Starting phenix.real_space_refine on Sun Mar 17 01:46:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p53_17445/03_2024/8p53_17445_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p53_17445/03_2024/8p53_17445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p53_17445/03_2024/8p53_17445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p53_17445/03_2024/8p53_17445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p53_17445/03_2024/8p53_17445_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p53_17445/03_2024/8p53_17445_updated.pdb" } resolution = 2.7 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= 0.018 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 76 5.16 5 C 10253 2.51 5 N 2937 2.21 5 O 3025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 116": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16299 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2028 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain: "B" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2028 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain: "C" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2996 Classifications: {'peptide': 378} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 361} Chain breaks: 1 Chain: "D" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2989 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 360} Chain breaks: 1 Chain: "E" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3097 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 372} Chain: "F" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3097 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 372} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.85, per 1000 atoms: 0.54 Number of scatterers: 16299 At special positions: 0 Unit cell: (200.64, 74.58, 119.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 76 16.00 P 6 15.00 Mg 2 11.99 O 3025 8.00 N 2937 7.00 C 10253 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: 7.00 Conformation dependent library (CDL) restraints added in 3.1 seconds 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3850 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 14 sheets defined 43.3% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 24 through 38 Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 104 through 116 removed outlier: 4.328A pdb=" N SER A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASP A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 230 through 233 No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'A' and resid 238 through 252 removed outlier: 3.524A pdb=" N SER A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'B' and resid 24 through 38 Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 104 through 116 removed outlier: 4.325A pdb=" N SER B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 154 through 171 Processing helix chain 'B' and resid 186 through 203 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 230 through 233 No H-bonds generated for 'chain 'B' and resid 230 through 233' Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'C' and resid 14 through 26 Processing helix chain 'C' and resid 39 through 45 Processing helix chain 'C' and resid 66 through 76 removed outlier: 3.580A pdb=" N LYS C 71 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 111 through 128 Processing helix chain 'C' and resid 151 through 163 Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 208 through 216 removed outlier: 4.618A pdb=" N GLU C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N SER C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 236 No H-bonds generated for 'chain 'C' and resid 233 through 236' Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 252 through 264 Processing helix chain 'C' and resid 290 through 296 Processing helix chain 'C' and resid 301 through 307 Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 321 through 338 removed outlier: 4.722A pdb=" N ALA C 325 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 332 " --> pdb=" O ASN C 329 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU C 338 " --> pdb=" O MET C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 361 through 375 Processing helix chain 'D' and resid 14 through 26 Processing helix chain 'D' and resid 39 through 45 Processing helix chain 'D' and resid 66 through 76 removed outlier: 3.586A pdb=" N LYS D 71 " --> pdb=" O VAL D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 111 through 128 Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 180 through 189 Processing helix chain 'D' and resid 208 through 216 removed outlier: 4.620A pdb=" N GLU D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 252 through 264 Processing helix chain 'D' and resid 290 through 296 Processing helix chain 'D' and resid 301 through 307 Processing helix chain 'D' and resid 317 through 319 No H-bonds generated for 'chain 'D' and resid 317 through 319' Processing helix chain 'D' and resid 321 through 338 removed outlier: 4.771A pdb=" N ALA D 325 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE D 332 " --> pdb=" O ASN D 329 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 338 " --> pdb=" O MET D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 354 Processing helix chain 'D' and resid 361 through 375 Processing helix chain 'E' and resid 14 through 26 Processing helix chain 'E' and resid 39 through 45 removed outlier: 4.498A pdb=" N GLY E 45 " --> pdb=" O GLU E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 51 No H-bonds generated for 'chain 'E' and resid 49 through 51' Processing helix chain 'E' and resid 66 through 76 Processing helix chain 'E' and resid 111 through 131 removed outlier: 3.596A pdb=" N MET E 127 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP E 129 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLN E 130 " --> pdb=" O GLU E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 164 Processing helix chain 'E' and resid 180 through 189 Processing helix chain 'E' and resid 211 through 216 Processing helix chain 'E' and resid 233 through 236 No H-bonds generated for 'chain 'E' and resid 233 through 236' Processing helix chain 'E' and resid 247 through 249 No H-bonds generated for 'chain 'E' and resid 247 through 249' Processing helix chain 'E' and resid 252 through 263 Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 301 through 307 Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 321 through 337 removed outlier: 4.734A pdb=" N ALA E 325 " --> pdb=" O GLU E 322 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE E 332 " --> pdb=" O ASN E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 355 Processing