Starting phenix.real_space_refine on Fri Jun 20 10:26:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1t_36803/06_2025/8k1t_36803.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1t_36803/06_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_36803/06_2025/8k1t_36803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1t_36803/06_2025/8k1t_36803.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1t_36803/06_2025/8k1t_36803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1t_36803/06_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-5710/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: 18.74, per 1000 atoms: 0.79 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: 8.74 Conformation dependent library (CDL) restraints added in 4.9 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: 3.04 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: 11.17 Time building geometry restraints manager: 7.65 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: 41.700 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: 0.060 Extract box with map and model: 20.470 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 63.890 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.160 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:87.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 215.300 ------------------------------------------------------------------------------- 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 : 2.464 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: 1.5112 time to fit residues: 1445.1529 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 : 2.394 ------------------------------------------------------------------------------- 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 = 0.168332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128137 restraints weight = 26051.982| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.83 r_work: 0.3306 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24318 Z= 0.151 Angle : 0.573 9.526 33014 Z= 0.304 Chirality : 0.043 0.184 3998 Planarity : 0.004 0.044 4016 Dihedral : 10.126 84.232 3474 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.66 % Allowed : 13.29 % Favored : 83.05 % 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: 1.96 (0.15), residues: 3008 helix: 2.21 (0.12), residues: 1840 sheet: 1.14 (0.28), residues: 322 loop : -0.71 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 47 HIS 0.003 0.001 HIS I 168 PHE 0.034 0.002 PHE L 202 TYR 0.015 0.001 TYR I 270 ARG 0.008 0.001 ARG E 27 Details of bonding type rmsd hydrogen bonds : bond 0.05123 ( 1532) hydrogen bonds : angle 4.41675 ( 4413) covalent geometry : bond 0.00326 (24318) covalent geometry : angle 0.57318 (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 698 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 604 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7993 (tp30) cc_final: 0.7639 (tp30) REVERT: A 115 LYS cc_start: 0.7662 (mmtm) cc_final: 0.7382 (mttm) REVERT: C 39 GLU cc_start: 0.7963 (mp0) cc_final: 0.7763 (mp0) REVERT: C 48 TYR cc_start: 0.8342 (m-80) cc_final: 0.7968 (m-80) REVERT: C 56 ASN cc_start: 0.8693 (t0) cc_final: 0.8383 (t0) REVERT: C 59 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7055 (mt-10) REVERT: C 62 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7101 (mt-10) REVERT: C 111 LYS cc_start: 0.8524 (mmpt) cc_final: 0.8222 (mtpt) REVERT: C 128 MET cc_start: 0.8594 (mmm) cc_final: 0.8192 (mmp) REVERT: D 126 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8299 (ttmt) REVERT: D 134 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7823 (mm110) REVERT: E 138 ASP cc_start: 0.7370 (t70) cc_final: 0.6577 (m-30) REVERT: F 59 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7150 (mt-10) REVERT: F 62 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6942 (mt-10) REVERT: F 111 LYS cc_start: 0.8479 (mmpt) cc_final: 0.8212 (mtpt) REVERT: F 128 MET cc_start: 0.8604 (mmm) cc_final: 0.8224 (mmp) REVERT: F 131 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8374 (mttm) REVERT: H 115 LYS cc_start: 0.7783 (mmtm) cc_final: 0.7580 (mmmm) REVERT: I 110 GLU cc_start: 0.7541 (mt-10) cc_final: 0.6821 (mp0) REVERT: I 123 ILE cc_start: 0.7825 (pt) cc_final: 0.7531 (pt) REVERT: I 140 ILE cc_start: 0.8349 (tt) cc_final: 0.8146 (tt) REVERT: I 251 TYR cc_start: 0.8626 (t80) cc_final: 0.8220 (t80) REVERT: I 298 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8714 (mt) REVERT: I 340 ARG cc_start: 0.8465 (mtt180) cc_final: 0.7892 (mtt-85) REVERT: J 97 LEU cc_start: 0.7260 (mt) cc_final: 0.7004 (tp) REVERT: J 100 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5729 (mmm) REVERT: J 106 ILE cc_start: 0.7410 (mp) cc_final: 0.7134 (mm) REVERT: J 136 PHE cc_start: 0.7674 (t80) cc_final: 0.7395 (t80) REVERT: J 155 GLN cc_start: 0.7593 (tt0) cc_final: 0.7151 (tt0) REVERT: J 156 TYR cc_start: 0.7547 (m-80) cc_final: 0.7328 (m-80) REVERT: J 216 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.6132 (mtp) REVERT: J 222 LYS cc_start: 0.8098 (pttm) cc_final: 0.7868 (mmtt) REVERT: J 299 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8721 (tp) REVERT: J 344 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.8035 (mmtm) REVERT: K 97 LEU cc_start: 0.7305 (mt) cc_final: 0.6993 (tp) REVERT: K 100 MET cc_start: 0.6349 (mtm) cc_final: 0.6025 (mtm) REVERT: K 155 GLN cc_start: 0.7574 (tt0) cc_final: 0.7156 (tt0) REVERT: K 216 MET cc_start: 0.7456 (mmp) cc_final: 0.6128 (mtp) REVERT: K 250 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8593 (mm-30) REVERT: K 253 ASN cc_start: 0.8395 (t0) cc_final: 0.8156 (t160) REVERT: K 344 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8073 (mmtm) REVERT: L 110 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6805 (mp0) REVERT: L 123 ILE cc_start: 0.7805 (pt) cc_final: 0.7513 (pt) REVERT: L 251 TYR cc_start: 0.8590 (t80) cc_final: 0.8163 (t80) REVERT: L 298 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8671 (mt) REVERT: L 340 ARG cc_start: 0.8500 (mtt180) cc_final: 0.7881 (mtt-85) REVERT: L 373 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6503 (mt-10) REVERT: L 439 ASP cc_start: 0.8217 (m-30) cc_final: 0.8000 (m-30) outliers start: 94 outliers final: 34 residues processed: 658 average time/residue: 1.4925 time to fit residues: 1118.8467 Evaluate side-chains 601 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 557 time to evaluate : 2.375 ------------------------------------------------------------------------------- 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 