Starting phenix.real_space_refine on Fri May 23 01:59:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1t_36803/05_2025/8k1t_36803.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1t_36803/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1t_36803/05_2025/8k1t_36803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1t_36803/05_2025/8k1t_36803.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1t_36803/05_2025/8k1t_36803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1t_36803/05_2025/8k1t_36803.cif" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.088 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.05, per 1000 atoms: 0.59 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: 5.82 Conformation dependent library (CDL) restraints added in 3.0 seconds 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5620 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 18 sheets defined 64.7% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 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: 7.84 Time building geometry restraints manager: 6.77 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 139 or resid 301)) selection = chain 'B' selection = (chain 'G' and (resid 7 through 139 or resid 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: 2.470 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: 0.930 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 51.480 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.160 ------------------------------------------------------------------------------- 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 : 3.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (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 TRP 0.006 0.001 TRP L 47 HIS 0.002 0.001 HIS L 168 PHE 0.026 0.001 PHE K 202 TYR 0.005 0.001 TYR D 108 ARG 0.002 0.000 ARG L 417 Details of bonding type rmsd hydrogen bonds : bond 0.21630 ( 1532) hydrogen bonds : angle 6.62929 ( 4413) covalent geometry : bond 0.00374 (24318) covalent geometry : angle 0.52925 (33014) *********************** 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 : 2.603 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: 1.3616 time to fit residues: 1299.4714 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 : 2.573 ------------------------------------------------------------------------------- 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 255 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 236 optimal weight: 0.0970 chunk 91 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 274 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 8 GLN 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 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: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.168349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128157 restraints weight = 26043.579| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.83 r_work: 0.3305 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24318 Z= 0.151 Angle : 0.569 9.388 33014 Z= 0.301 Chirality : 0.043 0.179 3998 Planarity : 0.004 0.044 4016 Dihedral : 10.134 84.223 3474 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.70 % Allowed : 13.29 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.15), residues: 3008 helix: 2.19 (0.12), residues: 1840 sheet: 1.14 (0.28), residues: 322 loop : -0.70 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 47 HIS 0.003 0.001 HIS I 168 PHE 0.034 0.002 PHE L 202 TYR 0.013 0.001 TYR I 270 ARG 0.008 0.001 ARG E 27 Details of bonding type rmsd hydrogen bonds : bond 0.05348 ( 1532) hydrogen bonds : angle 4.42748 ( 4413) covalent geometry : bond 0.00331 (24318) covalent geometry : angle 0.56919 (33014) *********************** 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 699 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 604 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8002 (tp30) cc_final: 0.7644 (tp30) REVERT: A 115 LYS cc_start: 0.7662 (mmtm) cc_final: 0.7381 (mttm) REVERT: B 41 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7387 (mmtt) REVERT: C 48 TYR cc_start: 0.8340 (m-80) cc_final: 0.7967 (m-80) REVERT: C 56 ASN cc_start: 0.8704 (t0) cc_final: 0.8402 (t0) REVERT: C 59 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7086 (mt-10) REVERT: C 62 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7119 (mt-10) REVERT: C 111 LYS cc_start: 0.8532 (mmpt) cc_final: 0.8230 (mtpt) REVERT: C 128 MET cc_start: 0.8597 (mmm) cc_final: 0.8197 (mmp) REVERT: D 126 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8305 (ttmt) REVERT: D 134 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7842 (mm110) REVERT: E 138 ASP cc_start: 0.7383 (t70) cc_final: 0.6591 (m-30) REVERT: F 59 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7170 (mt-10) REVERT: F 62 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6962 (mt-10) REVERT: F 111 LYS cc_start: 0.8479 (mmpt) cc_final: 0.8213 (mtpt) REVERT: F 128 MET cc_start: 0.8608 (mmm) cc_final: 0.8252 (mmp) REVERT: G 41 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7424 (mmtt) REVERT: H 115 LYS cc_start: 0.7786 (mmtm) cc_final: 0.7581 (mmmm) REVERT: I 110 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6809 (mp0) REVERT: I 123 ILE cc_start: 0.7832 (pt) cc_final: 0.7539 (pt) REVERT: I 140 ILE cc_start: 0.8350 (tt) cc_final: 0.8148 (tt) REVERT: I 156 TYR cc_start: 0.6741 (m-80) cc_final: 0.6501 (m-80) REVERT: I 251 TYR cc_start: 0.8625 (t80) cc_final: 0.8227 (t80) REVERT: I 298 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8719 (mt) REVERT: I 340 ARG cc_start: 0.8464 (mtt180) cc_final: 0.7890 (mtt-85) REVERT: J 97 LEU cc_start: 0.7262 (mt) cc_final: 0.7005 (tp) REVERT: J 100 MET cc_start: 0.6120 (OUTLIER) cc_final: 0.5756 (mmm) REVERT: J 106 ILE cc_start: 0.7411 (mp) cc_final: 0.7139 (mm) REVERT: J 136 PHE cc_start: 0.7678 (t80) cc_final: 0.7404 (t80) REVERT: J 155 GLN cc_start: 0.7592 (tt0) cc_final: 0.7152 (tt0) REVERT: J 156 TYR cc_start: 0.7547 (m-80) cc_final: 0.7331 (m-80) REVERT: J 216 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6122 (mtp) REVERT: J 222 LYS cc_start: 0.8092 (pttm) cc_final: 0.7864 (mmtt) REVERT: J 299 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8723 (tp) REVERT: K 97 LEU cc_start: 0.7274 (mt) cc_final: 0.6962 (tp) REVERT: K 100 MET cc_start: 0.6313 (mtm) cc_final: 0.5988 (mtm) REVERT: K 155 GLN cc_start: 0.7570 (tt0) cc_final: 0.7152 (tt0) REVERT: K 216 MET cc_start: 0.7454 (mmp) cc_final: 0.6122 (mtp) REVERT: K 250 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8591 (mm-30) REVERT: K 253 ASN cc_start: 0.8391 (t0) cc_final: 0.8155 (t160) REVERT: K 344 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8081 (mmtm) REVERT: L 110 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6804 (mp0) REVERT: L 123 ILE cc_start: 0.7806 (pt) cc_final: 0.7516 (pt) REVERT: L 251 TYR cc_start: 0.8591 (t80) cc_final: 0.8160 (t80) REVERT: L 298 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8674 (mt) REVERT: L 340 ARG cc_start: 0.8502 (mtt180) cc_final: 0.7886 (mtt-85) REVERT: L 439 ASP cc_start: 0.8215 (m-30) cc_final: 0.7999 (m-30) outliers start: 95 outliers final: 33 