helix chain 'E' and resid 361 through 375 Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'F' and resid 14 through 27 Processing helix chain 'F' and resid 39 through 45 removed outlier: 4.507A pdb=" N GLY F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 66 through 76 Processing helix chain 'F' and resid 111 through 131 removed outlier: 3.542A pdb=" N MET F 127 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP F 129 " --> pdb=" O ARG F 125 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLN F 130 " --> pdb=" O GLU F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 164 Processing helix chain 'F' and resid 180 through 189 Processing helix chain 'F' and resid 211 through 216 Processing helix chain 'F' and resid 233 through 236 No H-bonds generated for 'chain 'F' and resid 233 through 236' Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 252 through 263 Processing helix chain 'F' and resid 290 through 295 Processing helix chain 'F' and resid 301 through 307 Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 321 through 337 removed outlier: 4.723A pdb=" N ALA F 325 " --> pdb=" O GLU F 322 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE F 332 " --> pdb=" O ASN F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 355 Processing helix chain 'F' and resid 361 through 375 Processing helix chain 'F' and resid 388 through 390 No H-bonds generated for 'chain 'F' and resid 388 through 390' Processing sheet with id= A, first strand: chain 'A' and resid 207 through 214 removed outlier: 7.475A pdb=" N ALA A 180 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 213 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL A 146 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A 124 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL A 15 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 126 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG A 88 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 207 through 214 removed outlier: 7.489A pdb=" N ALA B 180 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 213 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL B 146 " --> pdb=" O ARG B 175 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 124 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL B 15 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 126 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG B 88 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 31 through 34 removed outlier: 6.654A pdb=" N LEU C 7 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N CYS C 34 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU C 9 " --> pdb=" O CYS C 34 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU C 57 " --> pdb=" O PRO C 81 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU C 83 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 310 through 313 Processing sheet with id= E, first strand: chain 'C' and resid 266 through 268 Processing sheet with id= F, first strand: chain 'D' and resid 31 through 34 removed outlier: 6.664A pdb=" N LEU D 7 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N CYS D 34 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU D 9 " --> pdb=" O CYS D 34 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU D 57 " --> pdb=" O PRO D 81 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU D 83 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 310 through 313 Processing sheet with id= H, first strand: chain 'D' and resid 266 through 268 Processing sheet with id= I, first strand: chain 'E' and resid 31 through 34 removed outlier: 6.614A pdb=" N LEU E 7 " --> pdb=" O LEU E 32 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N CYS E 34 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU E 9 " --> pdb=" O CYS E 34 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU E 57 " --> pdb=" O PRO E 81 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU E 83 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU E 84 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER E 104 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 311 through 314 removed outlier: 6.645A pdb=" N LEU E 171 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N MET E 314 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU E 173 " --> pdb=" O MET E 314 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 266 through 268 Processing sheet with id= L, first strand: chain 'F' and resid 31 through 34 removed outlier: 6.608A pdb=" N LEU F 7 " --> pdb=" O LEU F 32 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N CYS F 34 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU F 9 " --> pdb=" O CYS F 34 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU F 57 " --> pdb=" O PRO F 81 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU F 83 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU F 84 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER F 104 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 311 through 314 removed outlier: 6.665A pdb=" N LEU F 171 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N MET F 314 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU F 173 " --> pdb=" O MET F 314 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 266 through 268 623 hydrogen bonds defined for protein. 1707 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: 5.07 Time building geometry restraints manager: 7.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5600 1.34 - 1.46: 3057 1.46 - 1.58: 7778 1.58 - 1.70: 6 1.70 - 1.82: 136 Bond restraints: 16577 Sorted by residual: bond pdb=" O3A ACP A 302 " pdb=" PB ACP A 302 " ideal model delta sigma weight residual 1.698 1.586 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" O3A ACP B 302 " pdb=" PB ACP B 302 " ideal model delta sigma weight residual 1.698 1.587 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C3B ACP A 302 " pdb=" PG ACP A 302 " ideal model delta sigma weight residual 1.875 1.791 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C3B ACP B 302 " pdb=" PG ACP B 302 " ideal model delta sigma weight residual 1.875 1.794 0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" O5' ACP A 302 " pdb=" PA ACP A 302 " ideal model delta sigma weight residual 1.659 1.601 0.058 2.00e-02 2.50e+03 8.39e+00 ... (remaining 16572 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.65: 369 105.65 - 112.73: 8877 112.73 - 119.82: 5551 119.82 - 126.90: 7444 126.90 - 133.98: 193 Bond angle restraints: 22434 Sorted by residual: angle pdb=" N ALA C 222 " pdb=" CA ALA C 222 " pdb=" C ALA C 222 " ideal model delta sigma weight residual 114.56 109.80 4.76 1.27e+00 6.20e-01 1.40e+01 angle pdb=" N