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 150 ILE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain 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 J residue 344 LYS Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 344 LYS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 373 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 269 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 293 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 283 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.168725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.128531 restraints weight = 25944.552| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.84 r_work: 0.3315 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2740 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= 0.128 Angle : 0.526 7.552 33014 Z= 0.276 Chirality : 0.042 0.182 3998 Planarity : 0.004 0.044 4016 Dihedral : 9.586 77.960 3474 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.86 % Allowed : 14.38 % Favored : 81.76 % 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: 2.11 (0.15), residues: 3008 helix: 2.43 (0.12), residues: 1838 sheet: 0.83 (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 0.009 0.001 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 1532) hydrogen bonds : angle 4.15485 ( 4413) covalent geometry : bond 0.00276 (24318) covalent geometry : angle 0.52644 (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 684 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 585 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8024 (tp30) cc_final: 0.7690 (tp30) REVERT: A 89 THR cc_start: 0.8627 (t) cc_final: 0.8364 (p) REVERT: A 115 LYS cc_start: 0.7689 (mmtm) cc_final: 0.7447 (mttm) REVERT: B 127 ASP cc_start: 0.8124 (m-30) cc_final: 0.7909 (m-30) REVERT: C 23 LYS cc_start: 0.8618 (mtpm) cc_final: 0.8044 (mtmt) REVERT: C 24 GLU cc_start: 0.8479 (tp30) cc_final: 0.7960 (tp30) REVERT: C 48 TYR cc_start: 0.8343 (m-80) cc_final: 0.8004 (m-80) REVERT: C 56 ASN cc_start: 0.8657 (t0) cc_final: 0.8297 (t0) REVERT: C 59 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7047 (mt-10) REVERT: C 62 GLU cc_start: 0.7684 (mt-10) cc_final: 0.6983 (mt-10) REVERT: C 105 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: C 128 MET cc_start: 0.8517 (mmm) cc_final: 0.8100 (mmp) REVERT: D 115 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7957 (mptp) REVERT: D 134 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7396 (mp10) REVERT: E 134 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7912 (mm110) REVERT: E 138 ASP cc_start: 0.7182 (t70) cc_final: 0.6403 (m-30) REVERT: E 145 ILE cc_start: 0.6248 (OUTLIER) cc_final: 0.5953 (tt) REVERT: E 208 MET cc_start: 0.5782 (ptt) cc_final: 0.5375 (ptt) REVERT: F 23 LYS cc_start: 0.8639 (mtpm) cc_final: 0.8080 (mtmt) REVERT: F 56 ASN cc_start: 0.8600 (t0) cc_final: 0.8394 (t0) REVERT: F 111 LYS cc_start: 0.8457 (mmpt) cc_final: 0.8180 (mtpt) REVERT: F 128 MET cc_start: 0.8585 (mmm) cc_final: 0.8199 (mmp) REVERT: F 131 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8389 (mttm) REVERT: F 181 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6628 (mp) REVERT: G 127 ASP cc_start: 0.8264 (m-30) cc_final: 0.8062 (m-30) REVERT: H 89 THR cc_start: 0.8612 (t) cc_final: 0.8373 (p) REVERT: H 115 LYS cc_start: 0.7716 (mmtm) cc_final: 0.7469 (mttm) REVERT: I 106 ILE cc_start: 0.7977 (mm) cc_final: 0.7769 (mm) REVERT: I 110 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7182 (mp0) REVERT: I 123 ILE cc_start: 0.7715 (pt) cc_final: 0.7515 (pt) REVERT: I 140 ILE cc_start: 0.8389 (tt) cc_final: 0.8151 (tt) REVERT: I 150 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7674 (mp) REVERT: I 251 TYR cc_start: 0.8653 (t80) cc_final: 0.8289 (t80) REVERT: I 298 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8705 (mt) REVERT: I 340 ARG cc_start: 0.8439 (mtt180) cc_final: 0.7854 (mtt-85) REVERT: J 97 LEU cc_start: 0.7242 (mt) cc_final: 0.7012 (tp) REVERT: J 106 ILE cc_start: 0.7410 (mp) cc_final: 0.7048 (mm) REVERT: J 155 GLN cc_start: 0.7596 (tt0) cc_final: 0.7126 (tt0) REVERT: J 156 TYR cc_start: 0.7525 (m-80) cc_final: 0.7257 (m-80) REVERT: J 216 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.6147 (mtp) REVERT: J 222 LYS cc_start: 0.8077 (pttm) cc_final: 0.7871 (mmtt) REVERT: J 299 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8711 (tp) REVERT: J 374 GLN cc_start: 0.7817 (mp10) cc_final: 0.7563 (mp10) REVERT: K 97 LEU cc_start: 0.7392 (mt) cc_final: 0.7124 (tp) REVERT: K 100 MET cc_start: 0.6382 (mtm) cc_final: 0.6140 (mtm) REVERT: K 155 GLN cc_start: 0.7683 (tt0) cc_final: 0.7325 (tt0) REVERT: K 216 MET cc_start: 0.7523 (mmp) cc_final: 0.6140 (mtp) REVERT: K 220 ARG cc_start: 0.6317 (tpt170) cc_final: 0.5926 (tpt170) REVERT: K 222 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7858 (mmtt) REVERT: K 253 ASN cc_start: 0.8356 (t0) cc_final: 0.8123 (t160) REVERT: L 110 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7255 (mp0) REVERT: L 150 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7643 (mp) REVERT: L 251 TYR cc_start: 0.8619 (t80) cc_final: 0.8216 (t80) REVERT: L 298 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8672 (mt) REVERT: L 373 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6520 (mt-10) outliers start: 99 outliers final: 34 residues processed: 645 average time/residue: 1.4462 time to fit residues: 1063.7988 Evaluate side-chains 589 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 543 time to evaluate : 2.605 ------------------------------------------------------------------------------- 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 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 150 ILE Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 373 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 2 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 208 optimal weight: 0.7980 chunk 11 optimal weight: 0.0270 chunk 275 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 G 8 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 239 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.169282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129206 restraints weight = 26128.017| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.87 r_work: 0.3322 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24318 Z= 0.118 Angle : 0.511 7.630 33014 Z= 0.269 Chirality : 0.042 0.183 3998 Planarity : 0.004 0.046 4016 Dihedral : 9.422 77.108 3474 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.17 % Allowed : 14.85 % Favored : 80.98 % 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: 2.13 (0.15), residues: 3008 helix: 2.50 (0.12), residues: 1838 sheet: 0.66 (0.28), residues: 314 loop : -0.75 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 47 HIS 0.003 0.001 HIS I 168 PHE 0.035 0.001 PHE I 202 TYR 0.019 0.001 TYR I 270 ARG 0.009 0.001 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 1532) hydrogen bonds : angle 4.01050 ( 4413) covalent geometry : bond 0.00253 (24318) covalent geometry : angle 0.51099 (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 690 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 583 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8056 (tp30) cc_final: 0.7732 (tp30) REVERT: A 41 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7998 (mptp) REVERT: A 89 THR cc_start: 0.8607 (t) cc_final: 0.8385 (m) REVERT: A 115 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7364 (mptt) REVERT: B 62 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7198 (tp30) REVERT: B 127 ASP cc_start: 0.8133 (m-30) cc_final: 0.7931 (m-30) REVERT: C 23 LYS cc_start: 0.8586 (mtpm) cc_final: 0.8041 (mtmt) REVERT: C 24 GLU cc_start: 0.8414 (tp30) cc_final: 0.7777 (tp30) REVERT: C 48 TYR cc_start: 0.8358 (m-80) cc_final: 0.8074 (m-80) REVERT: C 56 ASN cc_start: 0.8626 (t0) cc_final: 0.8279 (t0) REVERT: C 62 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7511 (mt-10) REVERT: C 105 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: C 111 LYS cc_start: 0.8449 (mmpt) cc_final: 0.8196 (mtmt) REVERT: C 128 MET cc_start: 0.8515 (mmm) cc_final: 0.8092 (mmp) REVERT: C 208 MET cc_start: 0.6206 (ttp) cc_final: 0.5943 (ttm) REVERT: D 60 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: D 134 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7340 (mp10) REVERT: E 138 ASP cc_start: 0.7142 (t70) cc_final: 0.6389 (m-30) REVERT: E 145 ILE cc_start: 0.6221 (OUTLIER) cc_final: 0.5947 (tt) REVERT: E 208 MET cc_start: 0.5820 (ptt) cc_final: 0.5423 (ptt) REVERT: F 23 LYS cc_start: 0.8614 (mtpm) cc_final: 0.8151 (mttt) REVERT: F 62 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7377 (mt-10) REVERT: F 105 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: F 111 LYS cc_start: 0.8446 (mmpt) cc_final: 0.8177 (mtmt) REVERT: F 128 MET cc_start: 0.8578 (mmm) cc_final: 0.8210 (mmp) REVERT: F 181 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6743 (mp) REVERT: F 208 MET cc_start: 0.5958 (ttp) cc_final: 0.5736 (ttm) REVERT: G 41 LYS cc_start: 0.7923 (mmtm) cc_final: 0.7227 (mmtt) REVERT: G 62 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7058 (tp30) REVERT: G 72 GLU cc_start: 0.7731 (tt0) cc_final: 0.7371 (pt0) REVERT: H 89 THR cc_start: 0.8599 (t) cc_final: 0.8389 (m) REVERT: H 115 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7452 (mtpm) REVERT: I 110 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7307 (mp0) REVERT: I 140 ILE cc_start: 0.8393 (tt) cc_final: 0.8165 (tt) REVERT: I 150 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7381 (mp) REVERT: I 251 TYR cc_start: 0.8659 (t80) cc_final: 0.8339 (t80) REVERT: I 298 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8708 (mt) REVERT: J 97 LEU cc_start: 0.7353 (mt) cc_final: 0.7082 (tp) REVERT: J 100 MET cc_start: 0.6145 (mtm) cc_final: 0.5899 (mmm) REVERT: J 106 ILE cc_start: 0.7567 (mp) cc_final: 0.7237 (mm) REVERT: J 155 GLN cc_start: 0.7600 (tt0) cc_final: 0.7145 (tt0) REVERT: J 156 TYR cc_start: 0.7495 (m-80) cc_final: 0.7212 (m-80) REVERT: J 216 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6088 (mtp) REVERT: J 222 LYS cc_start: 0.8076 (pttm) cc_final: 0.7854 (mmtt) REVERT: J 299 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8731 (tp) REVERT: K 97 LEU cc_start: 0.7309 (mt) cc_final: 0.7075 (tp) REVERT: K 100 MET cc_start: 0.6430 (mtm) cc_final: 0.6191 (mtm) REVERT: K 155 GLN cc_start: 0.7710 (tt0) cc_final: 0.7369 (tt0) REVERT: K 156 TYR cc_start: 0.7540 (m-80) cc_final: 0.7324 (m-80) REVERT: K 216 MET cc_start: 0.7545 (mmp) cc_final: 0.6155 (mtp) REVERT: K 220 ARG cc_start: 0.6316 (tpt170) cc_final: 0.5989 (tpt170) REVERT: K 222 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7826 (mmtt) REVERT: L 110 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7344 (mp0) REVERT: L 150 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7369 (mp) REVERT: L 251 TYR cc_start: 0.8640 (t80) cc_final: 0.8259 (t80) REVERT: L 298 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8701 (mt) REVERT: L 373 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6462 (mt-10) outliers start: 107 outliers final: 38 residues processed: 645 average time/residue: 1.4158 time to fit residues: 1042.4450 Evaluate side-chains 611 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 558 time to evaluate : 2.649 ------------------------------------------------------------------------------- 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 114 GLU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 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 105 GLN Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain H residue 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 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 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 138 ILE Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 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 Chi-restraints excluded: chain L residue 373 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 234 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 198 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 82 optimal weight: 0.0970 chunk 120 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 G 134 GLN H 70 ASN I 18 GLN I 119 ASN I 239 ASN J 85 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.166615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.126451 restraints weight = 26264.421| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.84 r_work: 0.3275 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24318 Z= 0.172 Angle : 0.561 8.608 33014 Z= 0.296 Chirality : 0.044 0.201 3998 Planarity : 0.004 0.048 4016 Dihedral : 9.784 78.742 3474 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.64 % Allowed : 14.77 % Favored : 80.59 % 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: 2.35 (0.12), residues: 1838 sheet: 0.69 (0.29), residues: 302 loop : -0.79 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 47 HIS 0.005 0.001 HIS L 168 PHE 0.036 0.002 PHE L 202 TYR 0.017 0.001 TYR L 270 ARG 0.009 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 1532) hydrogen