residues processed: 659 average time/residue: 1.3894 time to fit residues: 1042.3827 Evaluate side-chains 593 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 553 time to evaluate : 2.619 ------------------------------------------------------------------------------- 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 B residue 89 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 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 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 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 344 LYS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 323 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 269 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 293 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 283 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 C 185 HIS D 8 GLN D 70 ASN D 185 HIS E 134 GLN E 185 HIS F 185 HIS G 8 GLN H 70 ASN I 18 GLN I 119 ASN I 155 GLN I 239 ASN J 85 GLN J 115 GLN J 253 ASN J 374 GLN K 85 GLN K 115 GLN K 272 GLN L 18 GLN L 119 ASN L 155 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.168544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128393 restraints weight = 25900.246| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.81 r_work: 0.3307 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2764 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= 0.131 Angle : 0.533 7.530 33014 Z= 0.279 Chirality : 0.042 0.183 3998 Planarity : 0.004 0.046 4016 Dihedral : 9.591 77.053 3474 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.98 % Allowed : 14.07 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.15), residues: 3008 helix: 2.39 (0.12), residues: 1838 sheet: 0.82 (0.28), residues: 314 loop : -0.71 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 47 HIS 0.003 0.001 HIS I 168 PHE 0.035 0.001 PHE L 202 TYR 0.019 0.001 TYR L 270 ARG 0.010 0.001 ARG H 27 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 1532) hydrogen bonds : angle 4.14325 ( 4413) covalent geometry : bond 0.00285 (24318) covalent geometry : angle 0.53259 (33014) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 587 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8043 (tp30) cc_final: 0.7703 (tp30) REVERT: A 89 THR cc_start: 0.8630 (t) cc_final: 0.8372 (p) REVERT: A 115 LYS cc_start: 0.7697 (mmtm) cc_final: 0.7411 (mttm) REVERT: B 41 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7418 (mmtt) REVERT: B 127 ASP cc_start: 0.8100 (m-30) cc_final: 0.7880 (m-30) REVERT: C 23 LYS cc_start: 0.8628 (mtpm) cc_final: 0.8034 (mtmt) REVERT: C 24 GLU cc_start: 0.8489 (tp30) cc_final: 0.7890 (tp30) REVERT: C 48 TYR cc_start: 0.8361 (m-80) cc_final: 0.8047 (m-80) REVERT: C 56 ASN cc_start: 0.8666 (t0) cc_final: 0.8331 (t0) REVERT: C 62 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7435 (mt-10) REVERT: C 105 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: C 128 MET cc_start: 0.8561 (mmm) cc_final: 0.8151 (mmp) REVERT: D 115 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7965 (mptp) REVERT: D 134 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7373 (mp10) REVERT: E 138 ASP cc_start: 0.7197 (t70) cc_final: 0.6398 (m-30) REVERT: E 145 ILE cc_start: 0.6290 (OUTLIER) cc_final: 0.5994 (tt) REVERT: E 208 MET cc_start: 0.5874 (ptt) cc_final: 0.5449 (ptt) REVERT: F 23 LYS cc_start: 0.8637 (mtpm) cc_final: 0.8089 (mtmt) REVERT: F 56 ASN cc_start: 0.8595 (t0) cc_final: 0.8356 (t0) REVERT: F 62 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7371 (mt-10) REVERT: F 111 LYS cc_start: 0.8446 (mmpt) cc_final: 0.8154 (mtpt) REVERT: F 128 MET cc_start: 0.8580 (mmm) cc_final: 0.8196 (mmp) REVERT: F 131 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8380 (mttm) REVERT: F 181 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6626 (mp) REVERT: G 41 LYS cc_start: 0.8011 (mmtm) cc_final: 0.7449 (mmtt) REVERT: H 89 THR cc_start: 0.8616 (t) cc_final: 0.8375 (p) REVERT: H 115 LYS cc_start: 0.7725 (mmtm) cc_final: 0.7474 (mttm) REVERT: I 110 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7242 (mp0) REVERT: I 140 ILE cc_start: 0.8394 (tt) cc_final: 0.8153 (tt) REVERT: I 150 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7661 (mp) REVERT: I 156 TYR cc_start: 0.6753 (m-80) cc_final: 0.6524 (m-80) REVERT: I 251 TYR cc_start: 0.8653 (t80) cc_final: 0.8288 (t80) REVERT: I 298 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8704 (mt) REVERT: I 340 ARG cc_start: 0.8447 (mtt180) cc_final: 0.7860 (mtt-85) REVERT: J 97 LEU cc_start: 0.7237 (mt) cc_final: 0.7026 (tp) REVERT: J 106 ILE cc_start: 0.7430 (mp) cc_final: 0.7058 (mm) REVERT: J 155 GLN cc_start: 0.7618 (tt0) cc_final: 0.7150 (tt0) REVERT: J 156 TYR cc_start: 0.7506 (m-80) cc_final: 0.7239 (m-80) REVERT: J 216 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.6163 (mtp) REVERT: J 222 LYS cc_start: 0.8069 (pttm) cc_final: 0.7852 (mmtt) REVERT: J 299 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8719 (tp) REVERT: K 97 LEU cc_start: 0.7395 (mt) cc_final: 0.7134 (tp) REVERT: K 100 MET cc_start: 0.6410 (mtm) cc_final: 0.6165 (mtm) REVERT: K 155 GLN cc_start: 0.7736 (tt0) cc_final: 0.7372 (tt0) REVERT: K 216 MET cc_start: 0.7513 (mmp) cc_final: 0.6151 (mtp) REVERT: K 220 ARG cc_start: 0.6895 (mmm160) cc_final: 0.6519 (tpt170) REVERT: K 253 ASN cc_start: 0.8359 (t0) cc_final: 0.8133 (t160) REVERT: L 110 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7264 (mp0) REVERT: L 150 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7650 (mp) REVERT: L 251 TYR cc_start: 0.8619 (t80) cc_final: 0.8214 (t80) REVERT: L 298 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8676 (mt) outliers start: 102 outliers final: 39 residues processed: 649 average time/residue: 1.3277 time to fit residues: 984.5019 Evaluate side-chains 597 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 547 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 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 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 439 ASP Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain 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 150 ILE Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 2 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 275 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 206 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 D 8 GLN D 70 ASN E 8 GLN F 185 HIS G 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 ** 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.168184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.127969 restraints weight = 26110.691| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.88 r_work: 0.3302 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24318 Z= 0.131 Angle : 0.528 7.759 33014 Z= 0.278 Chirality : 0.042 0.194 3998 Planarity : 0.004 0.047 4016 Dihedral : 9.546 76.750 3474 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.44 % Allowed : 14.22 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.15), residues: 3008 helix: 2.43 (0.12), residues: 1838 sheet: 0.72 (0.29), residues: 304 loop : -0.75 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 47 HIS 0.004 0.001 HIS