Starting phenix.real_space_refine on Sat Mar 16 15:35:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tah_41135/03_2024/8tah_41135_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tah_41135/03_2024/8tah_41135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tah_41135/03_2024/8tah_41135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tah_41135/03_2024/8tah_41135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tah_41135/03_2024/8tah_41135_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tah_41135/03_2024/8tah_41135_updated.pdb" } resolution = 2.89 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= 0.002 sd= 0.031 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 71 5.16 5 C 9529 2.51 5 N 2566 2.21 5 O 2804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14978 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3225 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2723 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 17, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2701 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Chain: "D" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2301 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain: "E" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1415 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "F" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1371 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain: "G" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1091 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "H" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 87 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.88, per 1000 atoms: 0.53 Number of scatterers: 14978 At special positions: 0 Unit cell: (100.8, 137.76, 140.28, 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 71 16.00 P 6 15.00 Mg 2 11.99 O 2804 8.00 N 2566 7.00 C 9529 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: 5.69 Conformation dependent library (CDL) restraints added in 2.9 seconds 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3534 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 17 sheets defined 35.1% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.827A pdb=" N TRP A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N SER A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 220 through 231 Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 273 through 282 removed outlier: 3.731A pdb=" N PHE A 276 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 277 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY A 278 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 3.627A pdb=" N PHE A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 273 through 282' Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.935A pdb=" N ALA A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.625A pdb=" N CYS A 408 " --> pdb=" O PRO A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.525A pdb=" N VAL B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.548A pdb=" N LEU B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 227 through 236 Processing helix chain 'B' and resid 256 through 264 removed outlier: 3.681A pdb=" N PHE B 259 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU B 260 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA B 261 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Proline residue: B 262 - end of helix No H-bonds generated for 'chain 'B' and resid 256 through 264' Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 313 through 328 Processing helix chain 'B' and resid 353 through 364 Processing helix chain 'B' and resid 375 through 379 Processing helix chain 'B' and resid 384 through 387 No H-bonds generated for 'chain 'B' and resid 384 through 387' Processing helix chain 'C' and resid 357 through 363 removed outlier: 3.656A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 64 through 70 removed outlier: 3.966A pdb=" N HIS D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 79 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 116 through 133 removed outlier: 4.705A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 186 Processing helix chain 'D' and resid 237 through 280 removed outlier: 4.432A pdb=" N THR D 246 " --> pdb=" O ASN D 242 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ARG D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 54 removed outlier: 4.755A pdb=" N LYS E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ALA E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 81 removed outlier: 3.571A pdb=" N LYS E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 99 Processing helix chain 'E' and resid 123 through 148 removed outlier: 3.905A pdb=" N GLU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'F' and resid 6 through 19 Processing helix chain 'F' and resid 37 through 40 No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 44 through 46 No H-bonds generated for 'chain 'F' and resid 44 through 46' Processing helix chain 'F' and resid 81 through 96 Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 128 through 166 removed outlier: 4.388A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 47 Processing helix chain 'G' and resid 51 through 58 Processing helix chain 'G' and resid 69 through 84 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 100 through 115 removed outlier: 4.385A pdb=" N GLU G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 136 removed outlier: 4.277A pdb=" N GLN G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 145 Processing sheet with id= A, first strand: chain 'A' and resid 139 through 143 removed outlier: 6.582A pdb=" N PHE A 110 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA A 142 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 112 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N CYS A 8 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR A 113 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N VAL A 10 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 60 through 62 Processing sheet with id= C, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.356A pdb=" N THR A 166 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N SER A 322 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE A 168 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 254 through 259 Processing sheet with id= E, first strand: chain 'B' and resid 30 through 33 removed outlier: 4.000A pdb=" N LYS B 19 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LYS B 106 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N CYS B 11 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU B 108 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B 13 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR B 110 " --> pdb=" O ASN B 13 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLY B 135 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU B 109 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR B 137 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLU B 111 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 139 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 301 through 304 removed outlier: 6.373A pdb=" N VAL B 155 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N SER B 304 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL B 157 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 242 through 245 Processing sheet with id= H, first strand: chain 'C' and resid 3 through 5 removed outlier: 4.693A pdb=" N ALA C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C 347 " --> pdb=" O ALA C 351 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.355A pdb=" N LYS C 36 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS C 44 " --> pdb=" O LYS C 36 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 87 through 91 removed outlier: 4.241A pdb=" N ALA C 76 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 131 through 137 Processing sheet with id= L, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.805A pdb=" N GLY C 160 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU C 148 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA C 158 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TRP C 150 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU C 156 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER C 170 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 194 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 243 removed outlier: 3.947A pdb=" N THR C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 209 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 249 through 254 removed outlier: 7.022A pdb=" N ALA C 263 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL C 252 