Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 22:01:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs6_29415/07_2023/8fs6_29415_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs6_29415/07_2023/8fs6_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_29415/07_2023/8fs6_29415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs6_29415/07_2023/8fs6_29415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs6_29415/07_2023/8fs6_29415_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs6_29415/07_2023/8fs6_29415_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 15 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: 10.86, per 1000 atoms: 0.49 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: 9.33 Conformation dependent library (CDL) restraints added in 3.2 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: 8.40 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: 9.05 Time building geometry restraints manager: 10.02 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: 12414 26.14 - 52.28: 1056 52.28 - 78.42: 177 78.42 - 104.56: 11 104.56 - 130.70: 3 Dihedral angle restraints: 13661 sinusoidal: 5967 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 13658 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: 6.990 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 17.610 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 63.640 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.160 ------------------------------------------------------------------------------- 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 : 18.334 130.697 8645 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 % 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 *********************** 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 : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 50 residues processed: 326 average time/residue: 1.3040 time to fit residues: 488.7451 Evaluate side-chains 312 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 262 time to evaluate : 2.676 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 45 residues processed: 6 average time/residue: 0.5066 time to fit residues: 7.6284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 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: 0.9980 chunk 152 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 22742 Z= 0.256 Angle : 0.530 7.741 30984 Z= 0.278 Chirality : 0.042 0.158 3582 Planarity : 0.004 0.077 3707 Dihedral : 15.291 142.767 3415 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 5.94 % 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: -0.34 (0.22), residues: 553 loop : -0.70 (0.21), residues: 812 *********************** 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 407 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 266 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 73 residues processed: 375 average time/residue: 1.1584 time to fit residues: 505.0135 Evaluate side-chains 326 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 253 time to evaluate : 2.501 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 60 residues processed: 14 average time/residue: 0.4819 time to fit residues: 12.8070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 198 optimal weight: 8.9990 chunk 162 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 chunk 238 optimal weight: 7.9990 chunk 257 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 81 optimal weight: 0.0770 chunk 191 optimal weight: 10.0000 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 351 HIS ** 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 C 184 HIS H 53 GLN H 122 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 22742 Z= 0.196 Angle : 0.497 8.496 30984 Z= 0.260 Chirality : 0.041 0.149 3582 Planarity : 0.004 0.059 3707 Dihedral : 15.275 134.937 3415 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 6.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.17), residues: 2577 helix: 0.26 (0.15), residues: 1202 sheet: -0.36 (0.22), residues: 562 loop : -0.53 (0.22), residues: 813 *********************** 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 416 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 268 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 148 outliers final: 80 residues processed: 388 average time/residue: 1.2237 time to fit residues: 549.4124 Evaluate side-chains 331 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 251 time to evaluate : 2.512 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 69 residues processed: 11 average time/residue: 0.3836 time to fit residues: 9.7046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 0.1980 chunk 179 optimal weight: 7.9990 chunk 123 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 253 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 8 GLN B 148 ASN C 74 ASN E 74 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: 0.7880 moved from start: 0.1670 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= 0.193 Angle : 0.498 8.775 30984 Z= 0.258 Chirality : 0.041 0.175 3582 Planarity : 0.004 0.057 3707 Dihedral : 15.277 137.415 3415 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 5.82 % 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: -0.17 (0.17), residues: 2577 helix: 0.39 (0.15), residues: 1202 sheet: -0.32 (0.22), residues: 562 loop : -0.45 (0.22), residues: 813 *********************** 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 405 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 267 time to evaluate : 2.539 Fit side-chains revert: symmetry clash outliers start: 138 outliers final: 89 residues processed: 381 average time/residue: 1.2162 time to fit residues: 536.5311 Evaluate side-chains 337 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 248 time to evaluate : 2.468 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 76 residues processed: 14 average time/residue: 0.4119 time to fit residues: 11.7137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 188 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 102 HIS C 74 ASN E 224 GLN H 53 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 22742 Z= 0.302 Angle : 0.555 10.721 30984 Z= 0.285 Chirality : 0.043 0.146 3582 Planarity : 0.004 0.059 3707 Dihedral : 15.409 144.884 3415 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 6.53 % 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: -0.30 (0.17), residues: 2577 helix: 0.25 (0.15), residues: 1202 sheet: -0.26 (0.21), residues: 566 loop : -0.55 (0.22), residues: 809 *********************** 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 410 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 255 time to evaluate : 2.566 Fit side-chains revert: symmetry clash outliers start: 155 outliers final: 88 residues processed: 381 average time/residue: 1.2074 time to fit residues: 536.3593 Evaluate side-chains 333 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 245 time to evaluate : 2.400 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 76 residues processed: 12 average time/residue: 0.6162 time to fit residues: 12.9959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0170 chunk 50 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 