I 168 PHE 0.035 0.001 PHE L 202 TYR 0.018 0.001 TYR I 270 ARG 0.010 0.001 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 1532) hydrogen bonds : angle 4.04477 ( 4413) covalent geometry : bond 0.00290 (24318) covalent geometry : angle 0.52834 (33014) *********************** 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 692 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 578 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8092 (tp30) cc_final: 0.7753 (tp30) REVERT: A 41 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7990 (mptp) REVERT: A 89 THR cc_start: 0.8630 (t) cc_final: 0.8428 (m) REVERT: A 115 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7412 (mtpm) REVERT: B 41 LYS cc_start: 0.7981 (mmtm) cc_final: 0.7424 (mmtt) REVERT: B 69 ARG cc_start: 0.8554 (mtt-85) cc_final: 0.8316 (mtt90) REVERT: B 127 ASP cc_start: 0.8149 (m-30) cc_final: 0.7930 (m-30) REVERT: C 23 LYS cc_start: 0.8611 (mtpm) cc_final: 0.8065 (mtmt) REVERT: C 48 TYR cc_start: 0.8344 (m-80) cc_final: 0.8114 (m-80) REVERT: C 56 ASN cc_start: 0.8635 (t0) cc_final: 0.8319 (t0) REVERT: C 59 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7280 (mm-30) REVERT: C 62 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7574 (mt-10) REVERT: C 105 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: C 111 LYS cc_start: 0.8459 (mmpt) cc_final: 0.8188 (mtmt) REVERT: C 128 MET cc_start: 0.8548 (mmm) cc_final: 0.8119 (mmp) REVERT: C 208 MET cc_start: 0.6207 (ttp) cc_final: 0.5951 (ttm) REVERT: D 60 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: E 138 ASP cc_start: 0.7145 (t70) cc_final: 0.6388 (m-30) REVERT: E 145 ILE cc_start: 0.6253 (OUTLIER) cc_final: 0.5976 (tt) REVERT: E 208 MET cc_start: 0.5853 (ptt) cc_final: 0.5511 (ptt) REVERT: F 23 LYS cc_start: 0.8602 (mtpm) cc_final: 0.8131 (mttt) REVERT: F 59 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7297 (mm-30) REVERT: F 105 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: F 111 LYS cc_start: 0.8469 (mmpt) cc_final: 0.8191 (mtpt) REVERT: F 128 MET cc_start: 0.8576 (mmm) cc_final: 0.8177 (mmp) REVERT: F 131 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8385 (mttm) REVERT: F 181 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6735 (mp) REVERT: G 41 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7447 (mmtt) REVERT: G 62 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7074 (tp30) REVERT: G 65 SER cc_start: 0.7872 (m) cc_final: 0.7666 (p) REVERT: G 72 GLU cc_start: 0.7723 (tt0) cc_final: 0.7321 (pt0) REVERT: H 41 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7955 (mptp) REVERT: H 115 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7433 (mttm) REVERT: I 110 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7197 (mp0) REVERT: I 140 ILE cc_start: 0.8375 (tt) cc_final: 0.8154 (tt) REVERT: I 150 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7351 (mp) REVERT: I 251 TYR cc_start: 0.8651 (t80) cc_final: 0.8311 (t80) REVERT: I 298 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8697 (mt) REVERT: J 97 LEU cc_start: 0.7386 (mt) cc_final: 0.7117 (tp) REVERT: J 100 MET cc_start: 0.6264 (mtm) cc_final: 0.5806 (mmm) REVERT: J 106 ILE cc_start: 0.7570 (mp) cc_final: 0.7245 (mm) REVERT: J 155 GLN cc_start: 0.7613 (tt0) cc_final: 0.7158 (tt0) REVERT: J 156 TYR cc_start: 0.7507 (m-80) cc_final: 0.7197 (m-80) REVERT: J 216 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6096 (mtp) REVERT: J 222 LYS cc_start: 0.8072 (pttm) cc_final: 0.7826 (mmtt) REVERT: J 299 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8731 (tp) REVERT: K 97 LEU cc_start: 0.7353 (mt) cc_final: 0.7093 (tp) REVERT: K 100 MET cc_start: 0.6477 (mtm) cc_final: 0.6235 (mtm) REVERT: K 155 GLN cc_start: 0.7724 (tt0) cc_final: 0.7381 (tt0) REVERT: K 216 MET cc_start: 0.7536 (mmp) cc_final: 0.6132 (mtp) REVERT: K 220 ARG cc_start: 0.6894 (mmm160) cc_final: 0.6531 (tpt170) REVERT: K 222 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7824 (mmtt) REVERT: L 110 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7329 (mp0) REVERT: L 150 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7360 (mp) REVERT: L 251 TYR cc_start: 0.8624 (t80) cc_final: 0.8223 (t80) REVERT: L 298 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8677 (mt) outliers start: 114 outliers final: 39 residues processed: 646 average time/residue: 1.4037 time to fit residues: 1038.7393 Evaluate side-chains 605 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 550 time to evaluate : 2.511 ------------------------------------------------------------------------------- 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 82 ILE Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 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 82 ILE Chi-restraints excluded: chain F residue 105 GLN 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 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 109 LYS Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 234 optimal weight: 1.9990 chunk 233 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 120 optimal weight: 0.0070 chunk 180 optimal weight: 9.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 8 GLN D 38 ASN D 70 ASN D 134 GLN E 8 GLN G 134 GLN H 70 ASN I 18 GLN I 119 ASN I 239 ASN J 85 GLN J 115 GLN J 253 ASN K 85 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 = 0.4008 r_free = 0.4008 target = 0.169395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.129499 restraints weight = 26335.111| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.85 r_work: 0.3323 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3119 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= 0.114 Angle : 0.506 9.060 33014 Z= 0.267 Chirality : 0.042 0.184 3998 Planarity : 0.004 0.047 4016 Dihedral : 9.373 75.787 3474 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.70 % Allowed : 15.94 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.15), residues: 3008 helix: 2.49 (0.12), residues: 1838 sheet: 0.58 (0.29), residues: 300 loop : -0.78 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 47 HIS 0.003 0.001 HIS I 168 PHE 0.034 0.001 PHE L 202 TYR 0.020 0.001 TYR E 107 ARG 0.009 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 1532) hydrogen bonds : angle 3.95105 ( 4413) covalent geometry : bond 0.00242 (24318) covalent geometry : angle 0.50580 (33014) *********************** 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 672 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 577 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8044 (tp30) cc_final: 0.7725 (tp30) REVERT: A 41 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7990 (mptp) REVERT: A 115 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7370 (mptt) REVERT: B 41 LYS cc_start: 0.8009 (mmtm) cc_final: 0.7437 (mmtt) REVERT: B 62 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7203 (tp30) REVERT: B 69 ARG cc_start: 0.8548 (mtt-85) cc_final: 0.8263 (mtt90) REVERT: B 127 ASP cc_start: 0.8070 (m-30) cc_final: 0.7849 (m-30) REVERT: C 23 LYS cc_start: 0.8605 (mtpm) cc_final: 0.8149 (mttt) REVERT: C 48 TYR cc_start: 0.8308 (m-80) cc_final: 0.7989 (m-80) REVERT: C 56 ASN cc_start: 0.8608 (t0) cc_final: 0.8261 (t0) REVERT: C 59 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7278 (mm-30) REVERT: C 62 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7600 (mt-10) REVERT: C 111 LYS cc_start: 0.8423 (mmpt) cc_final: 0.8178 (mtmt) REVERT: C 128 MET cc_start: 0.8508 (mmm) cc_final: 0.8087 (mmp) REVERT: C 208 MET cc_start: 0.6166 (ttp) cc_final: 0.5844 (ttm) REVERT: D 60 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: D 115 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7967 (mptp) REVERT: D 134 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7617 (mm110) REVERT: D 139 GLU cc_start: 0.7164 (pm20) cc_final: 0.6849 (pm20) REVERT: E 145 ILE cc_start: 0.6290 (OUTLIER) cc_final: 0.5998 (tt) REVERT: E 208 MET cc_start: 0.5909 (ptt) cc_final: 0.5488 (ptt) REVERT: F 23 LYS cc_start: 0.8593 (mtpm) cc_final: 0.8137 (mttt) REVERT: F 59 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7158 (mm-30) REVERT: F 62 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7659 (mt-10) REVERT: F 111 LYS cc_start: 0.8416 (mmpt) cc_final: 0.8163 (mtmt) REVERT: F 128 MET cc_start: 0.8530 (mmm) cc_final: 0.8135 (mmp) REVERT: F 131 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8377 (mttm) REVERT: G 41 LYS cc_start: 0.7998 (mmtm) cc_final: 0.7440 (mmtt) REVERT: G 62 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7129 (tp30) REVERT: G 72 GLU cc_start: 0.7690 (tt0) cc_final: 0.7274 (pt0) REVERT: G 127 ASP cc_start: 0.8096 (m-30) cc_final: 0.7867 (m-30) REVERT: H 41 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7947 (mptp) REVERT: H 115 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7381 (mtpm) REVERT: I 110 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7346 (mp0) REVERT: I 150 ILE cc_start: 0.7857 (pp) cc_final: 0.7418 (pt) REVERT: I 251 TYR cc_start: 0.8655 (t80) cc_final: 0.8329 (t80) REVERT: I 298 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8688 (mt) REVERT: J 100 MET cc_start: 0.6368 (mtm) cc_final: 0.6163 (mtm) REVERT: J 106 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7192 (mm) REVERT: J 155 GLN cc_start: 0.7612 (tt0) cc_final: 0.7119 (tt0) REVERT: J 156 TYR cc_start: 0.7497 (m-80) cc_final: 0.7169 (m-80) REVERT: J 216 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.6119 (mtp) REVERT: J 222 LYS cc_start: 0.8075 (pttm) cc_final: 0.7839 (mmtt) REVERT: J 299 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8731 (tp) REVERT: J 374 GLN cc_start: 0.7765 (mp10) cc_final: 0.7511 (mp10) REVERT: K 97 LEU cc_start: 0.7304 (mt) cc_final: 0.7082 (tp) REVERT: K 100 MET cc_start: 0.6474 (mtm) cc_final: 0.6192 (mtm) REVERT: K 155 GLN cc_start: 0.7748 (tt0) cc_final: 0.7481 (tt0) REVERT: K 216 MET cc_start: 0.7522 (mmp) cc_final: 0.6097 (mtp) REVERT: K 220 ARG cc_start: 0.6880 (mmm160) cc_final: 0.6507 (tpt170) REVERT: K 222 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7686 (mmtt) REVERT: L 110 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7348 (mp0) REVERT: L 150 ILE cc_start: 0.7860 (pp) cc_final: 0.7369 (mp) REVERT: L 251 TYR cc_start: 0.8637 (t80) cc_final: 0.8318 (t80) REVERT: L 298 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8676 (mt) outliers start: 95 outliers final: 45 residues processed: 633 average time/residue: 1.3458 time to fit residues: 972.4459 Evaluate side-chains 613 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 554 time to evaluate : 2.883 ------------------------------------------------------------------------------- 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 39 GLU 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 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 H residue 41 LYS 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 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 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 106 ILE 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 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 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 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 199 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 284 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 B 134 GLN D 8 GLN D 70 ASN E 8 GLN G 134 GLN H 70 ASN I 18 GLN I 119 ASN I 155 GLN I 239 ASN ** J 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN J 115 GLN J 253 ASN K 85 GLN 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.166204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125522 restraints weight = 25922.528| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.88 r_work: 0.3267 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24318 Z= 0.184 Angle : 0.570 8.117 33014 Z= 0.301 Chirality : 0.044 0.206 3998 Planarity : 0.004 0.047 4016 Dihedral : 9.831 79.882 3472 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.25 % Allowed : 16.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.15), residues: 3008 helix: 2.31 (0.12), residues: 1838 sheet: 0.61 (0.29), residues: 302 loop : -0.79 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 47 HIS 0.005 0.001 HIS I 168 PHE 0.036 0.002 PHE L 202 TYR 0.018 0.001 TYR I 270 ARG 0.009 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 1532) hydrogen bonds : angle 4.06579 ( 4413) covalent geometry : bond 0.00430 (24318) covalent geometry : angle 0.56963 (33014) *********************** 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 667 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 558 time to evaluate : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8039 (tp30) cc_final: 0.7645 (tp30) REVERT: A 41 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8002 (mptp) REVERT: B 41 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7423 (mmtt) REVERT: B 62 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7075 (tp30) REVERT: B 65 SER cc_start: 0.7888 (m) cc_final: 0.7603 (p) REVERT: B 69 ARG cc_start: 0.8616 (mtt-85) cc_final: 0.8322 (mtt90) REVERT: B 127 ASP cc_start: 0.8138 (m-30) cc_final: 0.7904 (m-30) REVERT: C 43 ASN cc_start: 0.8580 (m-40) cc_final: 0.8358 (m110) REVERT: C 48 TYR cc_start: 0.8376 (m-80) cc_final: 0.8170 (m-80) REVERT: C 56 ASN cc_start: 0.8637 (t0) cc_final: 0.8324 (t0) REVERT: C 59 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7305 (mm-30) REVERT: C 62 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7706 (mt-10) REVERT: C 111 LYS cc_start: 0.8527 (mmpt) cc_final: 0.8242 (mtmt) REVERT: C 128 MET cc_start: 0.8627 (mmm) cc_final: 0.8235 (mmp) REVERT: C 208 MET cc_start: 0.6189 (ttp) cc_final: 0.5853 (ttm) REVERT: D 60 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: D 115 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7972 (mptp) REVERT: D 134 GLN cc_start: 0.8067 (tp40) cc_final: 0.7658 (mm110) REVERT: E 138 ASP cc_start: 0.7210 (t70) cc_final: 0.6441 (m-30) REVERT: E 145 ILE cc_start: 0.6350 (OUTLIER) cc_final: 0.6070 (tt) REVERT: E 208 MET cc_start: 0.5825 (ptt) cc_final: 0.5421 (ptt) REVERT: F 23 LYS cc_start: 0.8583 (mtpm) cc_final: 0.8102 (mttt) REVERT: F 59 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7235 (mm-30) REVERT: F 111 LYS cc_start: 0.8508 (mmpt) cc_final: 0.8277 (mtpt) REVERT: F 128 MET cc_start: 0.8606 (mmm) cc_final: 0.8197 (mmp) REVERT: F 131 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8395 (mttm) REVERT: G 41 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7491 (mmtt) REVERT: G 62 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7135 (tp30) REVERT: H 41 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8006 (mptp) REVERT: I 150 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7444 (pt) REVERT: I 219 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6621 (mmt-90) REVERT: I 251 TYR cc_start: 0.8638 (t80) cc_final: 0.8316 (t80) REVERT: I 298 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8702 (mt) REVERT: J 100 MET cc_start: 0.6520 (mtm) cc_final: 0.6269 (mtm) REVERT: J 155 GLN cc_start: 0.7623 (tt0) cc_final: 0.7344 (tt0) REVERT: J 216 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6180 (mtp) REVERT: J 222 LYS cc_start: 0.8110 (pttm) cc_final: 0.7831 (mmtt) REVERT: J 299 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8777 (tp) REVERT: K 97 LEU cc_start: 0.7304 (mt) cc_final: 0.7096 (tp) REVERT: K 100 MET cc_start: 0.6486 (mtm) cc_final: 0.6201 (mtm) REVERT: K 155 GLN cc_start: 0.7725 (tt0) cc_final: 0.7453 (tt0) REVERT: K 216 MET cc_start: 0.7599 (mmp) cc_final: 0.6178 (mtp) REVERT: K 220 ARG cc_start: 0.6943 (mmm160) cc_final: 0.6541 (tpt170) REVERT: L 89 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8305 (mp) REVERT: L 116 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: L 150 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7423 (pt) REVERT: L 219 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6653 (mmt-90) REVERT: L 251 TYR cc_start: 0.8610 (t80) cc_final: 0.8265 (t80) REVERT: L 266 LEU cc_start: 0.8460 (mt) cc_final: 0.8215 (mt) REVERT: L 298 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8696 (mt) outliers start: 109 outliers final: 47 residues processed: 629 average time/residue: 1.4065 time to fit residues: 1011.6910 Evaluate side-chains 606 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 543 time to evaluate : 2.554 ------------------------------------------------------------------------------- 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 B residue 89 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 219 ARG Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 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 299 LEU Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 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 338 ILE Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 116 GLU Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 219 ARG Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 323 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 105 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 249 optimal weight: 0.8980 chunk 127 optimal weight: 0.0770 chunk 165 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 258 optimal weight: 0.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 134 GLN E 8 GLN E 134 GLN G 134 GLN H 70 ASN I 18 GLN I 119 ASN I 155 GLN I 239 ASN ** J 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN J 115 GLN J 253 ASN K 85 GLN 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.167710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127497 restraints weight = 26072.419| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.84 r_work: 0.3294 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24318 Z= 0.133 Angle : 0.532 7.546 33014 Z= 0.281 Chirality : 0.043 0.195 3998 Planarity : 0.004 0.046 4016 Dihedral : 9.640 79.287 3472 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.23 % Allowed : 17.50 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.15), residues: 3008 helix: 2.38 (0.12), residues: 1838 sheet: 0.56 (0.29), residues: 306 loop : -0.77 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 47 HIS 0.004 0.001 HIS L 168 PHE 0.036 0.002 PHE L 202 TYR 0.019 0.001 TYR E 107 ARG 0.009 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 1532) hydrogen bonds : angle 4.00330 ( 4413) covalent geometry : bond 0.00295 (24318) covalent geometry : angle 0.53170 (33014) *********************** 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 635 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 552 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8011 (tp30) cc_final: 0.7665 (tp30) REVERT: A 41 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7966 (mptp) REVERT: B 62 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7076 (tp30) REVERT: B 65 SER cc_start: 0.7834 (m) cc_final: 0.7613 (p) REVERT: B 69 ARG cc_start: 0.8586 (mtt-85) cc_final: 0.8308 (mtt90) REVERT: B 127 ASP cc_start: 0.8117 (m-30) cc_final: 0.7904 (m-30) REVERT: C 23 LYS cc_start: 0.8598 (mtpm) cc_final: 0.8115 (mttt) REVERT: C 43 ASN cc_start: 0.8570 (m-40) cc_final: 0.8327 (m110) REVERT: C 48 TYR cc_start: 0.8311 (m-80) cc_final: 0.8051 (m-80) REVERT: C 56 ASN cc_start: 0.8605 (t0) cc_final: 0.8293 (t0) REVERT: C 62 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7705 (mt-10) REVERT: C 111 LYS cc_start: 0.8467 (mmpt) cc_final: 0.8169 (mtmt) REVERT: C 128 MET cc_start: 0.8555 (mmm) cc_final: 0.8165 (mmp) REVERT: C 208 MET cc_start: 0.6125 (ttp) cc_final: 0.5903 (ttm) REVERT: D 60 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: D 115 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7995 (mptp) REVERT: D 134 GLN cc_start: 0.8179 (tp40) cc_final: 0.7656 (mm110) REVERT: E 120 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8557 (ttt180) REVERT: E 145 ILE cc_start: 0.6324 (OUTLIER) cc_final: 0.6025 (tt) REVERT: E 208 MET cc_start: 0.5940 (ptt) cc_final: 0.5537 (ptt) REVERT: F 23 LYS cc_start: 0.8561 (mtpm) cc_final: 0.8077 (mttt) REVERT: F 59 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7173 (mm-30) REVERT: F 62 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7688 (mt-10) REVERT: F 111 LYS cc_start: 0.8458 (mmpt) cc_final: 0.8227 (mtpt) REVERT: F 128 MET cc_start: 0.8555 (mmm) cc_final: 0.8144 (mmp) REVERT: F 131 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8378 (mttm) REVERT: G 41 LYS cc_start: 0.8067 (mmtm) cc_final: 0.7467 (mmtt) REVERT: G 62 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7224 (tp30) REVERT: G 72 GLU cc_start: 0.7695 (tt0) cc_final: 0.7246 (pt0) REVERT: G 127 ASP cc_start: 0.8149 (m-30) cc_final: 0.7913 (m-30) REVERT: H 41 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7947 (mptp) REVERT: I 116 GLU cc_start: 0.7152 (tp30) cc_final: 0.6948 (tp30) REVERT: I 150 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7416 (pt) REVERT: I 216 MET cc_start: 0.7706 (tpp) cc_final: 0.7113 (mtp) REVERT: I 219 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6651 (mmt-90) REVERT: I 237 MET cc_start: 0.8280 (mtt) cc_final: 0.8049 (mpp) REVERT: I 251 TYR cc_start: 0.8663 (t80) cc_final: 0.8377 (t80) REVERT: I 298 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8690 (mt) REVERT: J 100 MET cc_start: 0.6505 (mtm) cc_final: 0.6292 (mtm) REVERT: J 155 GLN cc_start: 0.7631 (tt0) cc_final: 0.7328 (tt0) REVERT: J 216 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.6164 (mtp) REVERT: J 222 LYS cc_start: 0.8100 (pttm) cc_final: 0.7846 (mmtt) REVERT: J 299 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8742 (tp) REVERT: J 374 GLN cc_start: 0.7783 (mp10) cc_final: 0.7531 (mp10) REVERT: K 34 LEU cc_start: 0.8430 (mp) cc_final: 0.8214 (mt) REVERT: K 100 MET cc_start: 0.6439 (mtm) cc_final: 0.6159 (mtm) REVERT: K 155 GLN cc_start: 0.7732 (tt0) cc_final: 0.7451 (tt0) REVERT: K 216 MET cc_start: 0.7605 (mmp) cc_final: 0.6174 (mtp) REVERT: K 220 ARG cc_start: 0.6939 (mmm160) cc_final: 0.6514 (tpt170) REVERT: L 150 ILE cc_start: 0.7876 (pp) cc_final: 0.7399 (pt) REVERT: L 216 MET cc_start: 0.7684 (tpp) cc_final: 0.7094 (mtp) REVERT: L 219 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6652 (mmt-90) REVERT: L 237 MET cc_start: 0.8263 (mtt) cc_final: 0.8032 (mpp) REVERT: L 251 TYR cc_start: 0.8643 (t80) cc_final: 0.8321 (t80) REVERT: L 298 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8704 (mt) outliers start: 83 outliers final: 48 residues processed: 603 average time/residue: 1.4563 time to fit residues: 996.1911 Evaluate side-chains 602 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 540 time to evaluate : 2.662 ------------------------------------------------------------------------------- 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 82 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 120 ARG 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 135 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 219 ARG Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE 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 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 441 GLU Chi-restraints excluded: chain K residue 41 THR 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 107 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 288 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 100 optimal weight: 0.0170 chunk 286 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- 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 134 GLN E 8 GLN G 134 GLN H 70 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 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 = 0.3995 r_free = 0.3995 target = 0.168297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128231 restraints weight = 26107.332| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.85 r_work: 0.3303 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3358 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= 0.123 Angle : 0.528 7.522 33014 Z= 0.279 Chirality : 0.042 0.191 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.478 79.146 3472 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.55 % Allowed : 17.85 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.15), residues: 3008 helix: 2.39 (0.12), residues: 1842 sheet: 0.44 (0.29), residues: 298 loop : -0.80 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 267 HIS 0.003 0.001 HIS I 168 PHE 0.034 0.001 PHE I 202 TYR 0.018 0.001 TYR I 270 ARG 0.008 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 1532) hydrogen bonds : angle 3.97022 ( 4413) covalent geometry : bond 0.00268 (24318) covalent geometry : angle 0.52771 (33014) *********************** 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 652 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 561 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7986 (tp30) cc_final: 0.7716 (tp30) REVERT: A 41 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7984 (mptp) REVERT: A 115 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7355 (mtpp) REVERT: B 41 LYS cc_start: 0.7953 (mmtm) cc_final: 0.7363 (mmtt) REVERT: B 62 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7093 (tp30) REVERT: B 65 SER cc_start: 0.7853 (m) cc_final: 0.7647 (p) REVERT: B 69 ARG cc_start: 0.8583 (mtt-85) cc_final: 0.8307 (mtt90) REVERT: B 127 ASP cc_start: 0.8122 (m-30) cc_final: 0.7900 (m-30) REVERT: C 23 LYS cc_start: 0.8579 (mtpm) cc_final: 0.8077 (mttt) REVERT: C 43 ASN cc_start: 0.8606 (m-40) cc_final: 0.8323 (m110) REVERT: C 48 TYR cc_start: 0.8298 (m-80) cc_final: 0.8082 (m-80) REVERT: C 59 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7335 (mm-30) REVERT: C 111 LYS cc_start: 0.8440 (mmpt) cc_final: 0.8153 (mtmt) REVERT: C 128 MET cc_start: 0.8509 (mmm) cc_final: 0.8080 (mmp) REVERT: C 208 MET cc_start: 0.6054 (ttp) cc_final: 0.5852 (ttm) REVERT: D 60 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: D 115 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7986 (mptp) REVERT: D 134 GLN cc_start: 0.8150 (tp40) cc_final: 0.7432 (mp10) REVERT: D 208 MET cc_start: 0.6127 (ptt) cc_final: 0.5874 (ptp) REVERT: E 145 ILE cc_start: 0.6263 (OUTLIER) cc_final: 0.6017 (tt) REVERT: E 208 MET cc_start: 0.5955 (ptt) cc_final: 0.5608 (ptt) REVERT: F 23 LYS cc_start: 0.8581 (mtpm) cc_final: 0.8095 (mttt) REVERT: F 62 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7737 (mt-10) REVERT: F 111 LYS cc_start: 0.8458 (mmpt) cc_final: 0.8225 (mtpt) REVERT: F 128 MET cc_start: 0.8536 (mmm) cc_final: 0.8114 (mmp) REVERT: F 131 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8389 (mttm) REVERT: G 41 LYS cc_start: 0.8060 (mmtm) cc_final: 0.7456 (mmtt) REVERT: G 62 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7227 (tp30) REVERT: G 72 GLU cc_start: 0.7660 (tt0) cc_final: 0.7232 (pt0) REVERT: G 127 ASP cc_start: 0.8174 (m-30) cc_final: 0.7948 (m-30) REVERT: H 41 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7978 (mptp) REVERT: I 110 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7632 (mp0) REVERT: I 150 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7479 (pt) REVERT: I 216 MET cc_start: 0.7718 (tpp) cc_final: 0.7148 (mtp) REVERT: I 219 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6680 (mmt-90) REVERT: I 237 MET cc_start: 0.8227 (mtt) cc_final: 0.8012 (mpp) REVERT: I 251 TYR cc_start: 0.8669 (t80) cc_final: 0.8398 (t80) REVERT: I 298 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8684 (mt) REVERT: J 34 LEU cc_start: 0.8434 (mp) cc_final: 0.8221 (mt) REVERT: J 100 MET cc_start: 0.6538 (mtm) cc_final: 0.6329 (mtm) REVERT: J 155 GLN cc_start: 0.7630 (tt0) cc_final: 0.7301 (tt0) REVERT: J 216 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6173 (mtp) REVERT: J 222 LYS cc_start: 0.8116 (pttm) cc_final: 0.7896 (mmtt) REVERT: J 299 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8744 (tp) REVERT: J 374 GLN cc_start: 0.7722 (mp10) cc_final: 0.7512 (mp10) REVERT: K 34 LEU cc_start: 0.8432 (mp) cc_final: 0.8221 (mt) REVERT: K 100 MET cc_start: 0.6448 (mtm) cc_final: 0.6182 (mtm) REVERT: K 155 GLN cc_start: 0.7679 (tt0) cc_final: 0.7383 (tt0) REVERT: K 216 MET cc_start: 0.7606 (mmp) cc_final: 0.6180 (mtp) REVERT: K 220 ARG cc_start: 0.6934 (mmm160) cc_final: 0.6523 (tpt170) REVERT: K 222 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7656 (mmtt) REVERT: L 110 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7648 (mp0) REVERT: L 150 ILE cc_start: 0.7922 (pp) cc_final: 0.7488 (pt) REVERT: L 216 MET cc_start: 0.7698 (tpp) cc_final: 0.7129 (mtp) REVERT: L 219 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6687 (mmt-90) REVERT: L 237 MET cc_start: 0.8246 (mtt) cc_final: 0.8033 (mpp) REVERT: L 251 TYR cc_start: 0.8643 (t80) cc_final: 0.8337 (t80) REVERT: L 298 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8693 (mt) outliers start: 91 outliers final: 45 residues processed: 615 average time/residue: 1.4053 time to fit residues: 981.6921 Evaluate side-chains 606 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 547 time to evaluate : 2.531 ------------------------------------------------------------------------------- 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 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 135 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 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 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 89 LEU 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 184 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 282 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 295 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 G 134 GLN H 70 ASN H 81 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.167760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127459 restraints weight = 26085.660| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.84 r_work: 0.3293 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3368 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= 0.139 Angle : 0.550 11.077 33014 Z= 0.290 Chirality : 0.043 0.195 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.544 80.352 3472 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.35 % Allowed : 18.67 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.15), residues: 3008 helix: 2.33 (0.12), residues: 1842 sheet: 0.47 (0.29), residues: 302 loop : -0.77 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 47 HIS 0.004 0.001 HIS I 168 PHE 0.035 0.002 PHE I 202 TYR 0.021 0.001 TYR L 270 ARG 0.010 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 1532) hydrogen bonds : angle 4.01081 ( 4413) covalent geometry : bond 0.00312 (24318) covalent geometry : angle 0.55003 (33014) *********************** 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 644 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 558 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8065 (tp30) cc_final: 0.7696 (tp30) REVERT: A 41 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7978 (mptp) REVERT: B 41 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7386 (mmtt) REVERT: B 62 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7223 (tp30) REVERT: B 69 ARG cc_start: 0.8597 (mtt-85) cc_final: 0.8311 (mtt90) REVERT: B 127 ASP cc_start: 0.8123 (m-30) cc_final: 0.7902 (m-30) REVERT: C 24 GLU cc_start: 0.8515 (tp30) cc_final: 0.8012 (tp30) REVERT: C 39 GLU cc_start: 0.8008 (mp0) cc_final: 0.7716 (mp0) REVERT: C 41 LYS cc_start: 0.8235 (mtpp) cc_final: 0.7857 (ttmt) REVERT: C 43 ASN cc_start: 0.8620 (m-40) cc_final: 0.8332 (m110) REVERT: C 48 TYR cc_start: 0.8306 (m-80) cc_final: 0.8090 (m-80) REVERT: C 59 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7302 (mm-30) REVERT: C 111 LYS cc_start: 0.8467 (mmpt) cc_final: 0.8172 (mtmt) REVERT: C 128 MET cc_start: 0.8580 (mmm) cc_final: 0.8196 (mmp) REVERT: D 60 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: D 115 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7947 (mptp) REVERT: D 134 GLN cc_start: 0.8128 (tp40) cc_final: 0.7327 (mp10) REVERT: D 139 GLU cc_start: 0.7146 (pm20) cc_final: 0.6819 (pm20) REVERT: D 208 MET cc_start: 0.6040 (ptt) cc_final: 0.5779 (ptp) REVERT: E 145 ILE cc_start: 0.6262 (OUTLIER) cc_final: 0.6016 (tt) REVERT: E 208 MET cc_start: 0.5966 (ptt) cc_final: 0.5617 (ptt) REVERT: F 23 LYS cc_start: 0.8567 (mtpm) cc_final: 0.8075 (mttt) REVERT: F 59 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7163 (mm-30) REVERT: F 65 SER cc_start: 0.8518 (m) cc_final: 0.8296 (t) REVERT: F 111 LYS cc_start: 0.8480 (mmpt) cc_final: 0.8232 (mtpt) REVERT: F 128 MET cc_start: 0.8562 (mmm) cc_final: 0.8147 (mmp) REVERT: F 131 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8395 (mttm) REVERT: G 41 LYS cc_start: 0.8103 (mmtm) cc_final: 0.7496 (mmtt) REVERT: G 62 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7231 (tp30) REVERT: G 72 GLU cc_start: 0.7666 (tt0) cc_final: 0.7238 (pt0) REVERT: H 41 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7967 (mptp) REVERT: I 110 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7641 (mp0) REVERT: I 150 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7508 (pt) REVERT: I 216 MET cc_start: 0.7730 (tpp) cc_final: 0.7163 (mtp) REVERT: I 219 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6709 (mmt-90) REVERT: I 251 TYR cc_start: 0.8669 (t80) cc_final: 0.8449 (t80) REVERT: I 298 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8707 (mt) REVERT: J 100 MET cc_start: 0.6526 (mtm) cc_final: 0.6313 (mtm) REVERT: J 155 GLN cc_start: 0.7638 (tt0) cc_final: 0.7293 (tt0) REVERT: J 216 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.6165 (mtp) REVERT: J 222 LYS cc_start: 0.8141 (pttm) cc_final: 0.7845 (mmtt) REVERT: J 299 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8761 (tp) REVERT: J 374 GLN cc_start: 0.7722 (mp10) cc_final: 0.7511 (mp10) REVERT: K 34 LEU cc_start: 0.8425 (mp) cc_final: 0.8217 (mt) REVERT: K 100 MET cc_start: 0.6498 (mtm) cc_final: 0.6221 (mtm) REVERT: K 155 GLN cc_start: 0.7692 (tt0) cc_final: 0.7379 (tt0) REVERT: K 216 MET cc_start: 0.7604 (mmp) cc_final: 0.6150 (mtp) REVERT: K 220 ARG cc_start: 0.6965 (mmm160) cc_final: 0.6559 (tpt170) REVERT: L 110 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7663 (mp0) REVERT: L 150 ILE cc_start: 0.7939 (pp) cc_final: 0.7499 (pt) REVERT: L 216 MET cc_start: 0.7708 (tpp) cc_final: 0.7135 (mtp) REVERT: L 219 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6717 (mmt-90) REVERT: L 251 TYR cc_start: 0.8653 (t80) cc_final: 0.8397 (t80) REVERT: L 298 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8713 (mt) REVERT: L 400 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7948 (mm-30) outliers start: 86 outliers final: 47 residues processed: 610 average time/residue: 1.4569 time to fit residues: 1013.4896 Evaluate side-chains 603 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 542 time to evaluate : 2.524 ------------------------------------------------------------------------------- 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 82 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 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 150 ILE Chi-restraints excluded: chain I residue 219 ARG Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 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 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 441 GLU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 41 THR 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 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 L residue 15 THR 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 30 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 101 optimal weight: 0.0770 chunk 296 optimal weight: 0.6980 chunk 235 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 chunk 199 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- 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 134 GLN C 134 GLN F 43 ASN F 