Starting phenix.real_space_refine on Fri Apr 12 22:27:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmh_38477/04_2024/8xmh_38477_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmh_38477/04_2024/8xmh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmh_38477/04_2024/8xmh_38477.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmh_38477/04_2024/8xmh_38477.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmh_38477/04_2024/8xmh_38477_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmh_38477/04_2024/8xmh_38477_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 13.20, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 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: 9.98 Conformation dependent library (CDL) restraints added in 5.1 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... running ksdssp... Secondary structure from input PDB file: 148 helices and 20 sheets defined 49.8% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.91 Creating SS restraints... Processing helix chain 'A' and resid 16 through 27 removed outlier: 3.646A pdb=" N SER A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 60 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 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 124 through 137 Processing helix chain 'A' and resid 211 through 220 removed outlier: 3.710A pdb=" N LYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 27 removed outlier: 3.645A pdb=" N SER B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 60 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 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 124 through 137 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.711A pdb=" N LYS B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 27 removed outlier: 3.645A pdb=" N SER C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 60 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 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 124 through 137 Processing helix chain 'C' and resid 211 through 220 removed outlier: 3.709A pdb=" N LYS C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 27 removed outlier: 3.645A pdb=" N SER D 20 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 60 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 68 through 70 No H-bonds generated for 'chain 'D' and resid 68 through 70' Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'D' and resid 211 through 220 removed outlier: 3.710A pdb=" N LYS D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 27 removed outlier: 3.646A pdb=" N SER E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 60 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 68 through 70 No H-bonds generated for 'chain 'E' and resid 68 through 70' Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 124 through 137 Processing helix chain 'E' and resid 211 through 220 removed outlier: 3.710A pdb=" N LYS E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 27 removed outlier: 3.646A pdb=" N SER F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 60 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 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 107 through 115 Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 211 through 220 removed outlier: 3.710A pdb=" N LYS F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 27 removed outlier: 3.646A pdb=" N SER G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 Processing helix chain 'G' and resid 60 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 68 through 70 No H-bonds generated for 'chain 'G' and resid 68 through 70' Processing helix chain 'G' and resid 82 through 94 Processing helix chain 'G' and resid 107 through 115 Processing helix chain 'G' and resid 124 through 137 Processing helix chain 'G' and resid 211 through 220 removed outlier: 3.710A pdb=" N LYS G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 27 removed outlier: 3.646A pdb=" N SER H 20 " --> pdb=" O ARG H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 Processing helix chain 'H' and resid 60 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 68 through 70 No H-bonds generated for 'chain 'H' and resid 68 through 70' Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'H' and resid 107 through 115 Processing helix chain 'H' and resid 124 through 137 Processing helix chain 'H' and resid 211 through 220 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 36 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 47 through 58 Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 74 through 89 Processing helix chain 'I' and resid 91 through 102 removed outlier: 3.646A pdb=" N LEU I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 117 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 127 through 156 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 159 through 173 removed outlier: 3.924A pdb=" N PHE I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 206 Processing helix chain 'I' and resid 209 through 217 Processing helix chain 'I' and resid 221 through 223 No H-bonds generated for 'chain 'I' and resid 221 through 223' Processing helix chain 'I' and resid 226 through 249 Processing helix chain 'I' and resid 262 through 274 Processing helix chain 'I' and resid 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 291 through 302 Processing helix chain 'I' and resid 316 through 330 Processing helix chain 'I' and resid 345 through 372 Processing helix chain 'I' and resid 377 through 388 Processing helix chain 'I' and resid 398 through 400 No H-bonds generated for 'chain 'I' and resid 398 through 400' Processing helix chain 'I' and resid 403 through 418 removed outlier: 3.518A pdb=" N CYS I 407 " --> pdb=" O THR I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 420 through 427 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 36 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 47 through 58 Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 74 through 89 Processing helix chain 'J' and resid 91 through 102 removed outlier: 3.647A pdb=" N LEU J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 117 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 127 through 156 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 159 through 173 removed outlier: 3.923A pdb=" N PHE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 192 through 206 Processing helix chain 'J' and resid 209 through 217 Processing helix chain 'J' and resid 221 through 223 No H-bonds generated for 'chain 'J' and resid 221 through 