bonds : angle 4.06499 ( 4413) covalent geometry : bond 0.00399 (24318) covalent geometry : angle 0.56108 (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 685 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 566 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8044 (tp30) cc_final: 0.7639 (tp30) REVERT: A 41 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8013 (mptp) REVERT: B 62 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7197 (tp30) REVERT: B 127 ASP cc_start: 0.8126 (m-30) cc_final: 0.7901 (m-30) REVERT: C 23 LYS cc_start: 0.8593 (mtpm) cc_final: 0.8132 (mttt) REVERT: C 24 GLU cc_start: 0.8382 (tp30) cc_final: 0.8151 (tp30) REVERT: C 48 TYR cc_start: 0.8361 (m-80) cc_final: 0.8109 (m-80) REVERT: C 56 ASN cc_start: 0.8639 (t0) cc_final: 0.8317 (t0) REVERT: C 62 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7679 (mt-10) REVERT: C 111 LYS cc_start: 0.8519 (mmpt) cc_final: 0.8248 (mtmt) REVERT: C 128 MET cc_start: 0.8610 (mmm) cc_final: 0.8215 (mmp) REVERT: C 208 MET cc_start: 0.6162 (ttp) cc_final: 0.5839 (ttm) REVERT: D 60 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: D 115 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7963 (mptp) REVERT: E 138 ASP cc_start: 0.7163 (t70) cc_final: 0.6415 (m-30) REVERT: E 145 ILE cc_start: 0.6276 (OUTLIER) cc_final: 0.5996 (tt) REVERT: E 208 MET cc_start: 0.5845 (ptt) cc_final: 0.5445 (ptt) REVERT: F 23 LYS cc_start: 0.8588 (mtpm) cc_final: 0.8124 (mttt) REVERT: F 59 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7207 (mm-30) REVERT: F 111 LYS cc_start: 0.8489 (mmpt) cc_final: 0.8257 (mtpt) REVERT: F 128 MET cc_start: 0.8620 (mmm) cc_final: 0.8216 (mmp) REVERT: F 131 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8388 (mttm) REVERT: G 62 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7146 (tp30) REVERT: G 72 GLU cc_start: 0.7731 (tt0) cc_final: 0.7319 (pt0) REVERT: H 41 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7990 (mptp) REVERT: H 115 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7484 (mttm) REVERT: I 110 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7292 (mp0) REVERT: I 150 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7476 (pt) REVERT: I 251 TYR cc_start: 0.8648 (t80) cc_final: 0.8348 (t80) REVERT: I 266 LEU cc_start: 0.8448 (mt) cc_final: 0.8210 (mt) REVERT: I 298 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8702 (mt) REVERT: J 155 GLN cc_start: 0.7625 (tt0) cc_final: 0.7366 (tt0) REVERT: J 216 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.6190 (mtp) REVERT: J 222 LYS cc_start: 0.8121 (pttm) cc_final: 0.7850 (mmtt) REVERT: J 299 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8765 (tp) REVERT: K 97 LEU cc_start: 0.7338 (mt) cc_final: 0.7075 (tp) REVERT: K 100 MET cc_start: 0.6458 (mtm) cc_final: 0.6184 (mtm) REVERT: K 155 GLN cc_start: 0.7689 (tt0) cc_final: 0.7431 (tt0) REVERT: K 216 MET cc_start: 0.7569 (mmp) cc_final: 0.6161 (mtp) REVERT: L 110 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7346 (mp0) REVERT: L 116 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7219 (tt0) REVERT: L 150 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7463 (pt) REVERT: L 251 TYR cc_start: 0.8635 (t80) cc_final: 0.8291 (t80) REVERT: L 266 LEU cc_start: 0.8458 (mt) cc_final: 0.8221 (mt) REVERT: L 298 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8711 (mt) REVERT: L 373 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6493 (mt-10) outliers start: 119 outliers final: 46 residues processed: 633 average time/residue: 1.3994 time to fit residues: 1010.0174 Evaluate side-chains 611 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 550 time to evaluate : 2.646 ------------------------------------------------------------------------------- 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 114 GLU 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 63 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 G residue 47 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 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 150 ILE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 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 338 ILE Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 165 SER 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 116 GLU Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 373 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 199 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 270 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 284 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 F 134 GLN G 134 GLN H 70 ASN I 18 GLN I 119 ASN I 239 ASN J 85 GLN J 115 GLN J 253 ASN K 85 GLN K 115 GLN K 253 ASN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.166421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126189 restraints weight = 25898.148| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.84 r_work: 0.3279 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24318 Z= 0.166 Angle : 0.558 7.894 33014 Z= 0.295 Chirality : 0.043 0.202 3998 Planarity : 0.004 0.046 4016 Dihedral : 9.811 80.050 3472 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.13 % Allowed : 16.25 % Favored : 79.62 % 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: 1.91 (0.15), residues: 3008 helix: 2.30 (0.12), residues: 1838 sheet: 0.62 (0.29), residues: 302 loop : -0.79 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 47 HIS 0.004 0.001 HIS I 168 PHE 0.037 0.002 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 0.04335 ( 1532) hydrogen bonds : angle 4.06466 ( 4413) covalent geometry : bond 0.00383 (24318) covalent geometry : angle 0.55842 (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 661 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 555 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8029 (tp30) cc_final: 0.7635 (tp30) REVERT: A 41 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8003 (mptp) REVERT: B 62 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7063 (tp30) REVERT: B 127 ASP cc_start: 0.8130 (m-30) cc_final: 0.7910 (m-30) REVERT: C 23 LYS cc_start: 0.8581 (mtpm) cc_final: 0.8098 (mttt) REVERT: C 24 GLU cc_start: 0.8259 (tp30) cc_final: 0.8028 (tm-30) REVERT: C 43 ASN cc_start: 0.8573 (m110) cc_final: 0.8300 (m110) REVERT: C 48 TYR cc_start: 0.8352 (m-80) cc_final: 0.8122 (m-80) REVERT: C 56 ASN cc_start: 0.8621 (t0) cc_final: 0.8299 (t0) REVERT: C 59 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7312 (mm-30) REVERT: C 62 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7702 (mt-10) REVERT: C 111 LYS cc_start: 0.8507 (mmpt) cc_final: 0.8223 (mtmt) REVERT: C 128 MET cc_start: 0.8608 (mmm) cc_final: 0.8208 (mmp) REVERT: C 208 MET cc_start: 0.6135 (ttp) cc_final: 0.5898 (ttm) REVERT: D 60 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: D 115 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7944 (mptp) REVERT: D 134 GLN cc_start: 0.8132 (tp40) cc_final: 0.7608 (mm110) REVERT: D 139 GLU cc_start: 0.7245 (pm20) cc_final: 0.6927 (pm20) REVERT: D 208 MET cc_start: 0.6092 (ptt) cc_final: 0.5799 (ptp) REVERT: E 145 ILE cc_start: 0.6351 (OUTLIER) cc_final: 0.6058 (tt) REVERT: E 208 MET cc_start: 0.5825 (ptt) cc_final: 0.5438 (ptt) REVERT: F 23 LYS cc_start: 0.8580 (mtpm) cc_final: 0.8111 (mttt) REVERT: F 62 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7763 (mt-10) REVERT: F 111 LYS cc_start: 0.8483 (mmpt) cc_final: 0.8248 (mtpt) REVERT: F 128 MET cc_start: 0.8588 (mmm) cc_final: 0.8182 (mmp) REVERT: F 131 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8387 (mttm) REVERT: G 62 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7162 (tp30) REVERT: G 64 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8202 (mm) REVERT: G 72 GLU cc_start: 0.7715 (tt0) cc_final: 0.7276 (pt0) REVERT: G 127 ASP cc_start: 0.8119 (m-30) cc_final: 0.7890 (m-30) REVERT: H 41 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8007 (mptp) REVERT: I 150 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7410 (pt) REVERT: I 219 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6594 (mmt-90) REVERT: I 237 MET cc_start: 0.8260 (mtt) cc_final: 0.8034 (mpp) REVERT: I 251 TYR cc_start: 0.8629 (t80) cc_final: 0.8316 (t80) REVERT: I 298 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8681 (mt) REVERT: J 155 GLN cc_start: 0.7642 (tt0) cc_final: 0.7356 (tt0) REVERT: J 216 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.6171 (mtp) REVERT: J 222 LYS cc_start: 0.8101 (pttm) cc_final: 0.7832 (mmtt) REVERT: J 299 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8758 (tp) REVERT: K 97 LEU cc_start: 0.7360 (mt) cc_final: 0.7123 (tp) REVERT: K 100 MET cc_start: 0.6483 (mtm) cc_final: 0.6201 (mtm) REVERT: K 155 GLN cc_start: 0.7711 (tt0) cc_final: 0.7443 (tt0) REVERT: K 216 MET cc_start: 0.7615 (mmp) cc_final: 0.6230 (mtp) REVERT: K 220 ARG cc_start: 0.6384 (tpt170) cc_final: 0.6071 (tpt170) REVERT: K 222 LYS cc_start: 0.8292 (mmtt) cc_final: 0.8001 (mmtt) REVERT: L 89 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8303 (mp) REVERT: L 150 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7415 (pt) REVERT: L 219 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6607 (mmt-90) REVERT: L 237 MET cc_start: 0.8233 (mtt) cc_final: 0.8011 (mpp) REVERT: L 251 TYR cc_start: 0.8630 (t80) cc_final: 0.8293 (t80) REVERT: L 266 LEU cc_start: 0.8457 (mt) cc_final: 0.8222 (mt) REVERT: L 298 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8677 (mt) REVERT: L 373 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6547 (mt-10) outliers start: 106 outliers final: 51 residues processed: 624 average time/residue: 1.4518 time to fit residues: 1037.1778 Evaluate side-chains 609 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 541 time to evaluate : 2.469 ------------------------------------------------------------------------------- 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 82 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain 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 F residue 181 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 64 LEU 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 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 86 ILE Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 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 74 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 219 ARG Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 373 GLU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 105 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 249 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 165 optimal weight: 0.2980 chunk 3 optimal weight: 0.0570 chunk 142 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 211 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 258 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 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 85 GLN K 115 GLN K 253 ASN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.168995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129290 restraints weight = 26111.418| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.81 r_work: 0.3318 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24318 Z= 0.114 Angle : 0.518 7.634 33014 Z= 0.272 Chirality : 0.042 0.183 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.425 77.897 3472 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.20 % Allowed : 17.73 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.04 (0.15), residues: 3008 helix: 2.45 (0.12), residues: 1838 sheet: 0.53 (0.29), residues: 306 loop : -0.79 (0.20), residues: 864 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 0.001 PHE I 202 TYR 0.020 0.001 TYR E 107 ARG 0.007 0.001 ARG D 27 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 1532) hydrogen bonds : angle 3.96252 ( 4413) covalent geometry : bond 0.00241 (24318) covalent geometry : angle 0.51796 (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 651 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 569 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8015 (tp30) cc_final: 0.7722 (tp30) REVERT: A 41 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7997 (mptp) REVERT: B 31 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 62 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7102 (tp30) REVERT: B 127 ASP cc_start: 0.8085 (m-30) cc_final: 0.7875 (m-30) REVERT: C 23 LYS cc_start: 0.8620 (mtpm) cc_final: 0.8152 (mttt) REVERT: C 24 GLU cc_start: 0.8267 (tp30) cc_final: 0.8048 (tm-30) REVERT: C 39 GLU cc_start: 0.7855 (mp0) cc_final: 0.7635 (mp0) REVERT: C 43 ASN cc_start: 0.8570 (m110) cc_final: 0.8229 (m110) REVERT: C 48 TYR cc_start: 0.8280 (m-80) cc_final: 0.8059 (m-80) REVERT: C 105 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: C 111 LYS cc_start: 0.8446 (mmpt) cc_final: 0.8181 (mtmt) REVERT: C 128 MET cc_start: 0.8487 (mmm) cc_final: 0.8069 (mmp) REVERT: D 60 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: D 115 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7970 (mptp) REVERT: D 134 GLN cc_start: 0.8095 (tp40) cc_final: 0.7589 (mm110) REVERT: E 145 ILE cc_start: 