Starting phenix.real_space_refine on Sun May 25 08:37:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1u_36804/05_2025/8k1u_36804.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1u_36804/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1u_36804/05_2025/8k1u_36804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1u_36804/05_2025/8k1u_36804.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1u_36804/05_2025/8k1u_36804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1u_36804/05_2025/8k1u_36804.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.61, per 1000 atoms: 0.62 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: 6.81 Conformation dependent library (CDL) restraints added in 4.0 seconds 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6364 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 20 sheets defined 57.6% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 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: 9.70 Time building geometry restraints manager: 7.91 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 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: 0.040 Extract box with map and model: 1.130 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 60.630 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.002 0.001 TRP C 101 HIS 0.004 0.001 HIS E 185 PHE 0.021 0.001 PHE L 202 TYR 0.005 0.001 TYR C 107 ARG 0.003 0.000 ARG J 220 Details of bonding type rmsd hydrogen bonds : bond 0.26662 ( 1588) hydrogen bonds : angle 7.47877 ( 4572) covalent geometry : bond 0.00210 (27468) covalent geometry : angle 0.50259 (37280) *********************** 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 : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.7279 (mmm) cc_final: 0.7002 (mmp) REVERT: C 41 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7985 (mmtt) 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: 1.2304 time to fit residues: 1253.2294 Evaluate side-chains 501 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 495 time to evaluate : 2.983 ------------------------------------------------------------------------------- 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 287 optimal weight: 0.9990 chunk 257 optimal weight: 3.9990 chunk 142 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 198 optimal weight: 0.6980 chunk 308 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 D 210 HIS F 30 HIS ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN G 134 GLN ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.180778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139814 restraints weight = 29573.640| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.36 r_work: 0.3328 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 27468 Z= 0.145 Angle : 0.546 7.751 37280 Z= 0.291 Chirality : 0.044 0.199 4486 Planarity : 0.004 0.036 4578 Dihedral : 9.119 75.918 3915 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.92 % Allowed : 12.59 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.13), residues: 3422 helix: 0.97 (0.11), residues: 1916 sheet: 0.34 (0.26), residues: 404 loop : -0.86 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 101 HIS 0.013 0.001 HIS G 185 PHE 0.043 0.002 PHE J 202 TYR 0.019 0.001 TYR F 107 ARG 0.007 0.001 ARG L 340 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 1588) hydrogen bonds : angle 4.56966 ( 4572) covalent geometry : bond 0.00319 (27468) covalent geometry : angle 0.54556 (37280) *********************** 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 611 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 526 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8604 (t) cc_final: 0.8299 (m) REVERT: A 128 MET cc_start: 0.8653 (mmm) cc_final: 0.8053 (mmp) REVERT: B 155 GLU cc_start: 0.6853 (tt0) cc_final: 0.6255 (mt-10) REVERT: B 183 ILE cc_start: 0.7495 (mt) cc_final: 0.6990 (mp) REVERT: B 213 ASP cc_start: 0.6949 (m-30) cc_final: 0.6604 (m-30) REVERT: C 147 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7261 (mp) REVERT: C 155 GLU cc_start: 0.6871 (tt0) cc_final: 0.6242 (mt-10) REVERT: C 213 ASP cc_start: 0.7034 (m-30) cc_final: 0.6770 (m-30) REVERT: D 27 ARG cc_start: 0.7854 (mtm110) cc_final: 0.7353 (ttm-80) REVERT: D 72 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: E 86 THR cc_start: 0.8852 (t) cc_final: 0.8536 (m) REVERT: E 95 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7680 (mt) REVERT: E 222 MET cc_start: 0.6293 (ttm) cc_final: 0.5997 (ttp) REVERT: F 128 MET cc_start: 0.8647 (mmm) cc_final: 0.8378 (mmm) REVERT: F 213 ASP cc_start: 0.7664 (m-30) cc_final: 0.7315 (p0) REVERT: G 128 MET cc_start: 0.8691 (mmm) cc_final: 0.8404 (mmm) REVERT: G 134 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7917 (mp10) REVERT: H 86 THR cc_start: 0.8799 (t) cc_final: 0.8483 (m) REVERT: I 97 LEU cc_start: 0.7656 (mt) cc_final: 0.7343 (mt) REVERT: I 106 ILE cc_start: 0.6905 (mm) cc_final: 0.6426 (tp) REVERT: I 217 LYS cc_start: 0.7520 (ptmt) cc_final: 0.7021 (mmtt) REVERT: I 222 LYS cc_start: 0.8475 (mmmt) cc_final: 0.7656 (ptmm) REVERT: I 266 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7923 (mm) REVERT: I 400 GLU cc_start: 0.7915 (mp0) cc_final: 0.7672 (mp0) REVERT: J 91 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7139 (t80) REVERT: K 91 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7080 (t80) REVERT: K 220 ARG cc_start: 0.6938 (mmt180) cc_final: 0.6552 (mmp80) REVERT: K 334 LYS cc_start: 0.8662 (mmtt) cc_final: 0.7917 (pttp) REVERT: L 36 MET cc_start: 0.7662 (mmm) cc_final: 0.7390 (mmm) REVERT: L 86 ILE cc_start: 0.8269 (mp) cc_final: 0.7986 (mp) REVERT: L 97 LEU cc_start: 0.7684 (mt) cc_final: 0.7437 (mt) REVERT: L 155 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: L 217 LYS cc_start: 0.7558 (ptmt) cc_final: 0.7051 (mmtt) REVERT: L 222 LYS cc_start: 0.8620 (ptmm) cc_final: 0.8012 (mmmt) REVERT: L 400 GLU cc_start: 0.7849 (mp0) cc_final: 0.7638 (mp0) outliers start: 85 outliers final: 21 residues processed: 581 average time/residue: 1.2194 time to fit residues: 833.3622 Evaluate side-chains 481 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 452 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE 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 E residue 47 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 314 ILE 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 