Starting phenix.real_space_refine on Sat Jul 4 21:31:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1t_36803/07_2026/8k1t_36803.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1t_36803/07_2026/8k1t_36803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k1t_36803/07_2026/8k1t_36803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1t_36803/07_2026/8k1t_36803.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k1t_36803/07_2026/8k1t_36803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1t_36803/07_2026/8k1t_36803.map" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.088 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 94 5.16 5 Na 4 4.78 5 C 15516 2.51 5 N 3888 2.21 5 O 4336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23866 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "B" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "C" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1498 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 3 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1643 Classifications: {'peptide': 208} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 202} Chain breaks: 2 Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1643 Classifications: {'peptide': 208} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 202} Chain breaks: 2 Chain: "F" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1498 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 3 Chain: "G" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "H" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "I" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "J" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "K" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "L" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Time building chain proxies: 4.84, per 1000 atoms: 0.20 Number of scatterers: 23866 At special positions: 0 Unit cell: (136.95, 176.79, 111.22, 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 94 16.00 P 24 15.00 Na 4 11.00 O 4336 8.00 N 3888 7.00 C 15516 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: 1.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5620 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 18 sheets defined 64.7% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 15 through 29 Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 59 through 66 removed outlier: 3.505A pdb=" N LEU A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'B' and resid 15 through 29 Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 59 through 66 removed outlier: 3.505A pdb=" N LEU B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 123 through 138 Processing helix chain 'C' and resid 15 through 29 removed outlier: 3.537A pdb=" N SER C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 59 through 66 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'C' and resid 106 through 116 Processing helix chain 'C' and resid 123 through 138 Processing helix chain 'C' and resid 211 through 217 Processing helix chain 'D' and resid 15 through 29 removed outlier: 3.536A pdb=" N SER D 20 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 59 through 66 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 81 through 95 Processing helix chain 'D' and resid 106 through 116 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'D' and resid 211 through 220 Processing helix chain 'E' and resid 15 through 29 removed outlier: 3.537A pdb=" N SER E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 59 through 66 Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 81 through 95 Processing helix chain 'E' and resid 106 through 116 Processing helix chain 'E' and resid 123 through 138 Processing helix chain 'E' and resid 171 through 176 Processing helix chain 'E' and resid 211 through 220 Processing helix chain 'F' and resid 15 through 29 removed outlier: 3.537A pdb=" N SER F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 46 Processing helix chain 'F' and resid 59 through 66 Processing helix chain 'F' and resid 67 through 71 Processing helix chain 'F' and resid 81 through 95 Processing helix chain 'F' and resid 106 through 116 Processing helix chain 'F' and resid 123 through 138 Processing helix chain 'F' and resid 211 through 217 Processing helix chain 'G' and resid 15 through 29 Processing helix chain 'G' and resid 38 through 45 Processing helix chain 'G' and resid 59 through 66 removed outlier: 3.504A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 81 through 95 Processing helix chain 'G' and resid 106 through 116 Processing helix chain 'G' and resid 123 through 138 Processing helix chain 'H' and resid 15 through 29 Processing helix chain 'H' and resid 38 through 45 Processing helix chain 'H' and resid 59 through 66 removed outlier: 3.505A pdb=" N LEU H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'H' and resid 81 through 95 Processing helix chain 'H' and resid 106 through 116 Processing helix chain 'H' and resid 123 through 138 Processing helix chain 'I' and resid 16 through 36 Processing helix chain 'I' and resid 37 through 41 removed outlier: 3.542A pdb=" N THR I 41 " --> pdb=" O PRO I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 59 Processing helix chain 'I' and resid 67 through 72 removed outlier: 3.554A pdb=" N PHE I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 90 Processing helix chain 'I' and resid 90 through 102 removed outlier: 3.873A pdb=" N PHE I 94 " --> pdb=" O GLY I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'I' and resid 125 through 157 removed outlier: 4.164A pdb=" N ARG I 151 " --> pdb=" O ILE I 147 " (cutoff:3.500A) Proline residue: I 154 - end of helix Processing helix chain 'I' and resid 158 through 174 removed outlier: 3.541A pdb=" N PHE I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 208 removed outlier: 4.415A pdb=" N GLY I 208 " --> pdb=" O THR I 204 " (cutoff:3.500A) 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 Processing helix chain 'I' and resid 290 through 303 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: 3.898A pdb=" N PHE I 427 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 36 Processing helix chain 'J' and resid 37 through 41 removed outlier: 3.541A pdb=" N THR J 41 " --> pdb=" O PRO J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 59 Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.555A pdb=" N PHE J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 90 Processing helix chain 'J' and resid 90 through 102 removed outlier: 3.873A pdb=" N PHE J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 118 Processing helix chain 'J' and resid 125 through 157 removed outlier: 4.164A 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: 3.541A pdb=" N PHE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 208 removed outlier: 4.414A pdb=" N GLY J 208 " --> pdb=" O THR J 204 " (cutoff:3.500A) 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 Processing helix chain 'J' and resid 290 through 303 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: 3.897A pdb=" N PHE J 427 " --> pdb=" O PHE J 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 36 Processing helix chain 'K' and resid 37 through 41 removed outlier: 3.542A pdb=" N THR K 41 " --> pdb=" O PRO K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 59 Processing helix chain 'K' and resid 67 through 72 removed outlier: 3.554A pdb=" N PHE K 72 " --> pdb=" O THR K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 90 Processing helix chain 'K' and resid 90 through 102 removed outlier: 3.873A pdb=" N PHE K 94 " --> pdb=" O GLY K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'K' and resid 125 through 157 removed outlier: 4.164A 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: 3.542A pdb=" N PHE K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 208 removed outlier: 4.414A pdb=" N GLY K 208 " --> pdb=" O THR K 204 " (cutoff:3.500A) 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 Processing helix chain 'K' and resid 290 through 303 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: 3.898A pdb=" N PHE K 427 " --> pdb=" O PHE K 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 36 Processing helix chain 'L' and resid 37 through 41 removed outlier: 3.541A pdb=" N THR L 41 " --> pdb=" O PRO L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 59 Processing helix chain 'L' and resid 67 through 72 removed outlier: 3.554A pdb=" N PHE L 72 " --> pdb=" O THR L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 90 Processing helix chain 'L' and resid 90 through 102 removed outlier: 3.873A pdb=" N PHE L 94 " --> pdb=" O GLY L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 118 Processing helix chain 'L' and resid 125 through 157 removed outlier: 4.164A pdb=" N ARG L 151 " --> pdb=" O ILE L 147 " (cutoff:3.500A) Proline residue: L 154 - end of helix Processing helix