ALA D 222 " pdb=" CA ALA D 222 " pdb=" C ALA D 222 " ideal model delta sigma weight residual 114.56 109.88 4.68 1.27e+00 6.20e-01 1.36e+01 angle pdb=" C3B ACP B 302 " pdb=" PB ACP B 302 " pdb=" O3A ACP B 302 " ideal model delta sigma weight residual 98.05 106.52 -8.47 3.00e+00 1.11e-01 7.96e+00 angle pdb=" CA ALA D 222 " pdb=" C ALA D 222 " pdb=" N PHE D 223 " ideal model delta sigma weight residual 119.26 116.12 3.14 1.14e+00 7.69e-01 7.61e+00 angle pdb=" CA ALA C 222 " pdb=" C ALA C 222 " pdb=" N PHE C 223 " ideal model delta sigma weight residual 119.26 116.12 3.14 1.14e+00 7.69e-01 7.59e+00 ... (remaining 22429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 9349 17.75 - 35.50: 695 35.50 - 53.25: 86 53.25 - 71.00: 29 71.00 - 88.75: 23 Dihedral angle restraints: 10182 sinusoidal: 4229 harmonic: 5953 Sorted by residual: dihedral pdb=" CA GLY F 360 " pdb=" C GLY F 360 " pdb=" N ASN F 361 " pdb=" CA ASN F 361 " ideal model delta harmonic sigma weight residual 180.00 -157.57 -22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA GLY E 360 " pdb=" C GLY E 360 " pdb=" N ASN E 361 " pdb=" CA ASN E 361 " ideal model delta harmonic sigma weight residual -180.00 -158.19 -21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ARG E 99 " pdb=" C ARG E 99 " pdb=" N ARG E 100 " pdb=" CA ARG E 100 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 10179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1952 0.048 - 0.095: 489 0.095 - 0.143: 104 0.143 - 0.190: 3 0.190 - 0.238: 2 Chirality restraints: 2550 Sorted by residual: chirality pdb=" C2' ACP B 302 " pdb=" C1' ACP B 302 " pdb=" C3' ACP B 302 " pdb=" O2' ACP B 302 " both_signs ideal model delta sigma weight residual False -2.75 -2.52 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C3' ACP B 302 " pdb=" C2' ACP B 302 " pdb=" C4' ACP B 302 " pdb=" O3' ACP B 302 " both_signs ideal model delta sigma weight residual False -2.57 -2.80 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU F 24 " pdb=" CB LEU F 24 " pdb=" CD1 LEU F 24 " pdb=" CD2 LEU F 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 2547 not shown) Planarity restraints: 2927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 305 " -0.021 2.00e-02 2.50e+03 2.03e-02 8.27e+00 pdb=" CG TYR E 305 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR E 305 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR E 305 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 305 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 305 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR E 305 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 305 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 305 " -0.021 2.00e-02 2.50e+03 1.97e-02 7.78e+00 pdb=" CG TYR F 305 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR F 305 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR F 305 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 305 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 305 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR F 305 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 305 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 141 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" C ASN F 141 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN F 141 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU F 142 " 0.013 2.00e-02 2.50e+03 ... (remaining 2924 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 97 2.53 - 3.13: 12400 3.13 - 3.72: 25339 3.72 - 4.31: 34774 4.31 - 4.90: 57814 Nonbonded interactions: 130424 Sorted by model distance: nonbonded pdb=" OG1 THR A 25 " pdb="MG MG A 301 " model vdw 1.943 2.170 nonbonded pdb=" OG1 THR B 25 " pdb="MG MG B 301 " model vdw 1.998 2.170 nonbonded pdb=" OG SER D 150 " pdb=" OD1 ASP D 323 " model vdw 2.046 2.440 nonbonded pdb=" OD2 ASP A 217 " pdb=" OG SER A 237 " model vdw 2.076 2.440 nonbonded pdb=" OD2 ASP B 217 " pdb=" OG SER B 237 " model vdw 2.077 2.440 ... (remaining 130419 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 4 through 392) selection = chain 'D' selection = (chain 'E' and (resid 4 through 129 or resid 142 through 392)) selection = (chain 'F' and (resid 4 through 129 or resid 142 through 392)) } 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: 9.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 34.900 Check model and map are aligned: 0.260 Set scattering table: 0.180 Process input model: 47.350 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 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:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 0.112 16577 Z= 0.253 Angle : 0.654 8.466 22434 Z= 0.329 Chirality : 0.043 0.238 2550 Planarity : 0.004 0.033 2927 Dihedral : 13.216 88.751 6332 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.11 % Allowed : 0.06 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % 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: -0.24 (0.18), residues: 2055 helix: 0.59 (0.17), residues: 995 sheet: -0.89 (0.31), residues: 235 loop : -0.74 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 358 HIS 0.005 0.001 HIS D 287 PHE 0.016 0.001 PHE F 143 TYR 0.049 0.002 TYR E 305 ARG 0.006 0.001 ARG E 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 496 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 155 THR cc_start: 0.8536 (p) cc_final: 0.8041 (p) REVERT: C 10 ILE cc_start: 0.8162 (mm) cc_final: 0.7904 (pt) REVERT: C 19 ASP cc_start: 0.7383 (t0) cc_final: 0.7040 (t0) REVERT: C 57 LEU cc_start: 0.7694 (tp) cc_final: 0.7302 (tp) REVERT: C 113 LYS cc_start: 0.7731 (mtmm) cc_final: 0.7470 (mtmm) REVERT: D 8 LEU cc_start: 0.8010 (mt) cc_final: 0.7803 (mt) REVERT: D 233 ARG cc_start: 0.8278 (mtp85) cc_final: 0.7927 (mtp85) REVERT: D 351 MET cc_start: 0.7451 (tmm) cc_final: 0.7086 (tmm) REVERT: D 370 GLU cc_start: 0.7423 (tp30) cc_final: 0.7063 (tp30) REVERT: E 212 GLU cc_start: 0.8041 (tp30) cc_final: 0.7772 (tp30) REVERT: E 259 LEU cc_start: 0.8900 (tp) cc_final: 0.8674 (tt) REVERT: E 295 GLU cc_start: 0.7273 (mp0) cc_final: 0.6735 (mp0) REVERT: E 336 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7612 (tt0) REVERT: F 106 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7385 (tm-30) REVERT: F 202 ASN cc_start: 0.8335 (t0) cc_final: 0.7923 (t0) REVERT: F 246 GLU cc_start: 0.7381 (pt0) cc_final: 0.7148 (pt0) REVERT: F 385 GLU cc_start: 0.8093 (mp0) cc_final: 0.7580 (mp0) outliers start: 2 outliers final: 2 residues processed: 496 average time/residue: 1.3994 time to fit residues: 758.2732 Evaluate side-chains 455 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 453 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain E residue 141 