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 352 LEU Chi-restraints excluded: chain L residue 155 GLN 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 398 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 297 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 66 optimal weight: 0.0980 chunk 74 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 131 optimal weight: 0.0970 chunk 133 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 C 143 ASN D 38 ASN D 210 HIS F 51 HIS F 56 ASN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 239 ASN I 253 ASN J 155 GLN J 434 ASN K 434 ASN L 85 GLN L 253 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.181419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.140752 restraints weight = 29679.375| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.42 r_work: 0.3356 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 27468 Z= 0.106 Angle : 0.482 7.549 37280 Z= 0.257 Chirality : 0.042 0.191 4486 Planarity : 0.003 0.037 4578 Dihedral : 8.486 76.193 3908 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.85 % Allowed : 14.48 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.14), residues: 3422 helix: 1.80 (0.11), residues: 1898 sheet: 0.10 (0.25), residues: 404 loop : -0.91 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP L 181 HIS 0.009 0.001 HIS F 185 PHE 0.034 0.001 PHE J 202 TYR 0.014 0.001 TYR F 107 ARG 0.008 0.000 ARG I 436 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 1588) hydrogen bonds : angle 4.18045 ( 4572) covalent geometry : bond 0.00221 (27468) covalent geometry : angle 0.48210 (37280) *********************** 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 583 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 500 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8559 (t) cc_final: 0.8209 (m) REVERT: A 128 MET cc_start: 0.8603 (mmm) cc_final: 0.7953 (mmp) REVERT: B 155 GLU cc_start: 0.6572 (tt0) cc_final: 0.6009 (mt-10) REVERT: B 213 ASP cc_start: 0.6818 (m-30) cc_final: 0.6491 (m-30) REVERT: C 128 MET cc_start: 0.8418 (mmm) cc_final: 0.8211 (mmm) REVERT: C 155 GLU cc_start: 0.6766 (tt0) cc_final: 0.6332 (mt-10) REVERT: C 213 ASP cc_start: 0.6826 (m-30) cc_final: 0.6597 (m-30) REVERT: D 181 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.5888 (mp) REVERT: E 213 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.6450 (t70) REVERT: E 222 MET cc_start: 0.6232 (ttm) cc_final: 0.5945 (ttp) REVERT: F 128 MET cc_start: 0.8532 (mmm) cc_final: 0.8228 (mmm) REVERT: F 134 GLN cc_start: 0.7821 (mm110) cc_final: 0.7286 (mp10) REVERT: F 138 ASP cc_start: 0.7547 (t0) cc_final: 0.7152 (m-30) REVERT: G 128 MET cc_start: 0.8524 (mmm) cc_final: 0.8200 (mmm) REVERT: G 134 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7786 (mp10) REVERT: G 138 ASP cc_start: 0.7567 (t0) cc_final: 0.7136 (m-30) REVERT: G 213 ASP cc_start: 0.7597 (m-30) cc_final: 0.7350 (p0) REVERT: H 95 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7479 (mt) REVERT: H 139 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6932 (pm20) REVERT: H 213 ASP cc_start: 0.6691 (OUTLIER) cc_final: 0.6477 (t70) REVERT: I 36 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7455 (mmt) REVERT: I 97 LEU cc_start: 0.7626 (mt) cc_final: 0.7323 (mt) REVERT: I 106 ILE cc_start: 0.6889 (mm) cc_final: 0.6399 (tp) REVERT: I 217 LYS cc_start: 0.7380 (ptmt) cc_final: 0.6922 (mmtt) REVERT: I 222 LYS cc_start: 0.8451 (mmmt) cc_final: 0.7634 (ptmm) REVERT: I 400 GLU cc_start: 0.7971 (mp0) cc_final: 0.7766 (mp0) REVERT: J 91 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7026 (t80) REVERT: J 142 LEU cc_start: 0.7554 (tp) cc_final: 0.7313 (tp) REVERT: J 220 ARG cc_start: 0.6844 (mmt180) cc_final: 0.6472 (mmp80) REVERT: J 352 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8117 (tt) REVERT: J 431 GLU cc_start: 0.5674 (OUTLIER) cc_final: 0.5301 (mt-10) REVERT: K 77 GLN cc_start: 0.8239 (mt0) cc_final: 0.8032 (mt0) REVERT: K 220 ARG cc_start: 0.6795 (mmt180) cc_final: 0.6430 (mmp80) REVERT: K 250 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7819 (mm-30) REVERT: K 334 LYS cc_start: 0.8621 (mmtt) cc_final: 0.7906 (pttp) REVERT: L 36 MET cc_start: 0.7580 (mmm) cc_final: 0.7326 (mmt) REVERT: L 97 LEU cc_start: 0.7674 (mt) cc_final: 0.7399 (mt) REVERT: L 155 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: L 217 LYS cc_start: 0.7430 (ptmt) cc_final: 0.6974 (mmtt) REVERT: L 266 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7822 (mm) REVERT: L 400 GLU cc_start: 0.7915 (mp0) cc_final: 0.7613 (mp0) outliers start: 83 outliers final: 18 residues processed: 548 average time/residue: 1.2585 time to fit residues: 807.6458 Evaluate side-chains 482 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 451 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 137 SER 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 95 LEU 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 33 VAL Chi-restraints excluded: chain I residue 36 MET Chi-restraints excluded: chain I residue 298 LEU 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 91 PHE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 431 GLU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 298 LEU 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 306 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 204 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 309 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN B 134 GLN C 134 GLN D 210 HIS G 134 GLN I 18 GLN I 85 GLN I 253 ASN J 155 GLN J 434 ASN K 119 ASN K 434 ASN L 85 GLN L 253 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.174314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.132386 restraints weight = 29741.248| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.41 r_work: 0.3254 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3888 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= 0.220 Angle : 0.601 8.465 37280 Z= 0.315 Chirality : 0.046 0.257 4486 Planarity : 0.004 0.038 4578 Dihedral : 9.046 80.513 3906 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.19 % Allowed : 13.83 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 3422 helix: 1.60 (0.11), residues: 1888 sheet: -0.02 (0.26), residues: 404 loop : -1.08 (0.16), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 47 HIS 0.006 