0.6338 (OUTLIER) cc_final: 0.6040 (tt) REVERT: E 208 MET cc_start: 0.5859 (ptt) cc_final: 0.5476 (ptt) REVERT: F 23 LYS cc_start: 0.8582 (mtpm) cc_final: 0.8118 (mttt) REVERT: F 59 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7133 (mm-30) REVERT: F 111 LYS cc_start: 0.8384 (mmpt) cc_final: 0.8173 (mtpt) REVERT: F 128 MET cc_start: 0.8508 (mmm) cc_final: 0.8126 (mmp) REVERT: G 31 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7689 (mt-10) REVERT: G 62 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7122 (tp30) REVERT: G 72 GLU cc_start: 0.7635 (tt0) cc_final: 0.7242 (pt0) REVERT: G 127 ASP cc_start: 0.8120 (m-30) cc_final: 0.7913 (m-30) REVERT: H 41 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7972 (mptp) REVERT: I 150 ILE cc_start: 0.7893 (pp) cc_final: 0.7401 (pt) REVERT: I 216 MET cc_start: 0.7742 (tpp) cc_final: 0.7130 (mtp) REVERT: I 219 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6682 (mmt-90) REVERT: I 237 MET cc_start: 0.8231 (mtt) cc_final: 0.8022 (mpp) REVERT: I 251 TYR cc_start: 0.8657 (t80) cc_final: 0.8385 (t80) REVERT: I 298 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8688 (mt) REVERT: J 155 GLN cc_start: 0.7648 (tt0) cc_final: 0.7353 (tt0) REVERT: J 216 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.6157 (mtp) REVERT: J 222 LYS cc_start: 0.8102 (pttm) cc_final: 0.7870 (mmtt) REVERT: J 374 GLN cc_start: 0.7731 (mp10) cc_final: 0.7521 (mp10) REVERT: K 34 LEU cc_start: 0.8466 (mp) cc_final: 0.8254 (mt) REVERT: K 100 MET cc_start: 0.6444 (mtm) cc_final: 0.6171 (mtm) REVERT: K 155 GLN cc_start: 0.7718 (tt0) cc_final: 0.7432 (tt0) REVERT: K 216 MET cc_start: 0.7642 (mmp) cc_final: 0.6223 (mtp) REVERT: L 116 GLU cc_start: 0.7512 (tp30) cc_final: 0.7205 (tt0) REVERT: L 150 ILE cc_start: 0.7884 (pp) cc_final: 0.7389 (pt) REVERT: L 216 MET cc_start: 0.7722 (tpp) cc_final: 0.7147 (mtp) REVERT: L 219 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6668 (mmt-90) REVERT: L 251 TYR cc_start: 0.8635 (t80) cc_final: 0.8330 (t80) REVERT: L 298 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8689 (mt) REVERT: L 373 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6466 (mt-10) outliers start: 82 outliers final: 37 residues processed: 619 average time/residue: 1.4587 time to fit residues: 1025.7246 Evaluate side-chains 598 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 549 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 219 ARG Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 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 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 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 373 GLU Chi-restraints excluded: chain L residue 421 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 107 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 288 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 286 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.166105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125538 restraints weight = 26072.907| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.87 r_work: 0.3268 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24318 Z= 0.180 Angle : 0.581 7.939 33014 Z= 0.307 Chirality : 0.044 0.207 3998 Planarity : 0.004 0.046 4016 Dihedral : 9.826 81.194 3472 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.09 % Allowed : 17.69 % Favored : 78.22 % 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: 2.28 (0.12), residues: 1840 sheet: 0.51 (0.29), residues: 302 loop : -0.82 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 47 HIS 0.005 0.001 HIS I 168 PHE 0.036 0.002 PHE I 202 TYR 0.022 0.002 TYR J 345 ARG 0.010 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 1532) hydrogen bonds : angle 4.07634 ( 4413) covalent geometry : bond 0.00419 (24318) covalent geometry : angle 0.58138 (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 654 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 549 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8052 (tp30) cc_final: 0.7697 (tp30) REVERT: A 41 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8013 (mptp) REVERT: A 63 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8042 (mp) REVERT: B 62 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7211 (tp30) REVERT: B 127 ASP cc_start: 0.8153 (m-30) cc_final: 0.7923 (m-30) REVERT: C 23 LYS cc_start: 0.8579 (mtpm) cc_final: 0.8103 (mttt) REVERT: C 24 GLU cc_start: 0.8281 (tp30) cc_final: 0.8056 (tm-30) REVERT: C 39 GLU cc_start: 0.7882 (mp0) cc_final: 0.7607 (mp0) REVERT: C 43 ASN cc_start: 0.8668 (m110) cc_final: 0.8326 (m110) REVERT: C 48 TYR cc_start: 0.8353 (m-80) cc_final: 0.8151 (m-80) REVERT: C 59 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7340 (mm-30) REVERT: C 111 LYS cc_start: 0.8515 (mmpt) cc_final: 0.8217 (mtmt) REVERT: C 128 MET cc_start: 0.8600 (mmm) cc_final: 0.8207 (mmp) REVERT: D 60 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: D 115 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7951 (mptp) REVERT: D 134 GLN cc_start: 0.8142 (tp40) cc_final: 0.7623 (mm110) REVERT: D 208 MET cc_start: 0.6108 (ptt) cc_final: 0.5820 (ptp) REVERT: E 145 ILE cc_start: 0.6386 (OUTLIER) cc_final: 0.6096 (tt) REVERT: E 208 MET cc_start: 0.5982 (ptt) cc_final: 0.5616 (ptt) REVERT: F 23 LYS cc_start: 0.8572 (mtpm) cc_final: 0.8148 (mttt) REVERT: F 111 LYS cc_start: 0.8494 (mmpt) cc_final: 0.8238 (mtpt) REVERT: F 128 MET cc_start: 0.8594 (mmm) cc_final: 0.8202 (mmp) REVERT: G 62 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7150 (tp30) REVERT: G 72 GLU cc_start: 0.7690 (tt0) cc_final: 0.7267 (pt0) REVERT: G 127 ASP cc_start: 0.8153 (m-30) cc_final: 0.7928 (m-30) REVERT: H 41 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8028 (mptp) REVERT: H 63 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8062 (mp) REVERT: I 110 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7664 (mp0) REVERT: I 150 ILE cc_start: 0.7977 (pp) cc_final: 0.7490 (pt) REVERT: I 216 MET cc_start: 0.7742 (tpp) cc_final: 0.7156 (mtp) REVERT: I 219 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6660 (mmt-90) REVERT: I 251 TYR cc_start: 0.8649 (t80) cc_final: 0.8354 (t80) REVERT: I 298 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8722 (mt) REVERT: J 100 MET cc_start: 0.6209 (mtm) cc_final: 0.5986 (mtm) REVERT: J 155 GLN cc_start: 0.7671 (tt0) cc_final: 0.7336 (tt0) REVERT: J 216 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.6163 (mtp) REVERT: J 222 LYS cc_start: 0.8090 (pttm) cc_final: 0.7844 (mmtt) REVERT: K 34 LEU cc_start: 0.8474 (mp) cc_final: 