Starting phenix.real_space_refine on Mon Jun 23 01:28:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmh_38477/06_2025/8xmh_38477.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmh_38477/06_2025/8xmh_38477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xmh_38477/06_2025/8xmh_38477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmh_38477/06_2025/8xmh_38477.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmh_38477/06_2025/8xmh_38477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmh_38477/06_2025/8xmh_38477.cif" } resolution = 2.85 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= 0.001 sd= 0.082 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 116 5.16 5 Na 4 4.78 5 C 17440 2.51 5 N 4420 2.21 5 O 4940 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: 26948 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "B" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "D" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "E" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "F" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "G" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "H" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "I" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "J" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "K" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "L" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" 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: "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: 17.31, per 1000 atoms: 0.64 Number of scatterers: 26948 At special positions: 0 Unit cell: (135.29, 135.29, 169.32, 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 116 16.00 P 24 15.00 Na 4 11.00 O 4940 8.00 N 4420 7.00 C 17440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.59 Conformation dependent library (CDL) restraints added in 3.6 seconds 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6360 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 20 sheets defined 57.8% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 15 through 28 removed outlier: 3.646A pdb=" N SER A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 59 through 66 removed outlier: 3.629A 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 'A' and resid 211 through 221 removed outlier: 3.710A pdb=" N LYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 28 removed outlier: 3.645A pdb=" N SER B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 59 through 66 removed outlier: 3.628A 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 'B' and resid 211 through 221 removed outlier: 3.711A pdb=" N LYS B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 28 removed outlier: 3.645A pdb=" N SER C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 45 Processing helix chain 'C' and resid 59 through 66 removed outlier: 3.629A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) 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 221 removed outlier: 3.709A pdb=" N LYS C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 28 removed outlier: 3.645A pdb=" N SER D 20 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 45 Processing helix chain 'D' and resid 59 through 66 removed outlier: 3.629A pdb=" N LEU D 66 " --> pdb=" O GLU D 62 " (cutoff:3.500A) 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 221 removed outlier: 3.710A pdb=" N LYS D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 28 removed outlier: 3.646A pdb=" N SER E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 45 Processing helix chain 'E' and resid 59 through 66 removed outlier: 3.629A pdb=" N LEU E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) 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 211 through 221 removed outlier: 3.710A pdb=" N LYS E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 28 removed outlier: 3.646A pdb=" N SER F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 45 Processing helix chain 'F' and resid 59 through 66 removed outlier: 3.629A pdb=" N LEU F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) 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 221 removed outlier: 3.710A pdb=" N LYS F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 28 removed outlier: 3.646A pdb=" N SER G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 45 Processing helix chain 'G' and resid 59 through 66 removed outlier: 3.629A 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 'G' and resid 211 through 221 removed outlier: 3.710A pdb=" N LYS G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 28 removed outlier: 3.646A pdb=" N SER H 20 " --> pdb=" O ARG H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 45 Processing helix chain 'H' and resid 59 through 66 removed outlier: 3.629A 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 'H' and resid 211 through 221 removed outlier: 3.710A pdb=" N LYS H 215 " --> pdb=" O LYS H 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 37 removed outlier: 3.528A pdb=" N LEU I 20 " --> pdb=" O PRO I 16 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE I 28 " --> pdb=" O PHE I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 59 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 73 through 90 Processing helix chain 'I' and resid 90 through 103 removed outlier: 4.040A pdb=" N PHE I 94 " --> pdb=" O GLY I 90 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 removed outlier: 3.552A pdb=" N LEU I 113 " --> pdb=" O LYS I 109 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL I 114 " --> pdb=" O GLU I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 157 removed outlier: 3.531A pdb=" N VAL I 130 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE I 150 " --> pdb=" O LEU I 146 " (cutoff:3.500A) removed outlier: 4.398A 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 LEU I 162 " --> pdb=" O TRP I 158 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 207 Processing helix chain 'I' and resid 208 through 218 Processing helix chain 'I' and resid 220 through 224 Processing helix chain 'I' and resid 225 through 250 Processing helix chain 'I' and resid 261 through 275 Processing helix chain 'I' and resid 285 through 289 removed outlier: 3.516A pdb=" N SER I 288 " --> pdb=" O ASP I 285 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET I 289 " --> pdb=" O PHE I 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 285 through 289' Processing helix chain 'I' and resid 290 through 303 removed outlier: 3.537A pdb=" N ILE I 303 " --> pdb=" O LEU I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 315 through 331 Processing helix chain 'I' and resid 344 through 373 Processing helix chain 'I' and resid 376 through 389 Processing helix chain 'I' and resid 397 through 401 Processing helix chain 'I' and resid 402 through 419 removed outlier: 3.518A pdb=" N CYS I 407 " --> pdb=" O THR I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 428 removed outlier: 4.129A pdb=" N PHE I 427 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 37 removed outlier: 3.529A pdb=" N LEU J 20 " --> pdb=" O PRO J 16 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE J 28 " --> pdb=" O PHE J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 59 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 73 through 90 Processing helix chain 'J' and resid 90 