223' Processing helix chain 'J' and resid 226 through 249 Processing helix chain 'J' and resid 262 through 274 Processing helix chain 'J' and resid 286 through 288 No H-bonds generated for 'chain 'J' and resid 286 through 288' Processing helix chain 'J' and resid 291 through 302 removed outlier: 3.638A pdb=" N LEU J 299 " --> pdb=" O VAL J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 330 Processing helix chain 'J' and resid 345 through 372 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 398 through 400 No H-bonds generated for 'chain 'J' and resid 398 through 400' Processing helix chain 'J' and resid 403 through 418 removed outlier: 3.519A pdb=" N CYS J 407 " --> pdb=" O THR J 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 420 through 427 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 36 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 47 through 58 Processing helix chain 'K' and resid 68 through 71 No H-bonds generated for 'chain 'K' and resid 68 through 71' Processing helix chain 'K' and resid 74 through 89 Processing helix chain 'K' and resid 91 through 102 removed outlier: 3.647A pdb=" N LEU K 97 " --> pdb=" O THR K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 117 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 127 through 156 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 159 through 173 removed outlier: 3.924A pdb=" N PHE K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 206 Processing helix chain 'K' and resid 209 through 217 Processing helix chain 'K' and resid 221 through 223 No H-bonds generated for 'chain 'K' and resid 221 through 223' Processing helix chain 'K' and resid 226 through 249 Processing helix chain 'K' and resid 262 through 274 Processing helix chain 'K' and resid 286 through 288 No H-bonds generated for 'chain 'K' and resid 286 through 288' Processing helix chain 'K' and resid 291 through 302 Processing helix chain 'K' and resid 316 through 330 Processing helix chain 'K' and resid 345 through 372 Processing helix chain 'K' and resid 377 through 388 Processing helix chain 'K' and resid 398 through 400 No H-bonds generated for 'chain 'K' and resid 398 through 400' Processing helix chain 'K' and resid 403 through 418 removed outlier: 3.519A pdb=" N CYS K 407 " --> pdb=" O THR K 403 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 427 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 36 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 47 through 58 Processing helix chain 'L' and resid 68 through 71 No H-bonds generated for 'chain 'L' and resid 68 through 71' Processing helix chain 'L' and resid 74 through 89 Processing helix chain 'L' and resid 91 through 102 removed outlier: 3.647A pdb=" N LEU L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 117 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 127 through 156 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 159 through 173 removed outlier: 3.923A pdb=" N PHE L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 206 Processing helix chain 'L' and resid 209 through 217 Processing helix chain 'L' and resid 221 through 223 No H-bonds generated for 'chain 'L' and resid 221 through 223' Processing helix chain 'L' and resid 226 through 249 Processing helix chain 'L' and resid 262 through 274 Processing helix chain 'L' and resid 286 through 288 No H-bonds generated for 'chain 'L' and resid 286 through 288' Processing helix chain 'L' and resid 291 through 302 Processing helix chain 'L' and resid 316 through 330 Processing helix chain 'L' and resid 345 through 372 Processing helix chain 'L' and resid 377 through 388 Processing helix chain 'L' and resid 398 through 400 No H-bonds generated for 'chain 'L' and resid 398 through 400' Processing helix chain 'L' and resid 403 through 418 removed outlier: 3.519A pdb=" N CYS L 407 " --> pdb=" O THR L 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 427 removed outlier: 4.130A pdb=" N PHE L 427 " --> pdb=" O PHE L 423 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.588A pdb=" N TYR A 73 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU A 31 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 11 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU A 33 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS A 51 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP A 36 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 53 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 141 through 146 removed outlier: 6.900A pdb=" N GLU A 155 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR A 144 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP A 146 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR A 151 " --> pdb=" O ASP A 146 " (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= C, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.587A pdb=" N TYR B 73 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU B 31 " --> pdb=" O PHE B 9 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL B 11 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU B 33 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS B 51 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP B 36 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL B 53 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 141 through 146 removed outlier: 6.900A pdb=" N GLU B 155 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR B 144 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP B 146 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR B 151 " --> pdb=" O ASP B 146 " (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= E, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.588A pdb=" N TYR C 73 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C 31 " --> pdb=" O PHE C 9 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL C 11 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU C 33 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS C 51 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP C 36 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL C 53 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 141 through 146 removed outlier: 6.900A pdb=" N GLU C 155 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR C 144 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP C 146 " --> pdb=" O TYR C 151 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N TYR C 151 " --> pdb=" O ASP C 146 " (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= G, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.588A pdb=" N TYR D 73 