0.001 HIS F 185 PHE 0.040 0.002 PHE K 202 TYR 0.012 0.002 TYR L 270 ARG 0.008 0.001 ARG L 340 Details of bonding type rmsd hydrogen bonds : bond 0.04801 ( 1588) hydrogen bonds : angle 4.46459 ( 4572) covalent geometry : bond 0.00530 (27468) covalent geometry : angle 0.60142 (37280) *********************** 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 591 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 469 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.8838 (mmm) cc_final: 0.8166 (mmp) REVERT: A 146 ASP cc_start: 0.7714 (m-30) cc_final: 0.7454 (t0) REVERT: A 189 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.7055 (tp) REVERT: B 155 GLU cc_start: 0.6864 (tt0) cc_final: 0.6276 (mt-10) REVERT: B 183 ILE cc_start: 0.7699 (mt) cc_final: 0.7227 (mp) REVERT: B 213 ASP cc_start: 0.6864 (m-30) cc_final: 0.6627 (m-30) REVERT: C 128 MET cc_start: 0.8372 (mmm) cc_final: 0.8166 (mmm) REVERT: C 134 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7620 (mp10) REVERT: C 155 GLU cc_start: 0.6854 (tt0) cc_final: 0.6350 (mt-10) REVERT: C 183 ILE cc_start: 0.7876 (mt) cc_final: 0.7374 (mp) REVERT: D 27 ARG cc_start: 0.7974 (mtm110) cc_final: 0.7758 (mtm110) REVERT: E 59 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7922 (mt-10) REVERT: E 134 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7687 (mp10) REVERT: E 139 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7038 (pm20) REVERT: E 213 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6500 (t70) REVERT: E 222 MET cc_start: 0.6330 (ttm) cc_final: 0.6130 (ttp) REVERT: F 128 MET cc_start: 0.8607 (mmm) cc_final: 0.8239 (mmm) REVERT: F 134 GLN cc_start: 0.7932 (mm110) cc_final: 0.7699 (mp10) REVERT: F 137 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8436 (p) REVERT: F 138 ASP cc_start: 0.7717 (t0) cc_final: 0.7362 (m-30) REVERT: G 111 LYS cc_start: 0.8442 (mtpt) cc_final: 0.7938 (mtpt) REVERT: G 128 MET cc_start: 0.8618 (mmm) cc_final: 0.8254 (mmm) REVERT: G 134 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: G 138 ASP cc_start: 0.7676 (t0) cc_final: 0.7307 (m-30) REVERT: H 59 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7935 (mt-10) REVERT: H 134 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: H 139 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: H 213 ASP cc_start: 0.6761 (OUTLIER) cc_final: 0.6541 (t70) REVERT: I 36 MET cc_start: 0.7646 (mmm) cc_final: 0.7318 (mmt) REVERT: I 97 LEU cc_start: 0.7547 (mt) cc_final: 0.7260 (mt) REVERT: I 106 ILE cc_start: 0.7094 (mm) cc_final: 0.6819 (tp) REVERT: I 158 TRP cc_start: 0.7711 (m100) cc_final: 0.6912 (m-90) REVERT: I 217 LYS cc_start: 0.7537 (ptmt) cc_final: 0.7033 (mmtt) REVERT: I 222 LYS cc_start: 0.8498 (mmmt) cc_final: 0.7777 (ptpt) REVERT: J 91 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7270 (t80) REVERT: J 109 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8177 (mmmm) REVERT: J 132 VAL cc_start: 0.8366 (m) cc_final: 0.7993 (p) REVERT: J 220 ARG cc_start: 0.7089 (mmt180) cc_final: 0.6731 (mmp80) REVERT: J 312 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8448 (t) REVERT: J 344 LYS cc_start: 0.7915 (tppt) cc_final: 0.7558 (tppt) REVERT: K 71 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: K 91 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7172 (t80) REVERT: K 132 VAL cc_start: 0.8333 (m) cc_final: 0.7986 (p) REVERT: K 220 ARG cc_start: 0.7116 (mmt180) cc_final: 0.6759 (mmp80) REVERT: K 250 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8254 (mm-30) REVERT: K 334 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7955 (pttp) REVERT: L 36 MET cc_start: 0.7585 (mmm) cc_final: 0.7200 (mmm) REVERT: L 97 LEU cc_start: 0.7715 (mt) cc_final: 0.7366 (mt) REVERT: L 155 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: L 217 LYS cc_start: 0.7572 (ptmt) cc_final: 0.7064 (mmtt) outliers start: 122 outliers final: 52 residues processed: 556 average time/residue: 1.2452 time to fit residues: 816.3209 Evaluate side-chains 510 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 440 time to evaluate : 2.968 ------------------------------------------------------------------------------- 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 145 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain 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 134 GLN 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 47 SER Chi-restraints excluded: chain F residue 135 SER 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 G residue 135 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 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 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 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 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 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 194 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 310 optimal weight: 7.9990 chunk 224 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 223 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 296 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 C 134 GLN D 210 HIS E 83 GLN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 HIS H 83 GLN I 253 ASN J 85 GLN J 119 ASN J 155 GLN J 434 ASN K 85 GLN K 119 ASN K 434 ASN L 18 GLN L 253 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.177541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136590 restraints weight = 29753.625| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.38 r_work: 0.3305 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 27468 Z= 0.124 Angle : 0.500 7.606 37280 Z= 0.266 Chirality : 0.043 0.242 4486 Planarity : 0.003 0.040 4578 Dihedral : 8.601 75.456 3906 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.26 % Allowed : 15.82 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.14), residues: 3422 helix: 1.85 (0.12), residues: 1900 sheet: -0.06 (0.26), residues: 416 loop : -0.96 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 47 HIS 0.006 0.001 HIS F 185 PHE 0.033 0.001 PHE J 202 TYR 0.013 0.001 TYR G 107 ARG 0.008 0.000 ARG L 436 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 1588) hydrogen bonds : angle 4.20246 ( 4572) covalent geometry : bond 0.00277 (27468) covalent geometry : angle 0.50018 (37280) *********************** 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 547 