Starting phenix.real_space_refine on Mon Mar 18 22:17:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs6_29415/03_2024/8fs6_29415_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs6_29415/03_2024/8fs6_29415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs6_29415/03_2024/8fs6_29415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs6_29415/03_2024/8fs6_29415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs6_29415/03_2024/8fs6_29415_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs6_29415/03_2024/8fs6_29415_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 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 71 5.49 5 Mg 4 5.21 5 S 115 5.16 5 C 13899 2.51 5 N 3821 2.21 5 O 4336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "E GLU 343": "OE1" <-> "OE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F GLU 427": "OE1" <-> "OE2" Residue "G GLU 105": "OE1" <-> "OE2" Residue "G GLU 215": "OE1" <-> "OE2" Residue "G GLU 307": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "H GLU 255": "OE1" <-> "OE2" Residue "H GLU 375": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22246 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3559 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2586 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "D" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2743 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Chain: "F" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2238 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 9, 'TRANS': 267} Chain breaks: 6 Chain: "G" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2366 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Chain breaks: 1 Chain: "H" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2314 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 4 Chain: "I" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "J" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 313 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.06, per 1000 atoms: 0.50 Number of scatterers: 22246 At special positions: 0 Unit cell: (115.092, 127.512, 138.276, 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 115 16.00 P 71 15.00 Mg 4 11.99 O 4336 8.00 N 3821 7.00 C 13899 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.00 Conformation dependent library (CDL) restraints added in 3.8 seconds 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5016 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 115 helices and 16 sheets defined 43.0% alpha, 13.9% beta 22 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 8.28 Creating SS restraints... Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 82 through 95 Processing helix chain 'A' and resid 119 through 130 removed outlier: 4.299A pdb=" N LYS A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 195 through 209 removed outlier: 3.846A pdb=" N ARG A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 249 No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 272 through 283 removed outlier: 3.518A pdb=" N LYS A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 280 " --> pdb=" O HIS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.768A pdb=" N TYR A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.743A pdb=" N ILE A 315 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 375 through 386 removed outlier: 5.377A pdb=" N ASN A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N THR A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.895A pdb=" N CYS A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 removed outlier: 3.706A pdb=" N GLU A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 430 Processing helix chain 'A' and resid 446 through 469 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 27 through 39 removed outlier: 3.704A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 70 removed outlier: 6.969A pdb=" N ARG B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 removed outlier: 3.990A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.841A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 170 through 182 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 245 through 256 removed outlier: 3.786A pdb=" N GLN B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 251 " --> pdb=" O ASP B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 282 through 301 Processing helix chain 'B' and resid 306 through 321 Processing helix chain 'C' and resid 10 through 12 No H-bonds generated for 'chain 'C' and resid 10 through 12' Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 34 through 43 removed outlier: 3.844A pdb=" N LYS C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 71 removed outlier: 3.526A pdb=" N VAL C 64 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 78 No H-bonds generated for 'chain 'C' and resid 75 through 78' Processing helix chain 'C' and resid 90 through 95 Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 201 removed outlier: 3.715A pdb=" N LYS C 195 " --> pdb=" O PRO C 191 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 196 " --> pdb=" O ASN C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 218 removed outlier: 3.597A pdb=" N SER C 214 " --> pdb=" O ASN C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.707A pdb=" N VAL C 247 " --> pdb=" O ASP C 243 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 269 Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.575A pdb=" N LYS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 312 removed outlier: 3.844A pdb=" N ASP C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 334 removed outlier: 3.527A pdb=" N SER C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 331 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 46 through 54 removed outlier: 4.105A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 removed outlier: 3.768A pdb=" N ALA D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 91 removed outlier: 4.077A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.948A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 147 through 153 removed outlier: 3.732A pdb=" N ALA D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 159 No H-bonds generated for 'chain 'D' and resid 156 through 159' Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 178 through 183 removed outlier: 3.568A pdb=" N ARG D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 207 Processing helix chain 'D' and resid 220 through 223 No H-bonds generated for 'chain 'D' and resid 220 through 223' Processing helix chain 'D' and resid 228 through 245 removed outlier: 3.510A pdb=" N TYR D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.993A pdb=" N GLU D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 276 Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.569A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER D 293 " --> pdb=" O THR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 310 removed outlier: 3.655A pdb=" N ASN D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 335 removed outlier: 3.756A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 20 through 31 Processing helix chain 'E' and resid 33 through 35 No H-bonds generated for 'chain 'E' and resid 33 through 35' Processing helix chain 'E' and resid 49 through 61 Processing helix chain 'E' and resid 98 through 101 Processing helix chain 'E' and resid 103 through 109 removed outlier: 4.430A pdb=" N ARG E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 115 No H-bonds generated for 'chain 'E' and resid 112 through 115' Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 152 through 160 removed outlier: 4.621A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 195 through 209 Processing helix chain 'E' and resid 216 through 226 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 292 removed outlier: 3.758A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 307 Processing helix chain 'E' and resid 315 through 333 Processing helix chain 'E' and resid 338 through 353 Processing helix chain 'F' and resid 13 through 29 removed outlier: 3.502A pdb=" N THR F 25 " --> pdb=" O THR F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 89 No H-bonds generated for 'chain 'F' and resid 87 through 89' Processing helix chain 'F' and resid 97 through 112 Processing helix chain 'F' and resid 214 through 218 Processing helix chain 'F' and resid 241 through 255 removed outlier: 4.567A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL F 253 " --> pdb=" O PHE F 249 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU F 254 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG F 255 " --> pdb=" O ARG F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 423 Processing helix chain 'G' and resid 18 through 27 removed outlier: 3.508A pdb=" N CYS G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 86 through 92 Processing helix chain 'G' and resid 160 through 172 Processing helix chain 'G' and resid 239 through 249 removed outlier: 4.133A pdb=" N LYS G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG G 246 " --> pdb=" O PHE G 242 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 329 Processing helix chain 'H' and resid 10 through 26 removed outlier: 3.586A pdb=" N VAL H 22 " --> pdb=" O ARG H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 102 Processing helix chain 'H' and resid 161 through 165 Processing helix chain 'H' and resid 234 through 243 Processing helix chain 'H' and resid 327 through 336 removed outlier: 3.674A pdb=" N ILE H 335 " --> pdb=" O ASN H 331 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 260 through 262 removed outlier: 6.531A pdb=" N ILE A 104 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 219 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU A 107 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 221 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLY A 109 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE A 223 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A 186 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR A 224 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 159 through 162 removed outlier: 6.206A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 162 through 166 removed outlier: 3.709A pdb=" N GLY C 53 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 185 through 189 removed outlier: 3.684A pdb=" N GLY D 65 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 186 through 190 removed outlier: 3.730A pdb=" N GLY E 43 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE E 75 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 79 through 82 Processing sheet with id= G, first strand: chain 'F' and resid 231 through 235 removed outlier: 3.811A pdb=" N MET F 231 " --> pdb=" O ILE F 432 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU F 68 " --> pdb=" O SER F 46 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER F 46 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS F 70 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE F 91 " --> pdb=" O PHE F 37 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR F 92 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL F 207 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 261 through 264 Processing sheet with id= I, first strand: chain 'F' and resid 282 through 286 Processing sheet with id= J, first strand: chain 'G' and resid 12 through 15 Processing sheet with id= K, first strand: chain 'G' and resid 80 through 85 removed outlier: 7.281A pdb=" N ASP G 36 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLU G 51 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP G 260 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 117 through 122 Processing sheet with id= M, first strand: chain 'G' and resid 177 through 183 Processing sheet with id= N, first strand: chain 'H' and resid 64 through 66 removed outlier: 6.586A pdb=" N GLU H 139 " --> pdb=" O LYS H 114 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE H 116 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL H 137 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE H 118 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE H 135 " --> pdb=" O ILE H 118 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 293 through 297 removed outlier: 6.826A pdb=" N CYS H 231 " --> pdb=" O GLU H 294 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR H 296 " --> pdb=" O TYR H 229 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR H 229 " --> pdb=" O TYR H 296 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN H 228 " --> pdb=" O PHE H 353 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE H 353 " --> pdb=" O ASN H 228 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASN H 348 " --> pdb=" O GLN H 365 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN H 365 " --> pdb=" O ASN H 348 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 321 through 324 removed outlier: 3.624A pdb=" N GLU H 251 " --> pdb=" O PHE H 266 " (cutoff:3.500A) 846 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 7.00 Time building geometry restraints manager: 9.