through 103 removed outlier: 4.039A pdb=" N PHE J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 118 removed outlier: 3.551A pdb=" N LEU J 113 " --> pdb=" O LYS J 109 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 157 removed outlier: 3.532A pdb=" N VAL J 130 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE J 150 " --> pdb=" O LEU J 146 " (cutoff:3.500A) removed outlier: 4.396A 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: 3.542A pdb=" N LEU J 162 " --> pdb=" O TRP J 158 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 207 Processing helix chain 'J' and resid 208 through 218 Processing helix chain 'J' and resid 220 through 224 Processing helix chain 'J' and resid 225 through 250 Processing helix chain 'J' and resid 261 through 275 Processing helix chain 'J' and resid 285 through 289 removed outlier: 3.516A pdb=" N SER J 288 " --> pdb=" O ASP J 285 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET J 289 " --> pdb=" O PHE J 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 285 through 289' Processing helix chain 'J' and resid 290 through 303 removed outlier: 3.638A pdb=" N LEU J 299 " --> pdb=" O VAL J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 331 Processing helix chain 'J' and resid 344 through 373 Processing helix chain 'J' and resid 376 through 389 Processing helix chain 'J' and resid 397 through 401 Processing helix chain 'J' and resid 402 through 419 removed outlier: 3.519A pdb=" N CYS J 407 " --> pdb=" O THR J 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 419 through 428 removed outlier: 4.129A pdb=" N PHE J 427 " --> pdb=" O PHE J 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 37 removed outlier: 3.529A pdb=" N LEU K 20 " --> pdb=" O PRO K 16 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE K 28 " --> pdb=" O PHE K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 59 Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 73 through 90 Processing helix chain 'K' and resid 90 through 103 removed outlier: 4.040A pdb=" N PHE K 94 " --> pdb=" O GLY K 90 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU K 97 " --> pdb=" O THR K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 removed outlier: 3.551A pdb=" N LEU K 113 " --> pdb=" O LYS K 109 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 157 removed outlier: 3.531A pdb=" N VAL K 130 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE K 150 " --> pdb=" O LEU K 146 " (cutoff:3.500A) removed outlier: 4.397A 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: 3.541A pdb=" N LEU K 162 " --> pdb=" O TRP K 158 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 207 Processing helix chain 'K' and resid 208 through 218 Processing helix chain 'K' and resid 220 through 224 Processing helix chain 'K' and resid 225 through 250 Processing helix chain 'K' and resid 261 through 275 Processing helix chain 'K' and resid 285 through 289 removed outlier: 3.515A pdb=" N SER K 288 " --> pdb=" O ASP K 285 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET K 289 " --> pdb=" O PHE K 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 285 through 289' Processing helix chain 'K' and resid 290 through 303 removed outlier: 3.536A pdb=" N ILE K 303 " --> pdb=" O LEU K 299 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 331 Processing helix chain 'K' and resid 344 through 373 Processing helix chain 'K' and resid 376 through 389 Processing helix chain 'K' and resid 397 through 401 Processing helix chain 'K' and resid 402 through 419 removed outlier: 3.519A pdb=" N CYS K 407 " --> pdb=" O THR K 403 " (cutoff:3.500A) Processing helix chain 'K' and resid 419 through 428 removed outlier: 4.130A pdb=" N PHE K 427 " --> pdb=" O PHE K 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 37 removed outlier: 3.528A pdb=" N LEU L 20 " --> pdb=" O PRO L 16 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE L 28 " --> pdb=" O PHE L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 59 Processing helix chain 'L' and resid 67 through 72 Processing helix chain 'L' and resid 73 through 90 Processing helix chain 'L' and resid 90 through 103 removed outlier: 4.040A pdb=" N PHE L 94 " --> pdb=" O GLY L 90 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 118 removed outlier: 3.551A pdb=" N LEU L 113 " --> pdb=" O LYS L 109 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL L 114 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 157 removed outlier: 3.531A pdb=" N VAL L 130 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE L 150 " --> pdb=" O LEU L 146 " (cutoff:3.500A) removed outlier: 4.396A 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 LEU L 162 " --> pdb=" O TRP L 158 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 207 Processing helix chain 'L' and resid 208 through 218 Processing helix chain 'L' and resid 220 through 224 Processing helix chain 'L' and resid 225 through 250 Processing helix chain 'L' and resid 261 through 275 Processing helix chain 'L' and resid 285 through 289 removed outlier: 3.516A pdb=" N SER L 288 " --> pdb=" O ASP L 285 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET L 289 " --> pdb=" O PHE L 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 285 through 289' Processing helix chain 'L' and resid 290 through 303 removed outlier: 3.537A pdb=" N ILE L 303 " --> pdb=" O LEU L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 331 Processing helix chain 'L' and resid 344 through 373 Processing helix chain 'L' and resid 376 through 389 Processing helix chain 'L' and resid 397 through 401 Processing helix chain 'L' and resid 402 through 419 removed outlier: 3.519A pdb=" N CYS L 407 " --> pdb=" O THR L 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 419 through 428 removed outlier: 4.130A 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: 3.588A pdb=" N TYR A 73 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 100 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE A 122 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A 102 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 141 through 146 removed outlier: 6.175A pdb=" N VAL A 141 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU A 157 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 143 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS A 204 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 182 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET A 208 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE A 180 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.587A pdb=" N TYR B 73 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 100 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE B 122 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 102 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 141 through 146 removed outlier: 6.174A pdb=" N VAL B 141 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU B 157 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN B 143 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS B 204 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 182 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET B 208 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE B 180 " --> pdb=" O MET B 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.588A pdb=" N TYR C 73 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 