.016 0.001 TYR G 107 PHE 0.031 0.001 PHE J 202 TRP 0.018 0.001 TRP I 181 HIS 0.006 0.001 HIS I 168 Details of bonding type rmsd covalent geometry : bond 0.00274 (27468) covalent geometry : angle 0.52330 (37280) hydrogen bonds : bond 0.03669 ( 1588) hydrogen bonds : angle 4.17090 ( 4572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 446 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8455 (mt) REVERT: A 72 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7943 (mm-30) REVERT: A 128 MET cc_start: 0.8276 (mmm) cc_final: 0.7854 (mmp) REVERT: A 145 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7788 (tt) REVERT: A 155 GLU cc_start: 0.7377 (tt0) cc_final: 0.6874 (mt-10) REVERT: A 189 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7101 (tp) REVERT: B 155 GLU cc_start: 0.6987 (tt0) cc_final: 0.6609 (mt-10) REVERT: B 183 ILE cc_start: 0.7895 (mt) cc_final: 0.7414 (mp) REVERT: C 59 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: C 155 GLU cc_start: 0.6998 (tt0) cc_final: 0.6646 (mt-10) REVERT: C 183 ILE cc_start: 0.8070 (mt) cc_final: 0.7605 (mp) REVERT: E 39 GLU cc_start: 0.7921 (mp0) cc_final: 0.7712 (mp0) REVERT: F 134 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7471 (mp10) REVERT: H 59 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7638 (mt-10) REVERT: H 86 THR cc_start: 0.8742 (t) cc_final: 0.8387 (m) REVERT: H 95 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7927 (mt) REVERT: H 139 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7031 (pm20) REVERT: I 71 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7728 (tp40) REVERT: I 97 LEU cc_start: 0.7757 (mt) cc_final: 0.7425 (mt) REVERT: I 158 TRP cc_start: 0.7744 (m100) cc_final: 0.7220 (m-90) REVERT: I 217 LYS cc_start: 0.7595 (ptmt) cc_final: 0.7341 (mmtt) REVERT: I 222 LYS cc_start: 0.8418 (mmmt) cc_final: 0.7987 (ptpt) REVERT: J 71 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: J 91 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7292 (t80) REVERT: J 220 ARG cc_start: 0.7542 (mmt180) cc_final: 0.7138 (mmp80) REVERT: K 71 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: K 104 LYS cc_start: 0.6169 (tttt) cc_final: 0.5950 (tttp) REVERT: K 220 ARG cc_start: 0.7509 (mmt180) cc_final: 0.7132 (mmp80) REVERT: K 334 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8184 (pttp) REVERT: K 373 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6375 (mm-30) REVERT: L 71 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7689 (tp40) REVERT: L 97 LEU cc_start: 0.7662 (mt) cc_final: 0.7384 (mt) REVERT: L 217 LYS cc_start: 0.7569 (ptmt) cc_final: 0.7333 (mmtt) REVERT: L 222 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8203 (ptpt) outliers start: 80 outliers final: 41 residues processed: 500 average time/residue: 0.5298 time to fit residues: 312.3075 Evaluate side-chains 480 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 425 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 71 GLN Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 249 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 99 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 258 optimal weight: 6.9990 chunk 265 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 269 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS B 134 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS G 105 GLN G 134 GLN I 85 GLN J 85 GLN J 119 ASN J 434 ASN ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 119 ASN K 434 ASN L 85 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.179241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.142230 restraints weight = 29380.665| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.27 r_work: 0.3349 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27468 Z= 0.150 Angle : 0.553 7.871 37280 Z= 0.290 Chirality : 0.044 0.228 4486 Planarity : 0.004 0.046 4578 Dihedral : 8.565 74.586 3910 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.54 % Allowed : 19.46 % Favored : 78.00 % 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: 1.07 (0.14), residues: 3422 helix: 1.86 (0.12), residues: 1922 sheet: -0.24 (0.27), residues: 380 loop : -0.96 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 27 TYR 0.018 0.001 TYR G 107 PHE 0.033 0.002 PHE J 202 TRP 0.016 0.001 TRP I 181 HIS 0.005 0.001 HIS I 168 Details of bonding type rmsd covalent geometry : bond 0.00347 (27468) covalent geometry : angle 0.55298 (37280) hydrogen bonds : bond 0.03966 ( 1588) hydrogen bonds : angle 4.24402 ( 4572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10604.69 seconds wall clock time: 181 minutes 10.52 seconds (10870.52 seconds total)