chain 'L' and resid 158 through 174 removed outlier: 3.542A pdb=" N PHE L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 208 removed outlier: 4.414A pdb=" N GLY L 208 " --> pdb=" O THR L 204 " (cutoff:3.500A) 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 Processing helix chain 'L' and resid 290 through 303 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: 3.897A 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: 3.817A pdb=" N TYR A 73 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 100 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE A 122 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 102 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.817A pdb=" N TYR B 73 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE B 100 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE B 122 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL B 102 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.747A pdb=" N TYR C 73 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE C 100 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE C 122 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C 102 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.644A pdb=" N ASN C 143 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET C 208 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE C 180 " --> pdb=" O MET C 208 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N LEU C 181 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER C 192 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE C 183 " --> pdb=" O CYS C 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.748A pdb=" N TYR D 73 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE D 100 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE D 122 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL D 102 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 143 through 145 removed outlier: 3.643A pdb=" N ASN D 143 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N MET D 208 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE D 180 " --> pdb=" O MET D 208 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE D 183 " --> pdb=" O CYS D 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 165 through 166 removed outlier: 3.682A pdb=" N LYS D 165 " --> pdb=" O ILE D 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 51 through 54 removed outlier: 3.747A pdb=" N TYR E 73 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE E 100 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE E 122 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL E 102 " --> pdb=" O ILE E 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 143 through 145 removed outlier: 3.643A pdb=" N ASN E 143 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET E 208 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE E 180 " --> pdb=" O MET E 208 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE E 183 " --> pdb=" O CYS E 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 165 through 166 removed outlier: 3.877A pdb=" N LYS E 165 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.747A pdb=" N TYR F 73 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE F 100 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE F 122 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL F 102 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 143 through 145 removed outlier: 3.643A pdb=" N ASN F 143 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET F 208 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE F 180 " --> pdb=" O MET F 208 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N LEU F 181 " --> pdb=" O SER F 192 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER F 192 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE F 183 " --> pdb=" O CYS F 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.817A pdb=" N TYR G 73 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE G 100 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE G 122 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL G 102 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 51 through 54 removed outlier: 3.817A pdb=" N TYR H 73 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE H 100 " --> pdb=" O ARG H 120 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE H 122 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL H 102 " --> pdb=" O ILE H 122 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 336 through 338 removed outlier: 4.633A pdb=" N THR I 336 " --> pdb=" O ILE I 343 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 336 through 338 removed outlier: 4.633A pdb=" N THR J 336 " --> pdb=" O ILE J 343 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 336 through 338 removed outlier: 4.634A pdb=" N THR K 336 " --> pdb=" O ILE K 343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 336 through 338 removed outlier: 4.634A pdb=" N THR L 336 " --> pdb=" O ILE L 343 " (cutoff:3.500A) 1532 hydrogen bonds defined for protein. 4413 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4015 1.32 - 1.44: 6056 1.44 - 1.57: 14037 1.57 - 1.69: 40 1.69 - 1.81: 170 Bond restraints: 24318 Sorted by residual: bond pdb=" CA LEU J 352 " pdb=" C LEU J 352 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.37e-02 5.33e+03 1.65e+01 bond pdb=" CA LEU L 352 " pdb=" C LEU L 352 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.32e-02 5.74e+03 1.36e+01 bond pdb=" CA LEU I 352 " pdb=" C LEU I 352 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.32e-02 5.74e+03 1.35e+01 bond pdb=" CA LEU K 352 " pdb=" C LEU K 352 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.37e-02 5.33e+03 1.03e+01 bond pdb=" CA SER K 283 " pdb=" CB SER K 283 " ideal model delta sigma weight residual 1.536 1.490 0.046 1.46e-02 4.69e+03 9.79e+00 ... (remaining 24313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 32718 2.04 - 4.07: 243 4.07 - 6.11: 35 6.11 - 8.15: 12 8.15 - 10.19: 6 Bond angle restraints: 33014 Sorted by residual: angle pdb=" N SER L 283 " pdb=" CA SER L 283 " pdb=" C SER L 283 " ideal model delta sigma weight residual 114.56 105.27 9.29 1.27e+00 6.20e-01 5.35e+01 angle pdb=" N SER I 283 " pdb=" CA SER I 283 " pdb=" C SER I 283 " ideal model delta sigma weight residual 114.56 105.35 9.21 1.27e+00 6.20e-01 5.26e+01 angle pdb=" N SER J 283 " pdb=" CA SER J 283 " pdb=" C SER J 283 " ideal model delta sigma weight residual 114.56 106.85 7.71 1.27e+00 6.20e-01 3.69e+01 angle pdb=" N SER K 283 " pdb=" CA SER K 283 " pdb=" C SER K 283 " ideal model delta sigma weight residual 114.56 106.95 7.61 1.27e+00 6.20e-01 3.59e+01 angle pdb=" C THR L 15 " pdb=" N PRO L 16 " pdb=" CA PRO L 16 " ideal model delta sigma weight residual 120.38 114.25 6.13 1.03e+00 9.43e-01 3.55e+01 ... (remaining 33009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13738 17.93 - 35.86: 597 35.86 - 53.79: 65 53.79 - 71.72: 46 71.72 - 89.66: 12 Dihedral angle restraints: 14458 sinusoidal: 5730 harmonic: 8728 Sorted by residual: dihedral pdb=" CA MET J 301 " pdb=" C MET J 301 " pdb=" N PHE J 302 " pdb=" CA PHE J 302 " ideal model delta harmonic sigma weight residual 180.00 164.71 15.29 0 5.00e+00 4.00e-02 9.36e+00 dihedral pdb=" CA MET K 301 " pdb=" C MET K 301 " pdb=" N PHE K 302 " pdb=" CA PHE K 302 " ideal model delta harmonic sigma weight residual 180.00 164.71 15.29 0 5.00e+00 4.00e-02 9.35e+00 dihedral pdb=" CA MET L 301 " pdb=" C MET L 301 " pdb=" N PHE L 302 " pdb=" CA PHE L 302 " ideal model delta harmonic sigma weight residual 180.00 164.71 15.29 0 5.00e+00 4.00e-02 9.35e+00 ... (remaining 14455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2497 0.032 - 0.065: 1101 0.065 - 0.097: 220 0.097 - 0.129: 157 0.129 - 0.162: 23 Chirality restraints: 3998 Sorted by residual: chirality pdb=" CA LEU E 87 " pdb=" N LEU E 87 " pdb=" C LEU E 87 " pdb=" CB LEU E 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" CA LEU D 87 " pdb=" N LEU D 87 " pdb=" C LEU D 87 " pdb=" CB LEU D 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE J 303 " pdb=" N ILE J 303 " pdb=" C ILE J 303 " pdb=" CB ILE J 303 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 ... (remaining 3995 not shown) Planarity restraints: 4016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA L 351 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C ALA L 351 " 0.037 2.00e-02 2.50e+03 pdb=" O ALA L 351 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU L 352 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 351 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.18e+00 pdb=" C ALA J 351 " -0.035 2.00e-02 2.50e+03 pdb=" O ALA J 351 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU J 352 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 86 " 0.009 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C THR G 86 " -0.029 2.00e-02 2.50e+03 pdb=" O THR G 86 