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU D 31 " --> pdb=" O PHE D 9 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL D 11 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU D 33 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS D 51 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASP D 36 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL D 53 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 141 through 146 removed outlier: 6.900A pdb=" N GLU D 155 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR D 144 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE D 153 " --> pdb=" O TYR D 144 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASP D 146 " --> pdb=" O TYR D 151 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N TYR D 151 " --> pdb=" O ASP D 146 " (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= I, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.588A pdb=" N TYR E 73 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU E 31 " --> pdb=" O PHE E 9 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL E 11 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU E 33 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS E 51 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP E 36 " --> pdb=" O HIS E 51 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL E 53 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 141 through 146 removed outlier: 6.900A pdb=" N GLU E 155 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR E 144 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE E 153 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASP E 146 " --> pdb=" O TYR E 151 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR E 151 " --> pdb=" O ASP E 146 " (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= K, first strand: chain 'F' and resid 120 through 122 removed outlier: 3.587A pdb=" N TYR F 73 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU F 31 " --> pdb=" O PHE F 9 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL F 11 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU F 33 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS F 51 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP F 36 " --> pdb=" O HIS F 51 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL F 53 " --> pdb=" O ASP F 36 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 141 through 146 removed outlier: 6.899A pdb=" N GLU F 155 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR F 144 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE F 153 " --> pdb=" O TYR F 144 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASP F 146 " --> pdb=" O TYR F 151 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR F 151 " --> pdb=" O ASP F 146 " (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= M, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.588A pdb=" N TYR G 73 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU G 31 " --> pdb=" O PHE G 9 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL G 11 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU G 33 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS G 51 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP G 36 " --> pdb=" O HIS G 51 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL G 53 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 141 through 146 removed outlier: 6.899A pdb=" N GLU G 155 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR G 144 " --> pdb=" O ILE G 153 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE G 153 " --> pdb=" O TYR G 144 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP G 146 " --> pdb=" O TYR G 151 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR G 151 " --> pdb=" O ASP G 146 " (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= O, first strand: chain 'H' and resid 120 through 122 removed outlier: 3.588A pdb=" N TYR H 73 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU H 31 " --> pdb=" O PHE H 9 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL H 11 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU H 33 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS H 51 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP H 36 " --> pdb=" O HIS H 51 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL H 53 " --> pdb=" O ASP H 36 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 141 through 146 removed outlier: 6.901A pdb=" N GLU H 155 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR H 144 " --> pdb=" O ILE H 153 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE H 153 " --> pdb=" O TYR H 144 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP H 146 " --> pdb=" O TYR H 151 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR H 151 " --> pdb=" O ASP H 146 " (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= Q, 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= R, 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= S, 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= T, 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) 1263 hydrogen bonds defined for protein. 3729 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: 8.96 Time building geometry restraints manager: 10.85 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: 100.43 - 108.37: 1163 108.37 - 116.32: 17714 116.32 - 124.27: 17909 124.27 - 132.21: 422 132.21 - 140.16: 52 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: 9249 2.86 - 3.43: 28733 3.43 - 4.00: 51456 4.00 - 4.57: 73186 4.57 - 5.14: 106691 Nonbonded interactions: 269315 Sorted by model distance: nonbonded pdb=" OE1 GLU A 60 " pdb=" OH TYR H 108 " model vdw 2.290 2.440 nonbonded pdb=" OH TYR D 108 " pdb=" OE1 GLU E 60 " model vdw 2.293 2.440 nonbonded pdb=" OE1 GLU D 60 " pdb=" OH TYR E 108 " model vdw 2.317 2.440 nonbonded pdb=" O ASN K 195 " pdb=" OG1 THR K 199 " model vdw 2.330 2.440 nonbonded pdb=" O ASN J 195 " pdb=" OG1 THR J 199 " model vdw 2.330 2.440 ... (remaining 269310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 3.280 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: 13.530 Check model and map are aligned: 0.390 Set scattering table: 0.260 Process input model: 70.210 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.030 ------------------------------------------------------------------------------- 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= 0.265 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 *********************** 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 fitting. rotamer