253 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 117 optimal weight: 0.0770 chunk 21 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN 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 8 GLN C 74 ASN E 74 GLN E 224 GLN E 292 HIS G 9 ASN H 53 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2056 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= 0.155 Angle : 0.498 8.779 30984 Z= 0.256 Chirality : 0.040 0.156 3582 Planarity : 0.004 0.057 3707 Dihedral : 15.325 133.998 3415 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 5.35 % 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: -0.02 (0.17), residues: 2577 helix: 0.55 (0.16), residues: 1205 sheet: -0.21 (0.22), residues: 553 loop : -0.47 (0.22), residues: 819 *********************** 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 383 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 256 time to evaluate : 2.564 Fit side-chains outliers start: 127 outliers final: 86 residues processed: 362 average time/residue: 1.2058 time to fit residues: 506.7870 Evaluate side-chains 327 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 241 time to evaluate : 2.585 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 78 residues processed: 9 average time/residue: 0.3163 time to fit residues: 8.0320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 144 optimal weight: 1.9990 chunk 185 optimal weight: 0.0870 chunk 143 optimal weight: 0.6980 chunk 213 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.7564 ------------------------------------------------------------------------------- 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 H 53 GLN H 132 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 22742 Z= 0.174 Angle : 0.503 9.872 30984 Z= 0.258 Chirality : 0.040 0.145 3582 Planarity : 0.004 0.058 3707 Dihedral : 15.293 131.977 3415 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 5.14 % 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 (0.16), residues: 1204 sheet: -0.17 (0.22), residues: 554 loop : -0.44 (0.22), residues: 819 *********************** 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 379 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 257 time to evaluate : 2.809 Fit side-chains outliers start: 122 outliers final: 91 residues processed: 359 average time/residue: 1.1825 time to fit residues: 494.8506 Evaluate side-chains 338 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 247 time to evaluate : 2.634 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 82 residues processed: 9 average time/residue: 0.2765 time to fit residues: 7.7391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 76 optimal weight: 0.0060 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN C 74 ASN G 9 ASN H 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 22742 Z= 0.170 Angle : 0.498 10.807 30984 Z= 0.256 Chirality : 0.040 0.168 3582 Planarity : 0.004 0.058 3707 Dihedral : 15.228 127.203 3415 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 5.02 % 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: 0.15 (0.17), residues: 2577 helix: 0.67 (0.15), residues: 1209 sheet: -0.11 (0.22), residues: 564 loop : -0.40 (0.22), residues: 804 *********************** 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 381 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 262 time to evaluate : 2.438 Fit side-chains outliers start: 119 outliers final: 90 residues processed: 357 average time/residue: 1.1662 time to fit residues: 487.1088 Evaluate side-chains 344 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 254 time to evaluate : 2.620 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 82 residues processed: 8 average time/residue: 0.3002 time to fit residues: 7.5366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 220 optimal weight: 0.0970 chunk 235 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 234 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN C 74 ASN C 292 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 22742 Z= 0.201 Angle : 0.520 11.939 30984 Z= 0.265 Chirality : 0.041 0.222 3582 Planarity : 0.004 0.058 3707 Dihedral : 15.226 127.803 3415 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 4.76 % 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: 0.15 (0.17), residues: 2577 helix: 0.66 (0.15), residues: 1205 sheet: -0.07 (0.22), residues: 565 loop : -0.40 (0.22), residues: 807 *********************** 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 365 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 252 time to evaluate : 2.583 Fit side-chains outliers start: 113 outliers final: 95 residues processed: 347 average time/residue: 1.2190 time to fit residues: 491.4669 Evaluate side-chains 340 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 245 time to evaluate : 2.567 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 85 residues processed: 10 average time/residue: 0.3844 time to fit residues: 9.1689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 240 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN C 74 ASN G 9 ASN G 88 HIS G 218 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2544 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= 0.302 Angle : 0.572 15.205 30984 Z= 0.292 Chirality : 0.043 0.212 3582 Planarity : 0.004 0.058 3707 Dihedral : 15.348 138.102 3415 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 4.30 % 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: -0.02 (0.17), residues: 2577 helix: 0.49 (0.15), residues: 1204 sheet: -0.12 (0.22), residues: 568 loop : -0.47 (0.22), residues: 805 ********************** 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 350 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 248 time to evaluate : 2.454 Fit side-chains outliers start: 102 outliers final: 85 residues processed: 340 average time/residue: 1.2843 time to fit residues: 506.9007 Evaluate side-chains 327 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 242 time to evaluate : 2.619 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 82 residues processed: 3 average time/residue: 0.2447 time to fit residues: 4.9138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 57 optimal weight: 0.2980 chunk 208 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** C 74 ASN G 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.179826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129774 restraints weight = 25145.097| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.75 r_work: 0.3280 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2544 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= 0.177 Angle : 0.529 15.096 30984 Z= 0.269 Chirality : 0.041 0.289 3582 Planarity : 0.004 0.058 3707 Dihedral : 15.250 132.625 3415 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 4.51 % 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: 0.18 (0.17), residues: 2577 helix: 0.67 (0.15), residues: 1205 sheet: -0.02 (0.22), residues: 562 loop : -0.39 (0.22), residues: 810 =============================================================================== Job complete usr+sys time: 8491.23 seconds wall clock time: 151 minutes 32.34 seconds (9092.34 seconds total)