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C 261 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N PHE C 254 " --> pdb=" O SER C 259 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N SER C 259 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 284 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN C 273 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE C 282 " --> pdb=" O ASN C 273 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 32 through 36 Processing sheet with id= P, first strand: chain 'D' and resid 142 through 144 Processing sheet with id= Q, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.620A pdb=" N LYS F 60 " --> pdb=" O ALA F 75 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1626 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: 4.60 Time building geometry restraints manager: 6.19 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: 4776 1.34 - 1.46: 2876 1.46 - 1.58: 7540 1.58 - 1.69: 8 1.69 - 1.81: 110 Bond restraints: 15310 Sorted by residual: bond pdb=" N ALA D 284 " pdb=" CA ALA D 284 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.33e-02 5.65e+03 4.16e+00 bond pdb=" N VAL G 151 " pdb=" CA VAL G 151 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.61e+00 bond pdb=" C LEU B 313 " pdb=" N PRO B 314 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 2.97e+00 bond pdb=" C ARG F 6 " pdb=" N PRO F 7 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.23e-02 6.61e+03 2.40e+00 bond pdb=" N GLY E 175 " pdb=" CA GLY E 175 " ideal model delta sigma weight residual 1.451 1.476 -0.025 1.60e-02 3.91e+03 2.36e+00 ... (remaining 15305 not shown) Histogram of bond angle deviations from ideal: 98.77 - 106.99: 489 106.99 - 115.20: 9241 115.20 - 123.41: 10407 123.41 - 131.62: 565 131.62 - 139.84: 34 Bond angle restraints: 20736 Sorted by residual: angle pdb=" N VAL A 55 " pdb=" CA VAL A 55 " pdb=" C VAL A 55 " ideal model delta sigma weight residual 112.29 108.25 4.04 9.40e-01 1.13e+00 1.85e+01 angle pdb=" C VAL C 335 " pdb=" N ASP C 336 " pdb=" CA ASP C 336 " ideal model delta sigma weight residual 121.54 128.94 -7.40 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C SER C 236 " pdb=" N VAL C 237 " pdb=" CA VAL C 237 " ideal model delta sigma weight residual 121.97 127.82 -5.85 1.80e+00 3.09e-01 1.06e+01 angle pdb=" CA LYS C 139 " pdb=" C LYS C 139 " pdb=" N PRO C 140 " ideal model delta sigma weight residual 118.44 123.47 -5.03 1.59e+00 3.96e-01 1.00e+01 angle pdb=" C ASN E 153 " pdb=" N ASP E 154 " pdb=" CA ASP E 154 " ideal model delta sigma weight residual 122.40 126.87 -4.47 1.45e+00 4.76e-01 9.50e+00 ... (remaining 20731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8532 17.89 - 35.78: 534 35.78 - 53.67: 139 53.67 - 71.56: 28 71.56 - 89.45: 6 Dihedral angle restraints: 9239 sinusoidal: 3765 harmonic: 5474 Sorted by residual: dihedral pdb=" CA ASN F 100 " pdb=" C ASN F 100 " pdb=" N PHE F 101 " pdb=" CA PHE F 101 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLN E 152 " pdb=" C GLN E 152 " pdb=" N ASN E 153 " pdb=" CA ASN E 153 " ideal model delta harmonic sigma weight residual -180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ASP C 336 " pdb=" C ASP C 336 " pdb=" N LYS C 337 " pdb=" CA LYS C 337 " ideal model delta harmonic sigma weight residual -180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 9236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1516 0.042 - 0.084: 523 0.084 - 0.127: 201 0.127 - 0.169: 37 0.169 - 0.211: 10 Chirality restraints: 2287 Sorted by residual: chirality pdb=" CB VAL A 311 " pdb=" CA VAL A 311 " pdb=" CG1 VAL A 311 " pdb=" CG2 VAL A 311 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL A 55 " pdb=" CA VAL A 55 " pdb=" CG1 VAL A 55 " pdb=" CG2 VAL A 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CA LYS C 139 " pdb=" N LYS C 139 " pdb=" C LYS C 139 " pdb=" CB LYS C 139 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 2284 not shown) Planarity restraints: 2666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 228 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO D 229 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 229 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 229 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 151 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO C 152 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 152 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 152 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 313 " -0.042 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO A 314 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 314 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 314 " -0.035 5.00e-02 4.00e+02 ... (remaining 2663 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 113 2.61 - 3.19: 11447 3.19 - 3.76: 22454 3.76 - 4.33: 32418 4.33 - 4.90: 53786 Nonbonded interactions: 120218 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O2B ATP A 502 " model vdw 2.043 2.170 nonbonded pdb="MG MG A 501 " pdb=" O1G ATP A 502 " model vdw 2.073 2.170 nonbonded pdb="MG MG B 501 " pdb=" O2G ATP B 502 " model vdw 2.282 2.170 nonbonded pdb=" O VAL G 142 " pdb=" OG1 THR G 146 " model vdw 2.326 2.440 nonbonded pdb=" O SER E 157 " pdb=" OG1 THR E 161 " model vdw 2.333 2.440 ... (remaining 120213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.250 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 41.170 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 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 : 0.005 0.054 15310 Z= 0.295 Angle : 0.656 7.888 20736 Z= 0.380 Chirality : 0.050 0.211 2287 Planarity : 0.007 0.083 2666 Dihedral : 13.050 89.449 5705 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.46 % Allowed : 8.62 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.21 (0.17), residues: 1862 helix: -2.37 (0.14), residues: 692 sheet: 0.21 (0.27), residues: 365 loop : -1.27 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 221 HIS 0.006 0.001 HIS C 224 PHE 0.023 0.002 PHE C 111 TYR 0.016 0.001 TYR D 250 ARG 0.003 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 470 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7623 (pp) REVERT: A 75 LYS cc_start: 0.7711 (mmtm) cc_final: 0.7370 (mmmm) REVERT: A 106 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7354 (mt-10) REVERT: A 161 ARG cc_start: 0.7106 (mtt90) cc_final: 0.6718 (mtt-85) REVERT: A 182 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 241 GLU cc_start: 0.6904 (tp30) cc_final: 0.6648 (mm-30) REVERT: A 244 LYS cc_start: 0.7136 (mttt) cc_final: 0.6902 (mtpt) REVERT: A 248 ASP cc_start: 0.7299 (t70) cc_final: 0.6755 (t0) REVERT: A 251 LYS cc_start: 0.7712 (tttt) cc_final: 0.7219 (ttpp) REVERT: A 253 ILE cc_start: 0.7716 (mt) cc_final: 0.7492 (OUTLIER) REVERT: A 255 GLN cc_start: 0.7459 (mp10) cc_final: 0.7222 (mp-120) REVERT: A 266 GLU cc_start: 0.6625 (mm-30) cc_final: 0.6276 (mm-30) REVERT: A 298 GLU cc_start: 0.6948 (mp0) cc_final: 0.6344 (mp0) REVERT: A 302 GLU cc_start: 0.7040 (tt0) cc_final: 0.6626 (tt0) REVERT: A 317 LYS cc_start: 0.7477 (ttpp) cc_final: 0.7002 (ttpp) REVERT: A 329 ARG cc_start: 0.7347 (mtp180) cc_final: 0.7034 (mtp180) REVERT: A 333 ARG cc_start: 0.7361 (mtp180) cc_final: 0.7042 (mtp180) REVERT: A 334 ARG cc_start: 0.7146 (ttt180) cc_final: 0.6918 (ttt180) REVERT: A 338 ASP cc_start: 0.6839 (m-30) cc_final: 0.6638 (m-30) REVERT: A 351 GLU cc_start: 0.6152 (mm-30) cc_final: 0.5857 (tp30) REVERT: A 364 ASP cc_start: 0.7394 (p0) cc_final: 0.7136 (p0) REVERT: A 368 ILE cc_start: 0.8148 (mp) cc_final: 0.7818 (mp) REVERT: A 391 TYR cc_start: 0.7712 (m-80) cc_final: 0.7436 (m-80) REVERT: A 393 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7136 (p) REVERT: A 414 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.6220 (m-80) REVERT: B 127 MET cc_start: 0.6907 (mmt) cc_final: 0.6604 (mmt) REVERT: B 232 LYS cc_start: 0.7314 (tttt) cc_final: 0.7091 (ttpp) REVERT: B 253 LYS cc_start: 0.7697 (mttt) cc_final: 0.7443 (mtmm) REVERT: B 257 GLU cc_start: 0.7552 (mp0) cc_final: 0.7053 (mp0) REVERT: B 263 GLU cc_start: 0.7224 (tp30) cc_final: 0.6591 (tp30) REVERT: B 292 ASP cc_start: 0.7816 (t0) cc_final: 0.7585 (t0) REVERT: B 327 GLU cc_start: 0.7203 (tt0) cc_final: 0.6938 (tt0) REVERT: B 328 ARG cc_start: 0.7564 (mtt180) cc_final: 0.7333 (mtt180) REVERT: B 345 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6705 (pt0) REVERT: B 346 ASP cc_start: 0.6981 (p0) cc_final: 0.6753 (p0) REVERT: B 365 MET cc_start: 0.5905 (mpt) cc_final: 0.4781 (tmt) REVERT: C 44 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7601 (ttpp) REVERT: C 46 HIS cc_start: 0.7818 (m-70) cc_final: 0.7450 (m-70) REVERT: C 65 ASP cc_start: 0.7633 (t70) cc_final: 0.7344 (t0) REVERT: C 85 VAL cc_start: 