100 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE C 122 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 102 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 141 through 146 removed outlier: 6.175A pdb=" N VAL C 141 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU C 157 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN C 143 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS C 204 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA C 182 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET C 208 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE C 180 " --> pdb=" O MET C 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.588A pdb=" N TYR D 73 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 100 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE D 122 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL D 102 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 141 through 146 removed outlier: 6.175A pdb=" N VAL D 141 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU D 157 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN D 143 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS D 204 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 182 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET D 208 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ILE D 180 " --> pdb=" O MET D 208 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 51 through 54 removed outlier: 3.588A pdb=" N TYR E 73 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE E 100 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE E 122 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL E 102 " --> pdb=" O ILE E 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 141 through 146 removed outlier: 6.175A pdb=" N VAL E 141 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU E 157 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN E 143 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS E 204 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 182 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET E 208 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE E 180 " --> pdb=" O MET E 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.587A pdb=" N TYR F 73 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE F 100 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE F 122 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL F 102 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 141 through 146 removed outlier: 6.175A pdb=" N VAL F 141 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU F 157 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN F 143 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS F 204 " --> pdb=" O LYS F 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA F 182 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET F 208 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE F 180 " --> pdb=" O MET F 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.588A pdb=" N TYR G 73 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE G 100 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE G 122 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL G 102 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 141 through 146 removed outlier: 6.175A pdb=" N VAL G 141 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU G 157 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN G 143 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS G 204 " --> pdb=" O LYS G 184 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA G 182 " --> pdb=" O VAL G 206 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET G 208 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE G 180 " --> pdb=" O MET G 208 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 51 through 54 removed outlier: 3.588A pdb=" N TYR H 73 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE H 100 " --> pdb=" O ARG H 120 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE H 122 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL H 102 " --> pdb=" O ILE H 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 141 through 146 removed outlier: 6.175A pdb=" N VAL H 141 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU H 157 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN H 143 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS H 204 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA H 182 " --> pdb=" O VAL H 206 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET H 208 " --> pdb=" O ILE H 180 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ILE H 180 " --> pdb=" O MET H 208 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 336 through 338 removed outlier: 4.695A pdb=" N THR I 336 " --> pdb=" O ILE I 343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 336 through 338 removed outlier: 4.695A pdb=" N THR J 336 " --> pdb=" O ILE J 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 336 through 338 removed outlier: 4.694A pdb=" N THR K 336 " --> pdb=" O ILE K 343 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 336 through 338 removed outlier: 4.694A pdb=" N THR L 336 " --> pdb=" O ILE L 343 " (cutoff:3.500A) 1572 hydrogen bonds defined for protein. 4560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.91 Time building geometry restraints manager: 7.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4315 1.29 - 1.42: 6694 1.42 - 1.55: 16188 1.55 - 1.68: 59 1.68 - 1.81: 196 Bond restraints: 27452 Sorted by residual: bond pdb=" CA LEU J 299 " pdb=" C LEU J 299 " ideal model delta sigma weight residual 1.524 1.430 0.093 1.29e-02 6.01e+03 5.25e+01 bond pdb=" C LEU I 298 " pdb=" O LEU I 298 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.19e-02 7.06e+03 4.39e+01 bond pdb=" C LEU E 87 " pdb=" O LEU E 87 " ideal model delta sigma weight residual 1.237 1.169 0.068 1.19e-02 7.06e+03 3.24e+01 bond pdb=" C LEU A 87 " pdb=" O LEU A 87 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.26e-02 6.30e+03 2.99e+01 bond pdb=" CA LEU D 87 " pdb=" C LEU D 87 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.35e-02 5.49e+03 2.66e+01 ... (remaining 27447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 36683 1.63 - 3.26: 452 3.26 - 4.89: 84 4.89 - 6.52: 20 6.52 - 8.15: 21 Bond angle restraints: 37260 Sorted by residual: angle pdb=" N LEU J 299 " pdb=" CA LEU J 299 " pdb=" C LEU J 299 " ideal model delta sigma weight residual 111.36 105.52 5.84 1.09e+00 8.42e-01 2.87e+01 angle pdb=" O THR I 297 " pdb=" C THR I 297 " pdb=" N LEU I 298 " ideal model delta sigma weight residual 122.27 116.17 6.10 1.23e+00 6.61e-01 2.46e+01 angle pdb=" CA THR I 297 " pdb=" C THR I 297 " pdb=" N LEU I 298 " ideal model delta sigma weight residual 117.72 123.94 -6.22 1.31e+00 5.83e-01 2.25e+01 angle pdb=" N THR L 275 " pdb=" CA THR L 275 " pdb=" C THR L 275 " ideal model delta sigma weight residual 109.81 116.83 -7.02 2.21e+00 2.05e-01 1.01e+01 angle pdb=" N THR J 275 " pdb=" CA THR J 275 " pdb=" C THR J 275 " ideal model delta sigma weight residual 109.81 116.82 -7.01 2.21e+00 2.05e-01 1.01e+01 ... (remaining 37255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 15437 15.76 - 31.51: 752 31.51 - 47.27: 135 47.27 - 63.03: 60 63.03 - 78.79: 32 Dihedral angle restraints: 16416 sinusoidal: 6532 harmonic: 