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 452 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8030 (mm-30) REVERT: A 85 SER cc_start: 0.8498 (OUTLIER) cc_final: 0.8224 (m) REVERT: A 128 MET cc_start: 0.8743 (mmm) cc_final: 0.8101 (mmp) REVERT: A 146 ASP cc_start: 0.7646 (m-30) cc_final: 0.7410 (t0) REVERT: A 189 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.7158 (tp) REVERT: B 69 ARG cc_start: 0.8813 (mtp85) cc_final: 0.8526 (mtp85) REVERT: B 155 GLU cc_start: 0.6783 (tt0) cc_final: 0.6223 (mt-10) REVERT: B 183 ILE cc_start: 0.7575 (mt) cc_final: 0.7043 (mp) REVERT: C 128 MET cc_start: 0.8293 (mmm) cc_final: 0.8052 (mmm) REVERT: C 155 GLU cc_start: 0.6835 (tt0) cc_final: 0.6376 (mt-10) REVERT: C 183 ILE cc_start: 0.7731 (mt) cc_final: 0.7259 (mp) REVERT: D 85 SER cc_start: 0.8522 (t) cc_final: 0.8227 (m) REVERT: E 139 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7010 (pm20) REVERT: E 213 ASP cc_start: 0.6753 (OUTLIER) cc_final: 0.6543 (t70) REVERT: F 128 MET cc_start: 0.8518 (mmm) cc_final: 0.8169 (mmm) REVERT: F 134 GLN cc_start: 0.7844 (mm110) cc_final: 0.7312 (mp10) REVERT: F 137 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8475 (p) REVERT: F 138 ASP cc_start: 0.7677 (t0) cc_final: 0.7360 (m-30) REVERT: G 128 MET cc_start: 0.8519 (mmm) cc_final: 0.8198 (mmm) REVERT: G 138 ASP cc_start: 0.7642 (t0) cc_final: 0.7331 (m-30) REVERT: H 59 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7788 (mt-10) REVERT: H 139 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7002 (pm20) REVERT: I 36 MET cc_start: 0.7569 (mmm) cc_final: 0.7263 (mmt) REVERT: I 97 LEU cc_start: 0.7502 (mt) cc_final: 0.7095 (mt) REVERT: I 106 ILE cc_start: 0.7039 (mm) cc_final: 0.6746 (tp) REVERT: I 158 TRP cc_start: 0.7671 (m100) cc_final: 0.6933 (m-90) REVERT: I 217 LYS cc_start: 0.7394 (ptmt) cc_final: 0.6939 (mmtt) REVERT: I 222 LYS cc_start: 0.8443 (mmmt) cc_final: 0.7784 (ptpt) REVERT: I 266 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7743 (mm) REVERT: J 109 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8072 (mmmm) REVERT: J 132 VAL cc_start: 0.8337 (m) cc_final: 0.7970 (p) REVERT: J 220 ARG cc_start: 0.6992 (mmt180) cc_final: 0.6641 (mmp80) REVERT: J 344 LYS cc_start: 0.7784 (tppt) cc_final: 0.7457 (tppt) REVERT: J 373 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6416 (mt-10) REVERT: K 132 VAL cc_start: 0.8299 (m) cc_final: 0.7940 (p) REVERT: K 220 ARG cc_start: 0.7060 (mmt180) cc_final: 0.6694 (mmp80) REVERT: K 250 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8011 (mm-30) REVERT: K 334 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7922 (pttp) REVERT: L 36 MET cc_start: 0.7554 (mmm) cc_final: 0.7193 (mmm) REVERT: L 97 LEU cc_start: 0.7738 (mt) cc_final: 0.7393 (mt) REVERT: L 155 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7532 (tt0) REVERT: L 217 LYS cc_start: 0.7414 (ptmt) cc_final: 0.6968 (mmtt) REVERT: L 400 GLU cc_start: 0.8309 (mp0) cc_final: 0.8084 (mp0) outliers start: 95 outliers final: 40 residues processed: 519 average time/residue: 1.2889 time to fit residues: 783.7257 Evaluate side-chains 489 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 436 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 141 VAL 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 G residue 95 LEU Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 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 266 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 314 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 123 ILE Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 187 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 76 optimal weight: 6.9990 chunk 314 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 305 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 334 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 118 optimal weight: 0.0670 chunk 267 optimal weight: 0.9990 overall best weight: 0.8126 ------------------------------------------------------------------------------- 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 D 210 HIS ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN J 85 GLN J 434 ASN K 85 GLN K 119 ASN K 434 ASN L 85 GLN L 253 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.177246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135474 restraints weight = 29683.412| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.44 r_work: 0.3299 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27468 Z= 0.118 Angle : 0.495 7.629 37280 Z= 0.262 Chirality : 0.042 0.218 4486 Planarity : 0.003 0.046 4578 Dihedral : 8.479 77.371 3906 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.40 % Allowed : 16.16 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.14), residues: 3422 helix: 1.93 (0.12), residues: 1922 sheet: -0.19 (0.27), residues: 380 loop : -0.85 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 181 HIS 0.007 0.001 HIS G 185 PHE 0.032 0.001 PHE J 202 TYR 0.013 0.001 TYR G 107 ARG 0.009 0.000 ARG F 27 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 1588) hydrogen bonds : angle 4.10554 ( 4572) covalent geometry : bond 0.00264 (27468) covalent geometry : angle 0.49537 (37280) *********************** 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 547 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 448 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8012 (mm-30) REVERT: A 85 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.8159 (m) REVERT: A 128 MET cc_start: 0.8736 (mmm) cc_final: 0.8510 (mmm) REVERT: A 146 ASP cc_start: 0.7610 (m-30) cc_final: 0.7325 (t0) REVERT: A 189 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.7093 (tp) REVERT: B 155 GLU cc_start: 0.6797 (tt0) cc_final: 0.6201 (mt-10) REVERT: B 183 ILE cc_start: 0.7547 (mt) cc_final: 0.7031 (mp) REVERT: C 59 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: C 128 MET cc_start: 0.8282 (mmm) cc_final: 0.7997 (mmm) REVERT: C 155 GLU cc_start: 0.6825 (tt0) cc_final: 0.6362 (mt-10) REVERT: C 183 ILE cc_start: 0.7644 (mt) cc_final: 0.7136 (mp) REVERT: D 85 SER cc_start: 0.8484 (t) cc_final: 0.8186 (m) REVERT: E 213 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6527 (t70) REVERT: F 93 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.7784 (tmtt) REVERT: F 128 MET cc_start: 0.8533 (mmm) cc_final: 0.8166 (mmm) REVERT: F 134 GLN