Starting phenix.real_space_refine on Thu Jan 18 23:41:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kb5_22787/01_2024/7kb5_22787.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kb5_22787/01_2024/7kb5_22787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kb5_22787/01_2024/7kb5_22787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kb5_22787/01_2024/7kb5_22787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kb5_22787/01_2024/7kb5_22787.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kb5_22787/01_2024/7kb5_22787.pdb" } resolution = 3.8 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= 0.001 sd= 0.016 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 40 5.16 5 C 6382 2.51 5 N 1645 2.21 5 O 1710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 25": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 186": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 145": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 185": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9777 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3269 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 19, 'TRANS': 407} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 229 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 435 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "D" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3244 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 24, 'TRANS': 385} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 11, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 68 Chain: "E" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1129 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 135} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1471 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 182} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.51, per 1000 atoms: 0.56 Number of scatterers: 9777 At special positions: 0 Unit cell: (99, 124.2, 135.9, 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 40 16.00 O 1710 8.00 N 1645 7.00 C 6382 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: 3.76 Conformation dependent library (CDL) restraints added in 1.7 seconds 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 67.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 28 through 49 removed outlier: 3.591A pdb=" N GLN A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 70 removed outlier: 3.742A pdb=" N ALA A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 98 removed outlier: 3.557A pdb=" N THR A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 137 removed outlier: 3.619A pdb=" N LEU A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.655A pdb=" N VAL A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 198 removed outlier: 3.672A pdb=" N LEU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 removed outlier: 3.643A pdb=" N ALA A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.676A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 262 removed outlier: 3.632A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 314 Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 341 through 347 removed outlier: 3.661A pdb=" N TYR A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.830A pdb=" N ASP A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 385 removed outlier: 3.636A pdb=" N THR A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU A 382 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 406 through 440 removed outlier: 3.564A pdb=" N ILE A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 444 through 466 removed outlier: 4.036A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 82 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 43 through 80 removed outlier: 3.732A pdb=" N TYR C 47 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix Processing helix chain 'D' and resid 68 through 78 Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'D' and resid 234 through 249 Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.784A pdb=" N ALA D 259 " --> pdb=" O HIS D 255 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.633A pdb=" N ILE D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 318 through 343 removed outlier: 4.125A pdb=" N ARG D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 362 Processing helix chain 'D' and resid 378 through 386 removed outlier: 4.416A pdb=" N THR D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 397 Processing helix chain 'D' and resid 399 through 408 removed outlier: 3.578A pdb=" N ILE D 403 " --> pdb=" O GLU D 399 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 423 removed outlier: 4.365A pdb=" N GLU D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 470 Processing helix chain 'D' and resid 480 through 486 removed outlier: 3.650A