Starting phenix.real_space_refine on Fri Mar 15 08:49:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqo_41510/03_2024/8tqo_41510.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqo_41510/03_2024/8tqo_41510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqo_41510/03_2024/8tqo_41510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqo_41510/03_2024/8tqo_41510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqo_41510/03_2024/8tqo_41510.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqo_41510/03_2024/8tqo_41510.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.080 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 7047 2.51 5 N 1959 2.21 5 O 2052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 111": "OD1" <-> "OD2" Residue "I TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 301": "OD1" <-> "OD2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 469": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11122 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3200 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "I" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2716 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2472 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2734 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 332} Time building chain proxies: 6.52, per 1000 atoms: 0.59 Number of scatterers: 11122 At special positions: 0 Unit cell: (131.095, 96.025, 129.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2052 8.00 N 1959 7.00 C 7047 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: 4.27 Conformation dependent library (CDL) restraints added in 2.1 seconds 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2722 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 37.2% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.705A pdb=" N TYR A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.648A pdb=" N LYS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.636A pdb=" N ASP A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.806A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 279 removed outlier: 3.515A pdb=" N ASN A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'I' and resid 24 through 27 Processing helix chain 'I' and resid 36 through 44 Processing helix chain 'I' and resid 85 through 93 Processing helix chain 'I' and resid 114 through 124 removed outlier: 3.784A pdb=" N LEU I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 removed outlier: 3.688A pdb=" N LYS I 189 " --> pdb=" O SER I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 218 removed outlier: 4.154A pdb=" N VAL I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP I 213 " --> pdb=" O LYS I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 235 Processing helix chain 'I' and resid 315 through 334 Proline residue: I 327 - end of helix removed outlier: 3.911A pdb=" N ALA I 332 " --> pdb=" O LYS I 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 4.216A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 128 through 146 removed outlier: 4.070A pdb=" N ASN D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.592A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.709A pdb=" N GLU D 299 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 337 through 344 removed outlier: 3.990A pdb=" N SER D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 240 removed outlier: 3.568A pdb=" N CYS E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 267 removed outlier: 4.006A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix removed outlier: 3.504A pdb=" N CYS E 266 " --> pdb=" O PHE E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 312 Processing helix chain 'E' and resid 314 through 325 removed outlier: 4.056A pdb=" N ALA E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 319 " --> pdb=" O ALA E 315 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 351 removed outlier: 3.878A pdb=" N THR E 351 " --> pdb=" O GLN E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 379 removed outlier: 3.986A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 419 through 430 removed outlier: 3.762A pdb=" N LEU E 425 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA E 429 " --> pdb=" O LEU E 425 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS E 430 " --> pdb=" O VAL E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 removed outlier: 3.647A pdb=" N LYS E 442 " --> pdb=" O GLU E 439 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 443 " --> pdb=" O THR E 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 439 through 443' Processing helix chain 'E' and resid 459 through 463 Processing helix chain 'E' and resid 511 through 517 removed outlier: 3.957A pdb=" N VAL E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 124 removed outlier: 6.611A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS A 247 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE A 184 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE A 249 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N