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU G 87 " 0.010 2.00e-02 2.50e+03 ... (remaining 4013 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 6808 2.82 - 3.40: 26062 3.40 - 3.98: 46778 3.98 - 4.56: 65663 4.56 - 5.14: 96579 Nonbonded interactions: 241890 Sorted by model distance: nonbonded pdb=" O ASN L 195 " pdb=" OG1 THR L 199 " model vdw 2.240 3.040 nonbonded pdb=" O ASN K 195 " pdb=" OG1 THR K 199 " model vdw 2.240 3.040 nonbonded pdb=" O ASN I 195 " pdb=" OG1 THR I 199 " model vdw 2.240 3.040 nonbonded pdb=" O ASN J 195 " pdb=" OG1 THR J 199 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR D 108 " pdb=" OE1 GLU E 60 " model vdw 2.296 3.040 ... (remaining 241885 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 301) selection = chain 'B' selection = (chain 'G' and resid 7 through 301) selection = chain 'H' } ncs_group { reference = (chain 'C' and resid 7 through 217) selection = (chain 'D' and (resid 7 through 172 or resid 179 through 192 or resid 205 throug \ h 217)) selection = (chain 'E' and (resid 7 through 172 or resid 179 through 192 or resid 205 throug \ h 217)) selection = (chain 'F' and resid 7 through 217) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.790 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24318 Z= 0.200 Angle : 0.529 10.186 33014 Z= 0.304 Chirality : 0.042 0.162 3998 Planarity : 0.003 0.031 4016 Dihedral : 10.972 89.655 8838 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.97 % Allowed : 3.66 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.14), residues: 3008 helix: 1.12 (0.11), residues: 1810 sheet: 1.39 (0.29), residues: 308 loop : -0.82 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 417 TYR 0.005 0.001 TYR D 108 PHE 0.026 0.001 PHE K 202 TRP 0.006 0.001 TRP L 47 HIS 0.002 0.001 HIS L 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.20 (24318) covalent geometry : angle 0.52925 / 0.30 (33014) hydrogen bonds : bond 0.21630 / 14.86 ( 1532) hydrogen bonds : angle 6.62929 / 4.72 ( 4413) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 813 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7166 (tp30) cc_final: 0.6932 (tp30) REVERT: C 48 TYR cc_start: 0.7996 (m-80) cc_final: 0.7784 (m-80) REVERT: C 128 MET cc_start: 0.7893 (mmm) cc_final: 0.7547 (mmp) REVERT: D 134 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7201 (mm110) REVERT: E 137 SER cc_start: 0.7971 (t) cc_final: 0.7742 (m) REVERT: F 128 MET cc_start: 0.7972 (mmm) cc_final: 0.7620 (mmp) REVERT: F 181 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7433 (mt) REVERT: I 110 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6819 (mp0) REVERT: I 123 ILE cc_start: 0.8073 (pt) cc_final: 0.7825 (pt) REVERT: I 140 ILE cc_start: 0.8609 (tt) cc_final: 0.8390 (tt) REVERT: I 166 LEU cc_start: 0.8782 (tp) cc_final: 0.8514 (tm) REVERT: I 251 TYR cc_start: 0.8479 (t80) cc_final: 0.8199 (t80) REVERT: I 298 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8875 (mt) REVERT: I 340 ARG cc_start: 0.7816 (mtt180) cc_final: 0.7455 (mtt-85) REVERT: J 97 LEU cc_start: 0.7358 (mt) cc_final: 0.7005 (tp) REVERT: J 136 PHE cc_start: 0.7749 (t80) cc_final: 0.7522 (t80) REVERT: J 156 TYR cc_start: 0.7498 (m-80) cc_final: 0.7260 (m-80) REVERT: J 166 LEU cc_start: 0.8060 (tp) cc_final: 0.7789 (tp) REVERT: K 156 TYR cc_start: 0.7480 (m-80) cc_final: 0.7252 (m-80) REVERT: K 166 LEU cc_start: 0.8071 (tp) cc_final: 0.7808 (tp) REVERT: K 250 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8296 (mm-30) REVERT: K 262 ILE cc_start: 0.7411 (mt) cc_final: 0.7134 (tp) REVERT: L 110 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6798 (mp0) REVERT: L 123 ILE cc_start: 0.8074 (pt) cc_final: 0.7847 (pt) REVERT: L 140 ILE cc_start: 0.8613 (tt) cc_final: 0.8404 (tt) REVERT: L 166 LEU cc_start: 0.8801 (tp) cc_final: 0.8529 (tm) REVERT: L 251 TYR cc_start: 0.8452 (t80) cc_final: 0.8083 (t80) REVERT: L 298 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8867 (mt) REVERT: L 340 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7454 (mtt-85) outliers start: 25 outliers final: 0 residues processed: 831 average time/residue: 0.6144 time to fit residues: 584.5533 Evaluate side-chains 572 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 569 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain L residue 298 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN A 81 ASN B 8 GLN B 38 ASN C 38 ASN C 185 HIS D 70 ASN D 185 HIS E 38 ASN E 61 ASN E 70 ASN E 134 GLN E 185 HIS F 38 ASN F 185 HIS G 8 GLN H 38 ASN H 43 ASN H 70 ASN H 81 ASN I 18 GLN I 119 ASN I 155 GLN I 195 ASN I 239 ASN ** J 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 GLN J 253 ASN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN K 155 GLN K 253 ASN K 272 GLN L 18 GLN L 119 ASN L 155 GLN L 195 ASN L 239 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.169205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.129233 restraints weight = 26175.036| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.85 r_work: 0.3314 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24318 Z= 0.143 Angle : 0.562 9.449 33014 Z= 0.298 Chirality : 0.043 0.174 3998 Planarity : 0.004 0.044 4016 Dihedral : 10.247 79.964 3474 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.47 % Allowed : 13.60 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.15), residues: 3008 helix: 2.21 (0.12), residues: 1840 sheet: 1.07 (0.28), residues: 332 loop : -0.53 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 27 TYR 0.014 0.001 TYR I 270 PHE 0.034 0.002 PHE I 202 TRP 0.005 0.001 TRP K 47 HIS 0.003 0.001 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (24318) covalent geometry : angle 0.56187 / 0.30 (33014) hydrogen bonds : bond 0.05116 / 3.49 ( 1532) hydrogen bonds : angle 4.42370 / 3.12 ( 4413) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 605 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8000 (tp30) cc_final: 0.7650 (tp30) REVERT: A 115 LYS cc_start: 0.7666 (mmtm) cc_final: 0.7329 (mptt) REVERT: C 39 GLU cc_start: 0.7962 (mp0) cc_final: 0.7755 (mp0) REVERT: C 48 TYR cc_start: 0.8341 (m-80) cc_final: 0.8037 (m-80) REVERT: C 56 ASN cc_start: 0.8700 (t0) cc_final: 0.8403 (t0) REVERT: C 59 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7066 (mt-10) REVERT: C 62 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7109 (mt-10) REVERT: C 111 LYS cc_start: 0.8534 (mmpt) cc_final: 0.8250 (mtpt) REVERT: C 128 MET cc_start: 0.8574 (mmm) cc_final: 0.8183 (mmp) REVERT: E 138 ASP cc_start: 0.7380 (t70) cc_final: 0.6595 (m-30) REVERT: F 59 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7175 (mt-10) REVERT: F 62 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6965 (mt-10) REVERT: F 111 LYS cc_start: 0.8487 (mmpt) cc_final: 0.8235 (mtpt) REVERT: F 128 MET cc_start: 0.8626 (mmm) cc_final: 0.8275 (mmp) REVERT: H 115 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7516 (mttm) REVERT: I 110 GLU cc_start: 0.7577 (mt-10) cc_final: 0.6861 (mp0) REVERT: I 123 ILE cc_start: 0.7826 (pt) cc_final: 0.7537 (pt) REVERT: I 140 ILE cc_start: 0.8355 (tt) cc_final: 0.8154 (tt) REVERT: I 150 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7693 (mp) REVERT: I 156 TYR cc_start: 0.6767 (m-80) cc_final: 0.6500 (m-80) REVERT: I 251 TYR cc_start: 0.8656 (t80) cc_final: 0.8274 (t80) REVERT: I 298 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8731 (mt) REVERT: I 340 ARG cc_start: 0.8478 (mtt180) cc_final: 0.7910 (mtt-85) REVERT: J 97 LEU cc_start: 0.7265 (mt) cc_final: 0.7024 (tp) REVERT: J 106 ILE cc_start: 0.7410 (mp) cc_final: 0.7110 (mm) REVERT: J 136 PHE cc_start: 0.7672 (t80) cc_final: 0.7404 (t80) REVERT: J 155 GLN cc_start: 0.7598 (tt0) cc_final: 0.7156 (tt0) REVERT: J 216 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6118 (mtp) REVERT: J 222 LYS cc_start: 0.8097 (pttm) cc_final: 0.7859 (mmtt) REVERT: J 299 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8727 (tp) REVERT: K 97 LEU cc_start: 0.7312 (mt) cc_final: 0.6996 (tp) REVERT: K 100 MET cc_start: 0.6276 (mtm) cc_final: 0.5972 (mtm) REVERT: K 155 GLN cc_start: 0.7580 (tt0) cc_final: 0.7163 (tt0) REVERT: K 216 MET cc_start: 0.7477 (mmp) cc_final: 0.6154 (mtp) REVERT: K 250 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8594 (mm-30) REVERT: K 253 ASN cc_start: 0.8397 (t0) cc_final: 0.8161 (t160) REVERT: K 344 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8080 (mmtm) REVERT: L 110 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6829 (mp0) REVERT: L 123 ILE cc_start: 0.7811 (pt) cc_final: 0.7537 (pt) REVERT: L 150 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7681 (mp) REVERT: L 151 ARG cc_start: 0.7691 (tpt-90) cc_final: 0.7437 (tpt-90) REVERT: L 156 TYR cc_start: 0.6786 (m-80) cc_final: 0.6518 (m-80) REVERT: L 251 TYR cc_start: 0.8598 (t80) cc_final: 0.8201 (t80) REVERT: L 298 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8697 (mt) REVERT: L 340 ARG cc_start: 0.8491 (mtt180) cc_final: 0.7920 (mtt-85) REVERT: L 373 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6483 (mt-10) REVERT: L 439 ASP cc_start: 0.8230 (m-30) cc_final: 0.8025 (m-30) outliers start: 89 outliers final: 28 residues processed: 654 average time/residue: 0.6879 time to fit residues: 512.8405 Evaluate side-chains 590 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 554 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 344 LYS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 373 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 275 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 267 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 251 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN A 70 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN B 134 GLN C 185 HIS D 70 ASN D 134 GLN D 185 HIS E 134 GLN E 185 HIS F 185 HIS G 8 GLN G 134 GLN H 70 ASN I 18 GLN I 119 ASN I 239 ASN J 85 GLN J 115 GLN J 253 ASN J 374 GLN K 85 GLN K 115 GLN K 272 GLN L 18 GLN L 119 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.166458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125979 restraints weight = 26201.406| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.85 r_work: 0.3272 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24318 Z= 0.180 Angle : 0.575 7.885 33014 Z= 0.303 Chirality : 0.044 0.197 3998 Planarity : 0.004 0.046 4016 Dihedral : 10.034 77.038 3474 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.25 % Allowed : 13.68 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.15), residues: 3008 helix: 2.27 (0.12), residues: 1840 sheet: 0.89 (0.28), residues: 300 loop : -0.58 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 27 TYR 0.017 0.001 TYR L 270 PHE 0.038 0.002 PHE L 202 TRP 0.006 0.001 TRP J 47 HIS 0.004 0.001 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (24318) covalent geometry : angle 0.57451 / 0.30 (33014) hydrogen bonds : bond 0.04885 / 3.34 ( 1532) hydrogen bonds : angle 4.26089 / 3.01 ( 4413) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 580 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8078 (tp30) cc_final: 0.7771 (tp30) REVERT: A 41 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8070 (mptp) REVERT: A 89 THR cc_start: 0.8690 (t) cc_final: 0.8456 (m) REVERT: B 127 ASP cc_start: 0.8088 (m-30) cc_final: 0.7867 (m-30) REVERT: C 23 LYS cc_start: 0.8685 (mtpm) cc_final: 0.8085 (mtmt) REVERT: C 48 TYR cc_start: 0.8356 (m-80) cc_final: 0.8153 (m-80) REVERT: C 56 ASN cc_start: 0.8691 (t0) cc_final: 0.8346 (t0) REVERT: C 59 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7046 (mt-10) REVERT: C 62 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7063 (mt-10) REVERT: C 105 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: C 128 MET cc_start: 0.8616 (mmm) cc_final: 0.8244 (mmp) REVERT: D 60 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: E 60 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: E 134 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7926 (mm110) REVERT: E 138 ASP cc_start: 0.7138 (t70) cc_final: 0.6410 (m-30) REVERT: E 145 ILE cc_start: 0.6311 (OUTLIER) cc_final: 0.6007 (tt) REVERT: E 208 MET cc_start: 0.5823 (ptt) cc_final: 0.5410 (ptt) REVERT: F 23 LYS cc_start: 0.8667 (mtpm) cc_final: 0.8083 (mtmt) REVERT: F 56 ASN cc_start: 0.8639 (t0) cc_final: 0.8376 (t0) REVERT: F 59 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7343 (mm-30) REVERT: F 62 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7488 (mt-10) REVERT: F 111 LYS cc_start: 0.8538 (mmpt) cc_final: 0.8257 (mtpt) REVERT: F 128 MET cc_start: 0.8608 (mmm) cc_final: 0.8233 (mmp) REVERT: F 131 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8399 (mttm) REVERT: H 41 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7981 (mptp) REVERT: H 89 THR cc_start: 0.8682 (t) cc_final: 0.8458 (m) REVERT: H 115 LYS cc_start: 0.7769 (mmtm) cc_final: 0.7563 (mmtm) REVERT: I 110 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7257 (mp0) REVERT: I 123 ILE cc_start: 0.7751 (pt) cc_final: 0.7530 (pt) REVERT: I 140 ILE cc_start: 0.8415 (tt) cc_final: 0.8146 (tt) REVERT: I 149 SER cc_start: 0.8321 (m) cc_final: 0.8120 (p) REVERT: I 150 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7651 (mp) REVERT: I 156 TYR cc_start: 0.6778 (m-80) cc_final: 0.6546 (m-80) REVERT: I 251 TYR cc_start: 0.8621 (t80) cc_final: 0.8282 (t80) REVERT: I 298 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8731 (mt) REVERT: I 340 ARG cc_start: 0.8481 (mtt180) cc_final: 0.7886 (mtt-85) REVERT: J 97 LEU cc_start: 0.7301 (mt) cc_final: 0.7063 (tp) REVERT: J 100 MET cc_start: 0.6323 (mtm) cc_final: 0.5791 (mmm) REVERT: J 136 PHE cc_start: 0.7696 (t80) cc_final: 0.7459 (t80) REVERT: J 155 GLN cc_start: 0.7696 (tt0) cc_final: 0.7333 (tt0) REVERT: J 216 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.6148 (mtp) REVERT: J 222 LYS cc_start: 0.8059 (pttm) cc_final: 0.7847 (mmtt) REVERT: J 299 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8755 (tp) REVERT: K 97 LEU cc_start: 0.7409 (mt) cc_final: 0.7132 (tp) REVERT: K 100 MET cc_start: 0.6425 (mtm) cc_final: 0.6127 (mtm) REVERT: K 155 GLN cc_start: 0.7700 (tt0) cc_final: 0.7356 (tt0) REVERT: K 216 MET cc_start: 0.7535 (mmp) cc_final: 0.6166 (mtp) REVERT: K 250 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8761 (mm-30) REVERT: K 253 ASN cc_start: 0.8379 (t0) cc_final: 0.8145 (t160) REVERT: L 110 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7267 (mp0) REVERT: L 150 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7632 (mp) REVERT: L 251 TYR cc_start: 0.8582 (t80) cc_final: 0.8189 (t80) REVERT: L 298 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8713 (mt) REVERT: L 373 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6599 (mt-10) REVERT: L 418 ILE cc_start: 0.8893 (tt) cc_final: 0.8688 (tp) outliers start: 109 outliers final: 47 residues processed: 646 average time/residue: 0.6359 time to fit residues: 469.8481 Evaluate side-chains 616 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 555 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 373 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 293 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 103 optimal weight: 0.0000 chunk 203 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN D 134 GLN G 8 GLN H 70 ASN I 18 GLN I 119 ASN I 155 GLN I 239 ASN J 85 GLN J 115 GLN J 253 ASN J 374 GLN K 85 GLN K 115 GLN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.168917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128674 restraints weight = 26161.420| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.83 r_work: 0.3313 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24318 Z= 0.119 Angle : 0.515 7.602 33014 Z= 0.273 Chirality : 0.042 0.181 3998 Planarity : 0.004 0.046 4016 Dihedral : 9.716 72.502 3474 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.90 % Allowed : 15.04 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.15), residues: 3008 helix: 2.43 (0.12), residues: 1838 sheet: 0.71 (0.29), residues: 304 loop : -0.54 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 27 TYR 0.019 0.001 TYR I 270 PHE 0.037 0.001 PHE L 202 TRP 0.006 0.001 TRP K 47 HIS 0.003 0.001 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (24318) covalent geometry : angle 0.51513 / 0.27 (33014) hydrogen bonds : bond 0.03931 / 2.69 ( 1532) hydrogen bonds : angle 4.06249 / 2.86 ( 4413) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 581 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8096 (tp30) cc_final: 0.7758 (tp30) REVERT: A 115 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7418 (mptt) REVERT: C 23 LYS cc_start: 0.8668 (mtpm) cc_final: 0.8115 (mtmt) REVERT: C 48 TYR cc_start: 0.8341 (m-80) cc_final: 0.8097 (m-80) REVERT: C 56 ASN cc_start: 0.8644 (t0) cc_final: 0.8359 (t0) REVERT: C 62 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7570 (mt-10) REVERT: C 111 LYS cc_start: 0.8446 (mmpt) cc_final: 0.8189 (mtpt) REVERT: C 128 MET cc_start: 0.8559 (mmm) cc_final: 0.8151 (mmp) REVERT: C 208 MET cc_start: 0.6248 (ttp) cc_final: 0.5996 (ttm) REVERT: D 60 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: D 115 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7982 (mptp) REVERT: E 138 ASP cc_start: 0.7235 (t70) cc_final: 0.6489 (m-30) REVERT: E 145 ILE cc_start: 0.6329 (OUTLIER) cc_final: 0.6044 (tt) REVERT: E 208 MET cc_start: 0.5857 (ptt) cc_final: 0.5468 (ptt) REVERT: F 23 LYS cc_start: 0.8660 (mtpm) cc_final: 0.8203 (mttt) REVERT: F 56 ASN cc_start: 0.8641 (t0) cc_final: 0.8440 (t0) REVERT: F 59 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7379 (mm-30) REVERT: F 105 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: F 111 LYS cc_start: 0.8455 (mmpt) cc_final: 0.8235 (mtpt) REVERT: F 128 MET cc_start: 0.8583 (mmm) cc_final: 0.8226 (mmp) REVERT: F 