pdb=" N ASP D 486 " --> pdb=" O GLU D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 removed outlier: 4.409A pdb=" N MET D 491 " --> pdb=" O PRO D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 541 removed outlier: 3.691A pdb=" N ASN D 541 " --> pdb=" O LYS D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 558 Processing helix chain 'E' and resid 72 through 86 removed outlier: 3.773A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 124 removed outlier: 4.197A pdb=" N LEU E 92 " --> pdb=" O HIS E 88 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 128 through 156 removed outlier: 3.855A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 182 removed outlier: 4.008A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 5.080A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.549A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG E 203 " --> pdb=" O ASN E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 203' Processing helix chain 'F' and resid 21 through 41 Processing helix chain 'F' and resid 52 through 67 Processing helix chain 'F' and resid 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 75 through 91 removed outlier: 3.727A pdb=" N LYS F 79 " --> pdb=" O ASN F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 120 removed outlier: 3.637A pdb=" N LEU F 105 " --> pdb=" O GLN F 101 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER F 111 " --> pdb=" O PHE F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 139 through 153 removed outlier: 3.940A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ARG F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 168 Processing helix chain 'F' and resid 175 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 278 through 284 Processing sheet with id=AA2, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA3, first strand: chain 'D' and resid 426 through 427 Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 434 removed outlier: 4.005A pdb=" N LYS D 432 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP D 434 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D 452 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.511A pdb=" N ILE D 604 " --> pdb=" O VAL D 590 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D 602 " --> pdb=" O VAL D 592 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 530 through 532 Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 6 609 hydrogen bonds defined for protein. 1779 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: 3.08 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3069 1.34 - 1.46: 1891 1.46 - 1.58: 4948 1.58 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 9971 Sorted by residual: bond pdb=" CB CYS E 167 " pdb=" SG CYS E 167 " ideal model delta sigma weight residual 1.808 1.762 0.046 3.30e-02 9.18e+02 1.96e+00 bond pdb=" C ILE A 418 " pdb=" N PRO A 419 " ideal model delta sigma weight residual 1.335 1.352 -0.016 1.36e-02 5.41e+03 1.44e+00 bond pdb=" CB GLN F 155 " pdb=" CG GLN F 155 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" C THR D 595 " pdb=" N ASP D 596 " ideal model delta sigma weight residual 1.333 1.319 0.014 1.41e-02 5.03e+03 9.83e-01 bond pdb=" C ILE D 531 " pdb=" N ILE D 532 " ideal model delta sigma weight residual 1.335 1.321 0.014 1.41e-02 5.03e+03 9.69e-01 ... (remaining 9966 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.68: 276 106.68 - 113.53: 5686 113.53 - 120.37: 3870 120.37 - 127.22: 3576 127.22 - 134.07: 97 Bond angle restraints: 13505 Sorted by residual: angle pdb=" N VAL E 205 " pdb=" CA VAL E 205 " pdb=" C VAL E 205 " ideal model delta sigma weight residual 112.17 108.28 3.89 9.50e-01 1.11e+00 1.68e+01 angle pdb=" N ILE E 126 " pdb=" CA ILE E 126 " pdb=" C ILE E 126 " ideal model delta sigma weight residual 113.71 110.11 3.60 9.50e-01 1.11e+00 1.44e+01 angle pdb=" C ILE A 417 " pdb=" N ILE A 418 " pdb=" CA ILE A 418 " ideal model delta sigma weight residual 120.33 122.80 -2.47 8.00e-01 1.56e+00 9.52e+00 angle pdb=" C PRO F 94 " pdb=" N TRP F 95 " pdb=" CA TRP F 95 " ideal model delta sigma weight residual 122.56 117.83 4.73 1.72e+00 3.38e-01 7.57e+00 angle pdb=" CA TYR F 190 " pdb=" CB TYR F 190 " pdb=" CG TYR F 190 " ideal model delta sigma weight residual 113.90 118.77 -4.87 1.80e+00 3.09e-01 7.33e+00 ... (remaining 13500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 5362 16.72 - 33.43: 526 33.43 - 50.15: 111 50.15 - 66.87: 9 66.87 - 83.58: 8 Dihedral angle restraints: 6016 sinusoidal: 2376 harmonic: 3640 Sorted by residual: dihedral pdb=" CA VAL D 437 " pdb=" C VAL D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ASP D 545 " pdb=" CB ASP D 545 " pdb=" CG ASP D 545 " pdb=" OD1 ASP D 545 " ideal model delta sinusoidal sigma weight residual -30.00 -88.94 58.94 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASN E 84 " pdb=" C ASN E 84 " pdb=" N GLU E 85 " pdb=" CA GLU E 85 " ideal model delta harmonic sigma weight residual -180.00 -163.25 -16.75 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 6013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 860 0.027 - 0.054: 499 0.054 - 0.081: 136 0.081 - 0.108: 82 0.108 - 0.135: 20 Chirality restraints: 1597 Sorted by residual: chirality pdb=" CA ILE D 470 " pdb=" N ILE D 470 " pdb=" C ILE D 470 " pdb=" CB ILE D 470 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE D 389 " pdb=" N ILE D 389 " pdb=" C ILE D 389 " pdb=" CB ILE D 389 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA PRO F 94 " pdb=" N PRO F 94 " pdb=" C PRO F 94 " pdb=" CB PRO F 94 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 1594 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO F 48 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 437 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO D 438 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 438 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 438 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 93 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO F 94 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 94 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 94 " -0.024 5.00e-02 4.00e+02 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 285 2.71 - 3.26: 10117 3.26 - 3.81: 14954 3.81 - 4.35: 17322 4.35 - 4.90: 29626 Nonbonded interactions: 72304 Sorted by model distance: nonbonded pdb=" OE1 GLN D 370 " pdb=" OG1 THR D 391 " model vdw 2.163 2.440 nonbonded pdb=" OG SER A 271 " pdb=" O VAL A 274 " model vdw 2.224 2.440 nonbonded pdb=" O PRO F 171 " pdb=" NH2 ARG F 177 " model vdw 2.252 2.520 nonbonded pdb=" O PRO A 18 " pdb=" NZ LYS A 119 " model vdw 2.260 2.520 nonbonded pdb=" O SER D 423 " pdb=" OG SER D 423 " model vdw 2.271 2.440 ... (remaining 72299 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 group one per residue 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: 2.400 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: 0.000 Extract box with map and model: 7.000 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.880 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9971 Z= 0.283 Angle : 0.635 9.382 13505 Z= 0.354 Chirality : 0.040 0.135 1597 Planarity : 0.004 0.044 1677 Dihedral : 13.760 83.585 3652 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % 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: -1.47 (0.22), residues: 1228 helix: -0.09 (0.17), residues: 753 sheet: -2.43 (0.54), residues: 85 loop : -2.26 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 156 HIS 0.004 0.001 HIS D 334 PHE 0.019 0.001 PHE D 356 TYR 0.022 0.002 TYR F 190 ARG 0.003 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.9334 (mmm) cc_final: 0.8861 (mmm) REVERT: B 71 LEU cc_start: 0.9403 (mt) cc_final: 0.9151 (tp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2424 time to fit residues: 26.5685 Evaluate side-chains 48 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 317 ASN A 336 GLN D 330 HIS D 390 HIS D 520 GLN E 88 HIS E 181 GLN F 68 ASN F 89 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9971 Z= 0.195 Angle : 0.552 7.597 13505 Z= 0.277 Chirality : 0.038 0.133 1597 Planarity : 0.004 0.045 1677 Dihedral : 3.737 20.282 1328 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.34 % Allowed : 13.29 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1228 helix: 1.52 (0.19), residues: 764 sheet: -2.02 (0.56), residues: 84 loop : -1.67 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 95 HIS 0.006 0.001 HIS D 309 PHE 0.008 0.001 PHE D 343 TYR 0.019 0.001 TYR D 227 ARG 0.004 0.000 ARG D 485 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 1.131 Fit side-chains REVERT: A 400 MET cc_start: 0.9272 (mmm) cc_final: 0.8743 (mmm) REVERT: B 71 LEU cc_start: 0.9387 (mt) cc_final: 0.9171 (tp) outliers start: 14 outliers final: 6 residues processed: 62 average time/residue: 0.1814 time to fit residues: 18.0409 Evaluate side-chains 51 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 198 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 120 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9971 Z= 0.177 Angle : 0.531 8.129 13505 Z= 0.263 Chirality : 0.037 0.134 1597 Planarity : 0.003 0.045 1677 Dihedral : 3.578 20.391 1328 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.01 % Allowed : 14.53 % Favored : 83.46 % 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: 1.17 (0.25), residues: 1228 helix: 2.09 (0.19), residues: 765 sheet: -1.73 (0.56), residues: 86 loop : -1.41 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 95 HIS 0.006 0.001 HIS D 309 PHE 0.023 0.001 PHE B 64 TYR 0.018 0.001 TYR D 227 ARG 0.003 0.000 ARG D 485 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 