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7201 1.36 - 1.51: 6039 1.51 - 1.65: 9331 1.65 - 1.80: 70 1.80 - 1.95: 101 Bond restraints: 22742 Sorted by residual: bond pdb=" C SER E 175 " pdb=" N PRO E 176 " ideal model delta sigma weight residual 1.334 1.365 -0.031 8.40e-03 1.42e+04 1.39e+01 bond pdb=" N ILE F 410 " pdb=" CA ILE F 410 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.18e+01 bond pdb=" N VAL F 267 " pdb=" CA VAL F 267 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N VAL A 148 " pdb=" CA VAL A 148 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" N ILE E 96 " pdb=" CA ILE E 96 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.14e-02 7.69e+03 9.39e+00 ... (remaining 22737 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.43: 596 105.43 - 113.09: 12774 113.09 - 120.75: 10089 120.75 - 128.41: 7352 128.41 - 136.07: 173 Bond angle restraints: 30984 Sorted by residual: angle pdb=" N MET F 231 " pdb=" CA MET F 231 " pdb=" C MET F 231 " ideal model delta sigma weight residual 107.61 115.83 -8.22 1.74e+00 3.30e-01 2.23e+01 angle pdb=" N HIS E 18 " pdb=" CA HIS E 18 " pdb=" CB HIS E 18 " ideal model delta sigma weight residual 110.49 118.30 -7.81 1.69e+00 3.50e-01 2.14e+01 angle pdb=" CA SER E 17 " pdb=" C SER E 17 " pdb=" O SER E 17 " ideal model delta sigma weight residual 121.39 116.30 5.09 1.12e+00 7.97e-01 2.06e+01 angle pdb=" CA HIS E 18 " pdb=" CB HIS E 18 " pdb=" CG HIS E 18 " ideal model delta sigma weight residual 113.80 118.22 -4.42 1.00e+00 1.00e+00 1.96e+01 angle pdb=" N ASN E 103 " pdb=" CA ASN E 103 " pdb=" C ASN E 103 " ideal model delta sigma weight residual 113.18 108.05 5.13 1.21e+00 6.83e-01 1.80e+01 ... (remaining 30979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.14: 12470 26.14 - 52.28: 1086 52.28 - 78.42: 183 78.42 - 104.56: 11 104.56 - 130.70: 3 Dihedral angle restraints: 13753 sinusoidal: 6059 harmonic: 7694 Sorted by residual: dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 70.70 -130.70 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 65.75 -125.75 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 58.13 -118.13 1 2.00e+01 2.50e-03 3.53e+01 ... (remaining 13750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3220 0.075 - 0.151: 330 0.151 - 0.226: 30 0.226 - 0.301: 1 0.301 - 0.377: 1 Chirality restraints: 3582 Sorted by residual: chirality pdb=" CG LEU G 327 " pdb=" CB LEU G 327 " pdb=" CD1 LEU G 327 " pdb=" CD2 LEU G 327 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CG LEU F 5 " pdb=" CB LEU F 5 " pdb=" CD1 LEU F 5 " pdb=" CD2 LEU F 5 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU B 319 " pdb=" CB LEU B 319 " pdb=" CD1 LEU B 319 " pdb=" CD2 LEU B 319 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3579 not shown) Planarity restraints: 3707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 541 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO A 542 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 542 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 542 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 333 " 0.016 2.00e-02 2.50e+03 3.03e-02 9.19e+00 pdb=" C ILE H 333 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE H 333 " 0.019 2.00e-02 2.50e+03 pdb=" N THR H 334 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E 185 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C CYS E 185 " 0.045 2.00e-02 2.50e+03 pdb=" O CYS E 185 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU E 186 " -0.015 2.00e-02 2.50e+03 ... (remaining 3704 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 248 2.62 - 3.19: 18584 3.19 - 3.76: 35767 3.76 - 4.33: 50260 4.33 - 4.90: 81618 Nonbonded interactions: 186477 Sorted by model distance: nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 402 " model vdw 2.045 2.170 nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.054 2.170 nonbonded pdb=" OG1 THR D 72 " pdb="MG MG D 402 " model vdw 2.097 2.170 nonbonded pdb=" OE2 GLU A 187 " pdb="MG MG A 602 " model vdw 2.102 2.170 nonbonded pdb=" O3A AGS A 601 " pdb="MG MG A 602 " model vdw 2.103 2.170 ... (remaining 186472 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: 5.210 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: 0.020 Extract box with map and model: 16.680 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 60.980 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 22742 Z= 0.234 Angle : 0.676 11.391 30984 Z= 0.403 Chirality : 0.046 0.377 3582 Planarity : 0.004 0.102 3707 Dihedral : 18.463 130.697 8737 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.53 % Allowed : 23.86 % Favored : 73.61 % 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: -0.78 (0.17), residues: 2577 helix: -0.24 (0.15), residues: 1213 sheet: -0.34 (0.23), residues: 542 loop : -0.75 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 352 HIS 0.016 0.001 HIS F 406 PHE 0.030 0.001 PHE E 124 TYR 0.031 0.001 TYR F 466 ARG 0.010 0.000 ARG B 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 274 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 332 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7001 (mt-10) REVERT: F 79 LEU cc_start: 0.1740 (OUTLIER) cc_final: 0.1391 (mt) REVERT: H 55 ARG cc_start: 0.7076 (mtt180) cc_final: 0.6846 (mtm-85) outliers start: 60 outliers final: 50 residues processed: 326 average time/residue: 1.2234 time to fit residues: 458.3827 Evaluate side-chains 313 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 262 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 268 ASN Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 256 