181 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6773 (mp) REVERT: G 62 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7071 (tp30) REVERT: G 72 GLU cc_start: 0.7740 (tt0) cc_final: 0.7355 (pt0) REVERT: G 127 ASP cc_start: 0.8126 (m-30) cc_final: 0.7910 (m-30) REVERT: H 115 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7460 (mtpp) REVERT: I 110 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7348 (mp0) REVERT: I 140 ILE cc_start: 0.8403 (tt) cc_final: 0.8188 (tt) REVERT: I 150 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7418 (mp) REVERT: I 251 TYR cc_start: 0.8673 (t80) cc_final: 0.8392 (t80) REVERT: I 298 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8694 (mt) REVERT: J 97 LEU cc_start: 0.7359 (mt) cc_final: 0.7148 (tp) REVERT: J 100 MET cc_start: 0.6399 (mtm) cc_final: 0.6179 (mtm) REVERT: J 136 PHE cc_start: 0.7632 (t80) cc_final: 0.7416 (t80) REVERT: J 155 GLN cc_start: 0.7747 (tt0) cc_final: 0.7390 (tt0) REVERT: J 156 TYR cc_start: 0.7575 (m-80) cc_final: 0.7337 (m-80) REVERT: J 216 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.6158 (mtp) REVERT: J 222 LYS cc_start: 0.8107 (pttm) cc_final: 0.7881 (mmtt) REVERT: J 299 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8753 (tp) REVERT: K 97 LEU cc_start: 0.7389 (mt) cc_final: 0.7132 (tp) REVERT: K 100 MET cc_start: 0.6511 (mtm) cc_final: 0.6243 (mtm) REVERT: K 155 GLN cc_start: 0.7752 (tt0) cc_final: 0.7408 (tt0) REVERT: K 156 TYR cc_start: 0.7624 (m-80) cc_final: 0.7394 (m-80) REVERT: K 216 MET cc_start: 0.7557 (mmp) cc_final: 0.6164 (mtp) REVERT: K 220 ARG cc_start: 0.6475 (tpm170) cc_final: 0.5494 (tpt170) REVERT: K 250 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8710 (mm-30) REVERT: K 253 ASN cc_start: 0.8403 (t0) cc_final: 0.8171 (t160) REVERT: L 110 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7404 (mp0) REVERT: L 150 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7363 (mp) REVERT: L 251 TYR cc_start: 0.8647 (t80) cc_final: 0.8308 (t80) REVERT: L 266 LEU cc_start: 0.8497 (mt) cc_final: 0.8261 (mt) REVERT: L 298 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8695 (mt) REVERT: L 373 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6511 (mt-10) outliers start: 100 outliers final: 39 residues processed: 644 average time/residue: 0.6297 time to fit residues: 462.9604 Evaluate side-chains 605 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 552 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 115 LYS Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 373 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 232 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN B 8 GLN B 38 ASN B 134 GLN D 134 GLN G 134 GLN H 70 ASN I 18 GLN I 119 ASN I 155 GLN I 239 ASN ** J 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN J 115 GLN J 253 ASN J 374 GLN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 115 GLN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.162983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122304 restraints weight = 26116.021| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.86 r_work: 0.3221 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 24318 Z= 0.327 Angle : 0.692 9.459 33014 Z= 0.366 Chirality : 0.050 0.228 3998 Planarity : 0.005 0.047 4016 Dihedral : 10.464 82.676 3474 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 5.07 % Allowed : 14.73 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.15), residues: 3008 helix: 1.89 (0.12), residues: 1840 sheet: 0.68 (0.28), residues: 310 loop : -0.65 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 27 TYR 0.018 0.002 TYR J 345 PHE 0.042 0.002 PHE I 202 TRP 0.010 0.001 TRP J 47 HIS 0.009 0.001 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00783 / 0.33 (24318) covalent geometry : angle 0.69249 / 0.37 (33014) hydrogen bonds : bond 0.05615 / 3.84 ( 1532) hydrogen bonds : angle 4.34868 / 3.08 ( 4413) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 563 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8131 (tp30) cc_final: 0.7694 (tp30) REVERT: A 41 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7796 (mptp) REVERT: A 60 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: B 62 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7054 (tp30) REVERT: C 23 LYS cc_start: 0.8656 (mtpm) cc_final: 0.8179 (mttt) REVERT: C 43 ASN cc_start: 0.8603 (m-40) cc_final: 0.8375 (m110) REVERT: C 56 ASN cc_start: 0.8689 (t0) cc_final: 0.8460 (t0) REVERT: C 59 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7412 (mm-30) REVERT: C 128 MET cc_start: 0.8684 (mmm) cc_final: 0.8285 (mmp) REVERT: C 208 MET cc_start: 0.6271 (ttp) cc_final: 0.5922 (ttm) REVERT: D 60 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: E 60 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: E 120 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8594 (ttt180) REVERT: E 138 ASP cc_start: 0.7470 (t70) cc_final: 0.6013 (p0) REVERT: E 208 MET cc_start: 0.5889 (ptt) cc_final: 0.5466 (ptt) REVERT: F 23 LYS cc_start: 0.8604 (mtpm) cc_final: 0.8159 (mttt) REVERT: F 43 ASN cc_start: 0.8616 (m110) cc_final: 0.8340 (m110) REVERT: F 111 LYS cc_start: 0.8621 (mmpt) cc_final: 0.8308 (mtpt) REVERT: F 128 MET cc_start: 0.8693 (mmm) cc_final: 0.8290 (mmp) REVERT: F 131 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8413 (mttm) REVERT: G 62 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7201 (tp30) REVERT: H 41 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7758 (mptp) REVERT: H 60 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7533 (tp30) REVERT: H 63 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.7982 (mp) REVERT: I 123 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7706 (pt) REVERT: I 140 ILE cc_start: 0.8416 (tt) cc_final: 0.8180 (tt) REVERT: I 150 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7429 (pt) REVERT: I 216 MET cc_start: 0.7730 (tpp) cc_final: 0.7090 (mtp) REVERT: I 219 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6492 (mmt-90) REVERT: I 251 TYR cc_start: 0.8553 (t80) cc_final: 0.8157 (t80) REVERT: I 266 LEU cc_start: 0.8464 (mt) cc_final: 0.8229 (mt) REVERT: I 298 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8765 (mt) REVERT: J 136 PHE cc_start: 0.7787 (t80) cc_final: 0.7476 (t80) REVERT: J 155 GLN cc_start: 0.7710 (tt0) cc_final: 0.7384 (tt0) REVERT: J 216 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.6171 (mtp) REVERT: J 222 LYS cc_start: 0.8017 (pttm) cc_final: 0.7807 (mmtp) REVERT: J 299 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8835 (tp) REVERT: J 333 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8029 (mmtt) REVERT: K 97 LEU cc_start: 0.7332 (mt) cc_final: 0.7131 (tp) REVERT: K 100 MET cc_start: 0.6475 (mtm) cc_final: 0.6190 (mtm) REVERT: K 155 GLN cc_start: 0.7731 (tt0) cc_final: 0.7436 (tt0) REVERT: K 216 MET cc_start: 0.7615 (mmp) cc_final: 0.6173 (mtp) REVERT: K 220 ARG cc_start: 0.6596 (tpm170) cc_final: 0.5570 (tpt170) REVERT: K 253 ASN cc_start: 0.8360 (t0) cc_final: 0.8133 (t160) REVERT: L 150 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7525 (pt) REVERT: L 216 MET cc_start: 0.7775 (tpp) cc_final: 0.7120 (mtp) REVERT: L 219 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6500 (mmt-90) REVERT: L 251 TYR cc_start: 0.8532 (t80) cc_final: 0.8142 (t80) REVERT: L 266 LEU cc_start: 0.8496 (mt) cc_final: 0.8246 (mt) REVERT: L 298 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8771 (mt) REVERT: L 373 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6688 (mt-10) outliers start: 130 outliers final: 51 residues processed: 643 average time/residue: 0.6402 time to fit residues: 469.8865 Evaluate side-chains 621 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 550 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 219 ARG Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 333 LYS Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain J residue 422 THR Chi-restraints excluded: chain J residue 441 GLU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 219 ARG Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 340 ARG Chi-restraints excluded: chain L residue 373 GLU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 184 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 267 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 GLN D 8 GLN D 134 GLN E 134 GLN G 134 GLN I 119 ASN I 239 ASN J 77 GLN J 85 GLN J 115 GLN J 253 ASN J 374 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.167266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127363 restraints weight = 26027.567| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.84 r_work: 0.3289 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24318 Z= 0.129 Angle : 0.542 7.995 33014 Z= 0.287 Chirality : 0.042 0.191 3998 Planarity : 0.004 0.044 4016 Dihedral : 9.995 75.652 3474 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.43 % Allowed : 17.26 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.15), residues: 3008 helix: 2.23 (0.12), residues: 1838 sheet: 0.56 (0.28), residues: 302 loop : -0.61 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 27 TYR 0.017 0.001 TYR J 345 PHE 0.037 0.002 PHE L 202 TRP 0.005 0.001 TRP J 267 HIS 0.004 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (24318) covalent geometry : angle 0.54198 / 0.29 (33014) hydrogen bonds : bond 0.04045 / 2.77 ( 1532) hydrogen bonds : angle 4.10145 / 2.88 ( 4413) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 569 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8040 (tp30) cc_final: 0.7726 (tp30) REVERT: A 41 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7979 (mptp) REVERT: B 62 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7106 (tp30) REVERT: C 23 LYS cc_start: 0.8604 (mtpm) cc_final: 0.8116 (mttt) REVERT: C 43 ASN cc_start: 0.8626 (m-40) cc_final: 0.8364 (m110) REVERT: C 56 ASN cc_start: 0.8677 (t0) cc_final: 0.8309 (t0) REVERT: C 59 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7365 (mm-30) REVERT: C 62 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7665 (mt-10) REVERT: C 111 LYS cc_start: 0.8514 (mmpt) cc_final: 0.8198 (mtpt) REVERT: C 128 MET cc_start: 0.8579 (mmm) cc_final: 0.8126 (mmp) REVERT: C 208 MET cc_start: 0.6154 (ttp) cc_final: 0.5928 (ttm) REVERT: D 115 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7940 (mptp) REVERT: D 139 GLU cc_start: 0.7195 (pm20) cc_final: 0.6843 (pm20) REVERT: E 145 ILE cc_start: 0.6362 (OUTLIER) cc_final: 0.6074 (tt) REVERT: E 208 MET cc_start: 0.5850 (ptt) cc_final: 0.5483 (ptt) REVERT: F 23 LYS cc_start: 0.8602 (mtpm) cc_final: 0.8197 (mttt) REVERT: F 62 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7751 (mt-10) REVERT: F 111 LYS cc_start: 0.8477 (mmpt) cc_final: 0.8244 (mtpt) REVERT: F 128 MET cc_start: 0.8577 (mmm) cc_final: 0.8189 (mmp) REVERT: G 62 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7167 (tp30) REVERT: G 72 GLU cc_start: 0.7770 (tt0) cc_final: 0.7338 (pt0) REVERT: G 127 ASP cc_start: 0.8159 (m-30) cc_final: 0.7940 (m-30) REVERT: H 41 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7996 (mptp) REVERT: I 150 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7422 (pt) REVERT: I 219 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6529 (mmt-90) REVERT: I 251 TYR cc_start: 0.8662 (t80) cc_final: 0.8337 (t80) REVERT: I 298 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8701 (mt) REVERT: J 136 PHE cc_start: 0.7709 (t80) cc_final: 0.7419 (t80) REVERT: J 155 GLN cc_start: 0.7693 (tt0) cc_final: 0.7391 (tt0) REVERT: J 216 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6155 (mtp) REVERT: J 222 LYS cc_start: 0.8086 (pttm) cc_final: 0.7874 (mmtt) REVERT: J 299 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8759 (tp) REVERT: K 34 LEU cc_start: 0.8473 (mp) cc_final: 0.8237 (mt) REVERT: K 100 MET cc_start: 0.6525 (mtm) cc_final: 0.6206 (mtm) REVERT: K 155 GLN cc_start: 0.7683 (tt0) cc_final: 0.7400 (tt0) REVERT: K 216 MET cc_start: 0.7615 (mmp) cc_final: 0.6207 (mtp) REVERT: K 220 ARG cc_start: 0.6571 (tpm170) cc_final: 0.5591 (tpt170) REVERT: K 253 ASN cc_start: 0.8399 (t0) cc_final: 0.8180 (t160) REVERT: L 89 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8325 (mp) REVERT: L 116 GLU cc_start: 0.7502 (tp30) cc_final: 0.7171 (tt0) REVERT: L 150 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7382 (pt) REVERT: L 216 MET cc_start: 0.7758 (tpp) cc_final: 0.7141 (mtp) REVERT: L 219 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6548 (mmt-90) REVERT: L 251 TYR cc_start: 0.8638 (t80) cc_final: 0.8323 (t80) REVERT: L 298 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8702 (mt) REVERT: L 373 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6664 (mt-10) outliers start: 88 outliers final: 37 residues processed: 620 average time/residue: 0.6601 time to fit residues: 465.6327 Evaluate side-chains 590 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 539 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 219 ARG Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 219 ARG Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 373 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 19 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 140 optimal weight: 0.0970 chunk 258 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 GLN C 134 GLN D 38 ASN D 134 GLN G 134 GLN I 119 ASN I 239 ASN ** J 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN J 115 GLN J 253 ASN J 374 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN K 272 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.166814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.126638 restraints weight = 26056.391| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.85 r_work: 0.3279 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24318 Z= 0.147 Angle : 0.558 8.891 33014 Z= 0.294 Chirality : 0.043 0.196 3998 Planarity : 0.004 0.046 4016 Dihedral : 9.850 75.475 3472 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.62 % Allowed : 17.69 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.15), residues: 3008 helix: 2.25 (0.12), residues: 1840 sheet: 0.48 (0.28), residues: 302 loop : -0.66 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 27 TYR 0.019 0.001 TYR L 270 PHE 0.036 0.002 PHE I 202 TRP 0.004 0.001 TRP J 267 HIS 0.004 0.001 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (24318) covalent geometry : angle 0.55827 / 0.29 (33014) hydrogen bonds : bond 0.04147 / 2.85 ( 1532) hydrogen bonds : angle 4.08181 / 2.87 ( 4413) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 550 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8069 (tp30) cc_final: 0.7723 (tp30) REVERT: A 41 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7989 (mptp) REVERT: B 62 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7156 (tp30) REVERT: C 23 LYS cc_start: 0.8614 (mtpm) cc_final: 0.8129 (mttt) REVERT: C 56 ASN cc_start: 0.8689 (t0) cc_final: 0.8441 (t0) REVERT: C 59 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7355 (mm-30) REVERT: C 111 LYS cc_start: 0.8574 (mmpt) cc_final: 0.8257 (mtpt) REVERT: C 128 MET cc_start: 0.8586 (mmm) cc_final: 0.8188 (mmp) REVERT: C 208 MET cc_start: 0.6163 (ttp) cc_final: 0.5921 (ttm) REVERT: D 115 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7974 (mptp) REVERT: E 145 ILE cc_start: 0.6330 (OUTLIER) cc_final: 0.6059 (tt) REVERT: E 208 MET cc_start: 0.5875 (ptt) cc_final: 0.5508 (ptt) REVERT: F 23 LYS cc_start: 0.8588 (mtpm) cc_final: 0.8114 (mttt) REVERT: F 59 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7100 (mm-30) REVERT: F 111 LYS cc_start: 0.8531 (mmpt) cc_final: 0.8210 (mtpt) REVERT: F 128 MET cc_start: 0.8588 (mmm) cc_final: 0.8174 (mmp) REVERT: F 131 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8409 (mttm) REVERT: G 62 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7182 (tp30) REVERT: G 72 GLU cc_start: 0.7731 (tt0) cc_final: 0.7294 (pt0) REVERT: G 127 ASP cc_start: 0.8174 (m-30) cc_final: 0.7948 (m-30) REVERT: H 41 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7978 (mptp) REVERT: I 150 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7397 (pt) REVERT: I 216 MET cc_start: 0.7734 (tpp) cc_final: 0.7142 (mtp) REVERT: I 219 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6631 (mmt-90) REVERT: I 251 TYR cc_start: 0.8661 (t80) cc_final: 0.8346 (t80) REVERT: I 298 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8728 (mt) REVERT: J 34 LEU cc_start: 0.8448 (mp) cc_final: 0.8228 (mt) REVERT: J 136 PHE cc_start: 0.7677 (t80) cc_final: 0.7387 (t80) REVERT: J 155 GLN cc_start: 0.7711 (tt0) cc_final: 0.7429 (tt0) REVERT: J 170 ILE cc_start: 0.8136 (mt) cc_final: 0.7915 (mp) REVERT: J 216 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.6132 (mtp) REVERT: J 222 LYS cc_start: 0.8108 (pttm) cc_final: 0.7864 (mmtt) REVERT: J 299 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8776 (tp) REVERT: K 34 LEU cc_start: 0.8459 (mp) cc_final: 0.8235 (mt) REVERT: K 100 MET cc_start: 0.6524 (mtm) cc_final: 0.6215 (mtm) REVERT: K 155 GLN cc_start: 0.7695 (tt0) cc_final: 0.7407 (tt0) REVERT: K 216 MET cc_start: 0.7629 (mmp) cc_final: 0.6174 (mtp) REVERT: K 253 ASN cc_start: 0.8395 (t0) cc_final: 0.8189 (t160) REVERT: L 150 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7428 (pt) REVERT: L 216 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7165 (mtp) REVERT: L 219 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6606 (mmt-90) REVERT: L 251 TYR cc_start: 0.8656 (t80) cc_final: 0.8358 (t80) REVERT: L 298 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8732 (mt) REVERT: L 373 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6666 (mt-10) outliers start: 93 outliers final: 43 residues processed: 610 average time/residue: 0.7070 time to fit residues: 