0.5929 (t) cc_final: 0.5681 (m) REVERT: C 94 ARG cc_start: 0.8094 (mtm110) cc_final: 0.7883 (mtp180) REVERT: C 118 ARG cc_start: 0.7610 (mtm110) cc_final: 0.7370 (mtm110) REVERT: C 138 LYS cc_start: 0.8005 (ptmt) cc_final: 0.7623 (ptmm) REVERT: C 149 ASP cc_start: 0.7585 (t70) cc_final: 0.7215 (t0) REVERT: C 175 GLU cc_start: 0.7564 (mp0) cc_final: 0.6779 (mp0) REVERT: C 176 VAL cc_start: 0.7787 (t) cc_final: 0.7364 (m) REVERT: C 177 ASP cc_start: 0.7608 (m-30) cc_final: 0.7045 (m-30) REVERT: C 232 ASP cc_start: 0.7750 (t0) cc_final: 0.7392 (t0) REVERT: C 245 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7043 (pp20) REVERT: C 279 CYS cc_start: 0.7628 (t) cc_final: 0.7201 (t) REVERT: C 285 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7662 (mtpt) REVERT: C 290 LYS cc_start: 0.5735 (OUTLIER) cc_final: 0.5287 (tptp) REVERT: C 361 GLU cc_start: 0.6661 (pp20) cc_final: 0.6408 (pp20) REVERT: D 34 THR cc_start: 0.7911 (OUTLIER) cc_final: 0.7703 (p) REVERT: D 54 LYS cc_start: 0.6895 (mmtp) cc_final: 0.6655 (mttm) REVERT: D 62 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8045 (mtmm) REVERT: D 65 LYS cc_start: 0.7630 (mmmm) cc_final: 0.7393 (mmmm) REVERT: D 75 LEU cc_start: 0.6880 (tt) cc_final: 0.6576 (tp) REVERT: D 79 VAL cc_start: 0.7554 (OUTLIER) cc_final: 0.7318 (p) REVERT: D 98 ASP cc_start: 0.6365 (t70) cc_final: 0.5981 (t70) REVERT: D 100 GLU cc_start: 0.7009 (mp0) cc_final: 0.6281 (mp0) REVERT: D 115 MET cc_start: 0.7024 (mtt) cc_final: 0.6717 (mtm) REVERT: D 179 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6780 (ttmm) REVERT: D 213 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7212 (p0) REVERT: D 249 ASP cc_start: 0.7746 (m-30) cc_final: 0.7514 (m-30) REVERT: D 267 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7184 (mtt90) REVERT: D 269 LYS cc_start: 0.7220 (tppt) cc_final: 0.6974 (tptm) REVERT: E 22 LEU cc_start: 0.7626 (mp) cc_final: 0.7307 (mp) REVERT: E 50 LYS cc_start: 0.7025 (mtpp) cc_final: 0.6558 (mttp) REVERT: E 57 ASN cc_start: 0.7498 (m-40) cc_final: 0.7250 (m110) REVERT: E 73 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.6062 (mt) REVERT: E 81 LYS cc_start: 0.7064 (mmmt) cc_final: 0.6686 (mmmt) REVERT: F 37 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7477 (mm-30) REVERT: F 38 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.7261 (p) REVERT: F 53 ILE cc_start: 0.7558 (mp) cc_final: 0.7338 (mt) REVERT: F 91 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6869 (mmt) REVERT: F 96 MET cc_start: 0.7750 (ttp) cc_final: 0.7337 (ttp) REVERT: F 97 ARG cc_start: 0.7709 (mtt90) cc_final: 0.7314 (mtt90) REVERT: F 100 ASN cc_start: 0.7817 (m-40) cc_final: 0.7574 (m-40) REVERT: F 110 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7528 (mt-10) REVERT: F 148 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6654 (mm-30) REVERT: F 163 GLU cc_start: 0.7036 (tp30) cc_final: 0.6535 (tp30) REVERT: G 56 GLN cc_start: 0.6010 (OUTLIER) cc_final: 0.4870 (mp10) REVERT: G 146 THR cc_start: 0.7596 (OUTLIER) cc_final: 0.7376 (p) REVERT: H 24 THR cc_start: 0.7014 (OUTLIER) cc_final: 0.6436 (p) outliers start: 72 outliers final: 23 residues processed: 517 average time/residue: 1.4371 time to fit residues: 804.4595 Evaluate side-chains 477 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 438 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 153 ASN Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 MET Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN B 76 ASN C 30 HIS D 254 HIS F 125 GLN F 167 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 15310 Z= 0.508 Angle : 0.575 7.113 20736 Z= 0.308 Chirality : 0.048 0.162 2287 Planarity : 0.005 0.064 2666 Dihedral : 8.303 82.097 2184 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 4.96 % Allowed : 13.33 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.18), residues: 1862 helix: -0.24 (0.19), residues: 680 sheet: 0.22 (0.27), residues: 367 loop : -0.95 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 378 HIS 0.007 0.002 HIS C 54 PHE 0.027 0.002 PHE F 101 TYR 0.025 0.002 TYR D 43 ARG 0.005 0.001 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 467 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.6708 (mtm-85) cc_final: 0.6111 (mtm-85) REVERT: A 121 GLU cc_start: 0.6787 (mp0) cc_final: 0.6301 (mp0) REVERT: A 161 ARG cc_start: 0.7108 (mtt90) cc_final: 0.6698 (mtt-85) REVERT: A 182 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7317 (mm-30) REVERT: A 199 ASP cc_start: 0.6765 (m-30) cc_final: 0.6553 (m-30) REVERT: A 251 LYS cc_start: 0.7774 (tttt) cc_final: 0.7247 (ttmm) REVERT: A 298 GLU cc_start: 0.6753 (mp0) cc_final: 0.6347 (mp0) REVERT: A 317 LYS cc_start: 0.7500 (ttpp) cc_final: 0.7248 (ttpp) REVERT: A 329 ARG cc_start: 0.7127 (mtp180) cc_final: 0.6704 (mtm-85) REVERT: A 333 ARG cc_start: 0.7312 (mtp180) cc_final: 0.7108 (mtp180) REVERT: A 338 ASP cc_start: 0.6727 (m-30) cc_final: 0.6470 (m-30) REVERT: A 342 THR cc_start: 0.7435 (t) cc_final: 0.7231 (t) REVERT: A 364 ASP cc_start: 0.7209 (p0) cc_final: 0.6924 (p0) REVERT: A 368 ILE cc_start: 0.8169 (mp) cc_final: 0.7952 (mp) REVERT: A 388 PRO cc_start: 0.7696 (Cg_endo) cc_final: 0.7402 (Cg_exo) REVERT: A 391 TYR cc_start: 0.7765 (m-80) cc_final: 0.7400 (m-80) REVERT: A 392 GLN cc_start: 0.6931 (mp10) cc_final: 0.6103 (mp10) REVERT: A 414 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.6348 (m-80) REVERT: B 74 MET cc_start: 0.5047 (mmm) cc_final: 0.4839 (mmm) REVERT: B 127 MET cc_start: 0.6836 (mmt) cc_final: 0.6433 (mmt) REVERT: B 180 ARG cc_start: 0.7044 (mmt-90) cc_final: 0.6338 (mmp80) REVERT: B 232 LYS cc_start: 0.7185 (tttt) cc_final: 0.6949 (ttpp) REVERT: B 253 LYS cc_start: 0.7707 (mttt) cc_final: 0.7427 (mttp) REVERT: B 257 GLU cc_start: 0.7565 (mp0) cc_final: 0.7101 (mp0) REVERT: B 292 ASP cc_start: 0.7819 (t0) cc_final: 0.7568 (t0) REVERT: B 341 LYS cc_start: 0.7674 (mttt) cc_final: 0.7323 (mttt) REVERT: B 343 ARG cc_start: 0.7312 (tpt90) cc_final: 0.6932 (tpt90) REVERT: B 346 ASP cc_start: 0.6908 (p0) cc_final: 0.6651 (p0) REVERT: B 365 MET cc_start: 0.5938 (mpt) cc_final: 0.4793 (tmt) REVERT: C 44 LYS cc_start: 0.8098 (ttpt) cc_final: 0.7705 (ttpp) REVERT: C 46 HIS cc_start: 0.7797 (m-70) cc_final: 0.7429 (m-70) REVERT: C 56 THR cc_start: 0.7534 (p) cc_final: 0.7325 (p) REVERT: C 65 ASP cc_start: 0.7673 (t70) cc_final: 0.7408 (t0) REVERT: C 131 TRP cc_start: 0.5860 (OUTLIER) cc_final: 0.5021 (p90) REVERT: C 149 ASP cc_start: 0.7672 (t70) cc_final: 0.7314 (t0) REVERT: C 175 GLU cc_start: 0.7551 (mp0) cc_final: 0.6723 (mp0) REVERT: C 176 VAL cc_start: 0.7820 (t) cc_final: 0.7506 (m) REVERT: C 245 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7019 (pp20) REVERT: C 270 MET cc_start: 0.8268 (mtp) cc_final: 0.8062 (mtp) REVERT: C 287 ASP cc_start: 0.7408 (t0) cc_final: 0.7159 (t0) REVERT: C 290 LYS cc_start: 0.5797 (OUTLIER) cc_final: 0.5299 (tptp) REVERT: C 361 GLU cc_start: 0.6563 (pp20) cc_final: 0.6324 (pp20) REVERT: D 12 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6899 (mt-10) REVERT: D 62 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7947 (mtmm) REVERT: D 75 LEU cc_start: 0.6831 (tt) cc_final: 0.6501 (tp) REVERT: D 98 ASP cc_start: 0.6170 (t70) cc_final: 0.5866 (t70) REVERT: D 100 GLU cc_start: 0.6981 (mp0) cc_final: 0.6236 (mp0) REVERT: D 115 MET cc_start: 0.6952 (mtt) cc_final: 0.6621 (mtp) REVERT: D 179 LYS cc_start: 0.6820 (mtmp) cc_final: 0.6614 (mtmp) REVERT: D 213 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7273 (p0) REVERT: D 237 ARG cc_start: 0.7031 (ttp-170) cc_final: 0.6755 (ttp-170) REVERT: D 249 ASP cc_start: 0.7723 (m-30) cc_final: 0.7506 (m-30) REVERT: D 269 LYS cc_start: 0.7257 (tppt) cc_final: 0.7050 (tptm) REVERT: E 22 LEU cc_start: 0.7513 (mp) cc_final: 0.7024 (mm) REVERT: E 62 ASN cc_start: 0.6964 (t0) cc_final: 0.6502 (t0) REVERT: E 81 LYS cc_start: 0.6974 (mmmt) cc_final: 0.6583 (mmmt) REVERT: F 37 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7316 (mm-30) REVERT: F 44 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7430 (mmtt) REVERT: F 57 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: F 59 GLU cc_start: 0.7749 (tt0) cc_final: 0.7344 (tt0) REVERT: F 100 ASN cc_start: 0.7763 (m-40) cc_final: 0.7424 (m-40) REVERT: F 110 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7551 (mt-10) REVERT: F 163 GLU cc_start: 0.6968 (tp30) cc_final: 0.6647 (tp30) REVERT: G 56 GLN cc_start: 0.6189 (OUTLIER) cc_final: 0.5098 (mp10) REVERT: G 146 THR cc_start: 0.7407 (OUTLIER) cc_final: 0.7053 (p) REVERT: H 24 THR cc_start: 0.7334 (OUTLIER) cc_final: 0.6846 (p) outliers start: 80 outliers final: 39 residues processed: 507 average time/residue: 1.4687 time to fit residues: 805.8922 Evaluate side-chains 514 