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 1.9990 chunk 198 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 203 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN C 140 ASN D 352 GLN F 226 ASN H 122 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22742 Z= 0.250 Angle : 0.530 7.691 30984 Z= 0.278 Chirality : 0.042 0.159 3582 Planarity : 0.004 0.077 3707 Dihedral : 15.987 143.480 3587 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.06 % Allowed : 21.59 % Favored : 73.36 % 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: -0.57 (0.16), residues: 2577 helix: 0.00 (0.15), residues: 1212 sheet: -0.35 (0.22), residues: 553 loop : -0.70 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 69 HIS 0.012 0.001 HIS E 18 PHE 0.019 0.002 PHE F 37 TYR 0.016 0.001 TYR F 16 ARG 0.006 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 268 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ASP cc_start: 0.6994 (m-30) cc_final: 0.6647 (m-30) REVERT: A 351 HIS cc_start: 0.7678 (OUTLIER) cc_final: 0.7094 (m170) REVERT: A 372 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.7904 (p) REVERT: C 199 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: C 332 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6963 (mt-10) REVERT: E 164 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7736 (p0) REVERT: F 79 LEU cc_start: 0.1383 (OUTLIER) cc_final: 0.1147 (mt) REVERT: F 119 MET cc_start: -0.0441 (mmm) cc_final: -0.0702 (mmm) REVERT: F 413 LYS cc_start: 0.5560 (OUTLIER) cc_final: 0.5017 (ttpp) REVERT: H 55 ARG cc_start: 0.7164 (mtt180) cc_final: 0.6680 (mtm-85) REVERT: H 139 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6986 (mm-30) REVERT: H 227 ILE cc_start: 0.5470 (OUTLIER) cc_final: 0.4656 (pp) REVERT: H 277 LEU cc_start: 0.6980 (tp) cc_final: 0.6650 (tp) REVERT: H 358 ASP cc_start: 0.7412 (m-30) cc_final: 0.6249 (p0) outliers start: 120 outliers final: 53 residues processed: 359 average time/residue: 1.1554 time to fit residues: 479.8057 Evaluate side-chains 318 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 257 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 372 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 198 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 238 optimal weight: 0.0670 chunk 257 optimal weight: 4.9990 chunk 212 optimal weight: 0.8980 chunk 236 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 102 HIS C 74 ASN F 247 HIS G 9 ASN G 17 HIS H 122 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 22742 Z= 0.329 Angle : 0.559 9.942 30984 Z= 0.292 Chirality : 0.043 0.151 3582 Planarity : 0.004 0.071 3707 Dihedral : 15.975 145.117 3550 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 6.62 % Allowed : 19.90 % Favored : 73.48 % 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: -0.57 (0.16), residues: 2577 helix: 0.00 (0.15), residues: 1204 sheet: -0.37 (0.21), residues: 564 loop : -0.67 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 69 HIS 0.008 0.001 HIS E 18 PHE 0.023 0.002 PHE A 279 TYR 0.018 0.002 TYR G 181 ARG 0.006 0.001 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 262 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8908 (mt) REVERT: A 241 ASP cc_start: 0.7195 (m-30) cc_final: 0.6842 (m-30) REVERT: A 351 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.7110 (m170) REVERT: A 372 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.7846 (p) REVERT: B 100 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7942 (ttmm) REVERT: B 183 ASP cc_start: 0.7970 (t0) cc_final: 0.7737 (t0) REVERT: C 199 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: C 332 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6976 (mt-10) REVERT: D 38 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8168 (mt-10) REVERT: E 74 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7193 (mm110) REVERT: E 119 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.5737 (mpp) REVERT: E 156 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7375 (tpt-90) REVERT: E 197 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6118 (mt-10) REVERT: E 204 ASP cc_start: 0.6606 (m-30) cc_final: 0.6387 (t0) REVERT: F 100 LEU cc_start: 0.2023 (OUTLIER) cc_final: 0.1438 (tt) REVERT: F 119 MET cc_start: -0.0213 (mmm) cc_final: -0.0751 (ptp) REVERT: F 413 LYS cc_start: 0.5589 (OUTLIER) cc_final: 0.5066 (ttpp) REVERT: G 25 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6619 (tt) REVERT: H 9 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7016 (tm-30) REVERT: H 55 ARG cc_start: 0.7176 (mtt180) cc_final: 0.6871 (mtm-85) REVERT: H 63 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: H 103 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7562 (p) REVERT: H 139 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6889 (mm-30) REVERT: H 227 ILE cc_start: 0.5608 (OUTLIER) cc_final: 0.4889 (pp) REVERT: H 277 LEU cc_start: 0.6997 (tp) cc_final: 0.6654 (tp) REVERT: H 358 ASP cc_start: 0.7328 (m-30) cc_final: 0.6310 (p0) outliers start: 157 outliers final: 71 residues processed: 383 average time/residue: 1.2098 time to fit residues: 533.4775 Evaluate side-chains 334 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 248 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 372 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 113 optimal weight: 0.3980 chunk 160 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 226 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN C 74 ASN C 184 HIS E 224 GLN G 9 ASN G 17 HIS ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22742 Z= 0.199 Angle : 0.499 8.949 30984 Z= 0.260 Chirality : 0.041 0.157 3582 Planarity : 0.004 0.055 3707 Dihedral : 15.880 138.406 3542 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.51 % Allowed : 22.72 % Favored : 72.77 % 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: -0.29 (0.17), residues: 2577 helix: 0.29 (0.15), residues: 1201 sheet: -0.33 (0.21), residues: 564 loop : -0.55 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 69 HIS 0.007 0.001 HIS E 93 PHE 0.018 0.001 PHE F 37 TYR 0.015 0.001 TYR G 181 ARG 0.006 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 263 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 ASP cc_start: 0.7115 (m-30) cc_final: 0.6741 (m-30) REVERT: A 351 HIS cc_start: 0.7678 (OUTLIER) cc_final: 0.7090 (m170) REVERT: A 372 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.7803 (p) REVERT: B 100 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7849 (ttmm) REVERT: C 172 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6598 (pt0) REVERT: C 332 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6809 (mt-10) REVERT: D 38 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8153 (mt-10) REVERT: E 74 GLN cc_start: 0.7426 (mm-40) cc_final: 0.7218 (mm110) REVERT: E 156 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7364 (tpt-90) REVERT: E 204 ASP cc_start: 0.6726 (m-30) cc_final: 0.6419 (t0) REVERT: F 119 MET cc_start: -0.0312 (mmm) cc_final: -0.0720 (mmm) REVERT: F 268 LYS cc_start: 0.1648 (tmtt) cc_final: 0.1364 (tppt) REVERT: F 413 LYS cc_start: 0.5618 (OUTLIER) cc_final: 0.5093 (ttpp) REVERT: G 25 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6682 (tt) REVERT: G 323 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6682 (tm-30) REVERT: H 9 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6987 (tm-30) REVERT: H 55 ARG cc_start: 0.7239 (mtt180) cc_final: 0.6888 (mtm-85) REVERT: H 63 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: H 227 ILE cc_start: 0.5605 (OUTLIER) cc_final: 0.4910 (pp) REVERT: H 277 LEU cc_start: 0.6996 (tp) cc_final: 0.6681 (tp) REVERT: H 358 ASP cc_start: 0.7369 (m-30) cc_final: 0.6321 (p0) outliers start: 107 outliers final: 55 residues processed: 345 average time/residue: 1.2436 time to fit residues: 492.2045 Evaluate side-chains 317 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 252 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 269 ILE Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 228 ASN Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 372 GLU Chi-restraints excluded: chain H residue 381 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 216 optimal weight: 0.9990 chunk 175 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 102 HIS C 74 ASN E 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22742 Z= 0.293 Angle : 0.539 9.764 30984 Z= 0.280 Chirality : 0.042 0.146 3582 Planarity : 0.004 0.059 3707 Dihedral : 15.946 146.742 3533 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 6.16 % Allowed : 21.54 % Favored : 72.30 % 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: -0.34 (0.17), residues: 2577 helix: 0.22 (0.15), residues: 1209 sheet: -0.27 (0.21), residues: 563 loop : -0.58 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 296 HIS 0.007 0.001 HIS E 93 PHE 0.027 0.002 PHE A 279 TYR 0.021 0.001 TYR B 186 ARG 0.006 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 253 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8914 (mt) REVERT: A 241 ASP cc_start: 0.7158 (m-30) cc_final: 0.6815 (m-30) REVERT: A 301 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8056 (mp) REVERT: A 351 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.7154 (m170) REVERT: A 372 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.7783 (p) REVERT: B 73 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7642 (p0) REVERT: B 100 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7910 (ttmm) REVERT: C 172 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6658 (pt0) REVERT: C 332 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6861 (mt-10) REVERT: D 234 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8276 (mp) REVERT: E 74 GLN cc_start: 0.7439 (mm-40) cc_final: 0.7166 (mm-40) REVERT: E 93 HIS cc_start: 0.8736 (OUTLIER) cc_final: 0.7975 (p-80) REVERT: E 134 ARG cc_start: 0.4422 (OUTLIER) cc_final: 0.3081 (mmt90) REVERT: E 156 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7442 (tpt-90) REVERT: E 204 ASP cc_start: 0.6686 (m-30) cc_final: 0.6372 (t0) REVERT: F 100 LEU cc_start: 0.1651 (OUTLIER) cc_final: 0.1172 (tt) REVERT: F 119 MET cc_start: -0.0270 (mmm) cc_final: -0.0870 (ptp) REVERT: F 413 LYS cc_start: 0.5606 (OUTLIER) cc_final: 0.5149 (ttpp) REVERT: G 25 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6628 (tt) REVERT: G 155 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7451 (pp20) REVERT: G 202 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.5600 (t80) REVERT: G 323 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6612 (tm-30) REVERT: H 9 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6943 (tm-30) REVERT: H 55 ARG cc_start: 0.7254 (mtt180) cc_final: 0.6997 (mtm-85) REVERT: H 63 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: H 139 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6923 (mm-30) REVERT: H 227 ILE cc_start: 0.5692 (OUTLIER) cc_final: 0.5004 (pp) REVERT: H 277 LEU cc_start: 0.6977 (tp) cc_final: 0.6643 (tp) REVERT: H 358 ASP cc_start: 0.7359 (m-30) cc_final: 0.6328 (p0) outliers start: 146 outliers final: 75 residues processed: 370 average time/residue: 1.2158 time to fit residues: 517.3079 Evaluate side-chains 351 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 256 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 134 ARG Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 228 ASN Chi-restraints excluded: chain H residue 247 ASN Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 83 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS C 74 ASN E 224 GLN E 292 HIS G 52 ASN H 53 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22742 Z= 0.207 Angle : 0.505 8.744 30984 Z= 0.262 Chirality : 0.041 0.175 3582 Planarity : 0.004 0.057 3707 Dihedral : 15.835 140.331 3533 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.14 % Allowed : 22.64 % Favored : 72.22 % 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: -0.16 (0.17), residues: 2577 helix: 0.39 (0.15), residues: 1208 sheet: -0.23 (0.22), residues: 563 loop : -0.51 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 296 HIS 0.006 0.001 HIS E 93 PHE 0.014 0.001 PHE G 154 TYR 0.020 0.001 TYR B 186 ARG 0.007 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 266 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8418 (tt) REVERT: A 162 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7041 (mp10) REVERT: A 189 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8925 (mt) REVERT: A 241 