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 144 GLN A 227 GLN B 11 GLN B 53 ASN B 209 GLN B 227 GLN D 13 ASN E 72 GLN E 277 ASN F 72 GLN F 190 HIS F 277 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 16577 Z= 0.505 Angle : 0.647 7.013 22434 Z= 0.331 Chirality : 0.048 0.173 2550 Planarity : 0.005 0.070 2927 Dihedral : 5.848 71.788 2341 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 2.68 % Allowed : 10.62 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % 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: -0.44 (0.18), residues: 2055 helix: 0.38 (0.17), residues: 988 sheet: -0.78 (0.32), residues: 204 loop : -0.86 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 39 HIS 0.007 0.001 HIS C 287 PHE 0.032 0.002 PHE F 143 TYR 0.035 0.002 TYR E 124 ARG 0.010 0.001 ARG E 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 483 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8628 (mtm-85) cc_final: 0.8356 (mtm180) REVERT: A 214 ILE cc_start: 0.8956 (mm) cc_final: 0.8639 (mm) REVERT: B 41 ARG cc_start: 0.8382 (mpp-170) cc_final: 0.8147 (mpp-170) REVERT: B 73 ARG cc_start: 0.8705 (mtm-85) cc_final: 0.8492 (mtm180) REVERT: C 16 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7553 (ttm170) REVERT: C 57 LEU cc_start: 0.7966 (tp) cc_final: 0.7669 (tp) REVERT: C 72 GLN cc_start: 0.7673 (mp10) cc_final: 0.7468 (mp10) REVERT: C 113 LYS cc_start: 0.8015 (mtmm) cc_final: 0.7737 (mtmm) REVERT: C 296 ASP cc_start: 0.7660 (m-30) cc_final: 0.7345 (m-30) REVERT: C 351 MET cc_start: 0.7605 (tmm) cc_final: 0.7065 (tmm) REVERT: D 19 ASP cc_start: 0.7325 (t0) cc_final: 0.7105 (t0) REVERT: D 106 GLU cc_start: 0.7804 (pp20) cc_final: 0.7578 (tm-30) REVERT: D 175 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7672 (mt-10) REVERT: D 214 GLU cc_start: 0.8114 (tp30) cc_final: 0.7895 (tp30) REVERT: D 351 MET cc_start: 0.7536 (tmm) cc_final: 0.7029 (tmm) REVERT: D 370 GLU cc_start: 0.7517 (tp30) cc_final: 0.7262 (tp30) REVERT: E 6 LYS cc_start: 0.8157 (mttp) cc_final: 0.7768 (mttp) REVERT: E 192 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8317 (mttp) REVERT: E 202 ASN cc_start: 0.8409 (t0) cc_final: 0.8152 (t0) REVERT: E 210 LEU cc_start: 0.8418 (tp) cc_final: 0.8113 (tp) REVERT: E 212 GLU cc_start: 0.8083 (tp30) cc_final: 0.7678 (tp30) REVERT: E 230 ARG cc_start: 0.6832 (tmm-80) cc_final: 0.6528 (tmm-80) REVERT: E 295 GLU cc_start: 0.7348 (mp0) cc_final: 0.6759 (mp0) REVERT: E 322 GLU cc_start: 0.7733 (pm20) cc_final: 0.7498 (pm20) REVERT: E 336 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7710 (mt-10) REVERT: E 355 ARG cc_start: 0.8065 (mtp180) cc_final: 0.7389 (mtp180) REVERT: F 6 LYS cc_start: 0.8149 (mttp) cc_final: 0.7941 (mttp) REVERT: F 100 ARG cc_start: 0.6677 (ttm-80) cc_final: 0.6477 (ttt90) REVERT: F 106 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7386 (tm-30) REVERT: F 126 GLU cc_start: 0.7094 (tp30) cc_final: 0.6878 (tp30) REVERT: F 202 ASN cc_start: 0.8257 (t0) cc_final: 0.8011 (t0) REVERT: F 230 ARG cc_start: 0.6730 (tmm-80) cc_final: 0.6390 (tmm-80) REVERT: F 385 GLU cc_start: 0.8092 (mp0) cc_final: 0.7782 (mp0) outliers start: 47 outliers final: 20 residues processed: 489 average time/residue: 1.4106 time to fit residues: 755.9003 Evaluate side-chains 500 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 478 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 314 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 185 optimal weight: 0.7980 chunk 200 optimal weight: 0.3980 chunk 165 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 162 GLN D 255 GLN E 72 GLN E 263 GLN E 277 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16577 Z= 0.236 Angle : 0.535 6.023 22434 Z= 0.271 Chirality : 0.041 0.155 2550 Planarity : 0.004 0.038 2927 Dihedral : 5.294 66.670 2337 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.86 % Allowed : 13.36 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % 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: -0.27 (0.18), residues: 2055 helix: 0.60 (0.17), residues: 988 sheet: -0.81 (0.32), residues: 204 loop : -0.84 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 76 HIS 0.005 0.001 HIS E 190 PHE 0.014 0.001 PHE D 223 TYR 0.028 0.001 TYR E 124 ARG 0.008 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 468 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8585 (mtm-85) cc_final: 0.8282 (mtm180) REVERT: A 202 ARG cc_start: 0.7180 (ttp-170) cc_final: 0.6979 (ttp-170) REVERT: A 214 ILE cc_start: 0.8940 (mm) cc_final: 0.8601 (mm) REVERT: C 7 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8041 (tt) REVERT: C 113 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7724 (mtmm) REVERT: C 292 LYS cc_start: 0.7720 (tptp) cc_final: 0.7305 (tptp) REVERT: C 296 ASP cc_start: 0.7640 (m-30) cc_final: 0.7097 (m-30) REVERT: C 351 MET cc_start: 0.7572 (tmm) cc_final: 0.7023 (tmm) REVERT: D 8 LEU cc_start: 0.7938 (mt) cc_final: 0.7594 (mt) REVERT: D 19 ASP cc_start: 0.7277 (t0) cc_final: 0.7052 (t0) REVERT: D 175 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7655 (mt-10) REVERT: D 214 GLU cc_start: 0.8101 (tp30) cc_final: 0.7875 (tp30) REVERT: D 322 GLU cc_start: 0.7809 (pm20) cc_final: 0.7553 (pm20) REVERT: D 329 ASN cc_start: 0.8540 (m-40) cc_final: 0.8325 (m-40) REVERT: D 351 MET cc_start: 0.7534 (tmm) cc_final: 0.7002 (tmm) REVERT: D 370 GLU cc_start: 0.7460 (tp30) cc_final: 0.7213 (tp30) REVERT: E 6 LYS cc_start: 0.8143 (mttp) cc_final: 0.7761 (mttp) REVERT: E 202 ASN cc_start: 0.8409 (t0) cc_final: 0.8154 (t0) REVERT: E 210 LEU cc_start: 0.8382 (tp) cc_final: 0.8019 (tp) REVERT: E 212 GLU cc_start: 0.8123 (tp30) cc_final: 0.7570 (tp30) REVERT: E 230 ARG cc_start: 0.6770 (tmm-80) cc_final: 0.6364 (tmm-80) REVERT: E 257 LYS cc_start: 0.8844 (mttm) cc_final: 0.8584 (mttt) REVERT: E 295 GLU cc_start: 0.7364 (mp0) cc_final: 0.6831 (mp0) REVERT: E 322 GLU cc_start: 0.7681 (pm20) cc_final: 0.7454 (pm20) REVERT: E 336 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7611 (mt-10) REVERT: E 355 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7389 (mtp180) REVERT: E 389 LYS cc_start: 0.8839 (ptpp) cc_final: 0.8497 (ptmm) REVERT: F 6 LYS cc_start: 0.8095 (mttp) cc_final: 0.7873 (mttp) REVERT: F 126 GLU cc_start: 0.7096 (tp30) cc_final: 0.6884 (tp30) REVERT: F 212 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7715 (mm-30) REVERT: F 230 ARG cc_start: 0.6712 (tmm-80) cc_final: 0.6271 (tmm-80) REVERT: F 247 ILE cc_start: 0.8363 (tt) cc_final: 0.8098 (pt) REVERT: F 336 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7388 (tt0) REVERT: F 385 GLU cc_start: 0.8017 (mp0) cc_final: 0.7722 (mp0) outliers start: 50 outliers final: 27 residues processed: 480 average