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 466 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 181 optimal weight: 0.3980 chunk 149 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 255 GLN B 226 ASN C 30 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15310 Z= 0.204 Angle : 0.458 6.760 20736 Z= 0.247 Chirality : 0.043 0.152 2287 Planarity : 0.004 0.054 2666 Dihedral : 7.346 74.446 2150 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 3.66 % Allowed : 16.49 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.19), residues: 1862 helix: 0.61 (0.20), residues: 687 sheet: 0.29 (0.26), residues: 369 loop : -0.76 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 221 HIS 0.005 0.001 HIS F 137 PHE 0.016 0.001 PHE F 101 TYR 0.015 0.001 TYR D 43 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 462 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.6699 (mtm-85) cc_final: 0.6097 (mtm-85) REVERT: A 114 GLU cc_start: 0.7969 (pt0) cc_final: 0.7703 (pt0) REVERT: A 132 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6755 (mm-30) REVERT: A 161 ARG cc_start: 0.7084 (mtt90) cc_final: 0.6696 (mtt-85) REVERT: A 182 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7282 (mm-30) REVERT: A 241 GLU cc_start: 0.6845 (tp30) cc_final: 0.6589 (mm-30) REVERT: A 251 LYS cc_start: 0.7695 (tttt) cc_final: 0.7159 (ttmm) REVERT: A 298 GLU cc_start: 0.6700 (mp0) cc_final: 0.6268 (mp0) REVERT: A 317 LYS cc_start: 0.7448 (ttpp) cc_final: 0.6942 (ttpp) REVERT: A 329 ARG cc_start: 0.7115 (mtp180) cc_final: 0.6672 (ttm-80) REVERT: A 342 THR cc_start: 0.7468 (t) cc_final: 0.7245 (t) REVERT: A 351 GLU cc_start: 0.5889 (tp30) cc_final: 0.5591 (tp30) REVERT: A 364 ASP cc_start: 0.7166 (p0) cc_final: 0.6896 (p0) REVERT: A 368 ILE cc_start: 0.8187 (mp) cc_final: 0.7966 (mp) REVERT: A 388 PRO cc_start: 0.7638 (Cg_endo) cc_final: 0.7349 (Cg_exo) REVERT: A 392 GLN cc_start: 0.6933 (mp10) cc_final: 0.6108 (mp10) REVERT: B 127 MET cc_start: 0.6837 (mmt) cc_final: 0.6417 (mmt) REVERT: B 180 ARG cc_start: 0.6914 (mmt-90) cc_final: 0.6447 (mmt-90) REVERT: B 214 ARG cc_start: 0.6884 (ttp80) cc_final: 0.6674 (ttp80) REVERT: B 232 LYS cc_start: 0.7164 (tttt) cc_final: 0.6908 (ttpp) REVERT: B 253 LYS cc_start: 0.7686 (mttt) cc_final: 0.7359 (mttp) REVERT: B 257 GLU cc_start: 0.7458 (mp0) cc_final: 0.7012 (mp0) REVERT: B 292 ASP cc_start: 0.7815 (t0) cc_final: 0.7497 (t0) REVERT: B 343 ARG cc_start: 0.7312 (tpt90) cc_final: 0.6921 (tpt90) REVERT: B 346 ASP cc_start: 0.6962 (p0) cc_final: 0.6632 (p0) REVERT: B 365 MET cc_start: 0.5954 (OUTLIER) cc_final: 0.4826 (tmt) REVERT: C 44 LYS cc_start: 0.8051 (ttpt) cc_final: 0.7718 (ttpp) REVERT: C 56 THR cc_start: 0.7546 (p) cc_final: 0.7317 (p) REVERT: C 65 ASP cc_start: 0.7607 (t70) cc_final: 0.7370 (t0) REVERT: C 131 TRP cc_start: 0.5544 (OUTLIER) cc_final: 0.4841 (p90) REVERT: C 149 ASP cc_start: 0.7482 (t70) cc_final: 0.7187 (t0) REVERT: C 175 GLU cc_start: 0.7575 (mp0) cc_final: 0.6745 (mp0) REVERT: C 176 VAL cc_start: 0.7774 (t) cc_final: 0.7505 (m) REVERT: C 232 ASP cc_start: 0.7356 (t0) cc_final: 0.7148 (t0) REVERT: C 245 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6984 (pp20) REVERT: C 287 ASP cc_start: 0.7381 (t0) cc_final: 0.7132 (t0) REVERT: C 290 LYS cc_start: 0.5779 (OUTLIER) cc_final: 0.5357 (tptp) REVERT: C 361 GLU cc_start: 0.6547 (pp20) cc_final: 0.6298 (pp20) REVERT: D 12 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6865 (mt-10) REVERT: D 62 LYS cc_start: 0.8287 (mtpp) cc_final: 0.7914 (mtmm) REVERT: D 100 GLU cc_start: 0.7084 (mp0) cc_final: 0.6312 (mp0) REVERT: D 115 MET cc_start: 0.6930 (mtt) cc_final: 0.6624 (mtm) REVERT: D 159 ASP cc_start: 0.7931 (p0) cc_final: 0.7683 (p0) REVERT: D 213 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7219 (p0) REVERT: D 237 ARG cc_start: 0.7006 (ttp-170) cc_final: 0.6719 (ttp-170) REVERT: D 258 SER cc_start: 0.7748 (m) cc_final: 0.7499 (m) REVERT: E 22 LEU cc_start: 0.7531 (mp) cc_final: 0.7052 (mm) REVERT: E 50 LYS cc_start: 0.6932 (mttp) cc_final: 0.6671 (mttp) REVERT: E 81 LYS cc_start: 0.6950 (mmmt) cc_final: 0.6580 (mmmt) REVERT: F 37 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7351 (mm-30) REVERT: F 44 LYS cc_start: 0.7652 (mmtt) cc_final: 0.7401 (mmtt) REVERT: F 57 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7194 (mm-30) REVERT: F 59 GLU cc_start: 0.7664 (tt0) cc_final: 0.7330 (tt0) REVERT: F 92 ARG cc_start: 0.7110 (mtp85) cc_final: 0.6673 (ttp80) REVERT: F 100 ASN cc_start: 0.7679 (m-40) cc_final: 0.7452 (m-40) REVERT: F 110 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7513 (mt-10) REVERT: F 152 SER cc_start: 0.7401 (m) cc_final: 0.7187 (p) REVERT: F 163 GLU cc_start: 0.6937 (tp30) cc_final: 0.6635 (tp30) REVERT: G 10 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6446 (tpm-80) REVERT: G 56 GLN cc_start: 0.6016 (OUTLIER) cc_final: 0.4901 (mp10) REVERT: G 146 THR cc_start: 0.7405 (OUTLIER) cc_final: 0.7058 (p) REVERT: H 24 THR cc_start: 0.7217 (OUTLIER) cc_final: 0.6748 (p) outliers start: 59 outliers final: 32 residues processed: 497 average time/residue: 1.4635 time to fit residues: 786.3052 Evaluate side-chains 495 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 453 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.4980 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 160 optimal weight: 0.0170 chunk 48 optimal weight: 8.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 255 GLN A 318 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN C 30 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN F 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15310 Z= 0.167 Angle : 0.441 6.443 20736 Z= 0.236 Chirality : 0.042 0.147 2287 Planarity : 0.004 0.048 2666 Dihedral : 6.789 68.889 2147 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 3.91 % Allowed : 17.17 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.19), residues: 1862 helix: 1.19 (0.20), residues: 680 sheet: 0.28 (0.27), residues: 370 loop : -0.61 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 PHE 0.015 0.001 PHE A 276 TYR 0.012 0.001 TYR D 43 ARG 0.004 0.000 ARG D 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 479 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.7877 (m-80) cc_final: 0.7557 (m-80) REVERT: A 79 ARG cc_start: 0.6687 (mtm-85) cc_final: 0.6089 (mtm-85) REVERT: A 132 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6727 (mm-30) REVERT: A 161 ARG cc_start: 0.7081 (mtt90) cc_final: 0.6699 (mtt-85) REVERT: A 248 ASP cc_start: 0.7258 (t70) cc_final: 0.6727 (t70) REVERT: A 250 SER cc_start: 0.8139 (p) cc_final: 0.7935 (m) REVERT: A 251 LYS cc_start: 0.7682 (tttt) cc_final: 0.7005 (ttmm) REVERT: A 253 ILE cc_start: 0.7682 (mt) cc_final: 0.7465 (OUTLIER) REVERT: A 280 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7002 (mm-30) REVERT: A 298 GLU cc_start: 0.6713 (mp0) cc_final: 0.6242 (mp0) REVERT: A 317 LYS cc_start: 0.7446 (ttpp) cc_final: 0.6925 (ttpp) REVERT: A 318 ASN cc_start: 0.7587 (t0) cc_final: 0.7293 (t0) REVERT: A 329 ARG cc_start: 0.7135 (mtp180) cc_final: 0.6717 (mtm-85) REVERT: A 333 ARG cc_start: 0.7165 (mtp180) cc_final: 0.6944 (mtp180) REVERT: A 342 THR cc_start: 0.7488 (t) cc_final: 0.7261 (t) REVERT: A 351 GLU cc_start: 0.6024 (tp30) cc_final: 0.5773 (tp30) REVERT: A 364 ASP cc_start: 0.7121 (p0) cc_final: 0.6863 (p0) REVERT: A 368 ILE cc_start: 0.8172 (mp) cc_final: 0.7913 (mp) REVERT: A 388 PRO cc_start: 0.7640 (Cg_endo) cc_final: 0.7371 (Cg_exo) REVERT: A 392 GLN cc_start: 0.6988 (mp10) cc_final: 0.6194 (mp10) REVERT: B 127 MET cc_start: 0.6806 (mmt) cc_final: 0.6379 (mmt) REVERT: B 180 ARG cc_start: 0.6880 (mmt-90) cc_final: 0.6420 (mmt-90) REVERT: B 214 ARG cc_start: 0.6865 (ttp80) cc_final: 0.6646 (ttp80) REVERT: B 232 LYS cc_start: 0.7141 (tttt) cc_final: 0.6878 (mtpp) REVERT: B 253 LYS cc_start: 0.7663 (mttt) cc_final: 0.7326 (mttp) REVERT: B 257 GLU cc_start: 0.7432 (mp0) cc_final: 0.6992 (mp0) REVERT: B 292 ASP cc_start: 0.7773 (t0) cc_final: 0.7500 (t0) REVERT: B 343 ARG cc_start: 0.7293 (tpt90) cc_final: 0.6905 (tpt90) REVERT: B 346 ASP cc_start: 0.6903 (p0) cc_final: 0.6616 (p0) REVERT: B 365 MET cc_start: 0.5954 (OUTLIER) cc_final: 0.4820 (tmt) REVERT: C 44 LYS cc_start: 0.8090 (ttpt) cc_final: 0.7641 (ttpp) REVERT: C 56 THR cc_start: 0.7519 (p) cc_final: 0.7278 (p) REVERT: C 65 ASP cc_start: 0.7620 (t70) cc_final: 0.7402 (t0) REVERT: C 131 TRP cc_start: 0.5401 (OUTLIER) cc_final: 0.4730 (p90) REVERT: C 175 GLU cc_start: 0.7581 (mp0) cc_final: 0.6745 (mp0) REVERT: C 176 VAL cc_start: 0.7796 (t) cc_final: 0.7510 (m) REVERT: C 232 ASP cc_start: 0.7346 (t0) cc_final: 0.7091 (t0) REVERT: C 245 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6924 (pp20) REVERT: C 287 ASP cc_start: 0.7383 (t0) cc_final: 