490.4045 Evaluate side-chains 603 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 545 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 219 ARG Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 219 ARG Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 373 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 19 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 277 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 233 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN B 8 GLN B 38 ASN B 134 GLN D 134 GLN G 38 ASN G 134 GLN H 81 ASN I 119 ASN I 239 ASN ** J 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN J 115 GLN J 253 ASN J 374 GLN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.165991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125865 restraints weight = 25859.960| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.83 r_work: 0.3268 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24318 Z= 0.174 Angle : 0.585 12.614 33014 Z= 0.308 Chirality : 0.044 0.204 3998 Planarity : 0.004 0.046 4016 Dihedral : 9.958 77.426 3472 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.55 % Allowed : 18.55 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.15), residues: 3008 helix: 2.19 (0.12), residues: 1840 sheet: 0.47 (0.28), residues: 302 loop : -0.67 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 436 TYR 0.021 0.001 TYR J 345 PHE 0.037 0.002 PHE I 202 TRP 0.004 0.001 TRP I 181 HIS 0.004 0.001 HIS L 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (24318) covalent geometry : angle 0.58518 / 0.31 (33014) hydrogen bonds : bond 0.04382 / 3.01 ( 1532) hydrogen bonds : angle 4.11981 / 2.90 ( 4413) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 542 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8027 (tp30) cc_final: 0.7722 (tp30) REVERT: A 41 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7978 (mptp) REVERT: B 62 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7210 (tp30) REVERT: C 56 ASN cc_start: 0.8690 (t0) cc_final: 0.8422 (t0) REVERT: C 59 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7238 (mm-30) REVERT: C 111 LYS cc_start: 0.8637 (mmpt) cc_final: 0.8194 (mtpt) REVERT: C 128 MET cc_start: 0.8591 (mmm) cc_final: 0.8178 (mmp) REVERT: C 208 MET cc_start: 0.6114 (ttp) cc_final: 0.5872 (ttm) REVERT: D 115 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7956 (mptp) REVERT: D 208 MET cc_start: 0.6108 (ptt) cc_final: 0.5848 (ptp) REVERT: E 120 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8553 (ttt180) REVERT: E 208 MET cc_start: 0.6009 (ptt) cc_final: 0.5664 (ptt) REVERT: F 23 LYS cc_start: 0.8594 (mtpm) cc_final: 0.8151 (mttt) REVERT: F 59 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7062 (mm-30) REVERT: F 111 LYS cc_start: 0.8551 (mmpt) cc_final: 0.8211 (mtpt) REVERT: F 128 MET cc_start: 0.8601 (mmm) cc_final: 0.8190 (mmp) REVERT: F 131 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8396 (mttm) REVERT: G 62 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7234 (tp30) REVERT: G 72 GLU cc_start: 0.7729 (tt0) cc_final: 0.7282 (pt0) REVERT: G 127 ASP cc_start: 0.8179 (m-30) cc_final: 0.7973 (m-30) REVERT: H 41 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7993 (mptp) REVERT: I 110 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7591 (mp0) REVERT: I 150 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7424 (pt) REVERT: I 216 MET cc_start: 0.7744 (tpp) cc_final: 0.7160 (mtp) REVERT: I 219 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6621 (mmt-90) REVERT: I 251 TYR cc_start: 0.8659 (t80) cc_final: 0.8338 (t80) REVERT: I 298 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8731 (mt) REVERT: J 34 LEU cc_start: 0.8441 (mp) cc_final: 0.8227 (mt) REVERT: J 100 MET cc_start: 0.6255 (mtm) cc_final: 0.5786 (mmm) REVERT: J 136 PHE cc_start: 0.7690 (t80) cc_final: 0.7413 (t80) REVERT: J 155 GLN cc_start: 0.7701 (tt0) cc_final: 0.7398 (tt0) REVERT: J 170 ILE cc_start: 0.8177 (mt) cc_final: 0.7940 (mp) REVERT: J 216 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.6203 (mtp) REVERT: J 222 LYS cc_start: 0.8012 (pttm) cc_final: 0.7810 (mmtt) REVERT: J 299 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8775 (tp) REVERT: K 34 LEU cc_start: 0.8450 (mp) cc_final: 0.8232 (mt) REVERT: K 100 MET cc_start: 0.6537 (mtm) cc_final: 0.6239 (mtm) REVERT: K 155 GLN cc_start: 0.7699 (tt0) cc_final: 0.7371 (tt0) REVERT: K 216 MET cc_start: 0.7639 (mmp) cc_final: 0.6178 (mtp) REVERT: K 222 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7311 (mmtm) REVERT: K 253 ASN cc_start: 0.8387 (t0) cc_final: 0.8167 (t160) REVERT: L 110 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7690 (mp0) REVERT: L 150 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7423 (pt) REVERT: L 216 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7166 (mtp) REVERT: L 219 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6625 (mmt-90) REVERT: L 237 MET cc_start: 0.8280 (mtt) cc_final: 0.8061 (mpp) REVERT: L 251 TYR cc_start: 0.8659 (t80) cc_final: 0.8358 (t80) REVERT: L 298 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8731 (mt) outliers start: 91 outliers final: 45 residues processed: 600 average time/residue: 0.7123 time to fit residues: 486.2001 Evaluate side-chains 588 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 529 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 219 ARG Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 219 ARG Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 179 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 297 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 250 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 199 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN B 38 ASN B 134 GLN C 134 GLN D 134 GLN G 134 GLN H 81 ASN I 119 ASN I 239 ASN J 85 GLN J 115 GLN J 253 ASN J 374 GLN K 85 GLN K 115 GLN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.167185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.126965 restraints weight = 26092.792| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.85 r_work: 0.3288 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24318 Z= 0.141 Angle : 0.556 9.890 33014 Z= 0.293 Chirality : 0.043 0.195 3998 Planarity : 0.004 0.044 4016 Dihedral : 9.790 76.341 3472 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.31 % Allowed : 18.94 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.15), residues: 3008 helix: 2.27 (0.12), residues: 1838 sheet: 0.42 (0.28), residues: 302 loop : -0.62 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 27 TYR 0.021 0.001 TYR J 345 PHE 0.037 0.002 PHE I 202 TRP 0.006 0.001 TRP J 267 HIS 0.004 0.001 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (24318) covalent geometry : angle 0.55623 / 0.29 (33014) hydrogen bonds : bond 0.04073 / 2.81 ( 1532) hydrogen bonds : angle 4.06487 / 2.86 ( 4413) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 548 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8082 (tp30) cc_final: 0.7646 (tp30) REVERT: A 41 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7988 (mptp) REVERT: B 62 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7207 (tp30) REVERT: C 23 LYS cc_start: 0.8591 (mtpm) cc_final: 0.8090 (mttt) REVERT: C 56 ASN cc_start: 0.8694 (t0) cc_final: 0.8424 (t0) REVERT: C 59 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7176 (mm-30) REVERT: C 111 LYS cc_start: 0.8600 (mmpt) cc_final: 0.8180 (mtpt) REVERT: C 128 MET cc_start: 0.8542 (mmm) cc_final: 0.8138 (mmp) REVERT: C 208 MET cc_start: 0.6103 (ttp) cc_final: 0.5865 (ttm) REVERT: D 115 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8001 (mptp) REVERT: D 139 GLU cc_start: 0.7184 (pm20) cc_final: 0.6864 (pm20) REVERT: D 208 MET cc_start: 0.6085 (ptt) cc_final: 0.5827 (ptp) REVERT: E 145 ILE cc_start: 0.6397 (OUTLIER) cc_final: 0.6147 (tt) REVERT: E 208 MET cc_start: 0.6025 (ptt) cc_final: 0.5688 (ptt) REVERT: F 23 LYS cc_start: 0.8581 (mtpm) cc_final: 0.8134 (mttt) REVERT: F 111 LYS cc_start: 0.8512 (mmpt) cc_final: 0.8213 (mtpt) REVERT: F 128 MET cc_start: 0.8577 (mmm) cc_final: 0.8150 (mmp) REVERT: F 131 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8391 (mttm) REVERT: G 62 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7204 (tp30) REVERT: G 72 GLU cc_start: 0.7720 (tt0) cc_final: 0.7281 (pt0) REVERT: H 41 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8000 (mptp) REVERT: I 110 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7651 (mp0) REVERT: I 150 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7481 (pt) REVERT: I 216 MET cc_start: 0.7732 (tpp) cc_final: 0.7158 (mtp) REVERT: I 219 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6629 (mmt-90) REVERT: I 251 TYR cc_start: 0.8683 (t80) cc_final: 0.8440 (t80) REVERT: I 298 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8716 (mt) REVERT: J 34 LEU cc_start: 0.8441 (mp) cc_final: 