9884 Sorted by residual: dihedral pdb=" CA GLU B 201 " pdb=" C GLU B 201 " pdb=" N GLN B 202 " pdb=" CA GLN B 202 " ideal model delta harmonic sigma weight residual -180.00 -163.34 -16.66 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA GLU A 201 " pdb=" C GLU A 201 " pdb=" N GLN A 202 " pdb=" CA GLN A 202 " ideal model delta harmonic sigma weight residual 180.00 -163.35 -16.65 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA GLU G 201 " pdb=" C GLU G 201 " pdb=" N GLN G 202 " pdb=" CA GLN G 202 " ideal model delta harmonic sigma weight residual -180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 16413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3124 0.040 - 0.080: 1019 0.080 - 0.121: 291 0.121 - 0.161: 44 0.161 - 0.201: 6 Chirality restraints: 4484 Sorted by residual: chirality pdb=" CA THR K 275 " pdb=" N THR K 275 " pdb=" C THR K 275 " pdb=" CB THR K 275 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA THR J 275 " pdb=" N THR J 275 " pdb=" C THR J 275 " pdb=" CB THR J 275 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CA THR I 275 " pdb=" N THR I 275 " pdb=" C THR I 275 " pdb=" CB THR I 275 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 4481 not shown) Planarity restraints: 4576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 298 " -0.009 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C LEU I 298 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU I 298 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU I 299 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR J 15 " -0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO J 16 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO J 16 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO J 16 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR L 15 " 0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO L 16 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO L 16 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 16 " 0.023 5.00e-02 4.00e+02 ... (remaining 4573 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 9213 2.86 - 3.43: 28452 3.43 - 4.00: 50971 4.00 - 4.57: 72756 4.57 - 5.14: 106687 Nonbonded interactions: 268079 Sorted by model distance: nonbonded pdb=" OE1 GLU A 60 " pdb=" OH TYR H 108 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR D 108 " pdb=" OE1 GLU E 60 " model vdw 2.293 3.040 nonbonded pdb=" OE1 GLU D 60 " pdb=" OH TYR E 108 " model vdw 2.317 3.040 nonbonded pdb=" O ASN K 195 " pdb=" OG1 THR K 199 " model vdw 2.330 3.040 nonbonded pdb=" O ASN J 195 " pdb=" OG1 THR J 199 " model vdw 2.330 3.040 ... (remaining 268074 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: 0.09 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 221) selection = (chain 'B' and resid 7 through 221) selection = (chain 'C' and resid 7 through 221) selection = (chain 'D' and resid 7 through 221) selection = (chain 'E' and resid 7 through 221) selection = (chain 'F' and resid 7 through 221) selection = (chain 'G' and resid 7 through 221) selection = (chain 'H' and resid 7 through 221) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.170 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 63.460 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:82.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 0.093 27452 Z= 0.217 Angle : 0.529 8.148 37260 Z= 0.285 Chirality : 0.043 0.201 4484 Planarity : 0.004 0.042 4576 Dihedral : 10.948 78.787 10056 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.55 % Allowed : 4.09 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.12), residues: 3420 helix: -1.51 (0.08), residues: 1852 sheet: 0.79 (0.27), residues: 416 loop : -0.81 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 181 HIS 0.003 0.001 HIS K 168 PHE 0.025 0.001 PHE I 202 TYR 0.006 0.001 TYR F 108 ARG 0.002 0.000 ARG L 111 Details of bonding type rmsd hydrogen bonds : bond 0.25057 ( 1572) hydrogen bonds : angle 7.78521 ( 4560) covalent geometry : bond 0.00401 (27452) covalent geometry : angle 0.52895 (37260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 831 time to evaluate : 2.832 Fit side-chains REVERT: F 128 MET cc_start: 0.7541 (mmm) cc_final: 0.7290 (mmt) REVERT: G 41 LYS cc_start: 0.8352 (mmtp) cc_final: 0.7977 (mmtt) REVERT: J 407 CYS cc_start: 0.7767 (m) cc_final: 0.7499 (m) REVERT: K 213 PHE cc_start: 0.7658 (t80) cc_final: 0.7315 (t80) REVERT: L 74 VAL cc_start: 0.7714 (t) cc_final: 0.7354 (p) REVERT: L 213 PHE cc_start: 0.7575 (t80) cc_final: 0.7267 (t80) outliers start: 45 outliers final: 5 residues processed: 857 average time/residue: 1.4615 time to fit residues: 1459.0194 Evaluate side-chains 491 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 486 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 352 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 0.6980 chunk 257 optimal weight: 0.8980 chunk 142 optimal weight: 0.3980 chunk 88 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 198 optimal weight: 0.6980 chunk 308 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 140 ASN C 134 GLN D 70 ASN D 81 ASN D 134 GLN E 134 GLN F 134 GLN H 70 ASN H 81 ASN H 134 GLN I 120 GLN I 253 ASN J 253 ASN J 282 ASN K 155 GLN K 195 ASN K 253 ASN K 261 HIS L 77 GLN L 253 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.199810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.161705 restraints weight = 28028.342| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.29 r_work: 0.3555 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27452 Z= 0.129 Angle : 0.530 6.853 37260 Z= 0.284 Chirality : 0.043 0.217 4484 Planarity : 0.004 0.043 4576 Dihedral : 9.081 74.731 3914 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.54 % Allowed : 14.80 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.13), residues: 3420 helix: 1.02 (0.11), residues: 1908 sheet: 0.30 (0.26), residues: 400 loop : -0.53 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 181 HIS 0.007 0.001 HIS C 185 PHE 0.039 0.002 PHE I 202 TYR 0.029 0.001 TYR F 107 ARG 0.006 0.000 ARG L 151 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 1572) hydrogen bonds : angle 4.59728 ( 4560) covalent geometry : bond 0.00279 (27452) covalent geometry : angle 0.52994 (37260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 523 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8234 (t) cc_final: 0.8015 (m) REVERT: B 134 GLN cc_start: 0.8607 (mp10) cc_final: 0.8064 (mp10) REVERT: C 128 MET cc_start: 0.8096 (mmm) cc_final: 0.7793 (mmm) REVERT: C 135 SER cc_start: 0.8738 (t) cc_final: 0.8437 (m) REVERT: D 95 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7583 (mt) REVERT: D 143 ASN cc_start: 0.8178 (t0) cc_final: 0.7955 (t0) REVERT: D 152 SER cc_start: 0.8575 (OUTLIER) cc_final: 0.8272 (m) REVERT: F 128 MET cc_start: 0.8499 (mmm) cc_final: 0.8176 (mmt) REVERT: F 189 ILE cc_start: 0.5776 (OUTLIER) cc_final: 0.5468 (tp) REVERT: G 41 LYS cc_start: 0.8309 (mmtp) cc_final: 0.8055 (mmtt) REVERT: G 134 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8142 (mp10) REVERT: H 85 SER cc_start: 0.8485 (t) cc_final: 0.8272 (m) REVERT: H 95 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7731 (mt) REVERT: H 152 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8201 (m) REVERT: I 250 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8384 (tp30) REVERT: K 71 GLN cc_start: 0.7053 (mm-40) cc_final: 0.6012 (tp40) REVERT: K 244 LEU cc_start: 0.8085 (tp) cc_final: 0.7861 (mm) REVERT: L 77 GLN cc_start: 0.7420 (mt0) cc_final: 0.7049 (mp10) REVERT: L 352 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8342 (tp) outliers start: 103 outliers final: 25 residues processed: 586 average time/residue: 1.4524 time to fit residues: 1010.6079 Evaluate side-chains 480 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 448 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 36 MET Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 371 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 242 optimal weight: 0.8980 chunk 338 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 264 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN D 70 ASN D 81 ASN D 134 GLN E 30 HIS E 134 GLN F 134 GLN H 70 ASN H 81 ASN H 134 GLN H 210 HIS I 115 GLN I 282 ASN I 432 GLN J 71 GLN J 432 GLN K 115 GLN K 253 ASN K 261 HIS K 432 GLN K 434 ASN L 115 GLN L 434 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.198220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.160072 restraints weight = 27871.912| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.11 r_work: 0.3534 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27452 Z= 0.134 Angle : 0.516 7.231 37260 Z= 0.273 Chirality : 0.043 0.215 4484 Planarity : 0.003 0.041 4576 Dihedral : 8.738 80.855 3906 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.71 % Allowed : 15.01 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.14), residues: 3420 helix: 1.73 (0.12), residues: 1920 sheet: 0.09 (0.26), residues: 400 loop : -0.63 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 181 HIS 0.006 0.001 HIS C 185 PHE 0.035 0.001 PHE I 202 TYR 0.009 0.001 TYR H 108 ARG 0.006 0.000 ARG J 151 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 1572) hydrogen bonds : angle 4.27815 ( 4560) covalent geometry : bond 0.00305 (27452) covalent geometry : angle 0.51643 (37260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 485 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 GLN cc_start: 0.8511 (mp10) cc_final: 0.7802 (mp10) REVERT: B 213 ASP cc_start: 0.6812 (m-30) cc_final: 0.5999 (t0) REVERT: C 128 MET cc_start: 0.8123 (mmm) cc_final: 0.7878 (mmm) REVERT: C 135 SER cc_start: 0.8699 (t) cc_final: 0.8463 (m) REVERT: D 85 SER cc_start: 0.8667 (t) cc_final: 0.8412 (m) REVERT: D 95 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7721 (mt) REVERT: D 152 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8369 (m) REVERT: E 139 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6662 (tp30) REVERT: F 128 MET cc_start: 0.8469 (mmm) cc_final: 0.8173 (mmt) REVERT: F 189 ILE cc_start: 0.5837 (OUTLIER) cc_final: 0.5531 (tp) REVERT: G 62 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8307 (mt-10) REVERT: H 95 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7716 (mt) REVERT: H 152 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8373 (m) REVERT: I 222 LYS cc_start: 0.8422 (mmtt) cc_final: 0.7996 (tttp) REVERT: K 24 PHE cc_start: 0.8074 (t80) cc_final: 0.7838 (t80) REVERT: K 25 PHE cc_start: 0.6620 (t80) cc_final: 0.6398 (t80) REVERT: K 71 GLN cc_start: 0.6994 (mm-40) cc_final: 0.6008 (tp40) REVERT: L 74 VAL cc_start: 0.7778 (t) cc_final: 0.7226 (p) REVERT: L 77 GLN cc_start: 0.7453 (mt0) cc_final: 0.7099 (mp10) REVERT: L 333 LYS cc_start: 0.8429 (mttt) cc_final: 0.8160 (mptp) outliers start: 108 outliers final: 40 residues processed: 552 average time/residue: 1.2185 time to fit residues: 795.5395 Evaluate side-chains 487 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 440 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 285 ASP Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 92 MET Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 284 optimal weight: 0.7980 chunk 324 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 304 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 276 optimal weight: 4.9990 chunk 265 optimal weight: 0.0970 chunk 154 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN D 70 ASN D 134 GLN E 134 GLN F 134 GLN H 70 ASN H 81 ASN J 85 GLN K 115 GLN K 253 ASN K 261 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.199469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.161213 restraints weight = 28106.574| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.21 r_work: 0.3555 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 27452 Z= 0.110 Angle : 0.486 7.420 37260 Z= 0.258 Chirality : 0.042 0.202 4484 Planarity : 0.003 0.041 4576 Dihedral : 8.482 78.237 3904 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.26 % Allowed : 16.55 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.14), residues: 3420 helix: 2.09 (0.12), residues: 1916 sheet: -0.04 (0.26), residues: 400 loop : -0.60 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 181 HIS 0.005 0.001 HIS K 261 PHE 0.033 0.001 PHE I 202 TYR 0.008 0.001 TYR F 107 ARG 0.009 0.000 ARG B 27 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 1572) hydrogen bonds : angle 4.09199 ( 4560) covalent geometry : bond 0.00239 (27452) covalent geometry : angle 0.48624 (37260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 473 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.6794 (m-30) cc_final: 0.5987 (t0) REVERT: C 128 MET cc_start: 0.8150 (mmm) cc_final: 0.7888 (mmm) REVERT: C 135 SER cc_start: 0.8697 (t) cc_final: 0.8464 (m) REVERT: D 85 SER cc_start: 0.8806 (t) cc_final: 0.8430 (m) REVERT: D 95 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7668 (mt) REVERT: F 128 MET cc_start: 0.8468 (mmm) cc_final: 0.8175 (mmt) REVERT: F 189 ILE cc_start: 0.5898 (OUTLIER) cc_final: 0.5610 (tp) REVERT: G 62 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8301 (mt-10) REVERT: H 95 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7675 (mt) REVERT: H 152 SER cc_start: 0.8783 (p) cc_final: 0.8445 (m) REVERT: I 222 LYS cc_start: 0.8394 (mmtt) cc_final: 0.8009 (tttp) REVERT: J 222 LYS cc_start: 0.8455 (mmtt) cc_final: 0.8017 (tttp) REVERT: K 71 GLN cc_start: 0.7050 (mm-40) cc_final: 0.5988 (tp40) REVERT: L 77 GLN cc_start: 0.7517 (mt0) cc_final: 0.7266 (mp10) REVERT: L 352 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8407 (tp) outliers start: 95 outliers final: 45 residues processed: 536 average time/residue: 1.2211 time to fit residues: 786.9859 Evaluate side-chains 485 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 435 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 36 MET Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 92 MET Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 371 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 238 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 221 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 303 optimal weight: 0.9980 chunk 316 optimal weight: 2.9990 chunk 339 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN D 70 ASN D 81 ASN D 134 GLN E 134 GLN F 134 GLN H 70 ASN H 81 ASN I 253 ASN J 261 HIS K 253 ASN L 115 GLN L 155 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.197725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.159247 restraints weight = 27910.016| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.08 r_work: 0.3529 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27452 Z= 0.130 Angle : 0.505 7.293 37260 Z= 0.267 Chirality : 0.042 