49 time to evaluate : 1.192 Fit side-chains REVERT: A 400 MET cc_start: 0.9275 (mmm) cc_final: 0.8802 (mmm) REVERT: D 330 HIS cc_start: 0.8379 (OUTLIER) cc_final: 0.7759 (t70) REVERT: D 421 VAL cc_start: 0.9076 (t) cc_final: 0.8867 (p) outliers start: 21 outliers final: 11 residues processed: 67 average time/residue: 0.1637 time to fit residues: 18.0213 Evaluate side-chains 57 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 330 HIS Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN D 307 GLN D 577 GLN E 181 GLN F 71 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9971 Z= 0.280 Angle : 0.577 8.033 13505 Z= 0.286 Chirality : 0.039 0.132 1597 Planarity : 0.003 0.045 1677 Dihedral : 3.683 20.072 1328 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.77 % Allowed : 16.63 % Favored : 80.59 % 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: 1.42 (0.25), residues: 1228 helix: 2.29 (0.19), residues: 765 sheet: -1.45 (0.59), residues: 81 loop : -1.38 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 156 HIS 0.006 0.001 HIS C 72 PHE 0.021 0.001 PHE B 64 TYR 0.019 0.001 TYR F 190 ARG 0.002 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 47 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: A 400 MET cc_start: 0.9273 (mmm) cc_final: 0.8796 (mmm) REVERT: D 330 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.7801 (t70) outliers start: 29 outliers final: 18 residues processed: 72 average time/residue: 0.1734 time to fit residues: 19.9569 Evaluate side-chains 61 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 42 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 330 HIS Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 414 LYS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 0.0060 chunk 0 optimal weight: 30.0000 chunk 60 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9971 Z= 0.286 Angle : 0.587 9.294 13505 Z= 0.289 Chirality : 0.039 0.132 1597 Planarity : 0.003 0.046 1677 Dihedral : 3.704 20.252 1328 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.49 % Allowed : 18.55 % Favored : 78.97 % 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: 1.56 (0.25), residues: 1228 helix: 2.40 (0.19), residues: 765 sheet: -1.42 (0.59), residues: 81 loop : -1.31 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 156 HIS 0.006 0.001 HIS C 72 PHE 0.019 0.001 PHE C 58 TYR 0.019 0.001 TYR F 190 ARG 0.002 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 46 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.9277 (mmm) cc_final: 0.9047 (mmm) REVERT: A 400 MET cc_start: 0.9286 (mmm) cc_final: 0.8892 (mmm) REVERT: D 330 HIS cc_start: 0.8503 (OUTLIER) cc_final: 0.7855 (t70) outliers start: 26 outliers final: 20 residues processed: 70 average time/residue: 0.1657 time to fit residues: 19.1980 Evaluate side-chains 65 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 44 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 330 HIS Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 414 LYS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9971 Z= 0.308 Angle : 0.603 10.169 13505 Z= 0.297 Chirality : 0.039 0.133 1597 Planarity : 0.003 0.047 1677 Dihedral : 3.761 20.094 1328 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.77 % Allowed : 18.83 % Favored : 78.39 % 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: 1.59 (0.25), residues: 1228 helix: 2.42 (0.19), residues: 765 sheet: -1.46 (0.59), residues: 81 loop : -1.28 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 156 HIS 0.005 0.001 HIS C 72 PHE 0.014 0.001 PHE D 356 TYR 0.020 0.001 TYR F 190 ARG 0.003 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 45 time to evaluate : 1.097 Fit side-chains REVERT: A 249 MET cc_start: 0.8570 (ppp) cc_final: 0.8317 (ppp) REVERT: A 400 MET cc_start: 0.9295 (mmm) cc_final: 0.8927 (mmm) REVERT: C 47 TYR cc_start: 0.8825 (t80) cc_final: 0.8344 (t80) REVERT: D 330 HIS cc_start: 0.8483 (OUTLIER) cc_final: 0.7884 (t70) outliers start: 29 outliers final: 21 residues processed: 72 average time/residue: 0.1645 time to fit residues: 19.2333 Evaluate side-chains 65 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 43 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 330 HIS Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9971 Z= 0.211 Angle : 0.568 10.306 13505 Z= 0.275 Chirality : 0.038 0.145 1597 Planarity : 0.003 0.049 1677 Dihedral : 3.641 19.897 1328 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.20 % Allowed : 20.55 % Favored : 77.25 % 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: 1.76 (0.25), residues: 1228 helix: 2.52 (0.19), residues: 766 sheet: -1.43 (0.59), residues: 86 loop : -1.12 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 156 HIS 0.004 0.001 HIS C 72 PHE 0.028 0.001 PHE C 58 TYR 0.017 0.001 TYR F 190 ARG 0.003 