Starting phenix.real_space_refine on Sun Aug 24 23:16:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1t_36803/08_2025/8k1t_36803.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1t_36803/08_2025/8k1t_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_36803/08_2025/8k1t_36803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1t_36803/08_2025/8k1t_36803.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k1t_36803/08_2025/8k1t_36803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1t_36803/08_2025/8k1t_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-2.0-5787/lib/python3.9/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, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.12, per 1000 atoms: 0.21 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: 1.41 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.03 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: 4.21 Time building geometry restraints manager: 2.07 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: 5.050 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.430 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 aren 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 covalent geometry : bond 0.00374 (24318) covalent geometry : angle 0.52925 (33014) hydrogen bonds : bond 0.21630 ( 1532) hydrogen bonds : angle 6.62929 ( 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 : 1.067 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: 0.6946 time to fit residues: 657.8459 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 : 0.991 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 GLN J 253 ASN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 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 = 0.4005 r_free = 0.4005 target = 0.168950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.128829 restraints weight = 26133.842| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.85 r_work: 0.3316 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24318 Z= 0.140 Angle : 0.561 9.265 33014 Z= 0.297 Chirality : 0.043 0.176 3998 Planarity : 0.004 0.044 4016 Dihedral : 10.099 84.553 3474 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.51 % Allowed : 13.60 % Favored : 82.89 % 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 aren not related in a simple way. whole: 1.96 (0.15), residues: 3008 helix: 2.22 (0.11), residues: 1840 sheet: 1.07 (0.28), residues: 332 loop : -0.72 (0.20), 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 0.008 0.001 TRP K 47 HIS 0.003 0.001 HIS I 168 Details of bonding type rmsd covalent geometry : bond 0.00301 (24318) covalent geometry : angle 0.56140 (33014) hydrogen bonds : bond 0.05086 ( 1532) hydrogen bonds : angle 4.40428 ( 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 700 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 610 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7984 (tp30) cc_final: 0.7612 (tp30) REVERT: A 115 LYS cc_start: 0.7644 (mmtm) cc_final: 0.7299 (mptt) REVERT: C 39 GLU cc_start: 0.7946 (mp0) cc_final: 0.7744 (mp0) REVERT: C 48 TYR cc_start: 0.8320 (m-80) cc_final: 0.8017 (m-80) REVERT: C 56 ASN cc_start: 0.8682 (t0) cc_final: 0.8374 (t0) REVERT: C 59 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7054 (mt-10) REVERT: C 62 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7094 (mt-10) REVERT: C 111 LYS cc_start: 0.8514 (mmpt) cc_final: 0.8222 (mtpt) REVERT: C 128 MET cc_start: 0.8585 (mmm) cc_final: 0.8185 (mmp) REVERT: D 126 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8294 (ttmt) REVERT: E 134 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7939 (mm110) REVERT: E 138 ASP cc_start: 0.7362 (t70) cc_final: 0.6576 (m-30) REVERT: F 62 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7213 (mt-10) REVERT: F 111 LYS cc_start: 0.8461 (mmpt) cc_final: 0.8233 (mtpt) REVERT: F 128 MET cc_start: 0.8605 (mmm) cc_final: 0.8241 (mmp) REVERT: G 41 LYS cc_start: 0.7995 (mmtm) cc_final: 0.7406 (mmtt) REVERT: H 115 LYS cc_start: 0.7755 (mmtm) cc_final: 0.7459 (mttm) REVERT: I 110 GLU cc_start: 0.7562 (mt-10) cc_final: 0.6828 (mp0) REVERT: I 123 ILE cc_start: 0.7817 (pt) cc_final: 0.7525 (pt) REVERT: I 140 ILE cc_start: 0.8340 (tt) cc_final: 0.8136 (tt) REVERT: I 156 TYR cc_start: 0.6763 (m-80) cc_final: 0.6538 (m-80) REVERT: I 251 TYR cc_start: 0.8647 (t80) cc_final: 0.8259 (t80) REVERT: I 298 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8704 (mt) REVERT: I 340 ARG cc_start: 0.8452 (mtt180) cc_final: 0.7882 (mtt-85) REVERT: J 97 LEU cc_start: 0.7254 (mt) cc_final: 0.6991 (tp) REVERT: J 100 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.5709 (mmm) REVERT: J 106 ILE cc_start: 0.7400 (mp) cc_final: 0.7104 (mm) REVERT: J 136 PHE cc_start: 0.7678 (t80) cc_final: 0.7400 (t80) REVERT: J 155 GLN cc_start: 0.7612 (tt0) cc_final: 0.7164 (tt0) REVERT: J 156 TYR cc_start: 0.7544 (m-80) cc_final: 0.7337 (m-80) REVERT: J 216 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6073 (mtp) REVERT: J 222 LYS cc_start: 0.8086 (pttm) cc_final: 0.7865 (mmtt) REVERT: J 344 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.8016 (mmtm) REVERT: K 97 LEU cc_start: 0.7301 (mt) cc_final: 0.6984 (tp) REVERT: K 100 MET cc_start: 0.6297 (mtm) cc_final: 0.5988 (mtm) REVERT: K 155 GLN cc_start: 0.7575 (tt0) cc_final: 0.7152 (tt0) REVERT: K 216 MET cc_start: 0.7435 (mmp) cc_final: 0.6116 (mtp) REVERT: K 250 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8559 (mm-30) REVERT: K 253 ASN cc_start: 0.8382 (t0) cc_final: 0.8141 (t160) REVERT: K 344 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8060 (mmtm) REVERT: L 110 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6806 (mp0) REVERT: L 123 ILE cc_start: 0.7799 (pt) cc_final: 0.7511 (pt) REVERT: L 156 TYR cc_start: 0.6783 (m-80) cc_final: 0.6510 (m-80) REVERT: L 251 TYR cc_start: 0.8592 (t80) cc_final: 0.8193 (t80) REVERT: L 298 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8658 (mt) REVERT: L 340 ARG cc_start: 0.8498 (mtt180) cc_final: 0.7915 (mtt-85) REVERT: L 439 ASP cc_start: 0.8213 (m-30) cc_final: 0.7999 (m-30) outliers start: 90 outliers final: 31 residues processed: 660 average time/residue: 0.7422 time to fit residues: 555.9201 Evaluate side-chains 590 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 552 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 D residue 126 LYS 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 100 MET 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 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 344 LYS 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 323 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 275 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 267 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 251 optimal weight: 0.0370 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.0660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 70 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN C 185 HIS D 70 ASN D 134 GLN D 185 HIS E 185 HIS F 185 HIS G 8 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.167782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.127465 restraints weight = 26158.703| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.84 r_work: 0.3293 