0.212 4484 Planarity : 0.003 0.043 4576 Dihedral : 8.614 80.325 3904 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.98 % Allowed : 16.00 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.14), residues: 3420 helix: 2.15 (0.12), residues: 1916 sheet: -0.11 (0.25), residues: 400 loop : -0.59 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 181 HIS 0.005 0.001 HIS C 185 PHE 0.033 0.001 PHE I 202 TYR 0.009 0.001 TYR E 45 ARG 0.010 0.001 ARG B 27 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 1572) hydrogen bonds : angle 4.10350 ( 4560) covalent geometry : bond 0.00296 (27452) covalent geometry : angle 0.50539 (37260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 450 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.6834 (m-30) cc_final: 0.6007 (t0) REVERT: C 128 MET cc_start: 0.8139 (mmm) cc_final: 0.7854 (mmm) REVERT: C 135 SER cc_start: 0.8784 (t) cc_final: 0.8560 (m) REVERT: D 85 SER cc_start: 0.8856 (t) cc_final: 0.8494 (m) REVERT: D 95 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7738 (mt) REVERT: F 59 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7837 (mm-30) REVERT: F 128 MET cc_start: 0.8468 (mmm) cc_final: 0.8176 (mmt) REVERT: F 189 ILE cc_start: 0.5853 (OUTLIER) cc_final: 0.5561 (tp) REVERT: G 62 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8297 (mt-10) REVERT: H 95 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7733 (mt) REVERT: H 152 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8404 (m) REVERT: I 91 PHE cc_start: 0.7298 (t80) cc_final: 0.6180 (t80) REVERT: I 222 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8032 (tttp) REVERT: J 18 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8232 (mp10) REVERT: J 135 LEU cc_start: 0.8534 (mm) cc_final: 0.8237 (mm) REVERT: J 222 LYS cc_start: 0.8533 (mmtt) cc_final: 0.8044 (tttp) REVERT: K 71 GLN cc_start: 0.6998 (mm-40) cc_final: 0.5909 (tp40) REVERT: K 86 ILE cc_start: 0.8168 (mt) cc_final: 0.7858 (mm) REVERT: K 213 PHE cc_start: 0.7479 (t80) cc_final: 0.7170 (t80) REVERT: L 71 GLN cc_start: 0.6721 (mm-40) cc_final: 0.5750 (tp40) REVERT: L 77 GLN cc_start: 0.7489 (mt0) cc_final: 0.7240 (mp10) REVERT: L 213 PHE cc_start: 0.7430 (t80) cc_final: 0.7117 (t80) REVERT: L 344 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7399 (mmpt) REVERT: L 352 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8425 (tp) outliers start: 116 outliers final: 52 residues processed: 531 average time/residue: 1.4449 time to fit residues: 903.7623 Evaluate side-chains 491 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 430 time to evaluate : 5.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 48 optimal weight: 0.7980 chunk 123 optimal weight: 0.0980 chunk 175 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 chunk 332 optimal weight: 1.9990 chunk 330 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 191 optimal weight: 0.0050 chunk 46 optimal weight: 0.0040 overall best weight: 0.5808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN D 70 ASN D 134 GLN E 134 GLN F 134 GLN H 70 ASN J 261 HIS K 115 GLN K 253 ASN K 272 GLN L 272 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.199185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.161376 restraints weight = 27954.154| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.15 r_work: 0.3548 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27452 Z= 0.107 Angle : 0.485 8.816 37260 Z= 0.256 Chirality : 0.042 0.193 4484 Planarity : 0.003 0.042 4576 Dihedral : 8.424 77.764 3904 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.09 % Allowed : 16.96 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.14), residues: 3420 helix: 2.27 (0.12), residues: 1920 sheet: -0.15 (0.25), residues: 400 loop : -0.55 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 181 HIS 0.009 0.001 HIS G 185 PHE 0.031 0.001 PHE I 202 TYR 0.008 0.001 TYR C 73 ARG 0.009 0.000 ARG B 27 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 1572) hydrogen bonds : angle 4.00683 ( 4560) covalent geometry : bond 0.00233 (27452) covalent geometry : angle 0.48456 (37260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 452 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7797 (mtt) REVERT: B 213 ASP cc_start: 0.6831 (m-30) cc_final: 0.6025 (t0) REVERT: C 128 MET cc_start: 0.8083 (mmm) cc_final: 0.7806 (mmm) REVERT: D 85 SER cc_start: 0.8782 (t) cc_final: 0.8445 (m) REVERT: D 95 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7671 (mt) REVERT: F 59 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7825 (mm-30) REVERT: F 128 MET cc_start: 0.8482 (mmm) cc_final: 0.8196 (mmt) REVERT: F 189 ILE cc_start: 0.5850 (OUTLIER) cc_final: 0.5591 (tp) REVERT: F 213 ASP cc_start: 0.7030 (m-30) cc_final: 0.6215 (t0) REVERT: G 62 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8312 (mt-10) REVERT: H 59 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7502 (pm20) REVERT: H 95 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7713 (mt) REVERT: H 152 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8471 (m) REVERT: I 222 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8044 (tttp) REVERT: J 18 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8227 (mp10) REVERT: J 222 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8016 (tttp) REVERT: K 71 GLN cc_start: 0.6960 (mm-40) cc_final: 0.6067 (tm-30) REVERT: K 77 GLN cc_start: 0.7434 (mt0) cc_final: 0.7113 (mp10) REVERT: K 86 ILE cc_start: 0.8199 (mt) cc_final: 0.7898 (mm) REVERT: K 213 PHE cc_start: 0.7481 (t80) cc_final: 0.7169 (t80) REVERT: L 36 MET cc_start: 0.7240 (mmm) cc_final: 0.6902 (mmp) REVERT: L 71 GLN cc_start: 0.6732 (mm-40) cc_final: 0.5741 (tp40) REVERT: L 77 GLN cc_start: 0.7491 (mt0) cc_final: 0.7224 (mp10) REVERT: L 213 PHE cc_start: 0.7438 (t80) cc_final: 0.7128 (t80) REVERT: L 352 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8413 (tp) outliers start: 90 outliers final: 50 residues processed: 515 average time/residue: 1.4216 time to fit residues: 863.6178 Evaluate side-chains 483 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 424 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 24 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 13 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 307 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 339 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 212 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 267 optimal weight: 9.9990 chunk 241 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 8 GLN D 70 ASN D 134 GLN E 134 GLN F 134 GLN H 70 ASN I 253 ASN J 261 HIS K 115 GLN K 253 ASN L 115 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.198300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.160202 restraints weight = 27945.875| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.16 r_work: 0.3547 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27452 Z= 0.120 Angle : 0.501 8.895 37260 Z= 0.263 Chirality : 0.042 0.206 4484 Planarity : 0.003 0.044 4576 Dihedral : 8.491 78.275 3904 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.26 % Allowed : 17.00 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.14), residues: 3420 helix: 2.27 (0.12), residues: 1908 sheet: -0.16 (0.25), residues: 400 loop : -0.56 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 181 HIS 0.007 0.001 HIS G 185 PHE 