outliers: 45 poor density : 831 time to evaluate : 2.978 Fit side-chains REVERT: F 128 MET cc_start: 0.7541 (mmm) cc_final: 0.7289 (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: 1.3495 time to fit residues: 1345.0924 Evaluate side-chains 490 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 485 time to evaluate : 3.543 ------------------------------------------------------------------------------- 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: 0.8980 chunk 257 optimal weight: 0.9980 chunk 142 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 chunk 308 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 140 ASN B 70 ASN B 134 GLN C 134 GLN D 70 ASN D 81 ASN D 134 GLN E 30 HIS ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 134 GLN H 70 ASN H 81 ASN H 134 GLN I 120 GLN I 253 ASN I 282 ASN I 432 GLN ** J 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 253 ASN J 282 ASN J 432 GLN K 155 GLN K 195 ASN K 253 ASN K 261 HIS K 432 GLN L 77 GLN L 253 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 27452 Z= 0.348 Angle : 0.598 8.692 37260 Z= 0.314 Chirality : 0.045 0.266 4484 Planarity : 0.004 0.046 4576 Dihedral : 9.553 86.547 3914 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.32 % Allowed : 13.80 % Favored : 80.87 % 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: 0.02 (0.13), residues: 3420 helix: 0.46 (0.11), residues: 1868 sheet: 0.48 (0.27), residues: 400 loop : -0.73 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 181 HIS 0.008 0.001 HIS C 185 PHE 0.043 0.002 PHE I 202 TYR 0.020 0.002 TYR F 107 ARG 0.005 0.001 ARG J 151 *********************** 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 650 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 495 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8335 (t) cc_final: 0.8068 (m) REVERT: A 145 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7964 (tt) REVERT: B 134 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: B 189 ILE cc_start: 0.6829 (OUTLIER) cc_final: 0.6226 (tp) REVERT: C 128 MET cc_start: 0.6725 (mmm) cc_final: 0.6465 (mmp) REVERT: C 135 SER cc_start: 0.8663 (t) cc_final: 0.8386 (m) REVERT: D 23 LYS cc_start: 0.8209 (mttp) cc_final: 0.7950 (mttm) REVERT: D 85 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8241 (m) REVERT: D 95 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7774 (mt) REVERT: D 131 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7914 (mtpt) REVERT: F 189 ILE cc_start: 0.6778 (OUTLIER) cc_final: 0.6230 (tp) REVERT: G 62 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: H 69 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7318 (mtm-85) REVERT: H 85 SER cc_start: 0.8457 (t) cc_final: 0.8236 (m) REVERT: H 95 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7657 (mt) REVERT: H 131 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7824 (mtpt) REVERT: I 110 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: K 71 GLN cc_start: 0.7151 (mm-40) cc_final: 0.6591 (tp40) REVERT: L 352 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8200 (tp) outliers start: 155 outliers final: 48 residues processed: 596 average time/residue: 1.2436 time to fit residues: 876.8236 Evaluate side-chains 498 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 437 time to evaluate : 3.165 ------------------------------------------------------------------------------- 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 72 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 131 LYS 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 D residue 207 ILE Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 152 SER 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 69 ARG Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 131 LYS Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 139 SER 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 I residue 394 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 139 SER 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 321 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 338 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 210 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 chunk 309 optimal weight: 0.9990 chunk 334 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 chunk 306 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN B 8 GLN B 134 GLN D 70 ASN D 81 ASN D 134 GLN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN H 70 ASN H 81 ASN H 134 GLN H 210 HIS ** J 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN K 119 ASN K 253 ASN K 261 HIS K 434 ASN L 115 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3011 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= 0.194 Angle : 0.509 7.129 37260 Z= 0.266 Chirality : 0.042 0.211 4484 Planarity : 0.003 0.047 4576 Dihedral : 8.840 83.704 3912 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.26 % Allowed : 16.76 % Favored : 79.98 % 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: 0.77 (0.14), residues: 3420 helix: 1.32 (0.11), residues: 1868 sheet: 0.34 (0.26), residues: 400 loop : -0.70 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 181 HIS 0.008 0.001 HIS G 185 PHE 0.035 0.001 PHE J 202 TYR 0.022 0.001 TYR F 107 ARG 0.005 0.000 ARG L 341 *********************** 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 573 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 478 time to evaluate : 3.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8246 (t) cc_final: 0.8014 (m) REVERT: A 145 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8046 (tt) REVERT: B 134 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7948 (mp10) REVERT: C 128 MET cc_start: 0.6752 (mmm) cc_final: 0.6469 (mmp) REVERT: C 135 SER cc_start: 0.8571 (t) cc_final: 0.8312 (m) REVERT: D 56 ASN cc_start: 0.8694 (t0) cc_final: 0.8459 (t0) REVERT: D 85 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8224 (m) REVERT: D 95 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7704 (mt) REVERT: F 59 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7258 (mm-30) REVERT: F 189 ILE cc_start: 0.6773 (OUTLIER) cc_final: 0.6231 (tp) REVERT: H 95 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7658 (mt) REVERT: J 18 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8072 (mp10) REVERT: K 71 GLN cc_start: 0.7156 (mm-40) cc_final: 0.6628 (tp40) REVERT: K 344 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7658 (mtpt) REVERT: L 344 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7738 (mtpt) outliers start: 95 outliers final: 39 residues processed: 