Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 21:45:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs5_29414/07_2023/8fs5_29414_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs5_29414/07_2023/8fs5_29414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs5_29414/07_2023/8fs5_29414.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs5_29414/07_2023/8fs5_29414.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs5_29414/07_2023/8fs5_29414_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs5_29414/07_2023/8fs5_29414_updated.pdb" } resolution = 2.76 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= 0.047 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 13862 2.51 5 N 3821 2.21 5 O 4338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E GLU 214": "OE1" <-> "OE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "E GLU 311": "OE1" <-> "OE2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "F PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 280": "OE1" <-> "OE2" Residue "F GLU 287": "OE1" <-> "OE2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F GLU 427": "OE1" <-> "OE2" Residue "F GLU 436": "OE1" <-> "OE2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "G GLU 128": "OE1" <-> "OE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G GLU 215": "OE1" <-> "OE2" Residue "G GLU 307": "OE1" <-> "OE2" Residue "G GLU 323": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H GLU 147": "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: 22211 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3559 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 2 Chain: "B" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2490 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 9, 'TRANS': 307} 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: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2787 Classifications: {'peptide': 353} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain: "F" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2337 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 5 Chain: "G" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2322 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 4, 'TRANS': 288} Chain breaks: 1 Chain: "H" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2193 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 6 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: 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: "C" 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: "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: 10.07, per 1000 atoms: 0.45 Number of scatterers: 22211 At special positions: 0 Unit cell: (116.748, 137.448, 139.104, 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 4338 8.00 N 3821 7.00 C 13862 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: 8.26 Conformation dependent library (CDL) restraints added in 3.2 seconds 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5008 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 16 sheets defined 45.2% alpha, 14.5% beta 22 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 7.17 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 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 82 through 95 Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.631A pdb=" N ILE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.937A 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 162 through 175 removed outlier: 4.503A pdb=" N PHE A 166 " --> pdb=" O MET A 163 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 168 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 171 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 173 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG A 174 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 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 270 through 282 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 311 through 322 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 374 through 386 removed outlier: 5.331A pdb=" N ASN A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N THR A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 409 removed outlier: 3.588A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.630A pdb=" N GLU A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 469 removed outlier: 4.356A pdb=" N TYR A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 removed outlier: 3.502A pdb=" N LEU A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.973A pdb=" N CYS A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) 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 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 55 through 74 removed outlier: 8.158A pdb=" N ARG B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N SER B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ALA B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ASP B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 removed outlier: 3.854A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.591A 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: 3.938A 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 157 removed outlier: 3.909A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 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 227 removed outlier: 3.622A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 245 through 254 removed outlier: 3.517A pdb=" N GLN B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.538A pdb=" N ARG B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 300 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 31 through 43 removed outlier: 3.990A pdb=" N LYS C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 78 removed outlier: 7.346A pdb=" N LYS C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASN C 74 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR C 75 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER C 76 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ASN C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.909A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) 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 134 removed outlier: 3.741A pdb=" N ARG C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) 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 