THR A 182 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE A 251 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL A 180 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLN A 286 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET A 181 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE A 287 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A 212 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP A 206 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 204 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 216 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE I 169 " --> pdb=" O GLY I 159 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP I 161 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU I 167 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 225 Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 338 removed outlier: 3.666A pdb=" N ILE A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU A 361 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU A 412 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.526A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 424 " --> pdb=" O LEU A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 6.459A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'I' and resid 76 through 77 removed outlier: 6.426A pdb=" N ALA I 5 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLN I 4 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU I 104 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL I 6 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N HIS I 203 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU I 131 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU I 204 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA I 129 " --> pdb=" O LEU I 204 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU I 128 " --> pdb=" O TYR I 301 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N HIS I 303 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N MET I 130 " --> pdb=" O HIS I 303 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N MET I 305 " --> pdb=" O MET I 130 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET I 132 " --> pdb=" O MET I 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 29 through 30 Processing sheet with id=AA9, first strand: chain 'I' and resid 353 through 354 removed outlier: 4.031A pdb=" N VAL I 354 " --> pdb=" O ILE I 370 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N SER I 369 " --> pdb=" O ILE I 387 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR I 386 " --> pdb=" O ILE I 404 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASN I 403 " --> pdb=" O ILE I 421 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP I 420 " --> pdb=" O LYS I 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'I' and resid 391 through 392 removed outlier: 6.647A pdb=" N LEU I 391 " --> pdb=" O ILE I 409 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL I 408 " --> pdb=" O ILE I 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 414 through 415 removed outlier: 7.350A pdb=" N VAL I 414 " --> pdb=" O ILE I 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 323 through 325 removed outlier: 6.846A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR D 167 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.403A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP E 362 " --> pdb=" O LEU E 386 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR E 336 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY E 404 " --> pdb=" O TYR E 336 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL E 401 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N CYS E 437 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU E 403 " --> pdb=" O CYS E 437 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 407 through 408 removed outlier: 3.604A pdb=" N VAL E 414 " --> pdb=" O THR E 492 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3705 1.34 - 1.46: 2234 1.46 - 1.58: 5289 1.58 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 11323 Sorted by residual: bond pdb=" CB GLU D 135 " pdb=" CG GLU D 135 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CG ARG A 145 " pdb=" CD ARG A 145 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CB GLU E 469 " pdb=" CG GLU E 469 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" C PHE D 278 " pdb=" N PRO D 279 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.89e-01 bond pdb=" C VAL I 326 " pdb=" N PRO I 327 " ideal model delta sigma weight residual 1.334 1.347 -0.013 1.51e-02 4.39e+03 7.50e-01 ... (remaining 11318 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.75: 338 106.75 - 113.56: 6428 113.56 - 120.36: 3897 120.36 - 127.17: 4581 127.17 - 133.97: 120 Bond angle restraints: 15364 Sorted by residual: angle pdb=" N VAL D 312 " pdb=" CA VAL D 312 " pdb=" C VAL D 312 " ideal model delta sigma weight residual 112.96 109.83 3.13 1.00e+00 1.00e+00 9.82e+00 angle pdb=" C GLU I 44 " pdb=" N