0.032 0.001 PHE I 202 TYR 0.010 0.001 TYR E 45 ARG 0.008 0.000 ARG B 27 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 1572) hydrogen bonds : angle 4.02379 ( 4560) covalent geometry : bond 0.00273 (27452) covalent geometry : angle 0.50107 (37260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 444 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.6863 (m-30) cc_final: 0.6065 (t0) REVERT: C 128 MET cc_start: 0.8149 (mmm) cc_final: 0.7848 (mmm) REVERT: D 85 SER cc_start: 0.8806 (t) cc_final: 0.8471 (m) REVERT: D 95 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7718 (mt) REVERT: F 59 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7809 (mm-30) REVERT: F 128 MET cc_start: 0.8484 (mmm) cc_final: 0.8158 (mmt) REVERT: F 189 ILE cc_start: 0.5902 (OUTLIER) cc_final: 0.5626 (tp) REVERT: F 213 ASP cc_start: 0.7025 (m-30) cc_final: 0.6228 (t0) REVERT: G 62 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: H 95 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7733 (mt) REVERT: H 152 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8497 (m) REVERT: I 222 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8064 (tttp) REVERT: J 18 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8228 (mp10) REVERT: J 135 LEU cc_start: 0.8565 (mm) cc_final: 0.8227 (mm) REVERT: J 222 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8044 (tttp) REVERT: K 71 GLN cc_start: 0.7096 (mm-40) cc_final: 0.5993 (tp40) REVERT: K 77 GLN cc_start: 0.7429 (mt0) cc_final: 0.7125 (mp10) REVERT: K 86 ILE cc_start: 0.8223 (mt) cc_final: 0.7918 (mm) REVERT: K 213 PHE cc_start: 0.7475 (t80) cc_final: 0.7151 (t80) REVERT: L 71 GLN cc_start: 0.6837 (mm-40) cc_final: 0.5885 (tp40) REVERT: L 213 PHE cc_start: 0.7467 (t80) cc_final: 0.7159 (t80) REVERT: L 344 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7423 (mmpt) REVERT: L 352 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8431 (tp) outliers start: 95 outliers final: 59 residues processed: 509 average time/residue: 1.2978 time to fit residues: 778.2640 Evaluate side-chains 496 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 428 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 24 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 371 ILE Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 125 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 9 optimal weight: 0.1980 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 271 optimal weight: 0.3980 chunk 142 optimal weight: 0.1980 chunk 161 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 318 optimal weight: 3.9990 chunk 330 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN D 70 ASN E 134 GLN F 134 GLN H 70 ASN H 81 ASN H 210 HIS J 261 HIS K 155 GLN K 253 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.199957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.162564 restraints weight = 28082.828| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.13 r_work: 0.3566 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27452 Z= 0.102 Angle : 0.492 11.851 37260 Z= 0.256 Chirality : 0.042 0.187 4484 Planarity : 0.003 0.045 4576 Dihedral : 8.236 74.870 3904 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.68 % Allowed : 18.03 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.14), residues: 3420 helix: 2.35 (0.12), residues: 1924 sheet: -0.17 (0.25), residues: 400 loop : -0.53 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 181 HIS 0.006 0.001 HIS G 185 PHE 0.031 0.001 PHE J 202 TYR 0.009 0.001 TYR G 73 ARG 0.007 0.000 ARG K 436 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 1572) hydrogen bonds : angle 3.94190 ( 4560) covalent geometry : bond 0.00221 (27452) covalent geometry : angle 0.49179 (37260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 456 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.6915 (m-30) cc_final: 0.6090 (t0) REVERT: C 27 ARG cc_start: 0.8490 (ttp80) cc_final: 0.8192 (ttp80) REVERT: C 128 MET cc_start: 0.8042 (mmm) cc_final: 0.7756 (mmm) REVERT: D 85 SER cc_start: 0.8763 (t) cc_final: 0.8416 (m) REVERT: D 95 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7591 (mt) REVERT: D 184 LYS cc_start: 0.7128 (ttpp) cc_final: 0.6849 (ptmt) REVERT: F 59 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7811 (mm-30) REVERT: F 128 MET cc_start: 0.8491 (mmm) cc_final: 0.8169 (mmt) REVERT: F 189 ILE cc_start: 0.5812 (OUTLIER) cc_final: 0.5577 (tp) REVERT: F 213 ASP cc_start: 0.7071 (m-30) cc_final: 0.6254 (t0) REVERT: G 62 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: G 145 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7331 (tp) REVERT: H 95 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7649 (mt) REVERT: H 152 SER cc_start: 0.8813 (p) cc_final: 0.8427 (m) REVERT: I 222 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8075 (tttp) REVERT: J 18 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: J 135 LEU cc_start: 0.8534 (mm) cc_final: 0.8236 (mm) REVERT: J 222 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8025 (tttp) REVERT: K 71 GLN cc_start: 0.7118 (mm-40) cc_final: 0.5955 (tp40) REVERT: K 86 ILE cc_start: 0.8179 (mt) cc_final: 0.7896 (mm) REVERT: K 91 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.6693 (p90) REVERT: K 213 PHE cc_start: 0.7465 (t80) cc_final: 0.7150 (t80) REVERT: L 36 MET cc_start: 0.7175 (mmm) cc_final: 0.6885 (mmp) REVERT: L 71 GLN cc_start: 0.6673 (mm-40) cc_final: 0.5729 (tp40) REVERT: L 213 PHE cc_start: 0.7440 (t80) cc_final: 0.7153 (t80) REVERT: L 344 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7423 (mmpt) REVERT: L 352 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8413 (tp) outliers start: 78 outliers final: 34 residues processed: 509 average time/residue: 1.2741 time to fit residues: 764.6691 Evaluate side-chains 474 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 430 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 172 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 218 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 290 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 59 optimal weight: 20.0000 chunk 154 optimal weight: 1.9990 chunk 280 optimal weight: 0.0980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN D 70 ASN F 134 GLN H 70 ASN I 253 ASN J 261 HIS K 115 GLN K 253 ASN ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.197836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.159984 restraints weight = 28007.170| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.15 r_work: 0.3540 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27452 Z= 0.125 Angle : 0.513 12.929 37260 Z= 0.269 Chirality : 0.042 0.201 4484 Planarity : 0.003 0.044 4576 Dihedral : 8.489 78.021 3904 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.37 % Allowed : 18.65 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.14), residues: 3420 helix: 2.26 (0.12), residues: 1928 sheet: -0.33 (0.24), residues: 416 loop : -0.55 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 181 HIS 0.006 0.001 HIS L 168 PHE 0.032 0.001 PHE I 202 TYR 0.010 0.001 TYR B 108 ARG 0.007 0.000 ARG L 341 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 1572) hydrogen bonds : angle 4.04545 ( 4560) covalent geometry : bond 0.00286 (27452) covalent geometry : angle 0.51342 (37260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 439 