538 average time/residue: 1.2814 time to fit residues: 811.0203 Evaluate side-chains 481 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 432 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 134 GLN 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 C residue 59 GLU Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 102 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 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 157 LEU Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 139 SER 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 I residue 357 THR Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 344 LYS 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 344 LYS 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 305 optimal weight: 3.9990 chunk 232 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 chunk 34 optimal weight: 0.2980 chunk 147 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 310 optimal weight: 9.9990 chunk 328 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN B 8 GLN B 134 GLN D 38 ASN D 70 ASN D 81 ASN D 134 GLN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 51 HIS F 134 GLN H 70 ASN H 81 ASN ** J 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN K 253 ASN L 115 GLN L 155 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27452 Z= 0.318 Angle : 0.564 7.413 37260 Z= 0.295 Chirality : 0.044 0.256 4484 Planarity : 0.003 0.047 4576 Dihedral : 8.927 85.941 3906 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.53 % Allowed : 16.69 % Favored : 78.78 % 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: 0.67 (0.14), residues: 3420 helix: 1.29 (0.12), residues: 1892 sheet: 0.15 (0.26), residues: 400 loop : -0.80 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 181 HIS 0.007 0.001 HIS G 185 PHE 0.036 0.002 PHE I 202 TYR 0.014 0.001 TYR F 107 ARG 0.009 0.001 ARG J 151 *********************** 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 586 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 454 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 SER cc_start: 0.8295 (t) cc_final: 0.8064 (m) REVERT: A 134 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7546 (mp-120) REVERT: A 145 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8089 (tt) REVERT: C 128 MET cc_start: 0.6783 (mmm) cc_final: 0.6573 (mmp) REVERT: C 135 SER cc_start: 0.8684 (t) cc_final: 0.8401 (m) REVERT: D 23 LYS cc_start: 0.8167 (mttp) cc_final: 0.7949 (mttp) REVERT: D 41 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8322 (mttt) REVERT: D 85 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.8384 (m) REVERT: D 95 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7796 (mt) REVERT: E 181 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6893 (mm) REVERT: F 59 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7276 (mm-30) REVERT: F 189 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6205 (tp) REVERT: G 62 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: H 69 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7298 (mtm-85) REVERT: H 95 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7664 (mt) REVERT: J 18 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: J 91 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.6228 (t80) REVERT: K 71 GLN cc_start: 0.7453 (mm-40) cc_final: 0.6804 (tp40) REVERT: K 213 PHE cc_start: 0.7471 (t80) cc_final: 0.7194 (t80) REVERT: K 344 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7642 (mtpt) REVERT: L 71 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6540 (mm-40) REVERT: L 213 PHE cc_start: 0.7481 (t80) cc_final: 0.7241 (t80) outliers start: 132 outliers final: 61 residues processed: 541 average time/residue: 1.2891 time to fit residues: 821.0563 Evaluate side-chains 507 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 431 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 85 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 85 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 152 SER 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 85 SER Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 85 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 157 LEU Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 140 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 257 LEU Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 357 THR 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 91 PHE Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 344 LYS Chi-restraints excluded: chain 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 71 GLN Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 422 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 0.9990 chunk 186 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 280 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 294 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN B 8 GLN D 70 ASN D 81 ASN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 134 GLN H 70 ASN H 81 ASN J 71 GLN K 155 GLN K 253 ASN L 155 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3429 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= 0.201 Angle : 0.503 7.495 37260 Z= 0.264 Chirality : 0.042 0.210 4484 Planarity : 0.003 0.045 4576 Dihedral : 8.647 82.685 3906 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.78 % Allowed : 17.45 % Favored : 78.78 % 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: 0.95 (0.14), residues: 3420 helix: 1.60 (0.12), residues: 1868 sheet: 0.15 (0.26), residues: 400 loop : -0.76 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 181 HIS 0.005 0.001 HIS G 185 PHE 0.032 0.001 PHE L 202 TYR 0.016 0.001 TYR F 107 ARG 0.007 0.000 ARG J 151 *********************** 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 555 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 445 time to evaluate : 3.