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24318 Z= 0.141 Angle : 0.543 7.736 33014 Z= 0.286 Chirality : 0.043 0.192 3998 Planarity : 0.004 0.047 4016 Dihedral : 9.703 78.710 3474 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.66 % Allowed : 14.54 % Favored : 81.80 % 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 aren not related in a simple way. whole: 2.04 (0.15), residues: 3008 helix: 2.38 (0.12), residues: 1840 sheet: 0.83 (0.28), residues: 314 loop : -0.78 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 27 TYR 0.017 0.001 TYR I 270 PHE 0.036 0.002 PHE I 202 TRP 0.006 0.001 TRP K 47 HIS 0.004 0.001 HIS I 168 Details of bonding type rmsd covalent geometry : bond 0.00314 (24318) covalent geometry : angle 0.54335 (33014) hydrogen bonds : bond 0.04474 ( 1532) hydrogen bonds : angle 4.16507 ( 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 672 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 578 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8058 (tp30) cc_final: 0.7732 (tp30) REVERT: A 89 THR cc_start: 0.8642 (t) cc_final: 0.8383 (p) REVERT: A 115 LYS cc_start: 0.7717 (mmtm) cc_final: 0.7414 (mttm) REVERT: B 127 ASP cc_start: 0.8115 (m-30) cc_final: 0.7899 (m-30) REVERT: C 23 LYS cc_start: 0.8585 (mtpm) cc_final: 0.8003 (mtmt) REVERT: C 48 TYR cc_start: 0.8363 (m-80) cc_final: 0.8153 (m-80) REVERT: C 56 ASN cc_start: 0.8701 (t0) cc_final: 0.8373 (t0) REVERT: C 59 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7050 (mt-10) REVERT: C 62 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7027 (mt-10) REVERT: C 105 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: C 128 MET cc_start: 0.8580 (mmm) cc_final: 0.8218 (mmp) REVERT: D 134 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7948 (mm110) REVERT: E 138 ASP cc_start: 0.7244 (t70) cc_final: 0.6446 (m-30) REVERT: E 145 ILE cc_start: 0.6276 (OUTLIER) cc_final: 0.5979 (tt) REVERT: E 208 MET cc_start: 0.5879 (ptt) cc_final: 0.5380 (ptt) REVERT: F 23 LYS cc_start: 0.8648 (mtpm) cc_final: 0.8069 (mtmt) REVERT: F 56 ASN cc_start: 0.8581 (t0) cc_final: 0.8337 (t0) REVERT: F 62 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7301 (mt-10) REVERT: F 111 LYS cc_start: 0.8505 (mmpt) cc_final: 0.8243 (mtmt) REVERT: F 128 MET cc_start: 0.8619 (mmm) cc_final: 0.8234 (mmp) REVERT: F 131 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8383 (mttm) REVERT: G 62 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6935 (tp30) REVERT: G 65 SER cc_start: 0.7862 (m) cc_final: 0.7641 (p) REVERT: H 89 THR cc_start: 0.8627 (t) cc_final: 0.8395 (p) REVERT: H 115 LYS cc_start: 0.7767 (mmtm) cc_final: 0.7458 (mttm) REVERT: I 110 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7217 (mp0) REVERT: I 123 ILE cc_start: 0.7724 (pt) cc_final: 0.7506 (pt) REVERT: I 140 ILE cc_start: 0.8394 (tt) cc_final: 0.8148 (tt) REVERT: I 150 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7659 (mp) REVERT: I 156 TYR cc_start: 0.6779 (m-80) cc_final: 0.6539 (m-80) REVERT: I 251 TYR cc_start: 0.8649 (t80) cc_final: 0.8280 (t80) REVERT: I 298 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8713 (mt) REVERT: I 340 ARG cc_start: 0.8445 (mtt180) cc_final: 0.7855 (mtt-85) REVERT: J 106 ILE cc_start: 0.7451 (mp) cc_final: 0.7073 (mm) REVERT: J 155 GLN cc_start: 0.7587 (tt0) cc_final: 0.7120 (tt0) REVERT: J 156 TYR cc_start: 0.7499 (m-80) cc_final: 0.7225 (m-80) REVERT: J 216 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6164 (mtp) REVERT: J 222 LYS cc_start: 0.8110 (pttm) cc_final: 0.7885 (mmtt) REVERT: K 97 LEU cc_start: 0.7412 (mt) cc_final: 0.7128 (tp) REVERT: K 100 MET cc_start: 0.6382 (mtm) cc_final: 0.6137 (mtm) REVERT: K 155 GLN cc_start: 0.7719 (tt0) cc_final: 0.7345 (tt0) REVERT: K 216 MET cc_start: 0.7525 (mmp) cc_final: 0.6140 (mtp) REVERT: K 220 ARG cc_start: 0.7053 (mmm160) cc_final: 0.6803 (mmm160) REVERT: K 222 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7328 (mmtm) REVERT: K 250 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8747 (mm-30) REVERT: K 253 ASN cc_start: 0.8362 (t0) cc_final: 0.8140 (t160) REVERT: L 110 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7231 (mp0) REVERT: L 150 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7662 (mp) REVERT: L 156 TYR cc_start: 0.6817 (m-80) cc_final: 0.6600 (m-80) REVERT: L 251 TYR cc_start: 0.8616 (t80) cc_final: 0.8221 (t80) REVERT: L 298 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8699 (mt) outliers start: 94 outliers final: 36 residues processed: 635 average time/residue: 0.7327 time to fit residues: 528.6114 Evaluate side-chains 591 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 547 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 105 GLN 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 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 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 96 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 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 165 SER Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR 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 123 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 K residue 421 LEU 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 236 LEU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 293 optimal weight: 0.8980 chunk 100 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 156 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 8 GLN B 38 ASN D 70 ASN 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 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 115 GLN K 272 GLN L 18 GLN L 119 ASN L 155 GLN L 239 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.168899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128721 restraints weight = 26119.913| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.83 r_work: 0.3311 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24318 Z= 0.120 Angle : 0.513 7.657 33014 Z= 0.271 Chirality : 0.042 0.186 3998 Planarity : 0.004 0.046 4016 Dihedral : 9.458 77.387 3474 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.25 % Allowed : 14.73 % Favored : 81.02 % 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 aren not related in a simple way. whole: 2.11 (0.15), residues: 3008 helix: 2.47 (0.12), residues: 1838 sheet: 0.69 (0.29), residues: 304 loop : -0.76 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 27 TYR 0.020 0.001 TYR I 270 PHE 0.035 0.001 PHE L 202 TRP 0.007 0.001 TRP K 47 HIS 0.003 0.001 HIS I 168 Details of bonding type rmsd covalent geometry : bond 0.00259 (24318) covalent geometry : angle 0.51344 (33014) hydrogen bonds : bond 0.03892 ( 1532) hydrogen bonds : angle 4.01866 ( 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 704 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 595 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8080 (tp30) cc_final: 0.7750 (tp30) REVERT: A 41 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8027 (mptp) REVERT: A 89 THR cc_start: 0.8614 (t) cc_final: 0.8405 (m) REVERT: A 115 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7376 (mptt) REVERT: B 62 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7179 (tp30) REVERT: B 127 ASP cc_start: 0.8153 (m-30) cc_final: 0.7941 (m-30) REVERT: C 23 LYS cc_start: 0.8654 (mtpm) cc_final: 0.8100 (mtmt) REVERT: C 48 TYR cc_start: 0.8322 (m-80) cc_final: 0.8068 (m-80) REVERT: C 56 ASN cc_start: 0.8637 (t0) cc_final: 0.8289 (t0) REVERT: C 62 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7512 (mt-10) REVERT: C 111 LYS cc_start: 0.8474 (mmpt) cc_final: 0.8214 (mtpt) REVERT: C 128 MET cc_start: 0.8537 (mmm) cc_final: 0.8117 (mmp) REVERT: C 208 MET cc_start: 0.6190 (ttp) cc_final: 0.5907 (ttm) REVERT: D 60 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: D 115 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7962 (mptp) REVERT: D 134 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7888 (mm110) REVERT: E 138 ASP cc_start: 0.7139 (t70) cc_final: 0.6412 (m-30) REVERT: E 145 ILE cc_start: 0.6302 (OUTLIER) cc_final: 0.6019 (tt) REVERT: E 208 MET cc_start: 0.5884 (ptt) cc_final: 0.5399 (ptt) REVERT: F 23 LYS cc_start: 0.8633 (mtpm) cc_final: 0.8161 (mttt) REVERT: F 56 ASN cc_start: 0.8613 (t0) cc_final: 0.8379 (t0) REVERT: F 62 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7411 (mt-10) REVERT: F 105 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: F 111 LYS cc_start: 0.8450 (mmpt) cc_final: 0.8184 (mtmt) REVERT: F 128 MET cc_start: 0.8591 (mmm) cc_final: 0.8228 (mmp) REVERT: F 181 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6764 (mp) REVERT: G 41 LYS cc_start: 0.8004 (mmtm) cc_final: 0.7322 (mmtt) REVERT: G 62 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7074 (tp30) REVERT: G 72 GLU cc_start: 0.7743 (tt0) cc_final: 0.7372 (pt0) REVERT: G 127 ASP cc_start: 0.8092 (m-30) cc_final: 0.7876 (m-30) REVERT: H 41 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7984 (mptp) REVERT: H 115 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7462 (mtpm) REVERT: I 110 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7262 (mp0) REVERT: I 140 ILE cc_start: 0.8409 (tt) cc_final: 0.8200 (tt) REVERT: I 150 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7408 (mp) REVERT: I 156 TYR cc_start: 0.6709 (m-80) cc_final: 0.6475 (m-80) REVERT: I 251 TYR cc_start: 0.8661 (t80) cc_final: 0.8333 (t80) REVERT: I 298 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8724 (mt) REVERT: J 100 MET cc_start: 0.6143 (mtm) cc_final: 0.5823 (mmm) REVERT: J 155 GLN cc_start: 0.7604 (tt0) cc_final: 0.7148 (tt0) REVERT: J 156 TYR cc_start: 0.7495 (m-80) cc_final: 0.7202 (m-80) REVERT: J 216 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.6085 (mtp) REVERT: J 222 LYS cc_start: 0.8083 (pttm) cc_final: 0.7847 (mmtt) REVERT: K 97 LEU cc_start: 0.7316 (mt) cc_final: 0.7097 (tp) REVERT: K 100 MET cc_start: 0.6441 (mtm) cc_final: 0.6212 (mtm) REVERT: K 155 GLN cc_start: 0.7752 (tt0) cc_final: 0.7428 (tt0) REVERT: K 216 MET cc_start: 0.7558 (mmp) cc_final: 0.6189 (mtp) REVERT: K 222 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7346 (mmtm) REVERT: K 253 ASN cc_start: 0.8387 (t0) cc_final: 0.8154 (t160) REVERT: L 110 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7354 (mp0) REVERT: L 150 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7408 (mp) REVERT: L 156 TYR cc_start: 0.6744 (m-80) cc_final: 0.6508 (m-80) REVERT: L 251 TYR cc_start: 0.8651 (t80) cc_final: 0.8285 (t80) REVERT: L 298 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8704 (mt) outliers start: 109 outliers final: 36 residues processed: 656 average time/residue: 0.7257 time to fit residues: 542.0478 Evaluate side-chains 602 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 552 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 115 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 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 63 LEU 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 H residue 41 LYS 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 150 ILE 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 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 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 224 optimal weight: 0.9980 chunk 232 optimal weight: 0.0370 chunk 244 optimal weight: 0.9990 chunk 240 optimal weight: 6.9990 chunk 229 optimal weight: 0.9980 chunk 190 optimal weight: 0.9980 chunk 177 optimal weight: 7.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 8 GLN B 38 ASN D 70 ASN E 8 GLN F 8 GLN G 134 GLN H 70 ASN I 18 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 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 = 0.4000 r_free = 0.4000 target = 0.168789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.129003 restraints weight = 26164.850| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.82 r_work: 0.3318 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24318 Z= 0.121 Angle : 0.514 9.191 33014 Z= 0.271 Chirality : 0.042 0.191 3998 Planarity : 0.004 0.047 4016 Dihedral : 9.384 76.967 3474 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.82 % Allowed : 15.94 % Favored : 80.24 % 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 aren not related in a simple way. whole: 2.11 (0.15), residues: 3008 helix: 2.49 (0.12), residues: 1838 sheet: 0.59 (0.29), residues: 304 loop : -0.75 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 27 TYR 0.017 0.001 TYR E 107 PHE 0.034 0.001 PHE L 202 TRP 0.008 0.001 TRP K 47 HIS 0.004 0.001 HIS I 168 Details of bonding type rmsd covalent geometry : bond 0.00263 (24318) covalent geometry : angle 0.51437 (33014) hydrogen bonds : bond 0.03810 ( 1532) hydrogen bonds : angle 3.95949 ( 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 673 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 575 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8032 (tp30) cc_final: 0.7771 (tp30) REVERT: A 41 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7962 (mptp) REVERT: A 115 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7367 (mtpp) REVERT: B 62 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7203 (tp30) REVERT: B 127 ASP cc_start: 0.8093 (m-30) cc_final: 0.7878 (m-30) REVERT: C 23 LYS cc_start: 0.8601 (mtpm) cc_final: 0.8105 (mttt) REVERT: C 48 TYR cc_start: 0.8305 (m-80) cc_final: 0.8051 (m-80) REVERT: C 56 ASN cc_start: 0.8608 (t0) cc_final: 0.8229 (t0) REVERT: C 59 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7274 (mm-30) REVERT: C 62 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7646 (mt-10) REVERT: C 111 LYS cc_start: 0.8484 (mmpt) cc_final: 0.8219 (mtpt) REVERT: C 128 MET cc_start: 0.8505 (mmm) cc_final: 0.8079 (mmp) REVERT: C 208 MET cc_start: 0.6186 (ttp) cc_final: 0.5864 (ttm) REVERT: D 60 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8132 (tt0) REVERT: D 115 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7969 (mptp) REVERT: D 134 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: D 139 GLU cc_start: 0.7174 (pm20) cc_final: 0.6863 (pm20) REVERT: E 145 ILE cc_start: 0.6267 (OUTLIER) cc_final: 0.5991 (tt) REVERT: E 208 MET cc_start: 0.5912 (ptt) cc_final: 0.5442 (ptt) REVERT: F 23 LYS cc_start: 0.8595 (mtpm) cc_final: 0.8131 (mttt) REVERT: F 56 ASN cc_start: 0.8644 (t0) cc_final: 0.8435 (t0) REVERT: F 62 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7565 (mt-10) REVERT: F 111 LYS cc_start: 0.8416 (mmpt) cc_final: 0.8143 (mtmt) REVERT: F 128 MET cc_start: 0.8529 (mmm) cc_final: 0.8130 (mmp) REVERT: F 131 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8378 (mttm) REVERT: G 62 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7169 (tp30) REVERT: G 72 GLU cc_start: 0.7698 (tt0) cc_final: 0.7304 (pt0) REVERT: G 127 ASP cc_start: 0.8107 (m-30) cc_final: 0.7874 (m-30) REVERT: H 41 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7969 (mptp) REVERT: H 115 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7367 (mttm) REVERT: I 110 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7309 (mp0) REVERT: I 150 ILE cc_start: 0.7860 (pp) cc_final: 0.7406 (pt) REVERT: I 251 TYR cc_start: 0.8652 (t80) cc_final: 0.8328 (t80) REVERT: I 298 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8691 (mt) REVERT: J 100 MET cc_start: 0.6367 (mtm) cc_final: 0.6125 (mtm) REVERT: J 155 GLN cc_start: 0.7611 (tt0) cc_final: 0.7118 (tt0) REVERT: J 156 TYR cc_start: 0.7498 (m-80) cc_final: 0.7169 (m-80) REVERT: J 216 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6129 (mtp) REVERT: J 222 LYS cc_start: 0.8099 (pttm) cc_final: 0.7857 (mmtt) REVERT: J 374 GLN cc_start: 0.7749 (mp10) cc_final: 0.7506 (mp10) REVERT: K 97 LEU cc_start: 0.7298 (mt) cc_final: 0.7074 (tp) REVERT: K 100 MET cc_start: 0.6454 (mtm) cc_final: 0.6178 (mtm) REVERT: K 155 GLN cc_start: 0.7744 (tt0) cc_final: 0.7492 (tt0) REVERT: K 216 MET cc_start: 0.7557 (mmp) cc_final: 0.6142 (mtp) REVERT: K 222 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7373 (mmtm) REVERT: L 110 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7388 (mp0) REVERT: L 150 ILE cc_start: 0.7862 (pp) cc_final: 0.7407 (pt) REVERT: L 251 TYR cc_start: 0.8644 (t80) cc_final: 0.8275 (t80) REVERT: L 266 LEU cc_start: 0.8444 (mt) cc_final: 0.8205 (mt) REVERT: L 298 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8685 (mt) outliers start: 98 outliers final: 47 residues processed: 631 average time/residue: 0.7447 time to fit residues: 532.6760 Evaluate side-chains 614 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 555 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 63 LEU 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 D residue 134 GLN 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 82 ILE Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 47 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 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 236 LEU 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 86 ILE Chi-restraints excluded: chain J residue 166 LEU 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 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 138 ILE Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 166 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 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 323 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 267 optimal weight: 10.0000 chunk 296 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 277 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 38 ASN D 70 ASN E 134 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 ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.167790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127630 restraints weight = 26101.067| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.84 r_work: 0.3292 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3188 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= 0.138 Angle : 0.533 7.608 33014 Z= 0.281 Chirality : 0.043 0.196 3998 Planarity : 0.004 0.049 4016 Dihedral : 9.505 77.727 3472 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.55 % Allowed : 16.95 % Favored : 79.50 % 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 aren not related in a simple way. whole: 2.05 (0.15), residues: 3008 helix: 2.43 (0.12), residues: 1838 sheet: 0.60 (0.29), residues: 306 loop : -0.77 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 27 TYR 0.017 0.001 TYR L 270 PHE 0.035 0.002 PHE I 202 TRP 0.006 0.001 TRP J 47 HIS 0.004 0.001 HIS I 168 Details of bonding type rmsd covalent geometry : bond 0.00310 (24318) covalent geometry : angle 0.53264 (33014) hydrogen bonds : bond 0.03994 ( 1532) hydrogen bonds : angle 3.97220 ( 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 643 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 552 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8043 (tp30) cc_final: 0.7679 (tp30) REVERT: A 41 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7972 (mptp) REVERT: A 115 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7378 (mtpp) REVERT: B 62 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7199 (tp30) REVERT: B 127 ASP cc_start: 0.8146 (m-30) cc_final: 0.7935 (m-30) REVERT: C 23 LYS cc_start: 0.8590 (mtpm) cc_final: 0.8082 (mttt) REVERT: C 24 GLU cc_start: 0.8453 (tp30) cc_final: 0.8120 (tm-30) REVERT: C 43 ASN cc_start: 0.8581 (m110) cc_final: 0.8299 (m110) REVERT: C 48 TYR cc_start: 0.8324 (m-80) cc_final: 0.8088 (m-80) REVERT: C 56 ASN cc_start: 0.8619 (t0) cc_final: 0.8258 (t0) REVERT: C 62 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7683 (mt-10) REVERT: C 111 LYS cc_start: 0.8505 (mmpt) cc_final: 0.8242 (mtpt) REVERT: C 128 MET cc_start: 0.8576 (mmm) cc_final: 0.8140 (mmp) REVERT: C 208 MET cc_start: 0.6138 (ttp) cc_final: 0.5789 (ttm) REVERT: D 60 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: D 115 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7987 (mptp) REVERT: D 134 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7813 (mm110) REVERT: E 145 ILE cc_start: 0.6289 (OUTLIER) cc_final: 0.6010 (tt) REVERT: E 208 MET cc_start: 0.6013 (ptt) cc_final: 0.5576 (ptt) REVERT: F 23 LYS cc_start: 0.8612 (mtpm) cc_final: 0.8144 (mttt) REVERT: F 56 ASN cc_start: 0.8670 (t0) cc_final: 0.8421 (t0) REVERT: F 62 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7584 (mt-10) REVERT: F 111 LYS cc_start: 0.8447 (mmpt) cc_final: 0.8176 (mtmt) REVERT: F 128 MET cc_start: 0.8562 (mmm) cc_final: 0.8154 (mmp) REVERT: F 131 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8399 (mttm) REVERT: G 62 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7161 (tp30) REVERT: G 72 GLU cc_start: 0.7701 (tt0) cc_final: 0.7306 (pt0) REVERT: H 41 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7945 (mptp) REVERT: H 115 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7423 (mttm) REVERT: I 150 ILE cc_start: 0.7867 (pp) cc_final: 0.7403 (pt) REVERT: I 219 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6646 (mmt-90) REVERT: I 251 TYR cc_start: 0.8655 (t80) cc_final: 0.8336 (t80) REVERT: I 298 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8696 (mt) REVERT: J 155 GLN cc_start: 0.7612 (tt0) cc_final: 0.7334 (tt0) REVERT: J 216 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.6153 (mtp) REVERT: J 222 LYS cc_start: 0.8139 (pttm) cc_final: 0.7878 (mmtt) REVERT: K 97 LEU cc_start: 0.7288 (mt) cc_final: 0.7075 (tp) REVERT: K 100 MET cc_start: 0.6483 (mtm) cc_final: 0.6182 (mtm) REVERT: K 155 GLN cc_start: 0.7729 (tt0) cc_final: 0.7451 (tt0) REVERT: K 216 MET cc_start: 0.7585 (mmp) cc_final: 0.6175 (mtp) REVERT: K 222 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7370 (mmtm) REVERT: L 150 ILE cc_start: 0.7862 (pp) cc_final: 0.7396 (pt) REVERT: L 237 MET cc_start: 0.8276 (mtt) cc_final: 