0.7123 (t0) REVERT: C 290 LYS cc_start: 0.5751 (OUTLIER) cc_final: 0.5306 (tptp) REVERT: C 337 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7737 (mmtm) REVERT: C 361 GLU cc_start: 0.6547 (pp20) cc_final: 0.6293 (pp20) REVERT: D 12 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6863 (mt-10) REVERT: D 62 LYS cc_start: 0.8279 (mtpp) cc_final: 0.7919 (mtmm) REVERT: D 98 ASP cc_start: 0.6474 (t70) cc_final: 0.6225 (t70) REVERT: D 100 GLU cc_start: 0.7224 (mp0) cc_final: 0.6484 (mp0) REVERT: D 115 MET cc_start: 0.6870 (mtt) cc_final: 0.6561 (mtm) REVERT: D 159 ASP cc_start: 0.7990 (p0) cc_final: 0.7753 (p0) REVERT: D 213 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7208 (p0) REVERT: D 237 ARG cc_start: 0.6977 (ttp-170) cc_final: 0.6755 (ttp-170) REVERT: D 258 SER cc_start: 0.7755 (m) cc_final: 0.7504 (m) REVERT: E 22 LEU cc_start: 0.7517 (mp) cc_final: 0.7046 (mm) REVERT: E 50 LYS cc_start: 0.6933 (mttp) cc_final: 0.6677 (mttp) REVERT: E 62 ASN cc_start: 0.6637 (t0) cc_final: 0.6187 (t0) REVERT: E 81 LYS cc_start: 0.6999 (mmmt) cc_final: 0.6631 (mmmt) REVERT: F 37 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7380 (mm-30) REVERT: F 44 LYS cc_start: 0.7639 (mmtt) cc_final: 0.7377 (mmtt) REVERT: F 57 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7180 (mm-30) REVERT: F 59 GLU cc_start: 0.7654 (tt0) cc_final: 0.7309 (tt0) REVERT: F 84 LYS cc_start: 0.6690 (tttt) cc_final: 0.6441 (ttpp) REVERT: F 91 MET cc_start: 0.7189 (mmt) cc_final: 0.6921 (mmt) REVERT: F 92 ARG cc_start: 0.7100 (mtp85) cc_final: 0.6675 (ttp80) REVERT: F 110 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7488 (mt-10) REVERT: F 163 GLU cc_start: 0.6928 (tp30) cc_final: 0.6611 (tp30) REVERT: G 10 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6468 (tpm-80) REVERT: G 56 GLN cc_start: 0.5912 (OUTLIER) cc_final: 0.4801 (mp10) REVERT: G 86 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6948 (t80) REVERT: G 146 THR cc_start: 0.7439 (OUTLIER) cc_final: 0.7088 (p) REVERT: H 24 THR cc_start: 0.7192 (OUTLIER) cc_final: 0.6663 (p) outliers start: 63 outliers final: 37 residues processed: 508 average time/residue: 1.4135 time to fit residues: 777.7428 Evaluate side-chains 525 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 478 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 219 GLN A 255 GLN B 226 ASN C 30 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN D 219 ASN F 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15310 Z= 0.397 Angle : 0.526 7.297 20736 Z= 0.280 Chirality : 0.046 0.158 2287 Planarity : 0.004 0.055 2666 Dihedral : 7.270 76.821 2145 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.54 % Favored : 96.40 % Rotamer: Outliers : 5.08 % Allowed : 16.12 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.19), residues: 1862 helix: 1.22 (0.21), residues: 675 sheet: 0.21 (0.26), residues: 380 loop : -0.66 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 104 HIS 0.006 0.001 HIS F 137 PHE 0.024 0.002 PHE F 101 TYR 0.024 0.002 TYR D 43 ARG 0.005 0.000 ARG D 281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 471 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7691 (pp) REVERT: A 79 ARG cc_start: 0.6672 (mtm-85) cc_final: 0.6095 (mtm-85) REVERT: A 121 GLU cc_start: 0.6735 (mp0) cc_final: 0.6244 (mp0) REVERT: A 161 ARG cc_start: 0.7058 (mtt90) cc_final: 0.6675 (mtt-85) REVERT: A 251 LYS cc_start: 0.7690 (tttt) cc_final: 0.6963 (ttmm) REVERT: A 280 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6876 (mm-30) REVERT: A 298 GLU cc_start: 0.6729 (mp0) cc_final: 0.6296 (mp0) REVERT: A 317 LYS cc_start: 0.7434 (ttpp) cc_final: 0.7168 (ttpp) REVERT: A 329 ARG cc_start: 0.7073 (mtp180) cc_final: 0.6655 (mtm-85) REVERT: A 342 THR cc_start: 0.7504 (t) cc_final: 0.7289 (t) REVERT: A 364 ASP cc_start: 0.7083 (p0) cc_final: 0.6799 (p0) REVERT: A 368 ILE cc_start: 0.8206 (mp) cc_final: 0.7936 (mp) REVERT: A 388 PRO cc_start: 0.7651 (Cg_endo) cc_final: 0.7385 (Cg_exo) REVERT: A 392 GLN cc_start: 0.7007 (mp10) cc_final: 0.6167 (mp10) REVERT: B 127 MET cc_start: 0.6835 (mmt) cc_final: 0.6381 (mmt) REVERT: B 180 ARG cc_start: 0.7001 (mmt-90) cc_final: 0.6407 (mmp80) REVERT: B 214 ARG cc_start: 0.6823 (ttp80) cc_final: 0.6580 (ttp80) REVERT: B 232 LYS cc_start: 0.7206 (tttt) cc_final: 0.6954 (ttmm) REVERT: B 253 LYS cc_start: 0.7673 (mttt) cc_final: 0.7366 (mttp) REVERT: B 257 GLU cc_start: 0.7522 (mp0) cc_final: 0.7154 (mp0) REVERT: B 265 LEU cc_start: 0.7533 (mt) cc_final: 0.7316 (mt) REVERT: B 292 ASP cc_start: 0.7824 (t0) cc_final: 0.7537 (t0) REVERT: B 343 ARG cc_start: 0.7319 (tpt90) cc_final: 0.6936 (tpt90) REVERT: B 346 ASP cc_start: 0.6846 (p0) cc_final: 0.6569 (p0) REVERT: B 365 MET cc_start: 0.5986 (OUTLIER) cc_final: 0.4886 (tmt) REVERT: C 44 LYS cc_start: 0.8040 (ttpt) cc_final: 0.7626 (ttpp) REVERT: C 56 THR cc_start: 0.7517 (p) cc_final: 0.7296 (p) REVERT: C 65 ASP cc_start: 0.7694 (t70) cc_final: 0.7433 (t0) REVERT: C 131 TRP cc_start: 0.5663 (OUTLIER) cc_final: 0.4911 (p90) REVERT: C 175 GLU cc_start: 0.7562 (mp0) cc_final: 0.6727 (mp0) REVERT: C 176 VAL cc_start: 0.7804 (t) cc_final: 0.7541 (m) REVERT: C 232 ASP cc_start: 0.7476 (t0) cc_final: 0.7215 (t0) REVERT: C 245 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6934 (pp20) REVERT: C 257 GLU cc_start: 0.7762 (tp30) cc_final: 0.7391 (tp30) REVERT: C 270 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7956 (mtt) REVERT: C 287 ASP cc_start: 0.7424 (t0) cc_final: 0.7157 (t0) REVERT: C 290 LYS cc_start: 0.5755 (OUTLIER) cc_final: 0.5324 (tptp) REVERT: C 337 LYS cc_start: 0.7962 (mmtm) cc_final: 0.7728 (mmtm) REVERT: C 361 GLU cc_start: 0.6570 (pp20) cc_final: 0.6304 (pp20) REVERT: D 12 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6898 (mt-10) REVERT: D 62 LYS cc_start: 0.8245 (mtpp) cc_final: 0.7895 (mtmm) REVERT: D 100 GLU cc_start: 0.7164 (mp0) cc_final: 0.6428 (mp0) REVERT: D 115 MET cc_start: 0.6936 (mtt) cc_final: 0.6593 (mtm) REVERT: D 159 ASP cc_start: 0.7959 (p0) cc_final: 0.7710 (p0) REVERT: D 237 ARG cc_start: 0.6975 (ttp-170) cc_final: 0.6768 (ttp-170) REVERT: E 22 LEU cc_start: 0.7484 (mp) cc_final: 0.6993 (mm) REVERT: E 50 LYS cc_start: 0.6897 (mttp) cc_final: 0.6653 (mttp) REVERT: E 81 LYS cc_start: 0.7003 (mmmt) cc_final: 0.6624 (mmmt) REVERT: F 37 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7339 (mm-30) REVERT: F 44 LYS cc_start: 0.7662 (mmtt) cc_final: 0.7411 (mmtt) REVERT: F 57 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7195 (mm-30) REVERT: F 59 GLU cc_start: 0.7693 (tt0) cc_final: 0.7397 (tt0) REVERT: F 110 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7470 (mt-10) REVERT: F 163 GLU cc_start: 0.6928 (tp30) cc_final: 0.6550 (tp30) REVERT: F 166 LYS cc_start: 0.7510 (ttmm) cc_final: 0.7295 (ttmt) REVERT: G 10 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6535 (tpm-80) REVERT: G 56 GLN cc_start: 0.5985 (OUTLIER) cc_final: 0.4885 (mp10) REVERT: G 146 THR cc_start: 0.7387 (OUTLIER) cc_final: 0.7010 (p) REVERT: H 24 THR cc_start: 0.7218 (OUTLIER) cc_final: 0.6750 (p) outliers start: 82 outliers final: 55 residues processed: 511 average time/residue: 1.4566 time to fit residues: 805.4823 Evaluate side-chains 534 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 468 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 219 GLN A 255 GLN A 318 ASN B 226 ASN C 28 ASN C 30 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN C 129 ASN ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN F 125 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15310 Z= 0.356 Angle : 0.511 7.625 20736 Z= 0.272 Chirality : 0.046 0.164 2287 Planarity : 0.004 0.054 2666 Dihedral : 7.322 77.073 2143 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 5.02 % Allowed : 16.74 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.19), residues: 1862 helix: 1.25 (0.21), residues: 681 sheet: 0.22 (0.26), residues: 380 loop : -0.62 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 221 HIS 0.006 0.001 HIS F 137 PHE 0.022 0.002 PHE F 101 TYR 0.021 0.002 TYR D 43 ARG 0.003 0.000 ARG D 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 459 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7695 (pp) REVERT: A 79 ARG cc_start: 0.6680 (mtm-85) cc_final: 0.6099 (mtm-85) REVERT: A 121 GLU cc_start: 0.6726 (mp0) cc_final: 0.6233 (mp0) REVERT: A 161 ARG cc_start: 0.7027 (mtt90) cc_final: 0.6630 (mtt-85) REVERT: A 251 LYS cc_start: 0.7611 (tttt) cc_final: 0.6951 (ttmm) REVERT: A 253 ILE cc_start: 0.7758 (mt) cc_final: 0.7538 (OUTLIER) REVERT: A 280 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6845 (mm-30) REVERT: A 298 GLU cc_start: 0.6735 (mp0) cc_final: 0.6293 (mp0) REVERT: A 317 LYS cc_start: 0.7449 (ttpp) cc_final: 0.7227 (ttpp) REVERT: A 329 ARG