159 Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 241 through 252 removed outlier: 3.764A pdb=" N LYS C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 270 removed outlier: 3.596A pdb=" N HIS C 260 " --> pdb=" O TRP C 256 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 4.048A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 removed outlier: 3.538A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 334 removed outlier: 3.949A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 4.154A 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 43 through 54 removed outlier: 4.370A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 4.257A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.935A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.797A 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 159 removed outlier: 3.671A pdb=" N LEU D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) 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: 3.505A 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 219 through 223 Processing helix chain 'D' and resid 228 through 245 removed outlier: 3.620A pdb=" N TYR D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 265 through 277 Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.764A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER D 293 " --> pdb=" O THR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 316 through 335 removed outlier: 3.603A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 351 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 removed outlier: 3.574A pdb=" N PHE E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) 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 118 removed outlier: 7.372A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN E 104 " --> pdb=" O MET E 101 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP E 105 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU E 112 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU E 113 " --> pdb=" O GLN E 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL E 116 " --> pdb=" O LEU E 113 " (cutoff:3.500A) 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 157 through 160 No H-bonds generated for 'chain 'E' and resid 157 through 160' Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.537A pdb=" N ASN E 244 " --> pdb=" O MET E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 292 removed outlier: 3.702A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 309 removed outlier: 3.834A pdb=" N ASP E 309 " --> pdb=" O PHE E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 333 Processing helix chain 'E' and resid 338 through 353 removed outlier: 3.731A pdb=" N ILE E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 29 removed outlier: 3.502A pdb=" N THR F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 61 No H-bonds generated for 'chain 'F' and resid 58 through 61' Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' 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: 4.569A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL F 253 " --> pdb=" O PHE F 249 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU F 254 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG F 255 " --> pdb=" O ARG F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 423 removed outlier: 3.625A pdb=" N CYS F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 26 Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 86 through 99 removed outlier: 4.136A pdb=" N VAL G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG G 98 " --> pdb=" O SER G 94 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASN G 99 " --> pdb=" O VAL G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 172 Processing helix chain 'G' and resid 239 through 251 removed outlier: 3.977A pdb=" N LYS G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ARG G 246 " --> pdb=" O PHE G 242 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS G 250 " --> pdb=" O ARG G 246 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE G 251 " --> pdb=" O LYS G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 329 Processing helix chain 'H' and resid 11 through 26 removed outlier: 3.542A pdb=" N TRP H 16 " --> pdb=" O LYS H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 60 No H-bonds generated for 'chain 'H' and resid 58 through 60' Processing helix chain 'H' and resid 98 through 104 removed outlier: 3.983A pdb=" N THR H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE H 104 " --> pdb=" O HIS H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 242 removed outlier: 4.004A pdb=" N PHE H 240 " --> pdb=" O LEU H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 336 removed outlier: 4.115A pdb=" N ASN H 331 " --> pdb=" O LYS H 327 " (cutoff:3.500A) removed outlier: 4.318A 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 264 removed outlier: 6.487A pdb=" N ILE A 104 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE A 263 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 106 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU A 219 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU A 107 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A 221 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N GLY A 109 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 223 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A 186 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.777A 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: 6.213A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.735A 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: 3.666A pdb=" N GLY C 53 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.726A 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: 3.606A pdb=" N GLY D 65 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.623A 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: 3.602A pdb=" N GLY E 43 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 79 through 83 removed outlier: 3.973A pdb=" N LEU F 79 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE F 6 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR F 81 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS F 4 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 91 through 95 removed outlier: 