0.8044 (mpp) REVERT: L 251 TYR cc_start: 0.8636 (t80) cc_final: 0.8325 (t80) REVERT: L 266 LEU cc_start: 0.8451 (mt) cc_final: 0.8203 (mt) REVERT: L 298 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8687 (mt) outliers start: 91 outliers final: 49 residues processed: 611 average time/residue: 0.7252 time to fit residues: 502.8146 Evaluate side-chains 601 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 539 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 63 LEU 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 D residue 134 GLN 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 82 ILE Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 170 LEU 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 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 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 138 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 166 LEU 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 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 165 SER Chi-restraints excluded: chain K residue 166 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 19 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 268 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 38 ASN B 134 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 ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.168659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.128640 restraints weight = 26164.700| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.84 r_work: 0.3309 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24318 Z= 0.122 Angle : 0.517 7.514 33014 Z= 0.274 Chirality : 0.042 0.189 3998 Planarity : 0.004 0.047 4016 Dihedral : 9.373 78.084 3472 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.27 % Allowed : 17.15 % Favored : 79.58 % 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 aren not related in a simple way. whole: 2.06 (0.15), residues: 3008 helix: 2.46 (0.12), residues: 1838 sheet: 0.53 (0.29), residues: 306 loop : -0.77 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 27 TYR 0.018 0.001 TYR E 107 PHE 0.035 0.002 PHE I 202 TRP 0.004 0.001 TRP J 267 HIS 0.003 0.001 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.00264 (24318) covalent geometry : angle 0.51750 (33014) hydrogen bonds : bond 0.03775 ( 1532) hydrogen bonds : angle 3.93622 ( 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 649 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 565 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8000 (tp30) cc_final: 0.7738 (tp30) REVERT: A 41 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7976 (mptp) REVERT: A 115 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7361 (mtpp) REVERT: B 31 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7775 (mt-10) REVERT: B 62 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7186 (tp30) REVERT: B 127 ASP cc_start: 0.8109 (m-30) cc_final: 0.7897 (m-30) REVERT: C 23 LYS cc_start: 0.8601 (mtpm) cc_final: 0.8108 (mttt) REVERT: C 24 GLU cc_start: 0.8407 (tp30) cc_final: 0.8101 (tm-30) REVERT: C 43 ASN cc_start: 0.8598 (m110) cc_final: 0.8263 (m110) REVERT: C 48 TYR cc_start: 0.8288 (m-80) cc_final: 0.8037 (m-80) REVERT: C 56 ASN cc_start: 0.8590 (t0) cc_final: 0.8221 (t0) REVERT: C 59 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7219 (mm-30) REVERT: C 62 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7686 (mt-10) REVERT: C 111 LYS cc_start: 0.8471 (mmpt) cc_final: 0.8218 (mtpt) REVERT: C 128 MET cc_start: 0.8501 (mmm) cc_final: 0.8073 (mmp) REVERT: C 208 MET cc_start: 0.6135 (ttp) cc_final: 0.5905 (ttm) REVERT: D 60 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: D 115 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7971 (mptp) REVERT: D 134 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7871 (mm110) REVERT: D 138 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.5678 (p0) REVERT: D 139 GLU cc_start: 0.7223 (pm20) cc_final: 0.6887 (pm20) REVERT: D 208 MET cc_start: 0.6086 (ptt) cc_final: 0.5839 (ptp) REVERT: E 145 ILE cc_start: 0.6300 (OUTLIER) cc_final: 0.6027 (tt) REVERT: E 208 MET cc_start: 0.5983 (ptt) cc_final: 0.5584 (ptt) REVERT: F 23 LYS cc_start: 0.8603 (mtpm) cc_final: 0.8143 (mttt) REVERT: F 56 ASN cc_start: 0.8628 (t0) cc_final: 0.8375 (t0) REVERT: F 62 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7572 (mt-10) REVERT: F 111 LYS cc_start: 0.8413 (mmpt) cc_final: 0.8197 (mtpt) REVERT: F 128 MET cc_start: 0.8537 (mmm) cc_final: 0.8120 (mmp) REVERT: F 131 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8389 (mttm) REVERT: G 62 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7134 (tp30) REVERT: G 72 GLU cc_start: 0.7674 (tt0) cc_final: 0.7269 (pt0) REVERT: G 127 ASP cc_start: 0.8130 (m-30) cc_final: 0.7895 (m-30) REVERT: G 128 MET cc_start: 0.8765 (mmm) cc_final: 0.8490 (mmt) REVERT: H 41 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7954 (mptp) REVERT: H 115 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7352 (mtpp) REVERT: I 150 ILE cc_start: 0.7896 (pp) cc_final: 0.7449 (pt) REVERT: I 219 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6668 (mmt-90) REVERT: I 237 MET cc_start: 0.8257 (mtt) cc_final: 0.8049 (mpp) REVERT: I 251 TYR cc_start: 0.8651 (t80) cc_final: 0.8397 (t80) REVERT: I 298 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8684 (mt) REVERT: J 155 GLN cc_start: 0.7611 (tt0) cc_final: 0.7308 (tt0) REVERT: J 216 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.6168 (mtp) REVERT: J 222 LYS cc_start: 0.8102 (pttm) cc_final: 0.7858 (mmtt) REVERT: J 374 GLN cc_start: 0.7739 (mp10) cc_final: 0.7490 (mp10) REVERT: K 100 MET cc_start: 0.6482 (mtm) cc_final: 0.6228 (mtm) REVERT: K 155 GLN cc_start: 0.7692 (tt0) cc_final: 0.7427 (tt0) REVERT: K 216 MET cc_start: 0.7612 (mmp) cc_final: 0.6181 (mtp) REVERT: K 222 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7360 (mmtm) REVERT: L 110 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7666 (mp0) REVERT: L 150 ILE cc_start: 0.7942 (pp) cc_final: 0.7515 (pt) REVERT: L 219 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6691 (mmt-90) REVERT: L 251 TYR cc_start: 0.8629 (t80) cc_final: 0.8333 (t80) REVERT: L 298 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8688 (mt) outliers start: 84 outliers final: 44 residues processed: 618 average time/residue: 0.7267 time to fit residues: 509.0997 Evaluate side-chains 608 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 549 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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 D residue 134 GLN Chi-restraints excluded: chain D residue 138 ASP 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 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 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 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 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 138 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR 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 165 SER Chi-restraints excluded: chain K residue 166 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 L residue 15 THR Chi-restraints excluded: chain L residue 109 LYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 19 