cc_start: 0.7829 (mm110) cc_final: 0.7242 (mp10) REVERT: F 137 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8355 (p) REVERT: F 138 ASP cc_start: 0.7471 (t0) cc_final: 0.7218 (m-30) REVERT: G 128 MET cc_start: 0.8539 (mmm) cc_final: 0.8174 (mmm) REVERT: G 134 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7876 (mp10) REVERT: G 135 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8325 (m) REVERT: G 138 ASP cc_start: 0.7558 (t0) cc_final: 0.7241 (m-30) REVERT: H 139 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6866 (pm20) REVERT: I 97 LEU cc_start: 0.7538 (mt) cc_final: 0.7206 (mt) REVERT: I 106 ILE cc_start: 0.6996 (mm) cc_final: 0.6726 (tp) REVERT: I 158 TRP cc_start: 0.7634 (m100) cc_final: 0.6894 (m-90) REVERT: I 217 LYS cc_start: 0.7332 (ptmt) cc_final: 0.6892 (mmtt) REVERT: I 222 LYS cc_start: 0.8465 (mmmt) cc_final: 0.7787 (ptpt) REVERT: J 109 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7964 (mmmm) REVERT: J 132 VAL cc_start: 0.8282 (m) cc_final: 0.7909 (p) REVERT: J 142 LEU cc_start: 0.7652 (tp) cc_final: 0.7428 (tp) REVERT: J 220 ARG cc_start: 0.6950 (mmt180) cc_final: 0.6612 (mmp80) REVERT: J 344 LYS cc_start: 0.7704 (tppt) cc_final: 0.7389 (tppt) REVERT: K 104 LYS cc_start: 0.5826 (tttt) cc_final: 0.5515 (tttp) REVERT: K 132 VAL cc_start: 0.8225 (m) cc_final: 0.7867 (p) REVERT: K 220 ARG cc_start: 0.6957 (mmt180) cc_final: 0.6603 (mmp80) REVERT: K 245 THR cc_start: 0.8484 (m) cc_final: 0.8178 (m) REVERT: K 334 LYS cc_start: 0.8540 (mmtt) cc_final: 0.7880 (pttp) REVERT: K 373 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6164 (mm-30) REVERT: L 97 LEU cc_start: 0.7634 (mt) cc_final: 0.7294 (mt) REVERT: L 155 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: L 217 LYS cc_start: 0.7289 (ptmt) cc_final: 0.6892 (mmtt) REVERT: L 400 GLU cc_start: 0.8380 (mp0) cc_final: 0.8107 (mp0) outliers start: 99 outliers final: 50 residues processed: 519 average time/residue: 1.2768 time to fit residues: 776.9977 Evaluate side-chains 492 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 429 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 141 VAL 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 D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 123 ILE 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 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 257 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 104 optimal weight: 5.9990 chunk 296 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 249 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 242 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS B 134 GLN C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS G 30 HIS I 253 ASN J 119 ASN J 155 GLN J 434 ASN K 119 ASN K 434 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.135120 restraints weight = 29857.146| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.54 r_work: 0.3277 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27468 Z= 0.134 Angle : 0.515 7.794 37280 Z= 0.270 Chirality : 0.043 0.209 4486 Planarity : 0.003 0.045 4578 Dihedral : 8.540 77.900 3906 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.36 % Allowed : 16.64 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.14), residues: 3422 helix: 1.90 (0.12), residues: 1922 sheet: -0.20 (0.27), residues: 380 loop : -0.87 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 181 HIS 0.005 0.001 HIS L 168 PHE 0.033 0.001 PHE J 202 TYR 0.012 0.001 TYR G 107 ARG 0.009 0.001 ARG F 27 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 1588) hydrogen bonds : angle 4.14669 ( 4572) covalent geometry : bond 0.00307 (27468) covalent geometry : angle 0.51451 (37280) *********************** 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 537 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 439 time to evaluate : 3.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8020 (mm-30) REVERT: A 85 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8215 (m) REVERT: A 128 MET cc_start: 0.8775 (mmm) cc_final: 0.8092 (mmp) REVERT: A 146 ASP cc_start: 0.7578 (m-30) cc_final: 0.7316 (t0) REVERT: A 189 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7108 (tp) REVERT: B 66 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8183 (mt) REVERT: B 155 GLU cc_start: 0.6735 (tt0) cc_final: 0.6127 (mt-10) REVERT: B 183 ILE cc_start: 0.7531 (mt) cc_final: 0.7020 (mp) REVERT: C 59 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: C 66 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8215 (mt) REVERT: C 128 MET cc_start: 0.8339 (mmm) cc_final: 0.8025 (mmm) REVERT: C 155 GLU cc_start: 0.6764 (tt0) cc_final: 0.6286 (mt-10) REVERT: C 183 ILE cc_start: 0.7628 (mt) cc_final: 0.7119 (mp) REVERT: D 85 SER cc_start: 0.8555 (t) cc_final: 0.8241 (m) REVERT: E 59 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7870 (mt-10) REVERT: E 139 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6867 (pm20) REVERT: E 213 ASP cc_start: 0.6703 (OUTLIER) cc_final: 0.6501 (t70) REVERT: F 128 MET cc_start: 0.8544 (mmm) cc_final: 0.8164 (mmm) REVERT: F 134 GLN cc_start: 0.7849 (mm110) cc_final: 0.7224 (mp10) REVERT: F 137 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8348 (p) REVERT: G 128 MET cc_start: 0.8536 (mmm) cc_final: 0.8161 (mmm) REVERT: G 135 SER cc_start: 0.8646 (OUTLIER) cc_final: 0.8338 (m) REVERT: G 138 ASP cc_start: 0.7609 (t0) cc_final: 0.7281 (m-30) REVERT: H 139 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7002 (pm20) REVERT: I 36 MET cc_start: 0.7605 (mmm) cc_final: 0.7337 (mmm) REVERT: I 97 LEU cc_start: 0.7528 (mt) cc_final: 0.7184 (mt) REVERT: I 158 TRP cc_start: 0.7601 (m100) cc_final: 0.6824 (m-90) REVERT: I 217 LYS cc_start: 0.7339 (ptmt) cc_final: 0.6886 (mmtt) REVERT: I 222 LYS cc_start: 0.8422 (mmmt) cc_final: 0.7764 (ptpt) REVERT: J 109 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8015 (mmmm) REVERT: J 132 VAL cc_start: 0.8250 (m) cc_final: 0.7884 (p) REVERT: J 220 ARG cc_start: 0.6965 (mmt180) cc_final: 0.6600 (mmp80) REVERT: J 373 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6109 (mm-30) REVERT: K 132 VAL cc_start: 0.8232 (m) cc_final: 0.7879 (p) REVERT: K 220 ARG cc_start: 0.6991 (mmt180) cc_final: 0.6471 (mmp80) REVERT: K 245 THR cc_start: 0.8485 (m) cc_final: 0.8181 (m) REVERT: K 334 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7888 (pttp) REVERT: K 