0.8248 (mt) REVERT: K 100 MET cc_start: 0.6500 (mtm) cc_final: 0.6232 (mtm) REVERT: K 155 GLN cc_start: 0.7671 (tt0) cc_final: 0.7372 (tt0) REVERT: K 216 MET cc_start: 0.7636 (mmp) cc_final: 0.6190 (mtp) REVERT: K 220 ARG cc_start: 0.6382 (tpt170) cc_final: 0.6014 (tpt170) REVERT: K 222 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7801 (mmtt) REVERT: L 110 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7684 (mp0) REVERT: L 150 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7424 (pt) REVERT: L 216 MET cc_start: 0.7725 (tpp) cc_final: 0.7147 (mtp) REVERT: L 219 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6656 (mmt-90) REVERT: L 237 MET cc_start: 0.8287 (mtt) cc_final: 0.8072 (mpp) REVERT: L 251 TYR cc_start: 0.8647 (t80) cc_final: 0.8330 (t80) REVERT: L 298 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8718 (mt) REVERT: L 373 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6549 (mt-10) outliers start: 105 outliers final: 43 residues processed: 615 average time/residue: 1.4490 time to fit residues: 1012.6557 Evaluate side-chains 596 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 539 time to evaluate : 2.472 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 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 135 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 219 ARG Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 219 ARG Chi-restraints excluded: chain L residue 252 SER 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 373 GLU 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: 0.8980 chunk 78 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 261 optimal weight: 0.0470 chunk 282 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.167308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127368 restraints weight = 26009.219| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.82 r_work: 0.3286 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 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 0.044 24318 Z= 0.145 Angle : 0.566 10.537 33014 Z= 0.297 Chirality : 0.043 0.198 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.703 81.292 3472 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.81 % Allowed : 19.37 % Favored : 77.83 % 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: 2.29 (0.12), residues: 1838 sheet: 0.47 (0.29), residues: 302 loop : -0.79 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 267 HIS 0.004 0.001 HIS L 168 PHE 0.036 0.002 PHE I 202 TYR 0.024 0.001 TYR J 345 ARG 0.010 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 1532) hydrogen bonds : angle 4.04638 ( 4413) covalent geometry : bond 0.00328 (24318) covalent geometry : angle 0.56601 (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 618 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 546 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8036 (tp30) cc_final: 0.7729 (tp30) REVERT: A 41 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7981 (mptp) REVERT: A 63 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8073 (mp) REVERT: B 62 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7245 (tp30) REVERT: B 127 ASP cc_start: 0.8130 (m-30) cc_final: 0.7921 (m-30) REVERT: C 23 LYS cc_start: 0.8591 (mtpm) cc_final: 0.8121 (mttt) REVERT: C 24 GLU cc_start: 0.8277 (tp30) cc_final: 0.8061 (tm-30) REVERT: C 48 TYR cc_start: 0.8324 (m-80) cc_final: 0.8094 (m-80) REVERT: C 59 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7228 (mm-30) REVERT: C 111 LYS cc_start: 0.8498 (mmpt) cc_final: 0.8211 (mtmt) REVERT: C 128 MET cc_start: 0.8599 (mmm) cc_final: 0.8207 (mmp) REVERT: D 60 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: D 115 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7947 (mptp) REVERT: D 134 GLN cc_start: 0.8142 (tp40) cc_final: 0.7632 (mm110) REVERT: D 139 GLU cc_start: 0.7183 (pm20) cc_final: 0.6801 (pm20) REVERT: E 145 ILE cc_start: 0.6320 (OUTLIER) cc_final: 0.6027 (tt) REVERT: E 208 MET cc_start: 0.6004 (ptt) cc_final: 0.5657 (ptt) REVERT: F 23 LYS cc_start: 0.8576 (mtpm) cc_final: 0.8155 (mttt) REVERT: F 111 LYS cc_start: 0.8488 (mmpt) cc_final: 0.8250 (mtpt) REVERT: F 128 MET cc_start: 0.8573 (mmm) cc_final: 0.8188 (mmp) REVERT: G 62 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7175 (tp30) REVERT: G 72 GLU cc_start: 0.7684 (tt0) cc_final: 0.7280 (pt0) REVERT: G 127 ASP cc_start: 0.8171 (m-30) cc_final: 0.7948 (m-30) REVERT: H 41 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7990 (mptp) REVERT: H 63 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8102 (mp) REVERT: I 110 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7684 (mp0) REVERT: I 116 GLU cc_start: 0.7149 (tp30) cc_final: 0.6935 (tp30) REVERT: I 150 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7513 (pt) REVERT: I 216 MET cc_start: 0.7746 (tpp) cc_final: 0.7156 (mtp) REVERT: I 219 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6670 (mmt-90) REVERT: I 251 TYR cc_start: 0.8658 (t80) cc_final: 0.8393 (t80) REVERT: I 298 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8726 (mt) REVERT: J 155 GLN cc_start: 0.7595 (tt0) cc_final: 0.7239 (tt0) REVERT: J 216 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.6176 (mtp) REVERT: J 222 LYS cc_start: 0.8115 (pttm) cc_final: 0.7883 (mmtt) REVERT: J 374 GLN cc_start: 0.7788 (mp10) cc_final: 0.7543 (mp10) REVERT: K 34 LEU cc_start: 0.8456 (mp) cc_final: 0.8238 (mt) REVERT: K 100 MET cc_start: 0.6546 (mtm) cc_final: 0.6265 (mtm) REVERT: K 155 GLN cc_start: 0.7669 (tt0) cc_final: 0.7351 (tt0) REVERT: K 216 MET cc_start: 0.7634 (mmp) cc_final: 0.6190 (mtp) REVERT: K 220 ARG cc_start: 0.6463 (tpt170) cc_final: 0.6112 (tpt170) REVERT: L 110 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7706 (mp0) REVERT: L 140 ILE cc_start: 0.8408 (tt) cc_final: 0.8190 (tt) REVERT: L 150 ILE cc_start: 0.7905 (pp) cc_final: 0.7464 (pt) REVERT: L 216 MET cc_start: 0.7749 (tpp) cc_final: 0.7183 (mtp) REVERT: L 219 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6704 (mmt-90) REVERT: L 298 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8729 (mt) REVERT: L 373 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6482 (mt-10) outliers start: 72 outliers final: 39 residues processed: 593 average time/residue: 1.4975 time to fit residues: 1013.9999 Evaluate side-chains 587 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 534 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 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 165 SER Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 