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 277 optimal weight: 0.6980 chunk 287 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 290 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 81 ASN B 38 ASN B 134 GLN D 8 GLN D 38 ASN F 134 GLN G 134 GLN H 81 ASN I 18 GLN I 119 ASN I 239 ASN J 85 GLN J 115 GLN J 253 ASN K 85 GLN K 115 GLN K 119 ASN K 253 ASN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.168480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128382 restraints weight = 25916.851| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.82 r_work: 0.3304 rms_B_bonded: 2.69 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: 0.8390 moved from start: 0.3332 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= 0.126 Angle : 0.533 8.291 33014 Z= 0.282 Chirality : 0.042 0.190 3998 Planarity : 0.004 0.046 4016 Dihedral : 9.363 78.580 3472 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.51 % Allowed : 18.08 % Favored : 78.41 % 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 aren not related in a simple way. whole: 2.02 (0.15), residues: 3008 helix: 2.41 (0.12), residues: 1842 sheet: 0.50 (0.29), residues: 306 loop : -0.75 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 27 TYR 0.018 0.001 TYR I 270 PHE 0.035 0.002 PHE I 202 TRP 0.004 0.001 TRP J 267 HIS 0.004 0.001 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.00278 (24318) covalent geometry : angle 0.53279 (33014) hydrogen bonds : bond 0.03829 ( 1532) hydrogen bonds : angle 3.94582 ( 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 653 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 563 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8056 (tp30) cc_final: 0.7673 (tp30) REVERT: A 41 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7988 (mptp) REVERT: A 115 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7369 (mtpp) REVERT: B 62 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7178 (tp30) REVERT: B 127 ASP cc_start: 0.8116 (m-30) cc_final: 0.7896 (m-30) REVERT: C 23 LYS cc_start: 0.8612 (mtpm) cc_final: 0.8118 (mttt) REVERT: C 24 GLU cc_start: 0.8407 (tp30) cc_final: 0.8125 (tm-30) REVERT: C 43 ASN cc_start: 0.8660 (m110) cc_final: 0.8329 (m110) REVERT: C 48 TYR cc_start: 0.8280 (m-80) cc_final: 0.8044 (m-80) REVERT: C 56 ASN cc_start: 0.8605 (t0) cc_final: 0.8259 (t0) REVERT: C 62 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7673 (mt-10) REVERT: C 111 LYS cc_start: 0.8483 (mmpt) cc_final: 0.8225 (mtmt) REVERT: C 128 MET cc_start: 0.8505 (mmm) cc_final: 0.8076 (mmp) REVERT: C 208 MET cc_start: 0.6098 (ttp) cc_final: 0.5863 (ttm) REVERT: D 60 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: D 115 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7975 (mptp) REVERT: D 134 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7848 (mm110) REVERT: D 138 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.5750 (p0) REVERT: E 145 ILE cc_start: 0.6257 (OUTLIER) cc_final: 0.6005 (tt) REVERT: E 208 MET cc_start: 0.6026 (ptt) cc_final: 0.5610 (ptt) REVERT: F 23 LYS cc_start: 0.8607 (mtpm) cc_final: 0.8146 (mttt) REVERT: F 56 ASN cc_start: 0.8636 (t0) cc_final: 0.8390 (t0) REVERT: F 62 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7600 (mt-10) REVERT: F 111 LYS cc_start: 0.8424 (mmpt) cc_final: 0.8206 (mtpt) REVERT: F 128 MET cc_start: 0.8550 (mmm) cc_final: 0.8125 (mmp) REVERT: F 131 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8401 (mttm) REVERT: G 62 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7151 (tp30) REVERT: G 72 GLU cc_start: 0.7681 (tt0) cc_final: 0.7286 (pt0) REVERT: H 41 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7993 (mptp) REVERT: H 115 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7365 (mtpp) REVERT: I 110 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7644 (mp0) REVERT: I 116 GLU cc_start: 0.7142 (tp30) cc_final: 0.6941 (tp30) REVERT: I 150 ILE cc_start: 0.7965 (pp) cc_final: 0.7524 (pt) REVERT: I 219 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6699 (mmt-90) REVERT: I 251 TYR cc_start: 0.8674 (t80) cc_final: 0.8420 (t80) REVERT: I 298 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8694 (mt) REVERT: J 34 LEU cc_start: 0.8433 (mp) cc_final: 0.8219 (mt) REVERT: J 155 GLN cc_start: 0.7621 (tt0) cc_final: 0.7282 (tt0) REVERT: J 216 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.6157 (mtp) REVERT: J 222 LYS cc_start: 0.8169 (pttm) cc_final: 0.7868 (mmtt) REVERT: J 374 GLN cc_start: 0.7717 (mp10) cc_final: 0.7473 (mp10) REVERT: K 34 LEU cc_start: 0.8437 (mp) cc_final: 0.8228 (mt) REVERT: K 100 MET cc_start: 0.6450 (mtm) cc_final: 0.6198 (mtm) REVERT: K 155 GLN cc_start: 0.7716 (tt0) cc_final: 0.7432 (tt0) REVERT: K 216 MET cc_start: 0.7582 (mmp) cc_final: 0.6148 (mtp) REVERT: K 222 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7347 (mmtm) REVERT: L 150 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7505 (pt) REVERT: L 219 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6724 (mmt-90) REVERT: L 237 MET cc_start: 0.8288 (mtt) cc_final: 0.8080 (mpp) REVERT: L 251 TYR cc_start: 0.8645 (t80) cc_final: 0.8356 (t80) REVERT: L 298 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8693 (mt) outliers start: 90 outliers final: 43 residues processed: 622 average time/residue: 0.7382 time to fit residues: 521.3221 Evaluate side-chains 607 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 548 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 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 D residue 134 GLN Chi-restraints excluded: chain D residue 138 ASP 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 G residue 47 SER Chi-restraints excluded: chain G residue 65 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 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 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 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 138 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR 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 165 SER Chi-restraints excluded: chain K residue 166 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 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: 0.6980 chunk 17 optimal weight: 6.9990 chunk 297 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 250 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 294 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 81 ASN B 38 ASN B 134 GLN E 8 GLN F 134 GLN G 134 GLN H 61 ASN H 81 ASN I 18 GLN I 119 ASN I 239 ASN J 85 GLN J 115 GLN J 253 ASN K 85 GLN 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.168783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.128616 restraints weight = 26169.264| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.83 r_work: 0.3309 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24318 Z= 0.125 Angle : 0.539 10.827 33014 Z= 0.284 Chirality : 0.042 0.191 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.348 79.145 3472 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.23 % Allowed : 18.63 % Favored : 78.14 % 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 aren not related in a simple way. whole: 2.01 (0.15), residues: 3008 helix: 2.41 (0.12), residues: 1842 sheet: 0.45 (0.29), residues: 