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8084 (tt) REVERT: B 59 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: C 128 MET cc_start: 0.6765 (mmm) cc_final: 0.6515 (mmp) REVERT: C 135 SER cc_start: 0.8628 (t) cc_final: 0.8354 (m) REVERT: D 85 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.8264 (m) REVERT: D 95 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7720 (mt) REVERT: F 59 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7251 (mm-30) REVERT: F 189 ILE cc_start: 0.6778 (OUTLIER) cc_final: 0.6220 (tp) REVERT: H 69 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7241 (mtm-85) REVERT: H 95 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7572 (mt) REVERT: I 18 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: I 91 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.6196 (t80) REVERT: J 18 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: J 291 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: K 71 GLN cc_start: 0.7437 (mm-40) cc_final: 0.6821 (tp40) REVERT: K 213 PHE cc_start: 0.7468 (t80) cc_final: 0.7188 (t80) REVERT: K 344 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7641 (mtpt) REVERT: L 71 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6578 (mm-40) REVERT: L 213 PHE cc_start: 0.7458 (t80) cc_final: 0.7205 (t80) REVERT: L 352 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8180 (tp) outliers start: 110 outliers final: 46 residues processed: 520 average time/residue: 1.3496 time to fit residues: 820.8286 Evaluate side-chains 487 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 426 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 59 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 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 152 SER 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 H residue 47 SER Chi-restraints excluded: chain H residue 69 ARG Chi-restraints excluded: chain H residue 85 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 157 LEU Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 140 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 357 THR 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 139 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 291 GLU Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 344 LYS 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 71 GLN Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 321 VAL 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 110 optimal weight: 3.9990 chunk 295 optimal weight: 0.0470 chunk 64 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 81 optimal weight: 0.0030 chunk 328 optimal weight: 0.9990 chunk 273 optimal weight: 0.8980 chunk 152 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 overall best weight: 0.4288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN D 70 ASN D 81 ASN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN H 70 ASN H 81 ASN K 115 GLN K 155 GLN K 253 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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= 0.131 Angle : 0.466 7.429 37260 Z= 0.244 Chirality : 0.041 0.177 4484 Planarity : 0.003 0.044 4576 Dihedral : 8.258 80.826 3906 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.06 % Allowed : 18.48 % Favored : 78.47 % 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: 1.28 (0.14), residues: 3420 helix: 1.93 (0.12), residues: 1872 sheet: 0.20 (0.26), residues: 400 loop : -0.69 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 181 HIS 0.004 0.001 HIS G 185 PHE 0.030 0.001 PHE I 202 TYR 0.011 0.001 TYR F 107 ARG 0.006 0.000 ARG L 436 *********************** 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 551 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 462 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8041 (tt) REVERT: B 59 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7169 (mm-30) REVERT: C 128 MET cc_start: 0.6672 (mmm) cc_final: 0.6431 (mmp) REVERT: C 135 SER cc_start: 0.8595 (t) cc_final: 0.8290 (m) REVERT: D 95 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7666 (mt) REVERT: F 59 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7176 (mm-30) REVERT: F 189 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6262 (tp) REVERT: H 95 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7640 (mt) REVERT: I 24 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7310 (t80) REVERT: I 91 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.6134 (t80) REVERT: I 135 LEU cc_start: 0.8430 (mm) cc_final: 0.8157 (mm) REVERT: J 135 LEU cc_start: 0.8405 (mm) cc_final: 0.8080 (mm) REVERT: J 418 ILE cc_start: 0.8620 (tp) cc_final: 0.8360 (tp) REVERT: K 213 PHE cc_start: 0.7472 (t80) cc_final: 0.7192 (t80) REVERT: K 344 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7604 (mtpt) REVERT: L 71 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6595 (mm-40) REVERT: L 213 PHE cc_start: 0.7462 (t80) cc_final: 0.7210 (t80) REVERT: L 352 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8192 (tp) outliers start: 89 outliers final: 37 residues processed: 517 average time/residue: 1.3195 time to fit residues: 800.5673 Evaluate side-chains 471 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 423 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 59 GLU 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 157 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 59 GLU 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 85 SER Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 85 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 15 THR Chi-restraints excluded: chain I residue 24 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 357 THR 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 357 THR Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 344 LYS Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 71 GLN Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 240 optimal weight: 7.9990 chunk 186 optimal weight: 0.8980 chunk 276 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 327 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN D 70 ASN D 81 ASN D 134 GLN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 134 GLN H 70 ASN H 81 ASN K 155 GLN K 253 ASN L 155 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27452 Z= 0.257 Angle : 0.531 7.993 37260 Z= 0.276 Chirality : 0.043 0.228 4484 Planarity : 0.003 0.045 4576 Dihedral : 8.592 82.844 3904 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.12 % Allowed : 17.72 % Favored : 78.16 % 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: 1.08 (0.14), residues: 3420 helix: 1.71 (0.12), residues: 1888 sheet: 0.09 (0.25), residues: 400 loop : -0.71 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 181 HIS 0.006 0.001 HIS L 168 PHE 0.032 0.002 PHE J 202 TYR 0.012 0.001 TYR F 107 ARG 0.007 0.000 ARG K 436 *********************** 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 549 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 429 time to evaluate : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8070 (tt) REVERT: B 59 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7189 (mm-30) REVERT: B 134 GLN cc_start: 0.8424 (mp10) cc_final: 0.7917 (mp10) REVERT: C 128 MET cc_start: 0.6820 (mmm) cc_final: 