time/residue: 1.4410 time to fit residues: 757.2362 Evaluate side-chains 478 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 450 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 314 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 186 optimal weight: 0.5980 chunk 197 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN C 162 GLN D 277 ASN D 289 ASN E 25 ASN E 277 ASN F 141 ASN F 186 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 ASN F 277 ASN F 308 ASN F 367 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16577 Z= 0.275 Angle : 0.541 6.280 22434 Z= 0.273 Chirality : 0.041 0.164 2550 Planarity : 0.004 0.057 2927 Dihedral : 5.257 67.137 2337 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.20 % Allowed : 15.71 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % 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: -0.20 (0.18), residues: 2055 helix: 0.67 (0.17), residues: 982 sheet: -0.85 (0.32), residues: 204 loop : -0.79 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 76 HIS 0.005 0.001 HIS E 190 PHE 0.017 0.001 PHE A 114 TYR 0.027 0.001 TYR E 124 ARG 0.009 0.001 ARG C 194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 464 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: A 73 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.8218 (mtm180) REVERT: A 214 ILE cc_start: 0.8943 (mm) cc_final: 0.8614 (mm) REVERT: B 73 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8438 (mtm180) REVERT: C 7 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8020 (tt) REVERT: C 296 ASP cc_start: 0.7666 (m-30) cc_final: 0.7282 (m-30) REVERT: C 351 MET cc_start: 0.7580 (tmm) cc_final: 0.7024 (tmm) REVERT: D 8 LEU cc_start: 0.7796 (mt) cc_final: 0.7535 (mt) REVERT: D 19 ASP cc_start: 0.7328 (t0) cc_final: 0.7101 (t0) REVERT: D 322 GLU cc_start: 0.7714 (pm20) cc_final: 0.7481 (pm20) REVERT: D 351 MET cc_start: 0.7544 (tmm) cc_final: 0.6995 (tmm) REVERT: D 370 GLU cc_start: 0.7502 (tp30) cc_final: 0.7255 (tp30) REVERT: E 6 LYS cc_start: 0.8123 (mttp) cc_final: 0.7727 (mttp) REVERT: E 194 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7892 (ttm110) REVERT: E 202 ASN cc_start: 0.8421 (t0) cc_final: 0.8161 (t0) REVERT: E 210 LEU cc_start: 0.8371 (tp) cc_final: 0.8021 (tp) REVERT: E 212 GLU cc_start: 0.8123 (tp30) cc_final: 0.7609 (tp30) REVERT: E 230 ARG cc_start: 0.6781 (tmm-80) cc_final: 0.6519 (tmm-80) REVERT: E 295 GLU cc_start: 0.7356 (mp0) cc_final: 0.6829 (mp0) REVERT: E 336 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7768 (mt-10) REVERT: E 355 ARG cc_start: 0.8036 (mtp180) cc_final: 0.7377 (mtp180) REVERT: F 151 ARG cc_start: 0.6240 (mmp-170) cc_final: 0.6020 (mmp-170) REVERT: F 212 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7714 (mm-30) REVERT: F 230 ARG cc_start: 0.6746 (tmm-80) cc_final: 0.6386 (tmm-80) REVERT: F 247 ILE cc_start: 0.8408 (tt) cc_final: 0.8140 (pt) REVERT: F 336 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7373 (tt0) REVERT: F 385 GLU cc_start: 0.8017 (mp0) cc_final: 0.7696 (mp0) outliers start: 56 outliers final: 31 residues processed: 477 average time/residue: 1.3985 time to fit residues: 730.1010 Evaluate side-chains 493 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 460 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 314 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 168 optimal weight: 0.4980 chunk 136 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 176 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 162 GLN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN E 277 ASN F 141 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16577 Z= 0.248 Angle : 0.536 6.119 22434 Z= 0.269 Chirality : 0.041 0.174 2550 Planarity : 0.004 0.057 2927 Dihedral : 5.177 65.970 2337 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.60 % Allowed : 16.73 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % 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: -0.03 (0.18), residues: 2055 helix: 0.85 (0.18), residues: 964 sheet: -0.89 (0.31), residues: 204 loop : -0.69 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 76 HIS 0.004 0.001 HIS E 190 PHE 0.022 0.001 PHE A 114 TYR 0.025 0.001 TYR E 124 ARG 0.010 0.000 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 465 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: A 73 ARG cc_start: 0.8531 (mtm-85) cc_final: 0.8211 (mtm180) REVERT: A 202 ARG cc_start: 0.7131 (ttp-170) cc_final: 0.6924 (ttp-170) REVERT: A 214 ILE cc_start: 0.8936 (mm) cc_final: 0.8601 (mm) REVERT: B 73 ARG cc_start: 0.8688 (mtm-85) cc_final: 0.8370 (mtm180) REVERT: B 166 LEU cc_start: 0.8804 (tt) cc_final: 0.8534 (tp) REVERT: B 260 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7065 (mtp180) REVERT: C 6 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8338 (mmmm) REVERT: C 7 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8046 (tt) REVERT: C 178 THR cc_start: 0.8678 (t) cc_final: 0.8411 (m) REVERT: C 296 ASP cc_start: 0.7668 (m-30) cc_final: 0.7348 (m-30) REVERT: C 329 ASN cc_start: 0.8591 (m-40) cc_final: 0.8352 (m110) REVERT: C 351 MET cc_start: 0.7581 (tmm) cc_final: 0.7019 (tmm) REVERT: D 8 LEU cc_start: 0.7795 (mt) cc_final: 0.7546 (mt) REVERT: D 19 ASP cc_start: 0.7308 (t0) cc_final: 0.7102 (t0) REVERT: D 107 MET cc_start: 0.6898 (tmm) cc_final: 0.6608 (tmm) REVERT: D 322 GLU cc_start: 0.7757 (pm20) cc_final: 0.7510 (pm20) REVERT: D 351 MET cc_start: 0.7550 (tmm) cc_final: 0.6988 (tmm) REVERT: D 370 GLU cc_start: 0.7460 (tp30) cc_final: 0.7203 (tp30) REVERT: D 385 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7631 (mm-30) REVERT: E 6 LYS cc_start: 0.8076 (mttp) cc_final: 0.7699 (mttp) REVERT: E 210 LEU cc_start: 0.8354 (tp) cc_final: 0.8013 (tp) REVERT: E 212 GLU cc_start: 0.8056 (tp30) cc_final: 0.7621 (tp30) REVERT: E 230 ARG cc_start: 0.6800 (tmm-80) cc_final: 0.6532 (tmm-80) REVERT: E 295 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: E 336 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7700 (mt-10) REVERT: E 355 ARG cc_start: 0.8025 (mtp180) cc_final: 0.7386 (mtp180) REVERT: E 370 GLU cc_start: 0.8138 (mp0) cc_final: 0.7835 (mp0) REVERT: F 77 ASP cc_start: 0.8004 (t0) cc_final: 0.7173 (t0) REVERT: F 106 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7321 (tm-30) REVERT: F 212 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7713 (mm-30) REVERT: F 230 ARG cc_start: 0.6740 (tmm-80) cc_final: 0.6402 (tmm-80) REVERT: F 245 ASP cc_start: 0.7327 (t0) cc_final: 0.7076 (m-30) REVERT: F 247 ILE cc_start: 0.8408 (tt) cc_final: 0.8120 (pt) REVERT: F 336 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7297 (tt0) REVERT: F 385 GLU cc_start: 0.7989 (mp0) cc_final: 0.7677 (mp0) outliers start: 63 outliers final: 38 residues processed: 485 average time/residue: 1.3911 time to fit residues: 740.0940 Evaluate side-chains 498 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 456 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 314 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.6980 chunk 177 optimal weight: 0.0770 chunk 38 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 91 optimal weight: 0.0870 chunk 16 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN D 255 GLN D 277 ASN D 289 ASN E 277 ASN F 186 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 ASN F 308 ASN F 367 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16577 Z= 0.197 Angle : 0.520 6.114 22434 Z= 0.261 Chirality : 0.040 0.177 2550 Planarity : 0.004 0.053 2927 Dihedral : 5.033 64.532 2337 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.08 % Allowed : 17.88 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % 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: 0.07 (0.19), residues: 2055 helix: 0.95 (0.18), residues: 963 sheet: -0.93 (0.32), residues: 201 loop : -0.63 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 76 HIS 0.004 0.001 HIS E 190 PHE 0.016 0.001 PHE A 114 TYR 0.025 0.001 TYR E 124 ARG 0.011 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 460 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: A 73 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.8152 (mtm180) REVERT: A 81 LEU cc_start: 0.8702 (mp) cc_final: 0.8426 (mp) REVERT: A 214 ILE cc_start: 0.8926 (mm) cc_final: 0.8593 (mm) REVERT: B 73 ARG cc_start: 0.8651 (mtm-85) cc_final: 0.8335 (mtm180) REVERT: B 166 LEU cc_start: 0.8737 (tt) cc_final: 0.8520 (tp) REVERT: B 260 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7016 (mtp180) REVERT: C 6 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8317 (mmmm) REVERT: C 10 ILE cc_start: 0.8407 (pt) cc_final: 0.8172 (pp) REVERT: C 178 THR cc_start: 0.8674 (t) cc_final: 0.8405 (m) REVERT: C 296 ASP cc_start: 0.7641 (m-30) cc_final: 0.7321 (m-30) REVERT: C 329 ASN cc_start: 0.8577 (m-40) cc_final: 0.8353 (m110) REVERT: C 351 MET cc_start: 0.7561 (tmm) cc_final: 0.7006 (tmm) REVERT: D 8 LEU cc_start: 0.7685 (mt) cc_final: 0.7431 (mt) REVERT: D 19 ASP cc_start: 0.7261 (t0) cc_final: 0.7056 (t0) REVERT: D 107 MET cc_start: 0.6864 (tmm) cc_final: 0.6559 (tmm) REVERT: D 178 THR cc_start: 0.8634 (t) cc_final: 0.8392 (p) REVERT: D 322 GLU cc_start: 0.7741 (pm20) cc_final: 0.7464 (pm20) REVERT: D 351 MET cc_start: 0.7553 (tmm) cc_final: 0.7001 (tmm) REVERT: D 370 GLU cc_start: 0.7473 (tp30) cc_final: 0.7142 (tp30) REVERT: D 385 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7661 (mm-30) REVERT: E 6 LYS cc_start: 0.8053 (mttp) cc_final: 0.7692 (mttp) REVERT: E 210 LEU cc_start: 0.8339 (tp) cc_final: 0.8025 (tp) REVERT: E 212 GLU cc_start: 0.8035 (tp30) cc_final: 0.7599 (tp30) REVERT: E 230 ARG cc_start: 0.6811 (tmm-80) cc_final: 0.6415 (tmm-80) REVERT: E 295 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: E 336 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7643 (mt-10) REVERT: E 355 ARG cc_start: 0.8017 (mtp180) cc_final: 0.7392 (mtp180) REVERT: E 370 GLU cc_start: 0.8143 (mp0) cc_final: 0.7803 (mp0) REVERT: F 77 ASP cc_start: 0.7949 (t0) cc_final: 0.7132 (t0) REVERT: F 106 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7279 (tm-30) REVERT: F 212 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7716 (mm-30) REVERT: F 230 ARG cc_start: 0.6767 (tmm-80) cc_final: 0.6433 (tmm-80) REVERT: F 245 ASP cc_start: 0.7320 (t0) cc_final: 0.7072 (m-30) REVERT: F 336 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7340 (tt0) REVERT: F 385 GLU cc_start: 0.7970 (mp0) cc_final: 0.7677 (mp0) outliers start: 54 outliers final: 40 residues processed: 470 average time/residue: 1.3990 time to fit residues: 720.2227 Evaluate side-chains 503 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 460 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 314 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.0670 chunk 22 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 144 optimal weight: 0.4980 chunk 111 optimal weight: 0.0050 chunk 166 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 0.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN D 277 ASN D 289 ASN E 277 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16577 Z= 0.180 Angle : 0.518 6.684 22434 Z= 0.260 Chirality : 0.040 0.182 2550 Planarity : 0.004 0.063 2927 Dihedral : 4.958 63.723 2337 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.14 % Allowed : 18.39 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % 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: 0.14 (0.19), residues: 2055 helix: 1.07 (0.18), residues: 952 sheet: -0.90 (0.32), residues: 201 loop : -0.67 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 76 HIS 0.004 0.001 HIS F 190 PHE 0.014 0.001 PHE A 114 TYR 0.024 0.001 TYR E 124 ARG 0.013 0.000 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 455 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: A 73 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.8097 (mtm180) REVERT: B 105 MET cc_start: 0.8076 (mtp) cc_final: 0.7860 (mtp) REVERT: B 166 LEU cc_start: 0.8723 (tt) cc_final: 0.8505 (tp) REVERT: B 260 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.6999 (mtp180) REVERT: C 6 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8232 (mmmm) REVERT: C 10 ILE cc_start: 0.8400 (pt) cc_final: 0.8186 (pp) REVERT: C 178 THR cc_start: 0.8665 (t) cc_final: 0.8403 (m) REVERT: C 296 ASP cc_start: 0.7633 (m-30) cc_final: 0.7296 (m-30) REVERT: C 351 MET cc_start: 0.7553 (tmm) cc_final: 0.7007 (tmm) REVERT: D 8 LEU cc_start: 0.7672 (mt) cc_final: 0.7438 (mt) REVERT: D 10 ILE cc_start: 0.8370 (pt) cc_final: 0.8084 (pp) REVERT: D 19 ASP cc_start: 0.7258 (t0) cc_final: 0.7043 (t0) REVERT: D 107 MET cc_start: 0.6852 (tmm) cc_final: 0.6549 (tmm) REVERT: D 178 THR cc_start: 0.8645 (t) cc_final: 0.8408 (p) REVERT: D 322 GLU cc_start: 0.7759 (pm20) cc_final: 0.7493 (pm20) REVERT: D 351 MET cc_start: 0.7551 (tmm) cc_final: 0.6998 (tmm) REVERT: D 370 GLU cc_start: 0.7461 (tp30) cc_final: 0.7100 (tp30) REVERT: E 6 LYS cc_start: 0.8038 (mttp) cc_final: 0.7683 (mttp) REVERT: E 160 MET cc_start: 0.8749 (ttm) cc_final: 0.8547 (mtp) REVERT: E 210 LEU cc_start: 0.8336 (tp) cc_final: 0.8012 (tp) REVERT: E 212 GLU cc_start: 0.8045 (tp30) cc_final: 0.7515 (tp30) REVERT: E 230 ARG cc_start: 0.6819 (tmm-80) cc_final: 0.6409 (tmm-80) REVERT: E 295 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: E 336 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7832 (mt-10) REVERT: E 355 ARG cc_start: 0.8022 (mtp180) cc_final: 0.7406 (mtp180) REVERT: F 77 ASP cc_start: 0.7922 (t0) cc_final: 0.7184 (t0) REVERT: F 106 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7248 (tm-30) REVERT: F 212 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7709 (mm-30) REVERT: F 230 ARG cc_start: 0.6778 (tmm-80) cc_final: 0.6443 (tmm-80) REVERT: F 245 ASP cc_start: 0.7310 (t0) cc_final: 0.7087 (m-30) REVERT: F 247 ILE cc_start: 0.8335 (tt) cc_final: 0.8081 (pt) REVERT: F 295 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6827 (mp0) REVERT: F 314 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8211 (mtm) REVERT: F 336 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7305 (tt0) REVERT: F 385 GLU cc_start: 0.7965 (mp0) cc_final: 0.7679 (mp0) outliers start: 55 outliers final: 40 residues processed: 468 average time/residue: 1.3732 time to fit residues: 704.6553 Evaluate side-chains 501 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 457 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 314 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 11 GLN C 162 GLN D 255 GLN D 289 ASN E 277 ASN E 356 HIS ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16577 Z= 0.321 Angle : 0.569 7.606 22434 Z= 0.287 Chirality : 0.042 0.200 2550 Planarity : 0.004 0.071 2927 Dihedral : 5.220 66.641 2337 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.86 % Allowed : 19.42 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % 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: 0.04 (0.19), residues: 2055 helix: 0.92 (0.18), residues: 952 sheet: -0.73 (0.30), residues: 220 loop : -0.67 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 76 HIS 0.004 0.001 HIS F 190 PHE 0.020 0.002 PHE A 114 TYR 0.027 0.001 TYR E 124 ARG 0.015 0.001 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 454 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.8117 (mtm180) REVERT: A 214 ILE cc_start: 0.8928 (mm) cc_final: 0.8591 (mm) REVERT: B 105 MET cc_start: 0.8098 (mtp) cc_final: 0.7867 (mtp) REVERT: B 166 LEU cc_start: 0.8753 (tt) cc_final: 0.8541 (tp) REVERT: B 260 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7099 (mtp180) REVERT: C 6 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8239 (mmmm) REVERT: C 10 ILE cc_start: 0.8415 (pt) cc_final: 0.8195 (pp) REVERT: C 178 THR cc_start: 0.8683 (t) cc_final: 0.8407 (m) REVERT: C 296 ASP cc_start: 0.7664 (m-30) cc_final: 0.7356 (m-30) REVERT: C 351 MET cc_start: 0.7587 (tmm) cc_final: 0.7018 (tmm) REVERT: D 8 LEU cc_start: 0.7654 (mt) cc_final: 0.7421 (mt) REVERT: D 10 ILE cc_start: 0.8388 (pt) cc_final: 0.8111 (pp) REVERT: D 107 MET cc_start: 0.6944 (tmm) cc_final: 0.6617 (tmm) REVERT: D 175 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: D 322 GLU cc_start: 0.7804 (pm20) cc_final: 0.7516 (pm20) REVERT: D 351 MET cc_start: 0.7565 (tmm) cc_final: 0.7006 (tmm) REVERT: D 370 GLU cc_start: 0.7489 (tp30) cc_final: 0.7158 (tp30) REVERT: E 6 LYS cc_start: 0.8106 (mttp) cc_final: 0.7719 (mttp) REVERT: E 210 LEU cc_start: 0.8336 (tp) cc_final: 0.8032 (tp) REVERT: E 212 GLU cc_start: 0.8066 (tp30) cc_final: 0.7550 (tp30) REVERT: E 230 ARG cc_start: 0.6814 (tmm-80) cc_final: 0.6432 (tmm-80) REVERT: E 295 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: E 336 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7675 (mt-10) REVERT: E 355 ARG cc_start: 0.8005 (mtp180) cc_final: 0.7306 (mtp180) REVERT: F 77 ASP cc_start: 0.7962 (t0) cc_final: 0.7187 (t0) REVERT: F 106 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7248 (tm-30) REVERT: F 107 MET cc_start: 0.8057 (tpt) cc_final: 0.7787 (mmm) REVERT: F 150 SER cc_start: 0.8382 (t) cc_final: 0.8055 (p) REVERT: F 212 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7693 (mm-30) REVERT: F 230 ARG cc_start: 0.6762 (tmm-80) cc_final: 0.6484 (tmm-80) REVERT: F 245 ASP cc_start: 0.7316 (t0) cc_final: 0.7080 (m-30) REVERT: F 247 ILE cc_start: 0.8361 (tt) cc_final: 0.8112 (pt) REVERT: F 295 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6820 (mp0) REVERT: F 385 GLU cc_start: 0.8037 (mp0) cc_final: 0.7708 (mp0) outliers start: 50 outliers final: 39 residues processed: 468 average time/residue: 1.3632 time to fit residues: 699.3729 Evaluate side-chains 497 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 455 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 314 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.2980 chunk 171 optimal weight: 0.0570 chunk 183 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 143 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 173 optimal weight: 0.0570 chunk 182 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 11 GLN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 GLN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN D 289 ASN E 277 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16577 Z= 0.171 Angle : 0.530 8.013 22434 Z= 0.266 Chirality : 0.040 0.193 2550 Planarity : 0.004 0.068 2927 Dihedral : 4.964 63.134 2337 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.11 % Allowed : 20.33 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % 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: 0.13 (0.19), residues: 2055 helix: 1.04 (0.18), residues: 953 sheet: -0.85 (0.33), residues: 194 loop : -0.65 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 76 HIS 0.003 0.001 HIS F 188 PHE 0.012 0.001 PHE C 223 TYR 0.025 0.001 TYR E 124 ARG 0.015 0.000 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 458 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8126 (mtm180) REVERT: A 81 LEU cc_start: 0.8698 (mp) cc_final: 0.8436 (mp) REVERT: B 166 LEU cc_start: 0.8715 (tt) cc_final: 0.8494 (tp) REVERT: B 202 ARG cc_start: 0.7236 (ttp-170) cc_final: 0.7018 (ttp-170) REVERT: B 260 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.6993 (mtp180) REVERT: B 263 LEU cc_start: 0.8748 (tp) cc_final: 0.8462 (tp) REVERT: C 6 LYS cc_start: 0.8607 (mmtt) cc_final: 0.8202 (mmmm) REVERT: C 10 ILE cc_start: 0.8420 (pt) cc_final: 0.8217 (pp) REVERT: C 178 THR cc_start: 0.8654 (t) cc_final: 0.8388 (m) REVERT: C 296 ASP cc_start: 0.7630 (m-30) cc_final: 0.7287 (m-30) REVERT: C 351 MET cc_start: 0.7552 (tmm) cc_final: 0.7000 (tmm) REVERT: D 8 LEU cc_start: 0.7596 (mt) cc_final: 0.7350 (mt) REVERT: D 10 ILE cc_start: 0.8409 (pt) cc_final: 0.8143 (pp) REVERT: D 107 MET cc_start: 0.6885 (tmm) cc_final: 0.6564 (tmm) REVERT: D 175 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7802 (mt-10) REVERT: D 178 THR cc_start: 0.8601 (t) cc_final: 0.8358 (p) REVERT: D 322 GLU cc_start: 0.7810 (pm20) cc_final: 0.7526 (pm20) REVERT: D 351 MET cc_start: 0.7550 (tmm) cc_final: 0.7005 (tmm) REVERT: D 370 GLU cc_start: 