0.8239 (mt) REVERT: J 100 MET cc_start: 0.6395 (mtm) cc_final: 0.5923 (mmm) REVERT: J 136 PHE cc_start: 0.7678 (t80) cc_final: 0.7376 (t80) REVERT: J 155 GLN cc_start: 0.7719 (tt0) cc_final: 0.7424 (tt0) REVERT: J 170 ILE cc_start: 0.8154 (mt) cc_final: 0.7925 (mp) REVERT: J 216 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.6221 (mtp) REVERT: J 222 LYS cc_start: 0.8056 (pttm) cc_final: 0.7827 (mmtt) REVERT: J 299 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8761 (tp) REVERT: K 34 LEU cc_start: 0.8445 (mp) cc_final: 0.8239 (mt) REVERT: K 100 MET cc_start: 0.6601 (mtm) cc_final: 0.6343 (mtm) REVERT: K 155 GLN cc_start: 0.7745 (tt0) cc_final: 0.7415 (tt0) REVERT: K 216 MET cc_start: 0.7620 (mmp) cc_final: 0.6158 (mtp) REVERT: K 222 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7326 (mmtm) REVERT: K 253 ASN cc_start: 0.8374 (t0) cc_final: 0.8172 (t160) REVERT: L 110 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7693 (mp0) REVERT: L 150 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7465 (pt) REVERT: L 216 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7182 (mtp) REVERT: L 219 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6625 (mmt-90) REVERT: L 237 MET cc_start: 0.8278 (mtt) cc_final: 0.8064 (mpp) REVERT: L 251 TYR cc_start: 0.8656 (t80) cc_final: 0.8370 (t80) REVERT: L 298 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8725 (mt) outliers start: 85 outliers final: 43 residues processed: 600 average time/residue: 0.7087 time to fit residues: 482.2837 Evaluate side-chains 601 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 544 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 219 ARG Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 219 ARG Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 79 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 300 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 294 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 252 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 chunk 297 optimal weight: 4.9990 chunk 254 optimal weight: 0.6980 chunk 246 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN B 38 ASN B 134 GLN D 38 ASN D 134 GLN G 38 ASN G 134 GLN H 81 ASN I 119 ASN I 239 ASN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 GLN J 253 ASN J 374 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.167952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127846 restraints weight = 26062.586| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.86 r_work: 0.3305 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24318 Z= 0.128 Angle : 0.558 11.068 33014 Z= 0.291 Chirality : 0.043 0.189 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.600 75.209 3472 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.38 % Allowed : 20.42 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.15), residues: 3008 helix: 2.26 (0.12), residues: 1842 sheet: 0.38 (0.28), residues: 302 loop : -0.60 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 27 TYR 0.021 0.001 TYR L 270 PHE 0.036 0.002 PHE I 202 TRP 0.006 0.001 TRP K 267 HIS 0.003 0.001 HIS L 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (24318) covalent geometry : angle 0.55780 / 0.29 (33014) hydrogen bonds : bond 0.03890 / 2.68 ( 1532) hydrogen bonds : angle 4.04736 / 2.85 ( 4413) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 553 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8057 (tp30) cc_final: 0.7710 (tp30) REVERT: A 41 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7980 (mptp) REVERT: B 62 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7194 (tp30) REVERT: C 23 LYS cc_start: 0.8575 (mtpm) cc_final: 0.8075 (mttt) REVERT: C 111 LYS cc_start: 0.8588 (mmpt) cc_final: 0.8172 (mtpt) REVERT: C 128 MET cc_start: 0.8488 (mmm) cc_final: 0.8043 (mmp) REVERT: C 208 MET cc_start: 0.6097 (ttp) cc_final: 0.5870 (ttm) REVERT: D 115 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7985 (mptp) REVERT: D 139 GLU cc_start: 0.7182 (pm20) cc_final: 0.6847 (pm20) REVERT: D 208 MET cc_start: 0.6058 (ptt) cc_final: 0.5809 (ptp) REVERT: E 145 ILE cc_start: 0.6390 (OUTLIER) cc_final: 0.6140 (tt) REVERT: E 208 MET cc_start: 0.6024 (ptt) cc_final: 0.5795 (ptt) REVERT: F 23 LYS cc_start: 0.8611 (mtpm) cc_final: 0.8108 (mttt) REVERT: F 59 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6892 (mm-30) REVERT: F 65 SER cc_start: 0.8557 (m) cc_final: 0.8314 (t) REVERT: F 128 MET cc_start: 0.8524 (mmm) cc_final: 0.8098 (mmp) REVERT: F 131 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8398 (mttm) REVERT: G 62 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7106 (tp30) REVERT: G 72 GLU cc_start: 0.7699 (tt0) cc_final: 0.7271 (pt0) REVERT: H 41 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7988 (mptp) REVERT: I 110 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7658 (mp0) REVERT: I 150 ILE cc_start: 0.7920 (pp) cc_final: 0.7471 (pt) REVERT: I 216 MET cc_start: 0.7742 (tpp) cc_final: 0.7172 (mtp) REVERT: I 219 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6650 (mmt-90) REVERT: I 237 MET cc_start: 0.8298 (mtt) cc_final: 0.8084 (mpp) REVERT: I 251 TYR cc_start: 0.8672 (t80) cc_final: 0.8436 (t80) REVERT: I 298 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8714 (mt) REVERT: J 34 LEU cc_start: 0.8408 (mp) cc_final: 0.8204 (mt) REVERT: J 100 MET cc_start: 0.6416 (mtm) cc_final: 0.5942 (mmm) REVERT: J 136 PHE cc_start: 0.7657 (t80) cc_final: 0.7371 (t80) REVERT: J 155 GLN cc_start: 0.7750 (tt0) cc_final: 0.7436 (tt0) REVERT: J 170 ILE cc_start: 0.8133 (mt) cc_final: 0.7890 (mp) REVERT: J 216 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.6179 (mtp) REVERT: J 222 LYS cc_start: 0.8053 (pttm) cc_final: 0.7825 (mmtt) REVERT: J 299 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8751 (tp) REVERT: K 100 MET cc_start: 0.6632 (mtm) cc_final: 0.6379 (mtm) REVERT: K 155 GLN cc_start: 0.7744 (tt0) cc_final: 0.7393 (tt0) REVERT: K 216 MET cc_start: 0.7626 (mmp) cc_final: 0.6170 (mtp) REVERT: K 222 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7301 (mmtm) REVERT: K 250 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8760 (mm-30) REVERT: K 383 GLU cc_start: 0.8579 (tp30) cc_final: 0.8329 (tp30) REVERT: L 110 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7660 (mp0) REVERT: L 140 ILE cc_start: 0.8402 (tt) cc_final: 0.8179 (tt) REVERT: L 150 ILE cc_start: 0.7904 (pp) cc_final: 0.7452 (pt) REVERT: L 216 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7217 (mtp) REVERT: L 219 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6682 (mmt-90) REVERT: L 237 MET cc_start: 0.8253 (mtt) cc_final: 0.8040 (mpp) REVERT: L 251 TYR cc_start: 0.8664 (t80) cc_final: 0.8394 (t80) REVERT: L 298 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8717 (mt) outliers start: 61 outliers final: 37 residues processed: 592 average time/residue: 0.6788 time to fit residues: 455.6168 Evaluate side-chains 588 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 539 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 219 ARG Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 340 ARG Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 219 ARG Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 209 optimal weight: 0.1980 chunk 285 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 269 optimal weight: 0.0970 chunk 262 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 300 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN B 38 ASN B 134 GLN D 134 GLN E 8 GLN G 38 ASN G 134 GLN H 81 ASN I 119 ASN I 239 ASN ** J 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN J 115 GLN J 253 ASN J 374 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN K 253 ASN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.169449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.129889 restraints weight = 26040.548| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.85 r_work: 0.3336 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24318 Z= 0.114 Angle : 0.543 9.666 33014 Z= 0.283 Chirality : 0.042 0.180 3998 Planarity : 0.004 0.044 4016 Dihedral : 9.334 75.412 3472 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.16 % Favored : 97.81 % Rotamer: Outliers : 2.07 % Allowed : 21.24 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.15), residues: 3008 helix: 2.29 (0.12), residues: 1848 sheet: 0.16 (0.29), residues: 294 loop : -0.51 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 27 TYR 0.023 0.001 TYR I 270 PHE 0.035 0.001 PHE I 202 TRP 0.007 0.001 TRP K 267 HIS 0.003 0.001 HIS L 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (24318) covalent geometry : angle 0.54317 / 0.28 (33014) hydrogen bonds : bond 0.03603 / 2.49 ( 1532) hydrogen bonds : angle 4.01662 / 2.82 ( 4413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12977.45 seconds wall clock time: 220 minutes 47.07 seconds (13247.07 seconds total)