0.6529 (mmp) REVERT: C 135 SER cc_start: 0.8669 (t) cc_final: 0.8377 (m) REVERT: D 41 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8350 (mttt) REVERT: D 95 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7772 (mt) REVERT: F 59 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7197 (mm-30) REVERT: F 189 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6175 (tp) REVERT: H 95 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7732 (mt) REVERT: I 24 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7375 (t80) REVERT: K 71 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.6924 (tp40) REVERT: K 213 PHE cc_start: 0.7472 (t80) cc_final: 0.7194 (t80) REVERT: L 213 PHE cc_start: 0.7453 (t80) cc_final: 0.7207 (t80) REVERT: L 344 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7472 (mmtm) REVERT: L 352 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8203 (tp) outliers start: 120 outliers final: 62 residues processed: 513 average time/residue: 1.2978 time to fit residues: 783.3067 Evaluate side-chains 484 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 412 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 59 GLU 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 C residue 85 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 85 SER 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 47 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 141 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 59 GLU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 85 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 157 LEU Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 24 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 181 TRP Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 357 THR 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 314 ILE Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR 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 202 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 208 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 257 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN B 210 HIS D 81 ASN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 134 GLN H 70 ASN H 81 ASN K 115 GLN K 155 GLN K 253 ASN L 115 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27452 Z= 0.171 Angle : 0.493 7.484 37260 Z= 0.257 Chirality : 0.042 0.199 4484 Planarity : 0.003 0.045 4576 Dihedral : 8.408 80.476 3904 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.75 % Allowed : 19.33 % Favored : 77.92 % 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: 1.25 (0.14), residues: 3420 helix: 1.86 (0.12), residues: 1880 sheet: 0.08 (0.25), residues: 416 loop : -0.62 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 181 HIS 0.005 0.001 HIS L 168 PHE 0.030 0.001 PHE L 202 TYR 0.012 0.001 TYR F 107 ARG 0.006 0.000 ARG L 436 *********************** 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 515 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 435 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8027 (tt) REVERT: B 28 MET cc_start: 0.7689 (mtt) cc_final: 0.7363 (mtt) REVERT: B 59 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7167 (mm-30) REVERT: B 134 GLN cc_start: 0.8368 (mp10) cc_final: 0.7908 (mp10) REVERT: C 128 MET cc_start: 0.6786 (mmm) cc_final: 0.6554 (mmp) REVERT: C 135 SER cc_start: 0.8691 (t) cc_final: 0.8409 (m) REVERT: D 41 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8346 (mttt) REVERT: D 95 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7705 (mt) REVERT: F 59 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7174 (mm-30) REVERT: F 189 ILE cc_start: 0.6736 (OUTLIER) cc_final: 0.6223 (tp) REVERT: H 95 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7688 (mt) REVERT: H 208 MET cc_start: 0.7769 (ptm) cc_final: 0.7521 (ptt) REVERT: I 18 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: I 24 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.7406 (t80) REVERT: J 135 LEU cc_start: 0.8405 (mm) cc_final: 0.8061 (mm) REVERT: K 71 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: K 213 PHE cc_start: 0.7460 (t80) cc_final: 0.7181 (t80) REVERT: L 71 GLN cc_start: 0.6998 (mm-40) cc_final: 0.6586 (tp40) REVERT: L 213 PHE cc_start: 0.7450 (t80) cc_final: 0.7199 (t80) REVERT: L 344 LYS cc_start: 0.8075 (mtmm) cc_final: 0.7470 (mmtm) REVERT: L 352 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8199 (tp) outliers start: 80 outliers final: 46 residues processed: 493 average time/residue: 1.3411 time to fit residues: 772.2753 Evaluate side-chains 480 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 423 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 59 GLU 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 C residue 65 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 85 SER 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 47 SER Chi-restraints excluded: chain E residue 85 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 85 SER Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 24 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 181 TRP Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 357 THR 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 314 ILE Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR 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 298 optimal weight: 0.8980 chunk 313 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 chunk 305 optimal weight: 0.0770 chunk 183 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 275 optimal weight: 0.8980 chunk 288 optimal weight: 5.9990 chunk 304 optimal weight: 6.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN H 70 ASN H 81 ASN J 85 GLN K 155 GLN K 253 ASN L 155 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 : 0.003 0.041 27452 Z= 0.187 Angle : 0.504 8.397 37260 Z= 0.263 Chirality : 0.042 0.205 4484 Planarity : 0.003 0.046 4576 Dihedral : 8.416 80.660 3904 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.58 % Allowed : 19.71 % Favored : 77.71 % 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: 1.23 (0.14), residues: 3420 helix: 1.82 (0.12), residues: 1904 sheet: 0.08 (0.25), residues: 416 loop : -0.63 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 181 HIS 0.007 0.001 HIS L 168 PHE 0.030 0.001 PHE L 202 TYR 0.025 0.001 TYR F 107 ARG 0.007 0.000 ARG L 341 *********************** 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 501 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 426 time to evaluate : 3.