134 GLN G 134 GLN H 81 ASN I 18 GLN I 119 ASN I 239 ASN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN K 253 ASN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.166963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.126626 restraints weight = 26144.085| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.85 r_work: 0.3284 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24318 Z= 0.155 Angle : 0.566 9.384 33014 Z= 0.299 Chirality : 0.044 0.201 3998 Planarity : 0.004 0.046 4016 Dihedral : 9.712 81.808 3472 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.08 % Allowed : 19.56 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.15), residues: 3008 helix: 2.27 (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 TRP 0.005 0.001 TRP L 181 HIS 0.004 0.001 HIS L 168 PHE 0.035 0.002 PHE I 202 TYR 0.020 0.001 TYR I 270 ARG 0.009 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 1532) hydrogen bonds : angle 4.05201 ( 4413) covalent geometry : bond 0.00353 (24318) covalent geometry : angle 0.56562 (33014) ********************** 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 623 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 544 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.8346 (ttp80) cc_final: 0.8100 (ttp80) REVERT: A 41 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8004 (mptp) REVERT: B 41 LYS cc_start: 0.7977 (mmtm) cc_final: 0.7425 (mmtt) REVERT: B 62 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7243 (tp30) REVERT: B 69 ARG cc_start: 0.8603 (mtt-85) cc_final: 0.8318 (mtt90) REVERT: B 127 ASP cc_start: 0.8123 (m-30) cc_final: 0.7900 (m-30) REVERT: C 24 GLU cc_start: 0.8494 (tp30) cc_final: 0.8001 (tp30) REVERT: C 48 TYR cc_start: 0.8340 (m-80) cc_final: 0.8113 (m-80) REVERT: C 59 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7284 (mm-30) REVERT: C 111 LYS cc_start: 0.8480 (mmpt) cc_final: 0.8187 (mtmt) REVERT: C 128 MET cc_start: 0.8574 (mmm) cc_final: 0.8174 (mmp) REVERT: D 115 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7943 (mptp) REVERT: D 134 GLN cc_start: 0.8136 (tp40) cc_final: 0.7354 (mp10) REVERT: D 208 MET cc_start: 0.6063 (ptt) cc_final: 0.5799 (ptp) REVERT: E 145 ILE cc_start: 0.6291 (OUTLIER) cc_final: 0.6041 (tt) REVERT: E 208 MET cc_start: 0.5991 (ptt) cc_final: 0.5741 (ptt) REVERT: F 23 LYS cc_start: 0.8563 (mtpm) cc_final: 0.8129 (mttt) REVERT: F 65 SER cc_start: 0.8538 (m) cc_final: 0.8312 (t) REVERT: F 111 LYS cc_start: 0.8500 (mmpt) cc_final: 0.8241 (mtpt) REVERT: F 128 MET cc_start: 0.8588 (mmm) cc_final: 0.8170 (mmp) REVERT: F 131 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8392 (mttm) REVERT: G 41 LYS cc_start: 0.8111 (mmtm) cc_final: 0.7485 (mmtt) REVERT: G 62 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7225 (tp30) REVERT: G 72 GLU cc_start: 0.7661 (tt0) cc_final: 0.7238 (pt0) REVERT: H 41 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7966 (mptp) REVERT: I 110 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7637 (mp0) REVERT: I 150 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7493 (pt) REVERT: I 216 MET cc_start: 0.7738 (tpp) cc_final: 0.7173 (mtp) REVERT: I 219 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6706 (mmt-90) REVERT: I 237 MET cc_start: 0.8246 (mtt) cc_final: 0.8037 (mpp) REVERT: I 251 TYR cc_start: 0.8641 (t80) cc_final: 0.8434 (t80) REVERT: I 298 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8709 (mt) REVERT: J 100 MET cc_start: 0.6581 (mtm) cc_final: 0.6369 (mtm) REVERT: J 155 GLN cc_start: 0.7654 (tt0) cc_final: 0.7300 (tt0) REVERT: J 216 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.6165 (mtp) REVERT: J 222 LYS cc_start: 0.8064 (pttm) cc_final: 0.7801 (mmtt) REVERT: J 299 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8771 (tp) REVERT: J 374 GLN cc_start: 0.7765 (mp10) cc_final: 0.7523 (mp10) REVERT: K 34 LEU cc_start: 0.8429 (mp) cc_final: 0.8212 (mt) REVERT: K 100 MET cc_start: 0.6554 (mtm) cc_final: 0.6267 (mtm) REVERT: K 155 GLN cc_start: 0.7703 (tt0) cc_final: 0.7404 (tt0) REVERT: K 216 MET cc_start: 0.7618 (mmp) cc_final: 0.6161 (mtp) REVERT: K 220 ARG cc_start: 0.6979 (mmm160) cc_final: 0.6548 (tpt170) REVERT: L 110 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7640 (mp0) REVERT: L 150 ILE cc_start: 0.7923 (pp) cc_final: 0.7489 (pt) REVERT: L 216 MET cc_start: 0.7729 (tpp) cc_final: 0.7174 (mtp) REVERT: L 219 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6710 (mmt-90) REVERT: L 251 TYR cc_start: 0.8657 (t80) cc_final: 0.8397 (t80) REVERT: L 298 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8722 (mt) REVERT: L 400 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7979 (mm-30) outliers start: 79 outliers final: 44 residues processed: 591 average time/residue: 1.4146 time to fit residues: 947.5062 Evaluate side-chains 588 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 531 time to evaluate : 2.517 ------------------------------------------------------------------------------- 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 82 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 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 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 150 ILE Chi-restraints excluded: chain I residue 219 ARG Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 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 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 441 GLU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 20 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 196 LEU 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 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 103 optimal weight: 6.9990 chunk 142 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 273 optimal weight: 1.9990 chunk 154 optimal weight: 0.0970 chunk 244 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 F 43 ASN G 134 GLN H 70 ASN H 81 ASN I 18 GLN I 119 ASN I 239 ASN J 85 GLN J 253 ASN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 ASN 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.168600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128772 restraints weight = 25958.855| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.81 r_work: 0.3310 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3483 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= 0.122 Angle : 0.539 9.356 33014 Z= 0.284 Chirality : 0.043 0.190 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.491 81.153 3472 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.38 % Allowed : 20.27 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.15), residues: 3008 helix: 2.34 (0.12), residues: 1832 sheet: 0.37 (0.29), residues: 302 loop : -0.74 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 267 HIS 0.003 0.001 HIS I 168 PHE 0.035 0.002 PHE I 202 TYR 0.021 0.001 TYR L 270 ARG 0.008 0.001 ARG E 27 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 1532) hydrogen bonds : angle 4.01271 ( 4413) covalent geometry : bond 0.00264 (24318) covalent geometry : angle 0.53943 (33014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26675.20 seconds wall clock time: 459 minutes 26.66 seconds (27566.66 seconds total)