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.6912 (m-30) cc_final: 0.6143 (t0) REVERT: C 128 MET cc_start: 0.8100 (mmm) cc_final: 0.7813 (mmm) REVERT: D 85 SER cc_start: 0.8813 (t) cc_final: 0.8495 (m) REVERT: D 95 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7746 (mt) REVERT: D 184 LYS cc_start: 0.7206 (ttpp) cc_final: 0.6876 (ptmt) REVERT: F 59 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: F 128 MET cc_start: 0.8515 (mmm) cc_final: 0.8192 (mmt) REVERT: F 189 ILE cc_start: 0.5874 (OUTLIER) cc_final: 0.5617 (tp) REVERT: F 213 ASP cc_start: 0.7116 (m-30) cc_final: 0.6255 (t0) REVERT: G 62 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: G 145 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7562 (tp) REVERT: H 95 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7757 (mt) REVERT: H 152 SER cc_start: 0.8853 (p) cc_final: 0.8469 (m) REVERT: I 222 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8100 (tttp) REVERT: J 18 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8248 (mp10) REVERT: J 119 ASN cc_start: 0.8378 (t0) cc_final: 0.8091 (t0) REVERT: J 135 LEU cc_start: 0.8530 (mm) cc_final: 0.8234 (mm) REVERT: J 216 MET cc_start: 0.8107 (mmt) cc_final: 0.7382 (mtp) REVERT: J 222 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8050 (tttp) REVERT: K 86 ILE cc_start: 0.8245 (mt) cc_final: 0.7959 (mm) REVERT: K 213 PHE cc_start: 0.7496 (t80) cc_final: 0.7181 (t80) REVERT: L 36 MET cc_start: 0.7214 (mmm) cc_final: 0.6905 (mmp) REVERT: L 213 PHE cc_start: 0.7470 (t80) cc_final: 0.7174 (t80) REVERT: L 344 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7404 (mmpt) REVERT: L 352 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8413 (tp) outliers start: 69 outliers final: 39 residues processed: 491 average time/residue: 1.2976 time to fit residues: 757.1402 Evaluate side-chains 476 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 428 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 216 MET Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 333 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 234 optimal weight: 0.0670 chunk 58 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 chunk 178 optimal weight: 0.0030 chunk 109 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 201 optimal weight: 0.7980 chunk 274 optimal weight: 0.1980 overall best weight: 0.3328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN D 70 ASN F 134 GLN H 70 ASN ** J 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 253 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.200517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.162661 restraints weight = 27938.158| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.14 r_work: 0.3594 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 27452 Z= 0.098 Angle : 0.490 10.019 37260 Z= 0.257 Chirality : 0.042 0.191 4484 Planarity : 0.003 0.043 4576 Dihedral : 8.114 74.332 3904 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.44 % Allowed : 19.92 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.14), residues: 3420 helix: 2.40 (0.12), residues: 1924 sheet: -0.25 (0.27), residues: 352 loop : -0.53 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 181 HIS 0.008 0.001 HIS L 168 PHE 0.029 0.001 PHE I 202 TYR 0.010 0.001 TYR G 73 ARG 0.009 0.000 ARG K 436 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 1572) hydrogen bonds : angle 3.92819 ( 4560) covalent geometry : bond 0.00208 (27452) covalent geometry : angle 0.49042 (37260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 448 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.6908 (m-30) cc_final: 0.6177 (t0) REVERT: C 27 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8156 (ttp80) REVERT: C 128 MET cc_start: 0.7959 (mmm) cc_final: 0.7687 (mmm) REVERT: D 85 SER cc_start: 0.8694 (t) cc_final: 0.8369 (m) REVERT: D 95 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7560 (mt) REVERT: D 184 LYS cc_start: 0.7210 (ttpp) cc_final: 0.6902 (ptmt) REVERT: F 128 MET cc_start: 0.8481 (mmm) cc_final: 0.8161 (mmt) REVERT: F 213 ASP cc_start: 0.7108 (m-30) cc_final: 0.6262 (t0) REVERT: G 27 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8160 (ttp80) REVERT: G 62 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8299 (mt-10) REVERT: G 138 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.8035 (m-30) REVERT: G 145 ILE cc_start: 0.7872 (tt) cc_final: 0.7502 (tp) REVERT: H 95 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7606 (mt) REVERT: H 152 SER cc_start: 0.8759 (p) cc_final: 0.8406 (m) REVERT: I 222 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8070 (tttp) REVERT: J 135 LEU cc_start: 0.8509 (mm) cc_final: 0.8217 (mm) REVERT: J 216 MET cc_start: 0.8038 (mmt) cc_final: 0.7357 (mtp) REVERT: J 222 LYS cc_start: 0.8382 (mmtt) cc_final: 0.8027 (tttp) REVERT: K 71 GLN cc_start: 0.7123 (mm-40) cc_final: 0.6261 (tm-30) REVERT: K 86 ILE cc_start: 0.8176 (mt) cc_final: 0.7933 (mm) REVERT: K 213 PHE cc_start: 0.7450 (t80) cc_final: 0.7147 (t80) REVERT: L 36 MET cc_start: 0.7214 (mmm) cc_final: 0.6936 (mmp) REVERT: L 71 GLN cc_start: 0.6758 (mm-40) cc_final: 0.5664 (tp40) REVERT: L 213 PHE cc_start: 0.7428 (t80) cc_final: 0.7133 (t80) REVERT: L 344 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7413 (mmpt) REVERT: L 352 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8402 (tp) outliers start: 42 outliers final: 24 residues processed: 475 average time/residue: 1.2915 time to fit residues: 721.1235 Evaluate side-chains 460 residues out of total 2912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 430 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 92 MET Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 344 LYS Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 111 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 299 optimal weight: 0.0000 chunk 18 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 189 optimal weight: 0.0870 chunk 264 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 chunk 327 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 overall best weight: 0.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN D 70 ASN F 134 GLN H 70 ASN H 81 ASN H 210 HIS ** J 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN K 253 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.199727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.161621 restraints weight = 28118.680| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.29 r_work: 0.3568 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27452 Z= 0.105 Angle : 0.498 9.921 37260 Z= 0.260 Chirality : 0.042 0.191 4484 Planarity : 0.003 0.044 4576 Dihedral : 8.147 76.877 3904 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.48 % Allowed : 20.12 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.14), residues: 3420 helix: 2.40 (0.12), residues: 1924 sheet: -0.43 (0.26), residues: 368 loop : -0.55 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 181 HIS 0.007 0.001 HIS J 261 PHE 0.030 0.001 PHE I 202 TYR 0.011 0.001 TYR B 108 ARG 0.010 0.000 ARG K 436 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 1572) hydrogen bonds : angle 3.94714 ( 4560) covalent geometry : bond 0.00227 (27452) covalent geometry : angle 0.49796 (37260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21754.29 seconds wall clock time: 380 minutes 7.61 seconds (22807.61 seconds total)