ASP cc_start: 0.7121 (m-30) cc_final: 0.6764 (m-30) REVERT: A 301 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 351 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.7206 (m170) REVERT: A 355 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8062 (t0) REVERT: A 372 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.7766 (p) REVERT: B 100 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7901 (ttmm) REVERT: B 272 ARG cc_start: 0.7352 (mtm110) cc_final: 0.6964 (mmm160) REVERT: C 172 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6630 (pt0) REVERT: C 332 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6794 (mt-10) REVERT: E 74 GLN cc_start: 0.7466 (mm-40) cc_final: 0.7191 (mm-40) REVERT: E 156 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7457 (tpt-90) REVERT: E 204 ASP cc_start: 0.6724 (m-30) cc_final: 0.6400 (t0) REVERT: F 100 LEU cc_start: 0.1523 (OUTLIER) cc_final: 0.1049 (tt) REVERT: F 119 MET cc_start: 0.0166 (mmm) cc_final: -0.0469 (ptp) REVERT: F 413 LYS cc_start: 0.5598 (OUTLIER) cc_final: 0.5119 (ttpp) REVERT: G 25 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6639 (tt) REVERT: G 125 PHE cc_start: 0.7647 (m-10) cc_final: 0.7379 (m-10) REVERT: G 155 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7470 (pp20) REVERT: G 202 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.5468 (t80) REVERT: G 323 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6565 (tm-30) REVERT: H 9 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6977 (tm-30) REVERT: H 44 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7332 (ttp) REVERT: H 53 GLN cc_start: 0.8494 (tt0) cc_final: 0.8272 (tt0) REVERT: H 55 ARG cc_start: 0.7257 (mtt180) cc_final: 0.6966 (mtm-85) REVERT: H 63 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: H 103 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7573 (p) REVERT: H 227 ILE cc_start: 0.5764 (OUTLIER) cc_final: 0.5139 (pp) REVERT: H 277 LEU cc_start: 0.6972 (tp) cc_final: 0.6646 (tp) REVERT: H 358 ASP cc_start: 0.7396 (m-30) cc_final: 0.6349 (p0) outliers start: 122 outliers final: 72 residues processed: 358 average time/residue: 1.3107 time to fit residues: 536.5741 Evaluate side-chains 349 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 258 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 228 ASN Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 372 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 185 optimal weight: 0.4980 chunk 143 optimal weight: 0.8980 chunk 213 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 252 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 116 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 148 ASN C 74 ASN E 224 GLN ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22742 Z= 0.154 Angle : 0.484 8.828 30984 Z= 0.252 Chirality : 0.040 0.154 3582 Planarity : 0.004 0.057 3707 Dihedral : 15.648 131.108 3532 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.60 % Allowed : 23.15 % Favored : 72.26 % 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: 0.05 (0.17), residues: 2577 helix: 0.61 (0.15), residues: 1203 sheet: -0.15 (0.22), residues: 555 loop : -0.47 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 259 HIS 0.006 0.001 HIS G 20 PHE 0.030 0.001 PHE A 279 TYR 0.020 0.001 TYR B 186 ARG 0.007 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 273 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8385 (tt) REVERT: A 162 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7111 (mp10) REVERT: A 189 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8917 (mt) REVERT: A 241 ASP cc_start: 0.7083 (m-30) cc_final: 0.6698 (m-30) REVERT: A 307 GLU cc_start: 0.7998 (tp30) cc_final: 0.7695 (tp30) REVERT: A 351 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7122 (m170) REVERT: A 372 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.7759 (p) REVERT: B 100 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7573 (tptm) REVERT: B 272 ARG cc_start: 0.7372 (mtm110) cc_final: 0.6993 (mmm160) REVERT: C 172 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6598 (pt0) REVERT: C 332 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6751 (mt-10) REVERT: D 38 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8121 (mt-10) REVERT: D 269 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8042 (mm) REVERT: E 74 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7201 (mm-40) REVERT: E 156 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7402 (tpt-90) REVERT: E 204 ASP cc_start: 0.6696 (m-30) cc_final: 0.6387 (t0) REVERT: E 214 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6154 (pm20) REVERT: F 100 LEU cc_start: 0.1530 (OUTLIER) cc_final: 0.1099 (tt) REVERT: F 119 MET cc_start: 0.0228 (mmm) cc_final: -0.0445 (ptp) REVERT: F 413 LYS cc_start: 0.5602 (OUTLIER) cc_final: 0.5114 (ttpp) REVERT: G 125 PHE cc_start: 0.7628 (m-10) cc_final: 0.7392 (m-10) REVERT: G 323 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6769 (tm-30) REVERT: H 9 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6943 (tm-30) REVERT: H 44 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7341 (ttp) REVERT: H 55 ARG cc_start: 0.7319 (mtt180) cc_final: 0.7013 (mtm-85) REVERT: H 63 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: H 227 ILE cc_start: 0.5829 (OUTLIER) cc_final: 0.5229 (pp) REVERT: H 277 LEU cc_start: 0.6919 (tp) cc_final: 0.6590 (tp) REVERT: H 358 ASP cc_start: 0.7386 (m-30) cc_final: 0.6272 (p0) outliers start: 109 outliers final: 66 residues processed: 353 average time/residue: 1.2248 time to fit residues: 496.3538 Evaluate side-chains 337 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 256 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 269 ILE Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 228 ASN Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 0.0980 chunk 100 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 76 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 198 optimal weight: 20.0000 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN C 74 ASN E 224 GLN ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22742 Z= 0.198 Angle : 0.501 9.454 30984 Z= 0.260 Chirality : 0.041 0.149 3582 Planarity : 0.004 0.056 3707 Dihedral : 15.609 130.777 3529 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.85 % Allowed : 23.44 % Favored : 71.71 % 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: 0.07 (0.17), residues: 2577 helix: 0.62 (0.15), residues: 1199 sheet: -0.15 (0.22), residues: 564 loop : -0.45 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 296 HIS 0.010 0.001 HIS E 93 PHE 0.014 0.001 PHE G 154 TYR 0.021 0.001 TYR B 186 ARG 0.007 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 263 time to evaluate : 2.161 Fit side-chains revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8405 (tt) REVERT: A 162 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7154 (mp10) REVERT: A 187 GLU cc_start: 0.8188 (tt0) cc_final: 0.7676 (tp30) REVERT: A 189 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8920 (mt) REVERT: A 241 ASP cc_start: 0.7199 (m-30) cc_final: 0.6820 (m-30) REVERT: A 283 GLN cc_start: 0.6944 (OUTLIER) cc_final: 0.6670 (mm110) REVERT: A 307 GLU cc_start: 0.7967 (tp30) cc_final: 0.7662 (tp30) REVERT: A 351 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.7125 (m170) REVERT: A 372 SER cc_start: 0.8457 (OUTLIER) cc_final: 0.7728 (p) REVERT: B 100 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7846 (ttmm) REVERT: B 272 ARG cc_start: 0.7363 (mtm110) cc_final: 0.6979 (mmm160) REVERT: C 172 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6635 (pt0) REVERT: C 245 LYS cc_start: 0.7907 (mppt) cc_final: 0.7197 (mttt) REVERT: C 292 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7691 (t0) REVERT: C 332 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6856 (mt-10) REVERT: D 269 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8079 (mm) REVERT: E 74 GLN cc_start: 0.7522 (mm-40) cc_final: 0.7308 (mm110) REVERT: E 156 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7433 (tpt-90) REVERT: E 204 ASP cc_start: 0.6708 (m-30) cc_final: 0.6439 (t0) REVERT: E 214 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6173 (pm20) REVERT: F 18 LEU cc_start: 0.2458 (OUTLIER) cc_final: 0.1924 (mm) REVERT: F 19 LEU cc_start: 0.3926 (OUTLIER) cc_final: 0.3526 (mm) REVERT: F 100 LEU cc_start: 0.1389 (OUTLIER) cc_final: 0.0952 (tt) REVERT: F 119 MET cc_start: 0.0285 (mmm) cc_final: -0.0410 (ptp) REVERT: F 413 LYS cc_start: 0.5601 (OUTLIER) cc_final: 0.5165 (ttpp) REVERT: G 125 PHE cc_start: 0.7611 (m-10) cc_final: 0.7084 (m-10) REVERT: G 155 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7519 (pp20) REVERT: G 323 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6766 (tm-30) REVERT: H 9 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6962 (tm-30) REVERT: H 44 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7384 (tpp) REVERT: H 53 GLN cc_start: 0.8488 (tt0) cc_final: 0.8240 (tt0) REVERT: H 55 ARG cc_start: 0.7340 (mtt180) cc_final: 0.7010 (mtm-85) REVERT: H 63 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: H 103 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7533 (p) REVERT: H 227 ILE cc_start: 0.5817 (OUTLIER) cc_final: 0.5246 (pp) REVERT: H 242 ASP cc_start: 0.7312 (m-30) cc_final: 0.7062 (t0) REVERT: H 277 LEU cc_start: 0.6937 (tp) cc_final: 0.6634 (tp) REVERT: H 358 ASP cc_start: 0.7371 (m-30) cc_final: 0.6261 (p0) outliers start: 115 outliers final: 74 residues processed: 350 average time/residue: 1.2858 time to fit residues: 516.2315 Evaluate side-chains 351 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 256 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 304 ILE Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 228 ASN Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 102 HIS C 74 ASN ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 22742 Z= 0.378 Angle : 0.592 10.015 30984 Z= 0.306 Chirality : 0.044 0.149 3582 Planarity : 0.004 0.057 3707 Dihedral : 15.829 144.531 3529 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.10 % Allowed : 23.31 % Favored : 71.59 % 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: -0.26 (0.16), residues: 2577 helix: 0.29 (0.15), residues: 1209 sheet: -0.16 (0.22), residues: 561 loop : -0.62 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 296 HIS 0.011 0.002 HIS E 93 PHE 0.028 0.002 PHE A 279 TYR 0.025 0.002 TYR B 186 ARG 0.005 0.001 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 252 time to evaluate : 2.665 Fit side-chains revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8424 (tt) REVERT: A 162 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7069 (mp10) REVERT: A 189 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8927 (mt) REVERT: A 241 ASP cc_start: 0.7298 (m-30) cc_final: 0.6847 (m-30) REVERT: A 283 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6629 (mm110) REVERT: A 286 LYS cc_start: 0.8669 (mttp) cc_final: 0.8338 (tptp) REVERT: A 307 GLU cc_start: 0.8004 (tp30) cc_final: 0.7647 (tp30) REVERT: A 351 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7238 (m170) REVERT: A 355 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.7998 (t0) REVERT: B 100 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8033 (ttmm) REVERT: B 272 ARG cc_start: 0.7413 (mtm110) cc_final: 0.7006 (mmm160) REVERT: C 172 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6753 (pp20) REVERT: C 195 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7583 (mptt) REVERT: C 332 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6883 (mt-10) REVERT: D 38 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8148 (mt-10) REVERT: E 74 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7262 (mm110) REVERT: E 156 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7498 (tpt-90) REVERT: E 204 ASP cc_start: 0.6761 (m-30) cc_final: 0.6482 (t0) REVERT: F 18 LEU cc_start: 0.2533 (OUTLIER) cc_final: 0.2056 (mm) REVERT: F 19 LEU cc_start: 0.3838 (OUTLIER) cc_final: 0.3491 (mm) REVERT: F 43 THR cc_start: 0.1411 (OUTLIER) cc_final: 0.1096 (m) REVERT: F 119 MET cc_start: 0.0203 (mmm) cc_final: -0.0369 (ptp) REVERT: F 413 LYS cc_start: 0.5590 (OUTLIER) cc_final: 0.5149 (ttpp) REVERT: G 25 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6723 (tt) REVERT: G 125 PHE cc_start: 0.7298 (m-10) cc_final: 0.6974 (m-10) REVERT: G 155 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7467 (pp20) REVERT: G 176 