373 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6194 (mm-30) REVERT: L 97 LEU cc_start: 0.7457 (mt) cc_final: 0.7095 (mt) REVERT: L 155 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: L 217 LYS cc_start: 0.7309 (ptmt) cc_final: 0.6877 (mmtt) REVERT: L 222 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8206 (ptpt) REVERT: L 400 GLU cc_start: 0.8413 (mp0) cc_final: 0.8154 (mp0) outliers start: 98 outliers final: 56 residues processed: 507 average time/residue: 1.2105 time to fit residues: 724.9448 Evaluate side-chains 506 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 433 time to evaluate : 2.946 ------------------------------------------------------------------------------- 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 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 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 135 SER Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL 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 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 123 ILE 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 37 LEU Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 323 optimal weight: 0.0270 chunk 284 optimal weight: 0.9990 chunk 320 optimal weight: 0.8980 chunk 339 optimal weight: 0.8980 chunk 60 optimal weight: 0.0010 chunk 273 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.5646 ------------------------------------------------------------------------------- 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 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS F 134 GLN G 134 GLN J 85 GLN J 119 ASN J 434 ASN K 85 GLN K 434 ASN L 85 GLN L 253 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.179491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137864 restraints weight = 29458.178| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.40 r_work: 0.3328 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27468 Z= 0.105 Angle : 0.487 7.533 37280 Z= 0.256 Chirality : 0.042 0.190 4486 Planarity : 0.003 0.043 4578 Dihedral : 8.278 77.978 3906 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.05 % Allowed : 17.09 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.14), residues: 3422 helix: 2.05 (0.12), residues: 1922 sheet: -0.24 (0.27), residues: 380 loop : -0.84 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 181 HIS 0.006 0.001 HIS F 185 PHE 0.031 0.001 PHE J 202 TYR 0.013 0.001 TYR G 107 ARG 0.009 0.001 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 1588) hydrogen bonds : angle 4.01485 ( 4572) covalent geometry : bond 0.00227 (27468) covalent geometry : angle 0.48660 (37280) *********************** 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 544 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 455 time to evaluate : 2.818 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 72 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8079 (mm-30) REVERT: A 85 SER cc_start: 0.8408 (OUTLIER) cc_final: 0.8192 (m) REVERT: A 128 MET cc_start: 0.8754 (mmm) cc_final: 0.8139 (mmp) REVERT: A 146 ASP cc_start: 0.7679 (m-30) cc_final: 0.7441 (t0) REVERT: A 155 GLU cc_start: 0.7281 (tt0) cc_final: 0.6644 (mt-10) REVERT: A 189 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.7016 (tp) REVERT: B 155 GLU cc_start: 0.6825 (tt0) cc_final: 0.6284 (mt-10) REVERT: B 183 ILE cc_start: 0.7580 (mt) cc_final: 0.7044 (mp) REVERT: C 59 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: C 128 MET cc_start: 0.8363 (mmm) cc_final: 0.8121 (mmm) REVERT: C 155 GLU cc_start: 0.6840 (tt0) cc_final: 0.6409 (mt-10) REVERT: C 183 ILE cc_start: 0.7690 (mt) cc_final: 0.7190 (mp) REVERT: D 85 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.8240 (m) REVERT: F 128 MET cc_start: 0.8607 (mmm) cc_final: 0.8316 (mmm) REVERT: F 134 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7526 (mp10) REVERT: F 146 ASP cc_start: 0.7092 (m-30) cc_final: 0.6787 (p0) REVERT: G 128 MET cc_start: 0.8645 (mmm) cc_final: 0.8333 (mmm) REVERT: G 134 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: G 138 ASP cc_start: 0.7704 (t0) cc_final: 0.7402 (m-30) REVERT: G 146 ASP cc_start: 0.7157 (m-30) cc_final: 0.6832 (p0) REVERT: H 95 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7680 (mt) REVERT: I 71 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7309 (tp40) REVERT: I 97 LEU cc_start: 0.7656 (mt) cc_final: 0.7340 (mt) REVERT: I 158 TRP cc_start: 0.7634 (m100) cc_final: 0.7004 (m-90) REVERT: I 217 LYS cc_start: 0.7339 (ptmt) cc_final: 0.6939 (mmtt) REVERT: I 222 LYS cc_start: 0.8422 (mmmt) cc_final: 0.7862 (ptpt) REVERT: J 109 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7945 (mmmm) REVERT: J 132 VAL cc_start: 0.8332 (m) cc_final: 0.7961 (p) REVERT: J 220 ARG cc_start: 0.7132 (mmt180) cc_final: 0.6784 (mmp80) REVERT: J 245 THR cc_start: 0.8531 (m) cc_final: 0.8192 (m) REVERT: K 104 LYS cc_start: 0.5986 (tttt) cc_final: 0.5677 (tttp) REVERT: K 132 VAL cc_start: 0.8322 (m) cc_final: 0.7963 (p) REVERT: K 220 ARG cc_start: 0.7121 (mmt180) cc_final: 0.6657 (mmp80) REVERT: K 245 THR cc_start: 0.8569 (m) cc_final: 0.8276 (m) REVERT: K 248 ILE cc_start: 0.9245 (mm) cc_final: 0.9028 (mt) REVERT: K 334 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8030 (pttp) REVERT: K 373 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6180 (mm-30) REVERT: L 71 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7272 (tp40) REVERT: L 97 LEU cc_start: 0.7583 (mt) cc_final: 0.7255 (mt) REVERT: L 155 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: L 158 TRP cc_start: 0.7720 (m100) cc_final: 0.7057 (m-90) REVERT: L 181 TRP cc_start: 0.8201 (m-90) cc_final: 0.7872 (p90) REVERT: L 217 LYS cc_start: 0.7394 (ptmt) cc_final: 0.6998 (mmtt) REVERT: L 222 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8168 (ptpt) outliers start: 89 outliers final: 46 residues processed: 518 average time/residue: 1.1632 time to fit residues: 711.9180 Evaluate side-chains 492 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 435 time to evaluate : 3.079 ------------------------------------------------------------------------------- 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 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 D residue 47 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 109 LYS 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 334 