3.594A pdb=" N LEU F 35 " --> pdb=" O MET F 93 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 67 through 70 removed outlier: 3.606A pdb=" N SER F 437 " --> pdb=" O SER F 433 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE F 432 " --> pdb=" O MET F 231 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET F 231 " --> pdb=" O ILE F 432 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 153 through 161 Processing sheet with id= J, first strand: chain 'F' and resid 405 through 411 Processing sheet with id= K, first strand: chain 'G' and resid 11 through 15 removed outlier: 4.095A pdb=" N GLU G 122 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 80 through 85 removed outlier: 7.207A pdb=" N ASP G 36 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLU G 51 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU G 270 " --> pdb=" O LYS G 254 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE G 154 " --> pdb=" O MET G 259 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 232 through 238 removed outlier: 4.671A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 63 through 66 removed outlier: 4.164A pdb=" N GLU H 63 " --> pdb=" O THR H 6 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU H 139 " --> pdb=" O LYS H 114 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE H 116 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL H 137 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE H 118 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE H 135 " --> pdb=" O ILE H 118 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL H 136 " --> pdb=" O TYR H 148 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR H 148 " --> pdb=" O VAL H 136 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 228 through 230 removed outlier: 3.655A pdb=" N PHE H 353 " --> pdb=" O ASN H 228 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 323 through 325 907 hydrogen bonds defined for protein. 2592 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 8.95 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: 7206 1.36 - 1.51: 5995 1.51 - 1.65: 9333 1.65 - 1.80: 74 1.80 - 1.95: 97 Bond restraints: 22705 Sorted by residual: bond pdb=" C SER E 175 " pdb=" N PRO E 176 " ideal model delta sigma weight residual 1.334 1.366 -0.032 8.40e-03 1.42e+04 1.47e+01 bond pdb=" CA SER F 51 " pdb=" CB SER F 51 " ideal model delta sigma weight residual 1.539 1.494 0.045 1.20e-02 6.94e+03 1.40e+01 bond pdb=" N HIS E 18 " pdb=" CA HIS E 18 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.31e-02 5.83e+03 8.30e+00 bond pdb=" N ILE F 468 " pdb=" CA ILE F 468 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.24e+00 bond pdb=" N LEU G 28 " pdb=" CA LEU G 28 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.27e-02 6.20e+03 7.24e+00 ... (remaining 22700 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.59: 875 106.59 - 114.00: 13285 114.00 - 121.40: 11011 121.40 - 128.80: 5597 128.80 - 136.21: 163 Bond angle restraints: 30931 Sorted by residual: angle pdb=" N GLU E 21 " pdb=" CA GLU E 21 " pdb=" C GLU E 21 " ideal model delta sigma weight residual 112.54 107.31 5.23 1.22e+00 6.72e-01 1.84e+01 angle pdb=" N GLU A 68 " pdb=" CA GLU A 68 " pdb=" C GLU A 68 " ideal model delta sigma weight residual 113.88 108.85 5.03 1.23e+00 6.61e-01 1.67e+01 angle pdb=" CA GLY G 303 " pdb=" C GLY G 303 " pdb=" O GLY G 303 " ideal model delta sigma weight residual 122.78 117.99 4.79 1.20e+00 6.94e-01 1.59e+01 angle pdb=" CA GLN A 65 " pdb=" C GLN A 65 " pdb=" O GLN A 65 " ideal model delta sigma weight residual 121.47 117.10 4.37 1.15e+00 7.56e-01 1.44e+01 angle pdb=" N TYR A 67 " pdb=" CA TYR A 67 " pdb=" C TYR A 67 " ideal model delta sigma weight residual 113.16 108.51 4.65 1.24e+00 6.50e-01 1.41e+01 ... (remaining 30926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 12935 35.10 - 70.20: 675 70.20 - 105.30: 22 105.30 - 140.40: 2 140.40 - 175.50: 1 Dihedral angle restraints: 13635 sinusoidal: 5953 harmonic: 7682 Sorted by residual: 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 -60.00 115.50 -175.50 1 2.00e+01 2.50e-03 4.79e+01 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 80.07 -140.07 1 2.00e+01 2.50e-03 4.24e+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 62.73 -122.73 1 2.00e+01 2.50e-03 3.70e+01 ... (remaining 13632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2781 0.046 - 0.092: 609 0.092 - 0.138: 174 0.138 - 0.183: 7 0.183 - 0.229: 3 Chirality restraints: 3574 Sorted by residual: chirality pdb=" CA ILE F 468 " pdb=" N ILE F 468 " pdb=" C ILE F 468 " pdb=" CB ILE F 468 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE E 211 " pdb=" CA ILE E 211 " pdb=" CG1 ILE E 211 " pdb=" CG2 ILE E 211 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA VAL C 133 " pdb=" N VAL C 133 " pdb=" C VAL C 133 " pdb=" CB VAL C 133 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.31e-01 ... (remaining 3571 not shown) Planarity restraints: 3703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " 0.080 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO E 63 " -0.208 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 336 " -0.054 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO H 337 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO H 337 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO H 337 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 235 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.67e+00 pdb=" N PRO F 236 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO F 236 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 236 " 0.030 5.00e-02 4.00e+02 ... (remaining 3700 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 267 2.63 - 3.19: 18901 3.19 - 3.76: 35765 3.76 - 4.33: 50611 4.33 - 4.90: 82572 Nonbonded interactions: 188116 Sorted by model distance: nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.057 2.170 nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.066 2.170 nonbonded pdb=" OE2 GLU A 187 " pdb="MG MG A 602 " model vdw 2.087 2.170 nonbonded pdb=" OG1 THR D 72 " pdb="MG MG D 402 " model vdw 2.095 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.122 2.170 ... (remaining 188111 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: 4.140 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: 17.400 