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8027 (tt) REVERT: B 59 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7173 (mm-30) REVERT: C 128 MET cc_start: 0.6791 (mmm) cc_final: 0.6574 (mmp) REVERT: C 135 SER cc_start: 0.8680 (t) cc_final: 0.8418 (m) REVERT: D 41 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8345 (mttt) REVERT: D 95 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7715 (mt) REVERT: F 59 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7153 (mm-30) REVERT: F 189 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.6294 (tp) REVERT: H 95 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7700 (mt) REVERT: H 208 MET cc_start: 0.7758 (ptm) cc_final: 0.7439 (ptt) REVERT: I 18 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8075 (mt0) REVERT: I 24 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7449 (t80) REVERT: K 71 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: K 213 PHE cc_start: 0.7435 (t80) cc_final: 0.7163 (t80) REVERT: L 71 GLN cc_start: 0.7042 (mm-40) cc_final: 0.6731 (tp40) REVERT: L 213 PHE cc_start: 0.7458 (t80) cc_final: 0.7204 (t80) REVERT: L 344 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7464 (mmtm) REVERT: L 352 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8200 (tp) outliers start: 75 outliers final: 53 residues processed: 488 average time/residue: 1.3601 time to fit residues: 784.9588 Evaluate side-chains 478 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 414 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 59 GLU 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 C residue 85 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 85 SER 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 47 SER Chi-restraints excluded: chain E residue 85 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 152 SER 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 85 SER Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 24 PHE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 181 TRP Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 357 THR 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 314 ILE Chi-restraints excluded: chain L residue 321 VAL Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR 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 200 optimal weight: 0.6980 chunk 322 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 153 optimal weight: 0.4980 chunk 224 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 chunk 311 optimal weight: 0.7980 chunk 269 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 165 optimal weight: 0.0870 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN B 210 HIS D 81 ASN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 134 GLN H 70 ASN H 81 ASN H 143 ASN K 115 GLN K 155 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27452 Z= 0.148 Angle : 0.484 9.943 37260 Z= 0.253 Chirality : 0.042 0.196 4484 Planarity : 0.003 0.047 4576 Dihedral : 8.251 80.746 3904 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.40 % Allowed : 20.02 % Favored : 77.58 % 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: 1.36 (0.14), residues: 3420 helix: 1.93 (0.12), residues: 1904 sheet: 0.14 (0.25), residues: 416 loop : -0.59 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 181 HIS 0.007 0.001 HIS L 168 PHE 0.029 0.001 PHE L 202 TYR 0.024 0.001 TYR F 107 ARG 0.007 0.000 ARG L 341 ********************** 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 500 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 430 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8025 (tt) REVERT: B 134 GLN cc_start: 0.8415 (mp10) cc_final: 0.7884 (mp10) REVERT: C 128 MET cc_start: 0.6698 (mmm) cc_final: 0.6447 (mmp) REVERT: C 135 SER cc_start: 0.8664 (t) cc_final: 0.8436 (m) REVERT: D 41 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8352 (mttt) REVERT: D 95 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7659 (mt) REVERT: F 189 ILE cc_start: 0.6757 (OUTLIER) cc_final: 0.6280 (tp) REVERT: H 95 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7649 (mt) REVERT: H 208 MET cc_start: 0.7780 (ptm) cc_final: 0.7498 (ptt) REVERT: K 71 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: K 213 PHE cc_start: 0.7427 (t80) cc_final: 0.7152 (t80) REVERT: L 71 GLN cc_start: 0.7028 (mm-40) cc_final: 0.6721 (tp40) REVERT: L 213 PHE cc_start: 0.7444 (t80) cc_final: 0.7191 (t80) REVERT: L 344 LYS cc_start: 0.8035 (mtmm) cc_final: 0.7458 (mmtm) REVERT: L 352 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8205 (tp) outliers start: 70 outliers final: 46 residues processed: 485 average time/residue: 1.2583 time to fit residues: 718.5113 Evaluate side-chains 470 residues out of total 2912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 417 time to evaluate : 2.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 ILE 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 C residue 181 LEU Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 85 SER 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 47 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 141 VAL 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 85 SER Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 357 THR Chi-restraints excluded: chain J residue 371 ILE Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 181 TRP Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 0.0980 chunk 287 optimal weight: 0.1980 chunk 82 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN B 210 HIS D 81 ASN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 134 GLN H 70 ASN H 81 ASN H 143 ASN K 253 ASN L 115 GLN L 253 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.196224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.158248 restraints weight = 27902.712| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.18 r_work: 0.3515 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27452 Z= 0.197 Angle : 0.513 11.609 37260 Z= 0.266 Chirality : 0.042 0.209 4484 Planarity : 0.003 0.047 4576 Dihedral : 8.378 80.594 3904 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.47 % Allowed : 20.19 % Favored : 77.34 % 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: 1.26 (0.14), residues: 3420 helix: 1.84 (0.12), residues: 1904 sheet: 0.12 (0.25), residues: 416 loop : -0.62 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 181 HIS 0.008 0.001 HIS L 168 PHE 0.030 0.001 PHE L 202 TYR 0.019 0.001 TYR F 107 ARG 0.006 0.000 ARG L 341 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11979.52 seconds wall clock time: 214 minutes 45.47 seconds (12885.47 seconds total)