0.7464 (tp30) cc_final: 0.7127 (tp30) REVERT: E 6 LYS cc_start: 0.8066 (mttp) cc_final: 0.7697 (mttp) REVERT: E 105 LEU cc_start: 0.7567 (mt) cc_final: 0.7341 (mp) REVERT: E 210 LEU cc_start: 0.8324 (tp) cc_final: 0.8012 (tp) REVERT: E 212 GLU cc_start: 0.8048 (tp30) cc_final: 0.7555 (tp30) REVERT: E 230 ARG cc_start: 0.6814 (tmm-80) cc_final: 0.6410 (tmm-80) REVERT: E 295 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: E 336 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7433 (tt0) REVERT: E 355 ARG cc_start: 0.8002 (mtp180) cc_final: 0.7370 (mtp180) REVERT: F 77 ASP cc_start: 0.7905 (t0) cc_final: 0.7153 (t0) REVERT: F 106 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7230 (tm-30) REVERT: F 150 SER cc_start: 0.8338 (t) cc_final: 0.8015 (p) REVERT: F 212 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7707 (mm-30) REVERT: F 230 ARG cc_start: 0.6784 (tmm-80) cc_final: 0.6467 (tmm-80) REVERT: F 245 ASP cc_start: 0.7303 (t0) cc_final: 0.7085 (m-30) REVERT: F 247 ILE cc_start: 0.8327 (tt) cc_final: 0.8090 (pt) REVERT: F 295 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6806 (mp0) REVERT: F 314 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8128 (mtm) REVERT: F 336 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7261 (tt0) REVERT: F 385 GLU cc_start: 0.7964 (mp0) cc_final: 0.7681 (mp0) outliers start: 37 outliers final: 27 residues processed: 470 average time/residue: 1.3564 time to fit residues: 698.5753 Evaluate side-chains 483 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 453 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 314 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 91 optimal weight: 0.0470 chunk 134 optimal weight: 2.9990 chunk 203 optimal weight: 0.3980 chunk 187 optimal weight: 4.9990 chunk 161 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 125 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 128 optimal weight: 0.0980 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN E 277 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16577 Z= 0.176 Angle : 0.542 9.427 22434 Z= 0.271 Chirality : 0.040 0.191 2550 Planarity : 0.004 0.077 2927 Dihedral : 4.896 62.541 2337 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.94 % Allowed : 21.13 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % 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: 0.19 (0.19), residues: 2055 helix: 1.09 (0.18), residues: 944 sheet: -0.79 (0.32), residues: 206 loop : -0.60 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 76 HIS 0.004 0.001 HIS F 190 PHE 0.013 0.001 PHE C 223 TYR 0.024 0.001 TYR E 124 ARG 0.016 0.000 ARG B 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 452 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.8130 (mtm180) REVERT: A 81 LEU cc_start: 0.8704 (mp) cc_final: 0.8441 (mp) REVERT: B 166 LEU cc_start: 0.8714 (tt) cc_final: 0.8492 (tp) REVERT: B 202 ARG cc_start: 0.7230 (ttp-170) cc_final: 0.7016 (ttp-170) REVERT: B 260 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.6946 (mtp180) REVERT: B 263 LEU cc_start: 0.8734 (tp) cc_final: 0.8496 (tp) REVERT: C 6 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8202 (mmmm) REVERT: C 178 THR cc_start: 0.8655 (t) cc_final: 0.8390 (m) REVERT: C 296 ASP cc_start: 0.7622 (m-30) cc_final: 0.7279 (m-30) REVERT: C 351 MET cc_start: 0.7540 (tmm) cc_final: 0.7027 (tmm) REVERT: D 8 LEU cc_start: 0.7618 (mt) cc_final: 0.7388 (mt) REVERT: D 10 ILE cc_start: 0.8420 (pt) cc_final: 0.8164 (pp) REVERT: D 107 MET cc_start: 0.6872 (tmm) cc_final: 0.6583 (tmm) REVERT: D 175 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: D 178 THR cc_start: 0.8613 (t) cc_final: 0.8369 (p) REVERT: D 322 GLU cc_start: 0.7816 (pm20) cc_final: 0.7539 (pm20) REVERT: D 344 ARG cc_start: 0.7269 (mmt180) cc_final: 0.6988 (mmt180) REVERT: D 351 MET cc_start: 0.7545 (tmm) cc_final: 0.6996 (tmm) REVERT: D 370 GLU cc_start: 0.7437 (tp30) cc_final: 0.7103 (tp30) REVERT: E 6 LYS cc_start: 0.8025 (mttp) cc_final: 0.7657 (mttp) REVERT: E 105 LEU cc_start: 0.7578 (mt) cc_final: 0.7353 (mp) REVERT: E 210 LEU cc_start: 0.8327 (tp) cc_final: 0.8015 (tp) REVERT: E 212 GLU cc_start: 0.8050 (tp30) cc_final: 0.7536 (tp30) REVERT: E 230 ARG cc_start: 0.6817 (tmm-80) cc_final: 0.6501 (tmm-80) REVERT: E 295 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: E 336 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7358 (tt0) REVERT: E 355 ARG cc_start: 0.7999 (mtp180) cc_final: 0.7371 (mtp180) REVERT: F 77 ASP cc_start: 0.7911 (t0) cc_final: 0.7155 (t0) REVERT: F 106 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7222 (tm-30) REVERT: F 212 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7707 (mm-30) REVERT: F 230 ARG cc_start: 0.6799 (tmm-80) cc_final: 0.6452 (tmm-80) REVERT: F 245 ASP cc_start: 0.7308 (t0) cc_final: 0.7094 (m-30) REVERT: F 247 ILE cc_start: 0.8348 (tt) cc_final: 0.8065 (pt) REVERT: F 295 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6796 (mp0) REVERT: F 314 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8105 (mtm) REVERT: F 336 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7241 (tt0) outliers start: 34 outliers final: 28 residues processed: 463 average time/residue: 1.3616 time to fit residues: 694.9209 Evaluate side-chains 484 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 452 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 314 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 23 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 166 optimal weight: 0.3980 chunk 20 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 144 GLN B 11 GLN C 162 GLN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN D 289 ASN E 277 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.150637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127236 restraints weight = 22357.219| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.14 r_work: 0.3558 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16577 Z= 0.220 Angle : 0.554 8.824 22434 Z= 0.277 Chirality : 0.040 0.197 2550 Planarity : 0.004 0.059 2927 Dihedral : 4.970 63.787 2337 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.28 % Allowed : 20.79 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % 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: 0.17 (0.19), residues: 2055 helix: 1.07 (0.18), residues: 943 sheet: -0.80 (0.32), residues: 206 loop : -0.63 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 76 HIS 0.004 0.001 HIS F 190 PHE 0.014 0.001 PHE D 223 TYR 0.025 0.001 TYR E 124 ARG 0.014 0.000 ARG C 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10621.37 seconds wall clock time: 186 minutes 42.82 seconds (11202.82 seconds total)