302 loop : -0.76 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 27 TYR 0.017 0.001 TYR L 270 PHE 0.035 0.001 PHE L 202 TRP 0.004 0.001 TRP K 267 HIS 0.003 0.001 HIS I 168 Details of bonding type rmsd covalent geometry : bond 0.00275 (24318) covalent geometry : angle 0.53949 (33014) hydrogen bonds : bond 0.03802 ( 1532) hydrogen bonds : angle 3.95487 ( 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 638 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 555 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8056 (tp30) cc_final: 0.7674 (tp30) REVERT: A 41 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7991 (mptp) REVERT: A 63 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8013 (mp) REVERT: A 115 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7354 (mtpp) REVERT: B 31 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7715 (mt-10) REVERT: B 62 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7229 (tp30) REVERT: B 127 ASP cc_start: 0.8113 (m-30) cc_final: 0.7894 (m-30) REVERT: C 23 LYS cc_start: 0.8606 (mtpm) cc_final: 0.8116 (mttt) REVERT: C 43 ASN cc_start: 0.8639 (m110) cc_final: 0.8276 (m110) REVERT: C 48 TYR cc_start: 0.8279 (m-80) cc_final: 0.8050 (m-80) REVERT: C 56 ASN cc_start: 0.8641 (t0) cc_final: 0.8437 (t0) REVERT: C 59 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7345 (mm-30) REVERT: C 128 MET cc_start: 0.8508 (mmm) cc_final: 0.8077 (mmp) REVERT: C 208 MET cc_start: 0.6063 (ttp) cc_final: 0.5827 (ttm) REVERT: D 60 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: D 115 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7967 (mptp) REVERT: D 134 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7914 (mm110) REVERT: D 138 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.5737 (p0) REVERT: D 139 GLU cc_start: 0.7158 (pm20) cc_final: 0.6760 (pm20) REVERT: D 208 MET cc_start: 0.6060 (ptt) cc_final: 0.5813 (ptp) REVERT: E 138 ASP cc_start: 0.7040 (OUTLIER) cc_final: 0.6325 (m-30) REVERT: E 145 ILE cc_start: 0.6206 (OUTLIER) cc_final: 0.5963 (tt) REVERT: E 208 MET cc_start: 0.5995 (ptt) cc_final: 0.5603 (ptt) REVERT: F 23 LYS cc_start: 0.8605 (mtpm) cc_final: 0.8155 (mttt) REVERT: F 56 ASN cc_start: 0.8625 (t0) cc_final: 0.8376 (t0) REVERT: F 62 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7549 (mt-10) REVERT: F 111 LYS cc_start: 0.8427 (mmpt) cc_final: 0.8207 (mtpt) REVERT: F 128 MET cc_start: 0.8518 (mmm) cc_final: 0.8103 (mmp) REVERT: F 131 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8396 (mttm) REVERT: G 62 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7212 (tp30) REVERT: G 72 GLU cc_start: 0.7670 (tt0) cc_final: 0.7274 (pt0) REVERT: G 127 ASP cc_start: 0.8105 (m-30) cc_final: 0.7901 (m-30) REVERT: H 41 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7963 (mptp) REVERT: I 110 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7650 (mp0) REVERT: I 150 ILE cc_start: 0.7926 (pp) cc_final: 0.7469 (pt) REVERT: I 216 MET cc_start: 0.7780 (tpp) cc_final: 0.7208 (mtp) REVERT: I 219 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6726 (mmt-90) REVERT: I 237 MET cc_start: 0.8250 (mtt) cc_final: 0.8049 (mpp) REVERT: I 251 TYR cc_start: 0.8670 (t80) cc_final: 0.8420 (t80) REVERT: I 298 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8691 (mt) REVERT: J 34 LEU cc_start: 0.8414 (mp) cc_final: 0.8205 (mt) REVERT: J 155 GLN cc_start: 0.7626 (tt0) cc_final: 0.7288 (tt0) REVERT: J 216 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.6158 (mtp) REVERT: J 222 LYS cc_start: 0.8150 (pttm) cc_final: 0.7836 (mmtt) REVERT: J 374 GLN cc_start: 0.7690 (mp10) cc_final: 0.7448 (mp10) REVERT: K 34 LEU cc_start: 0.8414 (mp) cc_final: 0.8208 (mt) REVERT: K 100 MET cc_start: 0.6446 (mtm) cc_final: 0.6184 (mtm) REVERT: K 155 GLN cc_start: 0.7651 (tt0) cc_final: 0.7361 (tt0) REVERT: K 216 MET cc_start: 0.7600 (mmp) cc_final: 0.6160 (mtp) REVERT: K 220 ARG cc_start: 0.7159 (mmm160) cc_final: 0.6621 (mmm160) REVERT: K 222 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7356 (mmtm) REVERT: L 110 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7667 (mp0) REVERT: L 150 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7466 (pt) REVERT: L 216 MET cc_start: 0.7805 (tpp) cc_final: 0.7207 (mtp) REVERT: L 219 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6751 (mmt-90) REVERT: L 237 MET cc_start: 0.8292 (mtt) cc_final: 0.8081 (mpp) REVERT: L 251 TYR cc_start: 0.8647 (t80) cc_final: 0.8368 (t80) REVERT: L 298 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8692 (mt) REVERT: L 400 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7940 (mm-30) outliers start: 83 outliers final: 44 residues processed: 602 average time/residue: 0.6504 time to fit residues: 444.2254 Evaluate side-chains 606 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 544 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 63 LEU 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 D residue 134 GLN Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 138 ASP 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 G residue 47 SER Chi-restraints excluded: chain G residue 65 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 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 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 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 138 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR 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 165 SER Chi-restraints excluded: chain K residue 166 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 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 Chi-restraints excluded: chain L residue 400 GLU 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: 1.9990 chunk 300 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 294 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 252 optimal weight: 0.6980 chunk 291 optimal weight: 0.7980 chunk 297 optimal weight: 0.0010 chunk 254 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 81 ASN B 38 ASN B 134 GLN C 134 GLN F 134 GLN G 134 GLN H 30 HIS H 61 ASN H 81 ASN I 18 GLN I 119 ASN I 155 GLN I 239 ASN J 85 GLN J 115 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 155 GLN L 239 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.168644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.128854 restraints weight = 26092.446| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.82 r_work: 0.3307 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24318 Z= 0.129 Angle : 0.548 9.622 33014 Z= 0.288 Chirality : 0.043 0.191 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.358 79.584 3472 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.88 % Allowed : 19.41 % Favored : 77.71 % 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 aren not related in a simple way. whole: 1.98 (0.15), residues: 3008 helix: 2.38 (0.12), residues: 1842 sheet: 0.44 (0.29), residues: 302 loop : -0.76 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 27 TYR 0.019 0.001 TYR I 270 PHE 0.035 0.002 PHE I 202 TRP 0.004 0.001 TRP J 267 HIS 0.003 0.001 HIS I 168 Details of bonding type rmsd covalent geometry : bond 0.00284 (24318) covalent geometry : angle 0.54813 (33014) hydrogen bonds : bond 0.03827 ( 