cc_start: 0.7063 (mtp180) cc_final: 0.6651 (mtm-85) REVERT: A 333 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6944 (mtp180) REVERT: A 342 THR cc_start: 0.7493 (t) cc_final: 0.7281 (t) REVERT: A 368 ILE cc_start: 0.8213 (mp) cc_final: 0.8003 (mp) REVERT: A 388 PRO cc_start: 0.7640 (Cg_endo) cc_final: 0.7389 (Cg_exo) REVERT: A 392 GLN cc_start: 0.7031 (mp10) cc_final: 0.6209 (mp10) REVERT: B 127 MET cc_start: 0.6837 (mmt) cc_final: 0.6378 (mmt) REVERT: B 180 ARG cc_start: 0.7012 (mmt-90) cc_final: 0.6485 (mmt-90) REVERT: B 214 ARG cc_start: 0.6852 (ttp80) cc_final: 0.6609 (ttp80) REVERT: B 232 LYS cc_start: 0.7226 (tttt) cc_final: 0.6963 (ttmm) REVERT: B 253 LYS cc_start: 0.7699 (mttt) cc_final: 0.7442 (mttp) REVERT: B 257 GLU cc_start: 0.7526 (mp0) cc_final: 0.7171 (mp0) REVERT: B 292 ASP cc_start: 0.7805 (t0) cc_final: 0.7495 (t0) REVERT: B 343 ARG cc_start: 0.7314 (tpt90) cc_final: 0.6907 (tpt90) REVERT: B 346 ASP cc_start: 0.6821 (p0) cc_final: 0.6528 (p0) REVERT: B 365 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.4916 (tmt) REVERT: C 44 LYS cc_start: 0.8032 (ttpt) cc_final: 0.7741 (ttpt) REVERT: C 65 ASP cc_start: 0.7709 (t70) cc_final: 0.7456 (t0) REVERT: C 131 TRP cc_start: 0.5699 (OUTLIER) cc_final: 0.4995 (p90) REVERT: C 175 GLU cc_start: 0.7568 (mp0) cc_final: 0.6724 (mp0) REVERT: C 176 VAL cc_start: 0.7792 (t) cc_final: 0.7530 (m) REVERT: C 232 ASP cc_start: 0.7488 (t0) cc_final: 0.7212 (t0) REVERT: C 245 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6924 (pp20) REVERT: C 257 GLU cc_start: 0.7753 (tp30) cc_final: 0.7375 (tp30) REVERT: C 287 ASP cc_start: 0.7440 (t0) cc_final: 0.7184 (t0) REVERT: C 290 LYS cc_start: 0.5787 (OUTLIER) cc_final: 0.5286 (tptp) REVERT: C 337 LYS cc_start: 0.7940 (mmtm) cc_final: 0.7694 (mmtm) REVERT: C 361 GLU cc_start: 0.6598 (pp20) cc_final: 0.6329 (pp20) REVERT: D 12 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6895 (mt-10) REVERT: D 62 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7981 (mtmm) REVERT: D 100 GLU cc_start: 0.7186 (mp0) cc_final: 0.6434 (mp0) REVERT: D 115 MET cc_start: 0.6923 (mtt) cc_final: 0.6576 (mtm) REVERT: D 159 ASP cc_start: 0.7988 (p0) cc_final: 0.7759 (p0) REVERT: D 167 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7471 (p) REVERT: D 213 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7203 (p0) REVERT: D 237 ARG cc_start: 0.6976 (ttp-170) cc_final: 0.6758 (ttp-170) REVERT: D 278 ASN cc_start: 0.7473 (t0) cc_final: 0.7241 (t0) REVERT: E 22 LEU cc_start: 0.7472 (mp) cc_final: 0.6983 (mm) REVERT: E 50 LYS cc_start: 0.6909 (mttp) cc_final: 0.6658 (mttp) REVERT: E 57 ASN cc_start: 0.7749 (m-40) cc_final: 0.7415 (m-40) REVERT: E 81 LYS cc_start: 0.7014 (mmmt) cc_final: 0.6634 (mmmt) REVERT: F 37 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7355 (mm-30) REVERT: F 44 LYS cc_start: 0.7656 (mmtt) cc_final: 0.7430 (mmtt) REVERT: F 57 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7167 (mm-30) REVERT: F 59 GLU cc_start: 0.7668 (tt0) cc_final: 0.7382 (tt0) REVERT: F 110 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7438 (mt-10) REVERT: F 163 GLU cc_start: 0.7030 (tp30) cc_final: 0.6690 (tp30) REVERT: G 10 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6559 (tpm-80) REVERT: G 56 GLN cc_start: 0.5972 (OUTLIER) cc_final: 0.4845 (mp10) REVERT: G 146 THR cc_start: 0.7354 (OUTLIER) cc_final: 0.6989 (p) REVERT: H 24 THR cc_start: 0.7264 (OUTLIER) cc_final: 0.6789 (p) outliers start: 81 outliers final: 52 residues processed: 496 average time/residue: 1.4843 time to fit residues: 795.3959 Evaluate side-chains 524 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 460 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 30.0000 chunk 20 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 255 GLN B 226 ASN C 30 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN F 100 ASN F 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15310 Z= 0.229 Angle : 0.468 7.836 20736 Z= 0.249 Chirality : 0.043 0.174 2287 Planarity : 0.004 0.052 2666 Dihedral : 6.975 73.861 2143 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 4.59 % Allowed : 17.42 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.20), residues: 1862 helix: 1.45 (0.21), residues: 680 sheet: 0.25 (0.26), residues: 380 loop : -0.48 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 PHE 0.017 0.001 PHE C 111 TYR 0.015 0.001 TYR D 43 ARG 0.003 0.000 ARG D 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 461 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.7890 (m-80) cc_final: 0.7592 (m-80) REVERT: A 19 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7696 (pp) REVERT: A 79 ARG cc_start: 0.6665 (mtm-85) cc_final: 0.6096 (mtm-85) REVERT: A 161 ARG cc_start: 0.7008 (mtt90) cc_final: 0.6633 (mtt-85) REVERT: A 170 SER cc_start: 0.7484 (t) cc_final: 0.6964 (p) REVERT: A 251 LYS cc_start: 0.7602 (tttt) cc_final: 0.6945 (ttmm) REVERT: A 280 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6947 (mm-30) REVERT: A 298 GLU cc_start: 0.6717 (mp0) cc_final: 0.6272 (mp0) REVERT: A 317 LYS cc_start: 0.7422 (ttpp) cc_final: 0.7167 (ttpp) REVERT: A 329 ARG cc_start: 0.7057 (mtp180) cc_final: 0.6649 (mtm-85) REVERT: A 333 ARG cc_start: 0.7151 (mtp180) cc_final: 0.6944 (mtp180) REVERT: A 342 THR cc_start: 0.7501 (t) cc_final: 0.7288 (t) REVERT: A 364 ASP cc_start: 0.7003 (p0) cc_final: 0.6736 (p0) REVERT: A 368 ILE cc_start: 0.8196 (mp) cc_final: 0.7950 (mp) REVERT: A 388 PRO cc_start: 0.7635 (Cg_endo) cc_final: 0.7385 (Cg_exo) REVERT: A 392 GLN cc_start: 0.7069 (mp10) cc_final: 0.6274 (mp10) REVERT: B 127 MET cc_start: 0.6838 (mmt) cc_final: 0.6400 (mmt) REVERT: B 180 ARG cc_start: 0.6913 (mmt-90) cc_final: 0.6401 (mmt-90) REVERT: B 214 ARG cc_start: 0.6855 (ttp80) cc_final: 0.6628 (ttp80) REVERT: B 232 LYS cc_start: 0.7208 (tttt) cc_final: 0.6868 (mtpp) REVERT: B 253 LYS cc_start: 0.7696 (mttt) cc_final: 0.7404 (mttp) REVERT: B 257 GLU cc_start: 0.7534 (mp0) cc_final: 0.7172 (mp0) REVERT: B 292 ASP cc_start: 0.7790 (t0) cc_final: 0.7493 (t0) REVERT: B 343 ARG cc_start: 0.7314 (tpt90) cc_final: 0.6912 (tpt90) REVERT: B 346 ASP cc_start: 0.6785 (p0) cc_final: 0.6576 (p0) REVERT: B 365 MET cc_start: 0.5938 (OUTLIER) cc_final: 0.4893 (tmt) REVERT: C 44 LYS cc_start: 0.8073 (ttpt) cc_final: 0.7787 (ttpt) REVERT: C 56 THR cc_start: 0.7512 (p) cc_final: 0.7275 (p) REVERT: C 65 ASP cc_start: 0.7694 (t70) cc_final: 0.7436 (t0) REVERT: C 131 TRP cc_start: 0.5560 (OUTLIER) cc_final: 0.4971 (p90) REVERT: C 175 GLU cc_start: 0.7573 (mp0) cc_final: 0.6750 (mp0) REVERT: C 176 VAL cc_start: 0.7826 (t) cc_final: 0.7575 (m) REVERT: C 183 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.7194 (t) REVERT: C 232 ASP cc_start: 0.7450 (t0) cc_final: 0.7193 (t0) REVERT: C 245 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6954 (pp20) REVERT: C 257 GLU cc_start: 0.7778 (tp30) cc_final: 0.7395 (tp30) REVERT: C 287 ASP cc_start: 0.7400 (t0) cc_final: 0.7123 (t0) REVERT: C 337 LYS cc_start: 0.7897 (mmtm) cc_final: 0.7624 (mmtm) REVERT: C 361 GLU cc_start: 0.6577 (pp20) cc_final: 0.6327 (pp20) REVERT: C 365 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6757 (pp30) REVERT: D 12 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6884 (mt-10) REVERT: D 62 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7975 (mtmm) REVERT: D 100 GLU cc_start: 0.7246 (mp0) cc_final: 0.6485 (mp0) REVERT: D 115 MET cc_start: 0.6891 (mtt) cc_final: 0.6550 (mtp) REVERT: D 159 ASP cc_start: 0.8017 (p0) cc_final: 0.7807 (p0) REVERT: D 167 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7421 (p) REVERT: D 213 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7167 (p0) REVERT: D 237 ARG cc_start: 0.6963 (ttp-170) cc_final: 0.6754 (ttp-170) REVERT: D 258 SER cc_start: 0.7716 (m) cc_final: 0.7448 (m) REVERT: E 22 LEU cc_start: 0.7465 (mp) cc_final: 0.7192 (mp) REVERT: E 50 LYS cc_start: 0.6890 (mttp) cc_final: 0.6667 (mttp) REVERT: E 57 ASN cc_start: 0.7733 (m-40) cc_final: 0.7444 (m-40) REVERT: E 62 ASN cc_start: 0.6751 (m-40) cc_final: 0.6521 (m-40) REVERT: E 81 LYS cc_start: 0.7034 (mmmt) cc_final: 0.6652 (mmmt) REVERT: F 37 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7348 (mm-30) REVERT: F 44 LYS cc_start: 0.7641 (mmtt) cc_final: 0.7404 (mmtt) REVERT: F 57 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7164 (mm-30) REVERT: F 59 GLU cc_start: 0.7666 (tt0) cc_final: 0.7380 (tt0) REVERT: F 110 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7463 (mt-10) REVERT: F 163 GLU cc_start: 0.6965 (tp30) cc_final: 0.6727 (tp30) REVERT: G 56 GLN cc_start: 0.5925 (OUTLIER) cc_final: 0.4809 (mp10) REVERT: G 146 THR cc_start: 0.7383 (OUTLIER) cc_final: 0.7023 (p) REVERT: H 24 THR cc_start: 0.7285 (OUTLIER) cc_final: 0.7030 (p) outliers