LYS cc_start: 0.7981 (pttp) cc_final: 0.7608 (pttt) REVERT: H 9 GLU cc_start: 0.7575 (mt-10) cc_final: 0.6949 (tm-30) REVERT: H 44 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7372 (ttp) REVERT: H 53 GLN cc_start: 0.8567 (tt0) cc_final: 0.8344 (tt0) REVERT: H 55 ARG cc_start: 0.7387 (mtt180) cc_final: 0.7044 (mtm-85) REVERT: H 63 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: H 103 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7479 (p) REVERT: H 227 ILE cc_start: 0.5967 (OUTLIER) cc_final: 0.5376 (pp) REVERT: H 242 ASP cc_start: 0.7336 (m-30) cc_final: 0.7082 (t0) REVERT: H 277 LEU cc_start: 0.6958 (tp) cc_final: 0.6636 (tp) REVERT: H 358 ASP cc_start: 0.7337 (m-30) cc_final: 0.6338 (p0) outliers start: 121 outliers final: 78 residues processed: 344 average time/residue: 1.2303 time to fit residues: 486.3045 Evaluate side-chains 343 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 247 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 228 ASN Chi-restraints excluded: chain H residue 247 ASN Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN A 362 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN E 224 GLN ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 GLN H 365 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22742 Z= 0.193 Angle : 0.517 9.294 30984 Z= 0.268 Chirality : 0.041 0.147 3582 Planarity : 0.004 0.056 3707 Dihedral : 15.700 135.837 3529 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.01 % Allowed : 24.66 % Favored : 71.33 % 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: -0.04 (0.17), residues: 2577 helix: 0.52 (0.15), residues: 1204 sheet: -0.15 (0.22), residues: 562 loop : -0.53 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 296 HIS 0.009 0.001 HIS E 93 PHE 0.019 0.001 PHE G 154 TYR 0.021 0.001 TYR B 186 ARG 0.008 0.000 ARG D 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 254 time to evaluate : 2.525 Fit side-chains revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8410 (tt) REVERT: A 162 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7139 (mp10) REVERT: A 187 GLU cc_start: 0.8202 (tt0) cc_final: 0.7699 (tp30) REVERT: A 189 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8910 (mt) REVERT: A 241 ASP cc_start: 0.7250 (m-30) cc_final: 0.6884 (m-30) REVERT: A 283 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6416 (mm110) REVERT: A 307 GLU cc_start: 0.7979 (tp30) cc_final: 0.7655 (tp30) REVERT: A 351 HIS cc_start: 0.7803 (OUTLIER) cc_final: 0.7292 (m170) REVERT: A 355 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8028 (t0) REVERT: B 100 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7901 (ttmm) REVERT: B 272 ARG cc_start: 0.7391 (mtm110) cc_final: 0.7021 (mmm160) REVERT: C 172 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6650 (pt0) REVERT: C 195 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7533 (mptt) REVERT: C 245 LYS cc_start: 0.7937 (mppt) cc_final: 0.7219 (mttt) REVERT: C 332 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6766 (mt-10) REVERT: E 74 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7283 (mm110) REVERT: E 156 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7452 (tpt-90) REVERT: E 204 ASP cc_start: 0.6715 (m-30) cc_final: 0.6425 (t0) REVERT: F 18 LEU cc_start: 0.2525 (OUTLIER) cc_final: 0.2095 (mm) REVERT: F 19 LEU cc_start: 0.3997 (OUTLIER) cc_final: 0.3609 (mm) REVERT: F 43 THR cc_start: 0.1343 (OUTLIER) cc_final: 0.1038 (m) REVERT: F 119 MET cc_start: 0.0334 (mmm) cc_final: -0.0368 (ptp) REVERT: F 413 LYS cc_start: 0.5702 (OUTLIER) cc_final: 0.5214 (ttpp) REVERT: G 125 PHE cc_start: 0.7276 (m-10) cc_final: 0.6977 (m-10) REVERT: G 155 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7493 (pp20) REVERT: G 176 LYS cc_start: 0.7923 (pttp) cc_final: 0.7588 (pttt) REVERT: G 197 LYS cc_start: 0.6638 (mmmt) cc_final: 0.6302 (mmtt) REVERT: H 9 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6939 (tm-30) REVERT: H 44 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7362 (ttp) REVERT: H 53 GLN cc_start: 0.8500 (tt0) cc_final: 0.8265 (tt0) REVERT: H 55 ARG cc_start: 0.7340 (mtt180) cc_final: 0.7021 (mtm-85) REVERT: H 63 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: H 103 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7539 (p) REVERT: H 227 ILE cc_start: 0.5842 (OUTLIER) cc_final: 0.5259 (pp) REVERT: H 242 ASP cc_start: 0.7328 (m-30) cc_final: 0.7074 (t0) REVERT: H 261 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5225 (pp) REVERT: H 263 ILE cc_start: 0.7607 (mt) cc_final: 0.7204 (mp) REVERT: H 277 LEU cc_start: 0.6911 (tp) cc_final: 0.6599 (tp) REVERT: H 358 ASP cc_start: 0.7326 (m-30) cc_final: 0.6348 (p0) outliers start: 95 outliers final: 68 residues processed: 322 average time/residue: 1.3237 time to fit residues: 487.0399 Evaluate side-chains 338 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 252 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 249 LYS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 228 ASN Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 191 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 208 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 213 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 102 HIS C 74 ASN G 218 GLN H 365 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.178443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.127486 restraints weight = 25146.715| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.94 r_work: 0.3228 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22742 Z= 0.220 Angle : 0.523 9.716 30984 Z= 0.270 Chirality : 0.041 0.152 3582 Planarity : 0.004 0.057 3707 Dihedral : 15.675 134.233 3529 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.38 % Allowed : 24.03 % Favored : 71.59 % 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: 0.01 (0.17), residues: 2577 helix: 0.56 (0.15), residues: 1204 sheet: -0.13 (0.22), residues: 562 loop : -0.50 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 296 HIS 0.010 0.001 HIS E 93 PHE 0.019 0.001 PHE G 154 TYR 0.022 0.001 TYR B 186 ARG 0.007 0.000 ARG D 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8507.68 seconds wall clock time: 151 minutes 14.98 seconds (9074.98 seconds total)