1532) hydrogen bonds : angle 3.96807 ( 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 624 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 550 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8062 (tp30) cc_final: 0.7706 (tp30) REVERT: A 41 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8011 (mptp) REVERT: A 63 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8040 (mp) REVERT: B 62 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7247 (tp30) REVERT: B 127 ASP cc_start: 0.8136 (m-30) cc_final: 0.7920 (m-30) REVERT: C 23 LYS cc_start: 0.8592 (mtpm) cc_final: 0.8098 (mttt) REVERT: C 39 GLU cc_start: 0.8005 (mp0) cc_final: 0.7747 (mp0) REVERT: C 43 ASN cc_start: 0.8695 (m110) cc_final: 0.8300 (m110) REVERT: C 48 TYR cc_start: 0.8281 (m-80) cc_final: 0.8062 (m-80) REVERT: C 56 ASN cc_start: 0.8673 (t0) cc_final: 0.8321 (t0) REVERT: C 59 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7291 (mm-30) REVERT: C 62 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7679 (mt-10) REVERT: C 65 SER cc_start: 0.8496 (m) cc_final: 0.8293 (t) REVERT: C 111 LYS cc_start: 0.8588 (mmpt) cc_final: 0.8193 (mtpt) REVERT: C 128 MET cc_start: 0.8515 (mmm) cc_final: 0.8093 (mmp) REVERT: C 208 MET cc_start: 0.6102 (ttp) cc_final: 0.5864 (ttm) REVERT: D 60 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: D 115 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7981 (mptp) REVERT: D 134 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7882 (mm110) REVERT: D 138 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.5788 (p0) REVERT: E 138 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6345 (m-30) REVERT: E 145 ILE cc_start: 0.6299 (OUTLIER) cc_final: 0.6049 (tt) REVERT: E 208 MET cc_start: 0.6035 (ptt) cc_final: 0.5710 (ptt) REVERT: F 23 LYS cc_start: 0.8621 (mtpm) cc_final: 0.8167 (mttt) REVERT: F 56 ASN cc_start: 0.8630 (t0) cc_final: 0.8376 (t0) REVERT: F 62 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7500 (mt-10) REVERT: F 111 LYS cc_start: 0.8441 (mmpt) cc_final: 0.8222 (mtpt) REVERT: F 128 MET cc_start: 0.8526 (mmm) cc_final: 0.8118 (mmp) REVERT: F 131 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8417 (mttm) REVERT: G 62 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7202 (tp30) REVERT: G 72 GLU cc_start: 0.7684 (tt0) cc_final: 0.7294 (pt0) REVERT: G 127 ASP cc_start: 0.8126 (m-30) cc_final: 0.7916 (m-30) REVERT: H 41 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7982 (mptp) REVERT: I 110 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7668 (mp0) REVERT: I 150 ILE cc_start: 0.7924 (pp) cc_final: 0.7479 (pt) REVERT: I 216 MET cc_start: 0.7764 (tpp) cc_final: 0.7210 (mtp) REVERT: I 219 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6730 (mmt-90) REVERT: I 237 MET cc_start: 0.8259 (mtt) cc_final: 0.8056 (mpp) REVERT: I 251 TYR cc_start: 0.8691 (t80) cc_final: 0.8448 (t80) REVERT: I 298 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8714 (mt) REVERT: J 34 LEU cc_start: 0.8433 (mp) cc_final: 0.8224 (mt) REVERT: J 155 GLN cc_start: 0.7684 (tt0) cc_final: 0.7329 (tt0) REVERT: J 216 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.6200 (mtp) REVERT: J 222 LYS cc_start: 0.8100 (pttm) cc_final: 0.7844 (mmtt) REVERT: J 374 GLN cc_start: 0.7686 (mp10) cc_final: 0.7451 (mp10) REVERT: K 34 LEU cc_start: 0.8430 (mp) cc_final: 0.8225 (mt) REVERT: K 100 MET cc_start: 0.6515 (mtm) cc_final: 0.6255 (mtm) REVERT: K 155 GLN cc_start: 0.7664 (tt0) cc_final: 0.7356 (tt0) REVERT: K 220 ARG cc_start: 0.7101 (mmm160) cc_final: 0.6586 (mmm160) REVERT: K 222 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7355 (mmtm) REVERT: L 110 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7683 (mp0) REVERT: L 150 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7477 (pt) REVERT: L 216 MET cc_start: 0.7817 (tpp) cc_final: 0.7233 (mtp) REVERT: L 219 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6756 (mmt-90) REVERT: L 237 MET cc_start: 0.8318 (mtt) cc_final: 0.8106 (mpp) REVERT: L 251 TYR cc_start: 0.8668 (t80) cc_final: 0.8392 (t80) REVERT: L 298 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8715 (mt) REVERT: L 400 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7932 (mm-30) outliers start: 74 outliers final: 43 residues processed: 595 average time/residue: 0.7613 time to fit residues: 512.1976 Evaluate side-chains 599 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 539 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 63 LEU 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 D residue 134 GLN Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 138 ASP 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 G residue 47 SER Chi-restraints excluded: chain G residue 65 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 H residue 135 SER Chi-restraints excluded: chain I residue 15 THR 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 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 166 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR 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 165 SER Chi-restraints excluded: chain K residue 166 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 219 ARG Chi-restraints excluded: chain L residue 291 GLU 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 Chi-restraints excluded: chain L residue 400 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 209 optimal weight: 0.5980 chunk 285 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 262 optimal weight: 0.7980 chunk 132 optimal weight: 0.0670 chunk 300 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 231 optimal weight: 0.3980 chunk 199 optimal weight: 0.8980 chunk 255 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN B 38 ASN B 134 GLN C 134 GLN F 134 GLN G 134 GLN H 61 ASN H 81 ASN I 18 GLN I 119 ASN I 155 GLN I 239 ASN J 85 GLN J 115 GLN J 253 ASN ** 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 155 GLN L 239 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.170198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130649 restraints weight = 26002.601| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.81 r_work: 0.3336 rms_B_bonded: 2.66 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: 0.8360 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24318 Z= 0.112 Angle : 0.529 9.312 33014 Z= 0.277 Chirality : 0.042 0.182 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.149 78.499 3472 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.70 % Favored : 98.27 % Rotamer: Outliers : 2.30 % Allowed : 19.99 % Favored : 77.71 % 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 aren not related in a simple way. whole: 2.01 (0.15), residues: 3008 helix: 2.41 (0.12), residues: 1838 sheet: 0.38 (0.28), residues: 298 loop : -0.72 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 27 TYR 0.017 0.001 TYR I 270 PHE 0.034 0.001 PHE I 202 TRP 0.005 0.001 TRP I 267 HIS 0.003 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00236 (24318) covalent geometry : angle 0.52876 (33014) hydrogen bonds : bond 0.03563 ( 1532) hydrogen bonds : angle 3.94549 ( 4413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13780.25 seconds wall clock time: 234 minutes 35.02 seconds (14075.02 seconds total)