ARG I 45 " pdb=" CA ARG I 45 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.67e+00 angle pdb=" CB GLU D 135 " pdb=" CG GLU D 135 " pdb=" CD GLU D 135 " ideal model delta sigma weight residual 112.60 117.21 -4.61 1.70e+00 3.46e-01 7.36e+00 angle pdb=" CA SER A 60 " pdb=" C SER A 60 " pdb=" N LYS A 61 " ideal model delta sigma weight residual 116.84 121.41 -4.57 1.71e+00 3.42e-01 7.14e+00 angle pdb=" C LEU I 351 " pdb=" N VAL I 352 " pdb=" CA VAL I 352 " ideal model delta sigma weight residual 121.97 126.76 -4.79 1.80e+00 3.09e-01 7.08e+00 ... (remaining 15359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5906 17.82 - 35.64: 761 35.64 - 53.45: 196 53.45 - 71.27: 28 71.27 - 89.09: 10 Dihedral angle restraints: 6901 sinusoidal: 2715 harmonic: 4186 Sorted by residual: dihedral pdb=" CA PHE A 57 " pdb=" C PHE A 57 " pdb=" N PRO A 58 " pdb=" CA PRO A 58 " ideal model delta harmonic sigma weight residual 180.00 140.19 39.81 0 5.00e+00 4.00e-02 6.34e+01 dihedral pdb=" CA ARG I 45 " pdb=" C ARG I 45 " pdb=" N VAL I 46 " pdb=" CA VAL I 46 " ideal model delta harmonic sigma weight residual 180.00 159.57 20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP A 147 " pdb=" CB ASP A 147 " pdb=" CG ASP A 147 " pdb=" OD1 ASP A 147 " ideal model delta sinusoidal sigma weight residual -30.00 -89.98 59.98 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 6898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1245 0.035 - 0.070: 362 0.070 - 0.106: 157 0.106 - 0.141: 55 0.141 - 0.176: 3 Chirality restraints: 1822 Sorted by residual: chirality pdb=" CB VAL I 54 " pdb=" CA VAL I 54 " pdb=" CG1 VAL I 54 " pdb=" CG2 VAL I 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CB ILE I 346 " pdb=" CA ILE I 346 " pdb=" CG1 ILE I 346 " pdb=" CG2 ILE I 346 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA ILE I 404 " pdb=" N ILE I 404 " pdb=" C ILE I 404 " pdb=" CB ILE I 404 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 1819 not shown) Planarity restraints: 1963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 57 " 0.077 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO A 58 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 395 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO E 396 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 396 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 396 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " 0.105 9.50e-02 1.11e+02 4.78e-02 2.13e+00 pdb=" NE ARG A 145 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " -0.001 2.00e-02 2.50e+03 ... (remaining 1960 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 803 2.74 - 3.28: 10959 3.28 - 3.82: 18019 3.82 - 4.36: 20823 4.36 - 4.90: 37285 Nonbonded interactions: 87889 Sorted by model distance: nonbonded pdb=" O PRO A 69 " pdb=" OH TYR A 306 " model vdw 2.202 2.440 nonbonded pdb=" OG SER I 402 " pdb=" O ALA I 419 " model vdw 2.214 2.440 nonbonded pdb=" N GLU E 469 " pdb=" OE1 GLU E 469 " model vdw 2.247 2.520 nonbonded pdb=" OG SER I 127 " pdb=" OH TYR I 210 " model vdw 2.253 2.440 nonbonded pdb=" O LEU D 265 " pdb=" OG1 THR D 322 " model vdw 2.254 2.440 ... (remaining 87884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.240 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 33.950 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 0.002 0.038 11323 Z= 0.133 Angle : 0.540 8.139 15364 Z= 0.282 Chirality : 0.043 0.176 1822 Planarity : 0.005 0.119 1963 Dihedral : 16.855 89.091 4179 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.16 % Allowed : 28.68 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1417 helix: 1.64 (0.26), residues: 456 sheet: -0.39 (0.38), residues: 193 loop : -0.72 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 51 HIS 0.011 0.001 HIS I 350 PHE 0.012 0.001 PHE D 177 TYR 0.021 0.001 TYR D 337 ARG 0.015 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.336 Fit side-chains REVERT: A 305 MET cc_start: 0.8541 (mmm) cc_final: 0.8318 (tpp) REVERT: I 424 CYS cc_start: 0.8171 (t) cc_final: 0.7903 (m) REVERT: D 20 GLU cc_start: 0.8183 (mp0) cc_final: 0.7938 (mp0) REVERT: D 292 GLU cc_start: 0.8418 (tp30) cc_final: 0.8124 (mt-10) outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.2270 time to fit residues: 37.4348 Evaluate side-chains 106 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 5.9990 chunk 107 optimal weight: 0.0970 chunk 59 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN D 162 ASN D 286 HIS E 274 HIS ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11323 Z= 0.337 Angle : 0.592 7.307 15364 Z= 0.307 Chirality : 0.047 0.169 1822 Planarity : 0.005 0.082 1963 Dihedral : 4.283 38.605 1555 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.57 % Allowed : 25.91 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.23), residues: 1417 helix: 1.43 (0.25), residues: 484 sheet: -0.71 (0.36), residues: 203 loop : -0.73 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 97 HIS 0.010 0.001 HIS I 350 PHE 0.014 0.002 PHE D 177 TYR 0.025 0.002 TYR I 231 ARG 0.006 