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 58.270 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 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:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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 : 0.003 0.060 22705 Z= 0.199 Angle : 0.687 9.200 30931 Z= 0.432 Chirality : 0.042 0.229 3574 Planarity : 0.005 0.121 3703 Dihedral : 18.235 175.496 8627 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 1.77 % 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: -0.31 (0.17), residues: 2575 helix: 0.33 (0.15), residues: 1216 sheet: -0.31 (0.23), residues: 542 loop : -0.71 (0.22), residues: 817 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 292 time to evaluate : 2.301 Fit side-chains outliers start: 42 outliers final: 31 residues processed: 325 average time/residue: 1.3374 time to fit residues: 496.2090 Evaluate side-chains 299 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 268 time to evaluate : 2.408 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 27 residues processed: 4 average time/residue: 0.2632 time to fit residues: 4.9240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 99 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN B 35 GLN B 102 HIS E 104 ASN E 243 ASN F 57 ASN G 52 ASN G 53 ASN G 87 ASN G 218 GLN H 100 HIS H 151 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 22705 Z= 0.376 Angle : 0.605 7.344 30931 Z= 0.317 Chirality : 0.046 0.178 3574 Planarity : 0.005 0.077 3703 Dihedral : 15.692 158.683 3412 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 5.74 % 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: -0.45 (0.17), residues: 2575 helix: 0.14 (0.15), residues: 1223 sheet: -0.30 (0.22), residues: 553 loop : -0.70 (0.23), residues: 799 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 287 time to evaluate : 2.437 Fit side-chains revert: symmetry clash outliers start: 136 outliers final: 64 residues processed: 386 average time/residue: 1.3436 time to fit residues: 591.4092 Evaluate side-chains 332 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 268 time to evaluate : 2.436 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 46 residues processed: 18 average time/residue: 0.5670 time to fit residues: 16.7617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 213 optimal weight: 0.0980 chunk 238 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN E 243 ASN G 53 ASN G 218 GLN H 151 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 22705 Z= 0.220 Angle : 0.511 6.595 30931 Z= 0.270 Chirality : 0.041 0.156 3574 Planarity : 0.004 0.077 3703 Dihedral : 15.633 148.388 3412 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 5.15 % 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: -0.19 (0.17), residues: 2575 helix: 0.41 (0.15), residues: 1227 sheet: -0.25 (0.22), residues: 552 loop : -0.63 (0.23), residues: 796 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 281 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 69 residues processed: 374 average time/residue: 1.3328 time to fit residues: 570.0043 Evaluate side-chains 336 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 267 time to evaluate : 2.651 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 54 residues processed: 15 average time/residue: 0.6331 time to fit residues: 15.7543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 241 optimal weight: 0.0370 chunk 255 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 35 GLN C 180 ASN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN E 224 GLN E 243 ASN ** E 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 GLN H 45 ASN H 151 GLN H 228 ASN H 247 ASN H 280 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 22705 Z= 0.340 Angle : 0.577 6.904 30931 Z= 0.300 Chirality : 0.044 0.164 3574 Planarity : 0.005 0.075 3703 Dihedral : 15.792 159.639 3412 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 6.20 % 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: 2575 helix: 0.28 (0.15), residues: 1222 sheet: -0.30 (0.22), residues: 554 loop : -0.64 (0.23), residues: 799 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 283 time to evaluate : 2.484 Fit side-chains revert: symmetry clash outliers start: 147 outliers final: 72 residues processed: 397 average time/residue: 1.3514 time to fit residues: 612.1726 Evaluate side-chains 334 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 262 time to evaluate : 2.371 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 57 residues processed: 15 average time/residue: 0.5707 time to fit residues: 14.6294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 190 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 217 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 229 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 ASN H 151 GLN H 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 22705 Z= 0.214 Angle : 0.508 6.967 30931 Z= 0.267 Chirality : 0.041 0.155 3574 Planarity : 0.004 0.074 3703 Dihedral : 15.729 153.199 3412 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 5.36 % 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: -0.06 (0.17), residues: 2575 helix: 0.53 (0.15), residues: 1226 sheet: -0.22 (0.22), residues: 551 loop : -0.57 (0.23), residues: 798 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 283 time to evaluate : 2.462 Fit side-chains outliers start: 127 outliers final: 72 residues processed: 383 average time/residue: 1.3322 time to fit residues: 586.2784 Evaluate side-chains 346 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 274 time to evaluate : 2.485 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 63 residues processed: 10 average time/residue: 0.3863 time to fit residues: 9.1311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.6980 chunk 229 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 212 optimal weight: 0.4980 chunk 118 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN A 298 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 243 ASN H 247 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 22705 Z= 0.174 Angle : 0.487 6.718 30931 Z= 0.257 Chirality : 0.040 0.156 3574 Planarity : 0.004 0.072 3703 Dihedral : 15.647 144.559 3412 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 4.81 % 