start: 74 outliers final: 48 residues processed: 499 average time/residue: 1.4572 time to fit residues: 786.4376 Evaluate side-chains 519 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 459 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 255 GLN B 226 ASN B 352 HIS C 30 HIS ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN F 100 ASN F 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15310 Z= 0.218 Angle : 0.471 7.488 20736 Z= 0.249 Chirality : 0.043 0.220 2287 Planarity : 0.004 0.052 2666 Dihedral : 6.783 72.619 2139 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 4.84 % Allowed : 17.73 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.20), residues: 1862 helix: 1.57 (0.21), residues: 680 sheet: 0.28 (0.26), residues: 380 loop : -0.42 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 221 HIS 0.005 0.001 HIS F 137 PHE 0.017 0.001 PHE A 276 TYR 0.015 0.001 TYR D 43 ARG 0.003 0.000 ARG D 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 458 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.7894 (m-80) cc_final: 0.7591 (m-80) REVERT: A 19 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7700 (pp) REVERT: A 79 ARG cc_start: 0.6616 (mtm-85) cc_final: 0.6057 (mtm-85) REVERT: A 161 ARG cc_start: 0.7011 (mtt90) cc_final: 0.6639 (mtt-85) REVERT: A 170 SER cc_start: 0.7465 (t) cc_final: 0.6991 (p) REVERT: A 251 LYS cc_start: 0.7581 (tttt) cc_final: 0.6996 (ttmm) REVERT: A 253 ILE cc_start: 0.7725 (mt) cc_final: 0.7519 (OUTLIER) REVERT: A 280 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6903 (mm-30) REVERT: A 298 GLU cc_start: 0.6720 (mp0) cc_final: 0.6247 (mp0) REVERT: A 317 LYS cc_start: 0.7432 (ttpp) cc_final: 0.7156 (ttpp) REVERT: A 329 ARG cc_start: 0.7043 (mtp180) cc_final: 0.6637 (mtm-85) REVERT: A 333 ARG cc_start: 0.7162 (mtp180) cc_final: 0.6937 (mtp180) REVERT: A 342 THR cc_start: 0.7507 (t) cc_final: 0.7286 (t) REVERT: A 364 ASP cc_start: 0.6989 (p0) cc_final: 0.6718 (p0) REVERT: A 388 PRO cc_start: 0.7632 (Cg_endo) cc_final: 0.7328 (Cg_exo) REVERT: A 391 TYR cc_start: 0.7722 (m-80) cc_final: 0.7238 (m-80) REVERT: A 392 GLN cc_start: 0.7077 (mp10) cc_final: 0.6274 (mp10) REVERT: B 127 MET cc_start: 0.6843 (mmt) cc_final: 0.6388 (mmt) REVERT: B 180 ARG cc_start: 0.6953 (mmt-90) cc_final: 0.6442 (mmt-90) REVERT: B 214 ARG cc_start: 0.6820 (ttp80) cc_final: 0.6589 (ttp80) REVERT: B 232 LYS cc_start: 0.7197 (tttt) cc_final: 0.6861 (mtpp) REVERT: B 253 LYS cc_start: 0.7697 (mttt) cc_final: 0.7410 (mttp) REVERT: B 257 GLU cc_start: 0.7529 (mp0) cc_final: 0.7170 (mp0) REVERT: B 292 ASP cc_start: 0.7784 (t0) cc_final: 0.7481 (t0) REVERT: B 343 ARG cc_start: 0.7312 (tpt90) cc_final: 0.6913 (tpt90) REVERT: B 365 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.4888 (tmt) REVERT: C 44 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7746 (ttpt) REVERT: C 65 ASP cc_start: 0.7686 (t70) cc_final: 0.7434 (t0) REVERT: C 175 GLU cc_start: 0.7577 (mp0) cc_final: 0.6758 (mp0) REVERT: C 176 VAL cc_start: 0.7857 (t) cc_final: 0.7604 (m) REVERT: C 183 THR cc_start: 0.7505 (OUTLIER) cc_final: 0.7199 (t) REVERT: C 232 ASP cc_start: 0.7450 (t0) cc_final: 0.7152 (t0) REVERT: C 245 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6931 (pp20) REVERT: C 257 GLU cc_start: 0.7772 (tp30) cc_final: 0.7387 (tp30) REVERT: C 287 ASP cc_start: 0.7381 (t0) cc_final: 0.7110 (t0) REVERT: C 337 LYS cc_start: 0.7900 (mmtm) cc_final: 0.7648 (mmtm) REVERT: C 361 GLU cc_start: 0.6573 (pp20) cc_final: 0.6341 (pp20) REVERT: C 365 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6763 (pp30) REVERT: D 12 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6884 (mt-10) REVERT: D 62 LYS cc_start: 0.8229 (mtpp) cc_final: 0.7939 (mtmm) REVERT: D 100 GLU cc_start: 0.7284 (mp0) cc_final: 0.6494 (mp0) REVERT: D 115 MET cc_start: 0.6886 (mtt) cc_final: 0.6533 (mtp) REVERT: D 159 ASP cc_start: 0.8020 (p0) cc_final: 0.7811 (p0) REVERT: D 167 THR cc_start: 0.7694 (OUTLIER) cc_final: 0.7409 (p) REVERT: D 213 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7155 (p0) REVERT: D 237 ARG cc_start: 0.6955 (ttp-170) cc_final: 0.6744 (ttp-170) REVERT: D 258 SER cc_start: 0.7747 (m) cc_final: 0.7488 (m) REVERT: E 22 LEU cc_start: 0.7459 (mp) cc_final: 0.7187 (mp) REVERT: E 50 LYS cc_start: 0.6887 (mttp) cc_final: 0.6663 (mttp) REVERT: E 57 ASN cc_start: 0.7715 (m-40) cc_final: 0.7428 (m-40) REVERT: E 62 ASN cc_start: 0.6760 (m-40) cc_final: 0.6514 (m-40) REVERT: E 81 LYS cc_start: 0.7057 (mmmt) cc_final: 0.6674 (mmmt) REVERT: E 147 LYS cc_start: 0.7190 (ttmm) cc_final: 0.6981 (ttmm) REVERT: F 35 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7846 (mttm) REVERT: F 44 LYS cc_start: 0.7627 (mmtt) cc_final: 0.7384 (mmtt) REVERT: F 57 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7167 (mm-30) REVERT: F 59 GLU cc_start: 0.7658 (tt0) cc_final: 0.7371 (tt0) REVERT: F 110 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7457 (mt-10) REVERT: F 163 GLU cc_start: 0.6958 (tp30) cc_final: 0.6718 (tp30) REVERT: G 10 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6572 (tpm-80) REVERT: G 16 VAL cc_start: 0.5947 (m) cc_final: 0.5705 (t) REVERT: G 56 GLN cc_start: 0.5954 (OUTLIER) cc_final: 0.4838 (mp10) REVERT: G 146 THR cc_start: 0.7383 (OUTLIER) cc_final: 0.7023 (p) REVERT: H 24 THR cc_start: 0.7348 (OUTLIER) cc_final: 0.7078 (p) outliers start: 78 outliers final: 58 residues processed: 493 average time/residue: 1.4969 time to fit residues: 798.5092 Evaluate side-chains 528 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 458 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 0.0170 chunk 155 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 157 optimal weight: 0.0370 chunk 165 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 255 GLN B 226 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN F 100 ASN F 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15310 Z= 0.167 Angle : 0.451 7.481 20736 Z= 0.239 Chirality : 0.042 0.187 2287 Planarity : 0.003 0.050 2666 Dihedral : 6.451 70.959 2139 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 4.53 % Allowed : 18.04 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.81 (0.20), residues: 1862 helix: 1.74 (0.21), residues: 677 sheet: 0.40 (0.26), residues: 369 loop : -0.37 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 PHE 0.017 0.001 PHE A 276 TYR 0.013 0.001 TYR D 250 ARG 0.003 0.000 ARG D 281 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 475 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.7899 (m-80) cc_final: 0.7585 (m-80) REVERT: A 19 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7706 (pp) REVERT: A 79 ARG cc_start: 0.6567 (mtm-85) cc_final: 0.6020 (mtm-85) REVERT: A 161 ARG cc_start: 0.7007 (mtt90) cc_final: 0.6642 (mtt-85) REVERT: A 170 SER cc_start: 0.7471 (t) cc_final: 0.7076 (p) REVERT: A 251 LYS cc_start: 0.7531 (tttt) cc_final: 0.7033 (ttmm) REVERT: A 253 ILE cc_start: 0.7683 (mt) cc_final: 0.7472 (OUTLIER) REVERT: A 280 GLU cc_start: 0.7443 (mm-30) cc_final: 0.6926 (mm-30) REVERT: A 298 GLU cc_start: 0.6734 (mp0) cc_final: 0.6259 (mp0) REVERT: A 317 LYS cc_start: 0.7431 (ttpp) cc_final: 0.7154 (ttpp) REVERT: A 329 ARG cc_start: 0.7053 (mtp180) cc_final: 0.6642 (mtm-85) REVERT: A 333 ARG cc_start: 0.7173 (mtp180) cc_final: 0.6946 (mtp180) REVERT: A 338 ASP cc_start: 0.6669 (OUTLIER) cc_final: 0.6103 (m-30) REVERT: A 342 THR cc_start: 0.7547 (t) cc_final: 0.7314 (t) REVERT: A 364 ASP cc_start: 0.7000 (p0) cc_final: 0.6726 (p0) REVERT: A 388 PRO cc_start: 0.7632 (Cg_endo) cc_final: 0.7337 (Cg_exo) REVERT: A 391 TYR cc_start: 0.7692 (m-80) cc_final: 0.7248 (m-80) REVERT: A 392 GLN cc_start: 0.7094 (mp10) cc_final: 0.6272 (mp10) REVERT: B 74 MET cc_start: 0.4920 (mmm) cc_final: 0.4572 (mmm) REVERT: B 127 MET cc_start: 0.6843 (mmt) cc_final: 0.6390 (mmt) REVERT: B 180 ARG cc_start: 0.6871 (mmt-90) cc_final: 0.6380 (mmt-90) REVERT: B 214 ARG cc_start: 0.6830 (ttp80) cc_final: 0.6610 (ttp80) REVERT: B 226 ASN cc_start: 0.6942 (t0) cc_final: 0.6610 (t160) REVERT: B 230 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: B 232 LYS cc_start: 0.7190 (tttt) cc_final: 0.6862 (mtpp) REVERT: B 246 LEU cc_start: 0.6858 (mt) cc_final: 0.6645 (mt) REVERT: B 253 LYS cc_start: 0.7690 (mttt) cc_final: 0.7401 (mttp) REVERT: B 257 GLU cc_start: 0.7520 (mp0) cc_final: 0.7123 (mp0) REVERT: B 292 ASP cc_start: 0.7776 (t0) cc_final: 0.7490 (t0) REVERT: B 343 ARG cc_start: 0.7306 (tpt90) cc_final: 0.6914 (tpt90) REVERT: B 365 MET cc_start: 0.5922 (OUTLIER) cc_final: 0.4891 (tmt) REVERT: C 44 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7761 (ttpt) REVERT: C 65 ASP cc_start: 0.7667 (t70) cc_final: 0.7418 (t0) REVERT: C 131 TRP cc_start: 0.5385 (OUTLIER) cc_final: 0.4932 (p90) REVERT: C 