0.001 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 115 time to evaluate : 1.376 Fit side-chains REVERT: A 104 GLU cc_start: 0.8624 (tp30) cc_final: 0.8171 (tp30) REVERT: I 8 MET cc_start: 0.8857 (mmt) cc_final: 0.8371 (mmt) REVERT: I 321 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8602 (tp30) REVERT: I 424 CYS cc_start: 0.8137 (t) cc_final: 0.7931 (m) REVERT: D 138 ASN cc_start: 0.8540 (m-40) cc_final: 0.8295 (m110) REVERT: D 180 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8874 (tm-30) outliers start: 44 outliers final: 30 residues processed: 153 average time/residue: 0.2287 time to fit residues: 51.0439 Evaluate side-chains 129 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 98 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 128 LEU Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 9.9990 chunk 40 optimal weight: 0.0270 chunk 107 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 139 optimal weight: 0.0980 chunk 115 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 162 ASN D 242 ASN D 286 HIS ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11323 Z= 0.135 Angle : 0.507 7.156 15364 Z= 0.259 Chirality : 0.043 0.153 1822 Planarity : 0.004 0.101 1963 Dihedral : 4.078 37.572 1552 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.01 % Allowed : 26.89 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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 (0.23), residues: 1417 helix: 1.60 (0.25), residues: 484 sheet: -0.59 (0.36), residues: 200 loop : -0.67 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 111 HIS 0.009 0.001 HIS I 350 PHE 0.011 0.001 PHE D 177 TYR 0.011 0.001 TYR I 319 ARG 0.005 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 104 time to evaluate : 1.331 Fit side-chains REVERT: A 170 LEU cc_start: 0.8655 (tp) cc_final: 0.8317 (tp) REVERT: I 8 MET cc_start: 0.8774 (mmt) cc_final: 0.8343 (mmt) REVERT: I 321 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8567 (tp30) REVERT: D 36 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7625 (ttp80) REVERT: D 180 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8905 (tm-30) REVERT: E 354 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7222 (mmt-90) outliers start: 37 outliers final: 21 residues processed: 135 average time/residue: 0.2326 time to fit residues: 45.3123 Evaluate side-chains 120 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 354 ARG Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 347 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11323 Z= 0.297 Angle : 0.562 8.066 15364 Z= 0.289 Chirality : 0.046 0.184 1822 Planarity : 0.004 0.096 1963 Dihedral : 4.264 39.465 1552 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.36 % Allowed : 25.26 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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 (0.23), residues: 1417 helix: 1.58 (0.25), residues: 485 sheet: -0.53 (0.37), residues: 194 loop : -0.72 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 97 HIS 0.009 0.001 HIS I 350 PHE 0.013 0.002 PHE D 177 TYR 0.014 0.001 TYR A 128 ARG 0.006 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 96 time to evaluate : 1.430 Fit side-chains revert: symmetry clash REVERT: I 4 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7933 (mt0) REVERT: I 321 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8546 (tp30) REVERT: D 180 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8866 (tm-30) REVERT: E 354 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7418 (mmt-90) REVERT: E 386 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8223 (pp) outliers start: 66 outliers final: 45 residues processed: 151 average time/residue: 0.2131 time to fit residues: 47.9457 Evaluate side-chains 141 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 92 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 354 ARG Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 8.9990 chunk 1 optimal weight: 0.1980 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 0.0050 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 242 ASN ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11323 Z= 0.138 Angle : 0.497 8.589 15364 Z= 0.255 Chirality : 0.043 0.151 1822 Planarity : 0.004 0.105 1963 Dihedral : 4.054 36.456 1552 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.82 % Allowed : 26.00 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.38 (0.23), residues: 1417 helix: 1.81 (0.25), residues: 480 sheet: -0.30 (0.38), residues: 187 loop : -0.62 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 97 HIS 0.008 0.001 HIS I 350 PHE 0.011 0.001 PHE D 177 TYR 0.015 0.001 TYR E 214 ARG 0.008 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 99 time to evaluate : 1.442 Fit side-chains revert: symmetry clash REVERT: I 4 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7925 (mt0) REVERT: I 133 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7722 (ttt90) REVERT: I 321 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8577 (tp30) REVERT: E 386 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8072 (pp) outliers start: 47 outliers final: 34 residues processed: 139 average time/residue: 0.2334 time to fit residues: 47.0243 Evaluate side-chains 127 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 90 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 133 ARG Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 80 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 114 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 72 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11323 Z= 0.160 Angle : 0.500 7.465 15364 Z= 0.255 Chirality : 0.044 0.191 1822 Planarity : 0.004 0.114 1963 Dihedral : 3.993 39.405 1552 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.90 % Allowed : 26.73 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.48 (0.23), residues: 1417 helix: 1.85 (0.25), residues: 479 sheet: -0.14 (0.39), residues: 186 loop : -0.55 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 97 HIS 0.009 0.001 HIS I 350 PHE 0.011 0.001 PHE D 177 TYR 0.015 0.001 TYR E 214 ARG 0.007 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 96 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: I 8 MET cc_start: 0.8765 (mmt) cc_final: 0.8475 (mmt) REVERT: I 133 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7738 (ttt90) REVERT: I 321 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8586 (tp30) REVERT: E 172 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7560 (t70) REVERT: E 354 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7318 (mmt-90) outliers start: 48 outliers final: 40 residues processed: 137 average time/residue: 0.2543 time to fit residues: 50.7825 Evaluate side-chains 135 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 92 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 133 ARG Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 396 VAL Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 354 ARG Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 ASN D 242 ASN D 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 11323 Z= 0.502 Angle : 0.645 9.129 15364 Z= 0.331 Chirality : 0.049 0.160 1822 Planarity : 0.005 0.120 1963 Dihedral : 4.574 41.603 1552 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 5.36 % Allowed : 25.26 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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 (0.23), residues: 1417 helix: 1.37 (0.25), residues: 492 sheet: -0.33 (0.39), residues: 190 loop : -0.77 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 97 HIS 0.008 0.001 HIS I 350 PHE 0.016 0.002 PHE A 56 TYR 0.019 0.002 TYR A 128 ARG 0.007 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 93 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7983 (mtt-85) REVERT: I 133 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7862 (ttt90) REVERT: I 158 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8998 (mp) REVERT: I 321 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8514 (tp30) REVERT: E 317 GLN cc_start: 0.6722 (OUTLIER) cc_final: 0.6132 (mm110) REVERT: E 354 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7562 (mmt-90) outliers start: 66 outliers final: 47 residues processed: 148 average time/residue: 0.2400 time to fit residues: 50.9102 Evaluate side-chains 141 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 89 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 133 ARG Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 224 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 396 VAL Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 317 GLN Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 354 ARG Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 12 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 242 ASN E 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11323 Z= 0.200 Angle : 0.539 9.079 15364 Z= 0.275 Chirality : 0.045 0.160 1822 Planarity : 0.004 0.120 1963 Dihedral : 4.369 40.449 1552 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.22 % Allowed : 26.48 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.23), residues: 1417 helix: 1.53 (0.25), residues: 493 sheet: -0.29 (0.39), residues: 186 loop : -0.71 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 97 HIS 0.007 0.001 HIS I 350 PHE 0.012 0.001 PHE D 177 TYR 0.019 0.001 TYR E 214 ARG 0.007 0.000 ARG I 431 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 94 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7977 (mtt-85) REVERT: I 133 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7840 (ttt90) REVERT: I 158 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8930 (mp) REVERT: I 321 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8508 (tp30) REVERT: D 217 MET cc_start: 0.8694 (ptt) cc_final: 0.8483 (ptt) REVERT: E 317 GLN cc_start: 0.6668 (OUTLIER) cc_final: 0.6086 (mm110) REVERT: E 354 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7450 (mmt-90) outliers start: 52 outliers final: 42 residues processed: 139 average time/residue: 