LYS Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 37 LEU 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 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 155 GLN Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 257 LEU 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 344 LYS 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 114 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 299 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 280 optimal weight: 0.9980 chunk 205 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS I 155 GLN I 253 ASN J 85 GLN J 119 ASN J 434 ASN K 85 GLN K 119 ASN K 434 ASN L 85 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.178153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136401 restraints weight = 29667.639| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.50 r_work: 0.3303 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 27468 Z= 0.126 Angle : 0.509 7.686 37280 Z= 0.268 Chirality : 0.043 0.197 4486 Planarity : 0.003 0.045 4578 Dihedral : 8.395 78.935 3906 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.92 % Allowed : 17.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.14), residues: 3422 helix: 2.00 (0.12), residues: 1922 sheet: -0.21 (0.27), residues: 380 loop : -0.85 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 181 HIS 0.005 0.001 HIS I 168 PHE 0.032 0.001 PHE J 202 TYR 0.012 0.001 TYR G 107 ARG 0.010 0.001 ARG F 27 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 1588) hydrogen bonds : angle 4.07763 ( 4572) covalent geometry : bond 0.00286 (27468) covalent geometry : angle 0.50938 (37280) *********************** 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 531 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 446 time to evaluate : 3.298 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 72 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8114 (mm-30) REVERT: A 85 SER cc_start: 0.8521 (OUTLIER) cc_final: 0.8285 (m) REVERT: A 128 MET cc_start: 0.8787 (mmm) cc_final: 0.8160 (mmp) REVERT: A 146 ASP cc_start: 0.7723 (m-30) cc_final: 0.7486 (t0) REVERT: A 189 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.7021 (tp) REVERT: B 155 GLU cc_start: 0.6936 (tt0) cc_final: 0.6318 (mt-10) REVERT: B 183 ILE cc_start: 0.7603 (mt) cc_final: 0.7073 (mp) REVERT: C 59 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: C 128 MET cc_start: 0.8439 (mmm) cc_final: 0.8160 (mmm) REVERT: C 155 GLU cc_start: 0.6912 (tt0) cc_final: 0.6459 (mt-10) REVERT: C 183 ILE cc_start: 0.7710 (mt) cc_final: 0.7209 (mp) REVERT: D 85 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8280 (m) REVERT: D 138 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7188 (t70) REVERT: E 59 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7953 (mt-10) REVERT: E 213 ASP cc_start: 0.6779 (t0) cc_final: 0.6453 (t70) REVERT: F 128 MET cc_start: 0.8657 (mmm) cc_final: 0.8337 (mmm) REVERT: F 134 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7551 (mp10) REVERT: G 128 MET cc_start: 0.8688 (mmm) cc_final: 0.8354 (mmm) REVERT: G 135 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8454 (m) REVERT: G 138 ASP cc_start: 0.7791 (t0) cc_final: 0.7467 (m-30) REVERT: G 146 ASP cc_start: 0.7168 (m-30) cc_final: 0.6834 (p0) REVERT: H 59 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7763 (mt-10) REVERT: H 139 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7036 (pm20) REVERT: I 71 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7336 (tp40) REVERT: I 97 LEU cc_start: 0.7621 (mt) cc_final: 0.7259 (mt) REVERT: I 158 TRP cc_start: 0.7651 (m100) cc_final: 0.7041 (m-90) REVERT: I 217 LYS cc_start: 0.7395 (ptmt) cc_final: 0.6960 (mmtt) REVERT: I 222 LYS cc_start: 0.8439 (mmmt) cc_final: 0.7861 (ptpt) REVERT: J 109 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7931 (mmmm) REVERT: J 132 VAL cc_start: 0.8327 (m) cc_final: 0.7964 (p) REVERT: J 220 ARG cc_start: 0.7159 (mmt180) cc_final: 0.6713 (mmp80) REVERT: J 248 ILE cc_start: 0.9207 (mm) cc_final: 0.8931 (mt) REVERT: K 104 LYS cc_start: 0.5971 (tttt) cc_final: 0.5685 (tttp) REVERT: K 132 VAL cc_start: 0.8291 (m) cc_final: 0.7934 (p) REVERT: K 220 ARG cc_start: 0.7142 (mmt180) cc_final: 0.6682 (mmp80) REVERT: K 248 ILE cc_start: 0.9252 (mm) cc_final: 0.9035 (mt) REVERT: K 334 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8012 (pttp) REVERT: K 373 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6189 (mm-30) REVERT: L 71 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7306 (tp40) REVERT: L 97 LEU cc_start: 0.7535 (mt) cc_final: 0.7210 (mt) REVERT: L 155 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: L 158 TRP cc_start: 0.7709 (m100) cc_final: 0.7022 (m-90) REVERT: L 181 TRP cc_start: 0.8249 (m-90) cc_final: 0.7843 (p90) REVERT: L 217 LYS cc_start: 0.7410 (ptmt) cc_final: 0.6999 (mmtt) REVERT: L 222 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8173 (ptpt) outliers start: 85 outliers final: 52 residues processed: 506 average time/residue: 1.2371 time to fit residues: 746.3902 Evaluate side-chains 506 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 442 time to evaluate : 2.885 ------------------------------------------------------------------------------- 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 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 116 GLU 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 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 249 LEU Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 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 222 LYS Chi-restraints excluded: chain L residue 257 LEU 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 344 LYS 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 299 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 291 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS H 30 HIS I 85 GLN I 155 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 = 0.4019 r_free = 0.4019 target = 0.177799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136811 restraints weight = 29399.324| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.34 r_work: 0.3310 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27468 Z= 0.128 Angle : 0.516 7.696 37280 Z= 0.271 Chirality : 0.043 0.209 4486 Planarity : 0.003 0.045 4578 Dihedral : 8.439 78.288 3906 