175 GLU cc_start: 0.7591 (mp0) cc_final: 0.6766 (mp0) REVERT: C 176 VAL cc_start: 0.7810 (t) cc_final: 0.7548 (m) REVERT: C 183 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7194 (t) REVERT: C 232 ASP cc_start: 0.7417 (t0) cc_final: 0.7115 (t0) REVERT: C 245 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6944 (pp20) REVERT: C 257 GLU cc_start: 0.7752 (tp30) cc_final: 0.7364 (tp30) REVERT: C 337 LYS cc_start: 0.7908 (mmtm) cc_final: 0.7632 (mmtm) REVERT: C 361 GLU cc_start: 0.6528 (pp20) cc_final: 0.6304 (pp20) REVERT: C 365 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6742 (pp30) REVERT: D 12 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6873 (mt-10) REVERT: D 62 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7938 (mtmm) REVERT: D 98 ASP cc_start: 0.7283 (t0) cc_final: 0.6867 (t0) REVERT: D 100 GLU cc_start: 0.7320 (mp0) cc_final: 0.6460 (mp0) REVERT: D 115 MET cc_start: 0.6882 (mtt) cc_final: 0.6557 (mtm) REVERT: D 159 ASP cc_start: 0.8038 (p0) cc_final: 0.7822 (p0) REVERT: D 167 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7388 (p) REVERT: D 237 ARG cc_start: 0.6947 (ttp-170) cc_final: 0.6743 (ttp-170) REVERT: D 258 SER cc_start: 0.7753 (m) cc_final: 0.7505 (m) REVERT: E 22 LEU cc_start: 0.7473 (mp) cc_final: 0.7206 (mp) REVERT: E 50 LYS cc_start: 0.6819 (mttp) cc_final: 0.6587 (mttp) REVERT: E 62 ASN cc_start: 0.6733 (m-40) cc_final: 0.6466 (m-40) REVERT: E 81 LYS cc_start: 0.7065 (mmmt) cc_final: 0.6692 (mmmt) REVERT: E 147 LYS cc_start: 0.7140 (ttmm) cc_final: 0.6938 (ttmm) REVERT: F 35 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7844 (mttm) REVERT: F 37 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7467 (mm-30) REVERT: F 44 LYS cc_start: 0.7627 (mmtt) cc_final: 0.7388 (mmtt) REVERT: F 57 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7189 (mm-30) REVERT: F 59 GLU cc_start: 0.7630 (tt0) cc_final: 0.7324 (tt0) REVERT: F 110 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7455 (mt-10) REVERT: F 163 GLU cc_start: 0.6934 (tp30) cc_final: 0.6680 (tp30) REVERT: G 10 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6558 (tpm-80) REVERT: G 16 VAL cc_start: 0.5942 (m) cc_final: 0.5706 (t) REVERT: G 146 THR cc_start: 0.7408 (OUTLIER) cc_final: 0.7052 (p) REVERT: H 24 THR cc_start: 0.7350 (OUTLIER) cc_final: 0.7066 (p) outliers start: 73 outliers final: 53 residues processed: 507 average time/residue: 1.4482 time to fit residues: 794.8840 Evaluate side-chains 535 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 469 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 122 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 219 GLN A 255 GLN A 373 GLN C 28 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN D 219 ASN F 125 GLN F 167 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15310 Z= 0.341 Angle : 0.517 8.299 20736 Z= 0.273 Chirality : 0.046 0.213 2287 Planarity : 0.004 0.054 2666 Dihedral : 6.849 75.686 2136 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 4.03 % Allowed : 18.60 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.20), residues: 1862 helix: 1.49 (0.21), residues: 688 sheet: 0.35 (0.26), residues: 377 loop : -0.44 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.006 0.001 HIS F 137 PHE 0.023 0.002 PHE F 101 TYR 0.022 0.002 TYR D 43 ARG 0.003 0.000 ARG D 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 465 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.7896 (m-80) cc_final: 0.7598 (m-80) REVERT: A 19 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7679 (pp) REVERT: A 79 ARG cc_start: 0.6663 (mtm-85) cc_final: 0.6093 (mtm-85) REVERT: A 121 GLU cc_start: 0.6750 (mp0) cc_final: 0.6197 (mp0) REVERT: A 161 ARG cc_start: 0.7014 (mtt90) cc_final: 0.6627 (mtt-85) REVERT: A 170 SER cc_start: 0.7540 (t) cc_final: 0.7019 (p) REVERT: A 251 LYS cc_start: 0.7578 (tttt) cc_final: 0.7082 (ttmm) REVERT: A 280 GLU cc_start: 0.7399 (mm-30) cc_final: 0.6830 (mm-30) REVERT: A 298 GLU cc_start: 0.6736 (mp0) cc_final: 0.6294 (mp0) REVERT: A 310 ASP cc_start: 0.7211 (p0) cc_final: 0.7005 (p0) REVERT: A 317 LYS cc_start: 0.7453 (ttpp) cc_final: 0.7206 (ttpp) REVERT: A 329 ARG cc_start: 0.7029 (mtp180) cc_final: 0.6623 (mtm-85) REVERT: A 342 THR cc_start: 0.7491 (t) cc_final: 0.7277 (t) REVERT: A 388 PRO cc_start: 0.7646 (Cg_endo) cc_final: 0.7345 (Cg_exo) REVERT: A 391 TYR cc_start: 0.7718 (m-80) cc_final: 0.7266 (m-80) REVERT: A 392 GLN cc_start: 0.7085 (mp10) cc_final: 0.6277 (mp10) REVERT: A 402 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6647 (mt-10) REVERT: B 127 MET cc_start: 0.6822 (mmt) cc_final: 0.6365 (mmt) REVERT: B 180 ARG cc_start: 0.6999 (mmt-90) cc_final: 0.6474 (mmt-90) REVERT: B 211 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6652 (mm-30) REVERT: B 214 ARG cc_start: 0.6815 (ttp80) cc_final: 0.6584 (ttp80) REVERT: B 232 LYS cc_start: 0.7200 (tttt) cc_final: 0.6844 (mtpp) REVERT: B 257 GLU cc_start: 0.7509 (mp0) cc_final: 0.7156 (mp0) REVERT: B 292 ASP cc_start: 0.7802 (t0) cc_final: 0.7498 (t0) REVERT: B 343 ARG cc_start: 0.7308 (tpt90) cc_final: 0.6897 (tpt90) REVERT: B 365 MET cc_start: 0.5934 (OUTLIER) cc_final: 0.4916 (tmt) REVERT: C 44 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7745 (ttpt) REVERT: C 65 ASP cc_start: 0.7703 (t70) cc_final: 0.7477 (t0) REVERT: C 175 GLU cc_start: 0.7563 (mp0) cc_final: 0.6742 (mp0) REVERT: C 176 VAL cc_start: 0.7780 (t) cc_final: 0.7520 (m) REVERT: C 245 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6944 (pp20) REVERT: C 257 GLU cc_start: 0.7746 (tp30) cc_final: 0.7375 (tp30) REVERT: C 287 ASP cc_start: 0.7415 (t0) cc_final: 0.7069 (t0) REVERT: C 361 GLU cc_start: 0.6568 (pp20) cc_final: 0.6339 (pp20) REVERT: C 365 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6758 (pp30) REVERT: D 12 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6901 (mt-10) REVERT: D 62 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7950 (mtmm) REVERT: D 115 MET cc_start: 0.6904 (mtt) cc_final: 0.6542 (mtm) REVERT: D 159 ASP cc_start: 0.8035 (p0) cc_final: 0.7809 (p0) REVERT: D 167 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7464 (p) REVERT: D 237 ARG cc_start: 0.6953 (ttp-170) cc_final: 0.6726 (ttp-170) REVERT: D 258 SER cc_start: 0.7705 (m) cc_final: 0.7449 (m) REVERT: E 22 LEU cc_start: 0.7471 (mp) cc_final: 0.7209 (mp) REVERT: E 50 LYS cc_start: 0.6912 (mttp) cc_final: 0.6676 (mttp) REVERT: E 62 ASN cc_start: 0.6772 (m-40) cc_final: 0.6501 (m-40) REVERT: E 78 CYS cc_start: 0.5183 (m) cc_final: 0.4881 (m) REVERT: E 81 LYS cc_start: 0.7036 (mmmt) cc_final: 0.6645 (mmmt) REVERT: E 147 LYS cc_start: 0.7194 (ttmm) cc_final: 0.6988 (ttmm) REVERT: F 35 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7909 (mttm) REVERT: F 37 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7352 (mm-30) REVERT: F 44 LYS cc_start: 0.7622 (mmtt) cc_final: 0.7390 (mmtt) REVERT: F 57 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7163 (mm-30) REVERT: F 59 GLU cc_start: 0.7663 (tt0) cc_final: 0.7385 (tt0) REVERT: F 110 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7435 (mt-10) REVERT: F 163 GLU cc_start: 0.6925 (tp30) cc_final: 0.6708 (tp30) REVERT: G 10 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6619 (tpm-80) REVERT: G 43 ASP cc_start: 0.7128 (m-30) cc_final: 0.6898 (m-30) REVERT: G 146 THR cc_start: 0.7402 (OUTLIER) cc_final: 0.7037 (p) REVERT: H 24 THR cc_start: 0.7396 (OUTLIER) cc_final: 0.7149 (p) outliers start: 65 outliers final: 52 residues processed: 497 average time/residue: 1.4256 time to fit residues: 767.1733 Evaluate side-chains 524 residues out of total 1650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 462 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 219 GLN A 243 ASN A 255 GLN B 226 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN D 219 ASN F 100 ASN F 125 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.130748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105343 restraints weight = 20882.804| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.99 r_work: 0.3153 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15310 Z= 0.223 Angle : 0.477 8.321 20736 Z= 0.253 Chirality : 0.044 0.198 2287 Planarity : 0.004 0.051 2666 Dihedral : 6.670 73.169 2136 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 3.91 % Allowed : 18.97 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.20), residues: 1862 helix: 1.63 (0.21), residues: 681 sheet: 0.31 (0.26), residues: 380 loop : -0.37 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.005 0.001 HIS F 137 PHE 0.017 0.001 PHE A 276 TYR 0.015 0.001 TYR D 43 ARG 0.003 0.000 ARG D 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10281.45 seconds wall clock time: 179 minutes 9.68 seconds (10749.68 seconds total)