0.2439 time to fit residues: 48.4766 Evaluate side-chains 136 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 89 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 133 ARG Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 317 GLN Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 354 ARG Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 0.1980 chunk 39 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 242 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11323 Z= 0.155 Angle : 0.525 8.749 15364 Z= 0.267 Chirality : 0.044 0.170 1822 Planarity : 0.004 0.124 1963 Dihedral : 4.222 41.420 1552 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.82 % Allowed : 26.81 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.39 (0.23), residues: 1417 helix: 1.69 (0.25), residues: 484 sheet: -0.01 (0.40), residues: 178 loop : -0.62 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 97 HIS 0.007 0.001 HIS I 350 PHE 0.012 0.001 PHE D 177 TYR 0.010 0.001 TYR A 128 ARG 0.008 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 92 time to evaluate : 1.471 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7934 (mtt-85) REVERT: I 133 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7793 (ttt90) REVERT: I 321 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8543 (tp30) REVERT: D 217 MET cc_start: 0.8680 (ptt) cc_final: 0.8452 (ptt) REVERT: E 317 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.6048 (mm110) REVERT: E 354 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7393 (mmt-90) outliers start: 47 outliers final: 39 residues processed: 134 average time/residue: 0.2369 time to fit residues: 45.7756 Evaluate side-chains 130 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 87 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 133 ARG Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 317 GLN Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 354 ARG Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 0.0050 chunk 141 optimal weight: 0.0060 chunk 130 optimal weight: 3.9990 chunk 112 optimal weight: 0.0770 chunk 11 optimal weight: 0.1980 chunk 87 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 overall best weight: 0.2568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 ASN ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11323 Z= 0.130 Angle : 0.513 8.272 15364 Z= 0.260 Chirality : 0.043 0.167 1822 Planarity : 0.004 0.123 1963 Dihedral : 4.062 38.590 1552 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.92 % Allowed : 27.86 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.23), residues: 1417 helix: 1.86 (0.25), residues: 478 sheet: 0.09 (0.40), residues: 178 loop : -0.55 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 97 HIS 0.011 0.001 HIS I 350 PHE 0.050 0.001 PHE A 57 TYR 0.017 0.001 TYR E 214 ARG 0.008 0.000 ARG A 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2834 Ramachandran restraints generated. 1417 Oldfield, 0 Emsley, 1417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 96 time to evaluate : 1.352 Fit side-chains revert: symmetry clash REVERT: I 133 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7659 (ttt90) REVERT: I 321 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8546 (tp30) REVERT: I 372 ARG cc_start: 0.8513 (mtp-110) cc_final: 0.8212 (mtp85) REVERT: D 217 MET cc_start: 0.8682 (ptt) cc_final: 0.8472 (ptt) REVERT: E 354 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7390 (mmt-90) outliers start: 36 outliers final: 31 residues processed: 128 average time/residue: 0.2284 time to fit residues: 42.3008 Evaluate side-chains 122 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 89 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain I residue 133 ARG Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 326 VAL Chi-restraints excluded: chain I residue 340 VAL Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 354 ARG Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.2980 chunk 112 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS D 242 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.113236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.079338 restraints weight = 18167.041| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.35 r_work: 0.2899 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11323 Z= 0.147 Angle : 0.516 8.013 15364 Z= 0.262 Chirality : 0.044 0.173 1822 Planarity : 0.004 0.124 1963 Dihedral : 3.995 41.315 1552 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.49 % Allowed : 27.38 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.62 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: 0.61 (0.23), residues: 1417 helix: 2.02 (0.25), residues: 472 sheet: 0.09 (0.40), residues: 178 loop : -0.54 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 97 HIS 0.012 0.001 HIS I 350 PHE 0.012 0.001 PHE D 272 TYR 0.025 0.001 TYR I 319 ARG 0.008 0.000 ARG A 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2413.51 seconds wall clock time: 44 minutes 11.36 seconds (2651.36 seconds total)