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.71 % Allowed : 17.98 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.14), residues: 3422 helix: 1.98 (0.12), residues: 1922 sheet: -0.24 (0.27), residues: 380 loop : -0.85 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 181 HIS 0.004 0.001 HIS L 168 PHE 0.032 0.001 PHE J 202 TYR 0.012 0.001 TYR G 107 ARG 0.010 0.001 ARG J 331 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 1588) hydrogen bonds : angle 4.09657 ( 4572) covalent geometry : bond 0.00292 (27468) covalent geometry : angle 0.51575 (37280) ********************** 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 517 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 438 time to evaluate : 2.856 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 72 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8118 (mm-30) REVERT: A 85 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8305 (m) REVERT: A 128 MET cc_start: 0.8783 (mmm) cc_final: 0.8160 (mmp) REVERT: A 138 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7276 (t70) REVERT: A 146 ASP cc_start: 0.7736 (m-30) cc_final: 0.7465 (t0) REVERT: A 189 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.7040 (tp) REVERT: B 155 GLU cc_start: 0.6948 (tt0) cc_final: 0.6313 (mt-10) REVERT: B 183 ILE cc_start: 0.7644 (mt) cc_final: 0.7114 (mp) REVERT: C 59 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: C 128 MET cc_start: 0.8436 (mmm) cc_final: 0.8163 (mmm) REVERT: C 155 GLU cc_start: 0.6920 (tt0) cc_final: 0.6469 (mt-10) REVERT: C 183 ILE cc_start: 0.7723 (mt) cc_final: 0.7204 (mp) REVERT: D 85 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8284 (m) REVERT: E 59 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7969 (mt-10) REVERT: E 213 ASP cc_start: 0.6785 (t0) cc_final: 0.6446 (t70) REVERT: F 128 MET cc_start: 0.8662 (mmm) cc_final: 0.8359 (mmm) REVERT: F 134 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7610 (mp10) REVERT: F 146 ASP cc_start: 0.7065 (m-30) cc_final: 0.6750 (p0) REVERT: G 128 MET cc_start: 0.8669 (mmm) cc_final: 0.8362 (mmm) REVERT: G 134 GLN cc_start: 0.8054 (mp10) cc_final: 0.7432 (mp10) REVERT: G 138 ASP cc_start: 0.7828 (t0) cc_final: 0.7508 (m-30) REVERT: G 146 ASP cc_start: 0.7111 (m-30) cc_final: 0.6772 (p0) REVERT: H 59 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7771 (mt-10) REVERT: H 139 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: I 71 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7410 (tp40) REVERT: I 97 LEU cc_start: 0.7634 (mt) cc_final: 0.7272 (mt) REVERT: I 158 TRP cc_start: 0.7677 (m100) cc_final: 0.6962 (m-90) REVERT: I 217 LYS cc_start: 0.7425 (ptmt) cc_final: 0.6997 (mmtt) REVERT: I 222 LYS cc_start: 0.8437 (mmmt) cc_final: 0.7876 (ptpt) REVERT: J 109 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7992 (mmmm) REVERT: J 132 VAL cc_start: 0.8332 (m) cc_final: 0.7978 (p) REVERT: J 220 ARG cc_start: 0.7186 (mmt180) cc_final: 0.6739 (mmp80) REVERT: J 248 ILE cc_start: 0.9211 (mm) cc_final: 0.8945 (mt) REVERT: J 373 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6137 (mm-30) REVERT: K 132 VAL cc_start: 0.8299 (m) cc_final: 0.7948 (p) REVERT: K 220 ARG cc_start: 0.7196 (mmt180) cc_final: 0.6753 (mmp80) REVERT: K 248 ILE cc_start: 0.9266 (mm) cc_final: 0.9037 (mt) REVERT: K 334 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8024 (pttp) REVERT: K 373 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6210 (mm-30) REVERT: L 71 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7398 (tp40) REVERT: L 97 LEU cc_start: 0.7459 (mt) cc_final: 0.7141 (mt) REVERT: L 141 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6769 (mt-10) REVERT: L 155 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: L 158 TRP cc_start: 0.7708 (m100) cc_final: 0.7013 (m-90) REVERT: L 217 LYS cc_start: 0.7416 (ptmt) cc_final: 0.7013 (mmtt) REVERT: L 222 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8182 (ptpt) outliers start: 79 outliers final: 54 residues processed: 491 average time/residue: 1.2148 time to fit residues: 701.8059 Evaluate side-chains 500 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 434 time to evaluate : 3.225 ------------------------------------------------------------------------------- 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 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 141 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 141 VAL 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 139 GLU Chi-restraints excluded: chain H residue 141 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 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 109 LYS Chi-restraints excluded: chain J residue 116 GLU 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 37 LEU Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 116 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 155 GLN Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 257 LEU 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 344 LYS 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 183 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 249 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 210 HIS G 134 GLN J 85 GLN J 119 ASN J 434 ASN K 85 GLN K 119 ASN K 434 ASN L 85 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.177155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.134981 restraints weight = 29618.784| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.41 r_work: 0.3290 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27468 Z= 0.138 Angle : 0.525 7.794 37280 Z= 0.276 Chirality : 0.043 0.205 4486 Planarity : 0.003 0.045 4578 Dihedral : 8.527 77.725 3906 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.68 % Allowed : 17.88 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.14), residues: 3422 helix: 1.91 (0.12), residues: 1926 sheet: -0.23 (0.27), residues: 380 loop : -0.87 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 181 HIS 0.005 0.001 HIS H 30 PHE 0.033 0.002 PHE J 202 TYR 0.011 0.001 TYR G 107 ARG 0.010 0.001 ARG F 27 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 1588) hydrogen bonds : angle 4.14629 ( 4572) covalent geometry : bond 0.00318 (27468) covalent geometry : angle 0.52510 (37280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23301.87 seconds wall clock time: 400 minutes 29.68 seconds (24029.68 seconds total)