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 373 GLU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 30 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 296 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 81 ASN B 38 ASN B 134 GLN C 134 GLN E 8 GLN F 43 ASN F 134 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 ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3958 r_free = 0.3958 target = 0.164832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124115 restraints weight = 26153.329| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.89 r_work: 0.3248 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24318 Z= 0.225 Angle : 0.634 9.604 33014 Z= 0.334 Chirality : 0.046 0.219 3998 Planarity : 0.004 0.046 4016 Dihedral : 10.158 84.167 3472 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.27 % Allowed : 19.37 % 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: 1.63 (0.15), residues: 3008 helix: 2.06 (0.12), residues: 1840 sheet: 0.49 (0.28), residues: 302 loop : -0.85 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 181 HIS 0.006 0.001 HIS L 168 PHE 0.037 0.002 PHE I 202 TYR 0.027 0.002 TYR J 345 ARG 0.010 0.001 ARG A 27 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 1532) hydrogen bonds : angle 4.18897 ( 4413) covalent geometry : bond 0.00531 (24318) covalent geometry : angle 0.63375 (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: 84 poor density : 539 time to evaluate : 3.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8019 (tp30) cc_final: 0.7722 (tp30) REVERT: A 27 ARG cc_start: 0.8380 (ttp80) cc_final: 0.8095 (ttp80) REVERT: A 41 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8042 (mptp) REVERT: A 63 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8121 (mp) REVERT: B 62 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7238 (tp30) REVERT: B 127 ASP cc_start: 0.8181 (m-30) cc_final: 0.7945 (m-30) REVERT: C 23 LYS cc_start: 0.8578 (mtpm) cc_final: 0.8144 (mttt) REVERT: C 24 GLU cc_start: 0.8284 (tp30) cc_final: 0.7859 (tp30) REVERT: C 128 MET cc_start: 0.8656 (mmm) cc_final: 0.8247 (mmp) REVERT: D 60 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: D 134 GLN cc_start: 0.8187 (tp40) cc_final: 0.7402 (mp10) REVERT: E 208 MET cc_start: 0.5969 (ptt) cc_final: 0.5601 (ptt) REVERT: F 23 LYS cc_start: 0.8590 (mtpm) cc_final: 0.8134 (mttt) REVERT: F 43 ASN cc_start: 0.8512 (m110) cc_final: 0.8288 (m110) REVERT: F 111 LYS cc_start: 0.8539 (mmpt) cc_final: 0.8272 (mtpt) REVERT: F 128 MET cc_start: 0.8642 (mmm) cc_final: 0.8245 (mmp) REVERT: G 62 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7206 (tp30) REVERT: H 41 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7721 (mptp) REVERT: H 63 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8142 (mp) REVERT: I 110 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7662 (mp0) REVERT: I 150 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7497 (pt) REVERT: I 216 MET cc_start: 0.7719 (tpp) cc_final: 0.7129 (mtp) REVERT: I 219 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6628 (mmt-90) REVERT: I 251 TYR cc_start: 0.8634 (t80) cc_final: 0.8362 (t80) REVERT: I 298 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8742 (mt) REVERT: J 155 GLN cc_start: 0.7650 (tt0) cc_final: 0.7307 (tt0) REVERT: J 216 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.6293 (mtp) REVERT: J 222 LYS cc_start: 0.8027 (pttm) cc_final: 0.7816 (mmtt) REVERT: K 100 MET cc_start: 0.6597 (mtm) cc_final: 0.6347 (mtm) REVERT: K 155 GLN cc_start: 0.7752 (tt0) cc_final: 0.7452 (tt0) REVERT: K 216 MET cc_start: 0.7682 (mmp) cc_final: 0.6277 (mtp) REVERT: K 222 LYS cc_start: 0.8264 (mmtt) cc_final: 0.8048 (mmtt) REVERT: L 110 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7679 (mp0) REVERT: L 140 ILE cc_start: 0.8413 (tt) cc_final: 0.8186 (tt) REVERT: L 150 ILE cc_start: 0.7930 (pp) cc_final: 0.7479 (pt) REVERT: L 216 MET cc_start: 0.7743 (tpp) cc_final: 0.7182 (mtp) REVERT: L 219 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6662 (mmt-90) REVERT: L 298 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8744 (mt) REVERT: L 373 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6581 (mt-10) outliers start: 84 outliers final: 35 residues processed: 592 average time/residue: 1.7656 time to fit residues: 1184.6036 Evaluate side-chains 578 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 531 time to evaluate : 2.547 ------------------------------------------------------------------------------- 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 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 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 G residue 65 SER Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 74 VAL 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 165 SER Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 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 219 ARG Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 373 GLU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 103 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 281 optimal weight: 0.6980 chunk 274 optimal weight: 4.9990 chunk 273 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 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 A 81 ASN B 38 ASN B 134 GLN C 134 GLN E 8 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** J 115 GLN J 253 ASN J 374 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN K 253 ASN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.167435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127626 restraints weight = 25940.902| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.83 r_work: 0.3289 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24318 Z= 0.136 Angle : 0.566 9.523 33014 Z= 0.296 Chirality : 0.043 0.197 3998 Planarity : 0.004 0.044 4016 Dihedral : 9.743 82.336 3472 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.38 % Allowed : 20.34 % Favored : 77.28 % 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: 1.81 (0.15), residues: 3008 helix: 2.22 (0.12), residues: 1834 sheet: 0.43 (0.29), residues: 302 loop : -0.73 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 267 HIS 0.004 0.001 HIS L 168 PHE 0.036 0.002 PHE I 202 TYR 0.020 0.001 TYR J 345 ARG 0.008 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 1532) hydrogen bonds : angle 4.07184 ( 4413) covalent geometry : bond 0.00305 (24318) covalent geometry : angle 0.56619 (33014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28970.25 seconds wall clock time: 499 minutes 47.36 seconds (29987.36 seconds total)