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: 2575 helix: 0.71 (0.15), residues: 1231 sheet: -0.12 (0.22), residues: 542 loop : -0.49 (0.23), residues: 802 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 282 time to evaluate : 2.581 Fit side-chains outliers start: 114 outliers final: 74 residues processed: 376 average time/residue: 1.3737 time to fit residues: 589.2225 Evaluate side-chains 345 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 271 time to evaluate : 2.266 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 65 residues processed: 10 average time/residue: 0.5626 time to fit residues: 10.7424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 254 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 32 GLN E 243 ASN H 151 GLN H 247 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 22705 Z= 0.216 Angle : 0.510 9.623 30931 Z= 0.267 Chirality : 0.041 0.154 3574 Planarity : 0.004 0.071 3703 Dihedral : 15.643 140.821 3412 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 4.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2575 helix: 0.73 (0.15), residues: 1224 sheet: -0.07 (0.22), residues: 540 loop : -0.45 (0.23), residues: 811 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 280 time to evaluate : 2.299 Fit side-chains revert: symmetry clash outliers start: 115 outliers final: 78 residues processed: 368 average time/residue: 1.4036 time to fit residues: 591.4588 Evaluate side-chains 352 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 274 time to evaluate : 2.463 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 66 residues processed: 13 average time/residue: 0.7444 time to fit residues: 15.5096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN A 351 HIS ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 32 GLN E 243 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 22705 Z= 0.249 Angle : 0.530 9.393 30931 Z= 0.277 Chirality : 0.042 0.159 3574 Planarity : 0.004 0.070 3703 Dihedral : 15.709 141.732 3412 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 3.88 % 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: 0.13 (0.17), residues: 2575 helix: 0.66 (0.15), residues: 1224 sheet: -0.08 (0.22), residues: 548 loop : -0.46 (0.23), residues: 803 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 275 time to evaluate : 2.685 Fit side-chains revert: symmetry clash outliers start: 92 outliers final: 73 residues processed: 353 average time/residue: 1.3898 time to fit residues: 559.6084 Evaluate side-chains 338 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 265 time to evaluate : 2.451 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 67 residues processed: 7 average time/residue: 0.6340 time to fit residues: 9.0747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 8.9990 chunk 222 optimal weight: 5.9990 chunk 237 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 186 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 214 optimal weight: 0.3980 chunk 224 optimal weight: 0.5980 chunk 236 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 203 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 35 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN E 19 ASN E 32 GLN E 243 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 22705 Z= 0.170 Angle : 0.496 11.071 30931 Z= 0.260 Chirality : 0.040 0.154 3574 Planarity : 0.004 0.070 3703 Dihedral : 15.615 135.147 3412 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 3.76 % 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: 0.36 (0.17), residues: 2575 helix: 0.90 (0.15), residues: 1217 sheet: 0.01 (0.22), residues: 537 loop : -0.39 (0.23), residues: 821 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 274 time to evaluate : 2.568 Fit side-chains revert: symmetry clash outliers start: 89 outliers final: 75 residues processed: 352 average time/residue: 1.3956 time to fit residues: 564.1853 Evaluate side-chains 334 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 259 time to evaluate : 2.717 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 67 residues processed: 9 average time/residue: 1.0554 time to fit residues: 14.7044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 203 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 35 GLN B 244 ASN B 250 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 32 GLN E 243 ASN F 56 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 22705 Z= 0.303 Angle : 0.562 8.990 30931 Z= 0.292 Chirality : 0.043 0.154 3574 Planarity : 0.004 0.069 3703 Dihedral : 15.712 134.701 3412 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 3.59 % 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: 0.13 (0.17), residues: 2575 helix: 0.63 (0.15), residues: 1218 sheet: -0.04 (0.22), residues: 549 loop : -0.44 (0.23), residues: 808 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 263 time to evaluate : 2.633 Fit side-chains revert: symmetry clash outliers start: 85 outliers final: 73 residues processed: 336 average time/residue: 1.3892 time to fit residues: 533.5987 Evaluate side-chains 333 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 260 time to evaluate : 2.501 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 66 residues processed: 8 average time/residue: 0.7054 time to fit residues: 10.6217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 184 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 243 ASN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS H 247 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.172557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.125357 restraints weight = 23293.712| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.70 r_work: 0.3330 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 22705 Z= 0.178 Angle : 0.504 8.363 30931 Z= 0.264 Chirality : 0.041 0.152 3574 Planarity : 0.004 0.070 3703 Dihedral : 15.621 131.324 3412 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 3.21 % 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: 0.36 (0.17), residues: 2575 helix: 0.86 (0.15), residues: 1216 sheet: 0.03 (0.22), residues: 544 loop : -0.36 (0.23), residues: 815 =============================================================================== Job complete usr+sys time: 8817.30 seconds wall clock time: 157 minutes 24.69 seconds (9444.69 seconds total)