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 46 time to evaluate : 1.144 Fit side-chains REVERT: A 194 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8720 (t80) REVERT: A 400 MET cc_start: 0.9315 (mmm) cc_final: 0.8974 (mmm) REVERT: C 47 TYR cc_start: 0.8825 (t80) cc_final: 0.8337 (t80) REVERT: C 70 LEU cc_start: 0.9590 (tt) cc_final: 0.9341 (mt) REVERT: D 330 HIS cc_start: 0.8476 (OUTLIER) cc_final: 0.7894 (t70) outliers start: 23 outliers final: 16 residues processed: 67 average time/residue: 0.1582 time to fit residues: 17.5453 Evaluate side-chains 62 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 44 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 330 HIS Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 chunk 93 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN E 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9971 Z= 0.149 Angle : 0.572 10.813 13505 Z= 0.267 Chirality : 0.037 0.139 1597 Planarity : 0.003 0.049 1677 Dihedral : 3.426 19.289 1328 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.53 % Allowed : 21.41 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.26), residues: 1228 helix: 2.70 (0.19), residues: 767 sheet: -1.33 (0.58), residues: 87 loop : -0.94 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 159 HIS 0.007 0.001 HIS D 309 PHE 0.010 0.001 PHE E 134 TYR 0.014 0.001 TYR F 190 ARG 0.003 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 1.105 Fit side-chains REVERT: A 194 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8755 (t80) REVERT: A 244 MET cc_start: 0.8303 (pmm) cc_final: 0.6664 (mmm) REVERT: A 400 MET cc_start: 0.9247 (mmm) cc_final: 0.8887 (mmm) REVERT: C 47 TYR cc_start: 0.8822 (t80) cc_final: 0.8344 (t80) REVERT: C 70 LEU cc_start: 0.9580 (tt) cc_final: 0.9331 (mt) REVERT: D 330 HIS cc_start: 0.8347 (OUTLIER) cc_final: 0.7837 (t70) outliers start: 16 outliers final: 11 residues processed: 65 average time/residue: 0.1597 time to fit residues: 17.2924 Evaluate side-chains 61 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 330 HIS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 179 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.2980 chunk 110 optimal weight: 9.9990 chunk 113 optimal weight: 0.4980 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9971 Z= 0.172 Angle : 0.585 11.472 13505 Z= 0.274 Chirality : 0.037 0.140 1597 Planarity : 0.003 0.048 1677 Dihedral : 3.405 19.139 1328 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.63 % Allowed : 21.89 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.25), residues: 1228 helix: 2.77 (0.19), residues: 764 sheet: -1.24 (0.58), residues: 86 loop : -0.85 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 159 HIS 0.005 0.001 HIS D 309 PHE 0.028 0.001 PHE C 58 TYR 0.023 0.001 TYR D 227 ARG 0.004 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 1.188 Fit side-chains REVERT: A 90 MET cc_start: 0.9120 (tmm) cc_final: 0.8740 (ppp) REVERT: A 194 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8733 (t80) REVERT: A 400 MET cc_start: 0.9251 (mmm) cc_final: 0.8898 (mmm) REVERT: B 66 PHE cc_start: 0.8496 (t80) cc_final: 0.7990 (t80) REVERT: C 47 TYR cc_start: 0.8845 (t80) cc_final: 0.8343 (t80) REVERT: C 70 LEU cc_start: 0.9586 (tt) cc_final: 0.9342 (mt) REVERT: C 72 HIS cc_start: 0.8857 (OUTLIER) cc_final: 0.8435 (t70) REVERT: D 330 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.7840 (t70) outliers start: 17 outliers final: 11 residues processed: 65 average time/residue: 0.1643 time to fit residues: 17.6851 Evaluate side-chains 61 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 330 HIS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.0870 chunk 55 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 0.0770 chunk 59 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 103 optimal weight: 0.0970 overall best weight: 0.8316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9971 Z= 0.143 Angle : 0.580 12.591 13505 Z= 0.267 Chirality : 0.037 0.139 1597 Planarity : 0.003 0.044 1677 Dihedral : 3.293 18.569 1328 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.43 % Allowed : 21.99 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.25), residues: 1228 helix: 2.79 (0.19), residues: 767 sheet: -1.14 (0.58), residues: 86 loop : -0.79 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 159 HIS 0.006 0.001 HIS D 309 PHE 0.014 0.001 PHE D 598 TYR 0.021 0.001 TYR D 227 ARG 0.002 0.000 ARG E 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 1.270 Fit side-chains REVERT: A 90 MET cc_start: 0.9098 (tmm) cc_final: 0.8718 (ppp) REVERT: A 194 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8695 (t80) REVERT: A 244 MET cc_start: 0.8245 (pmm) cc_final: 0.6754 (mmm) REVERT: A 400 MET cc_start: 0.9263 (mmm) cc_final: 0.8911 (mmm) REVERT: B 66 PHE cc_start: 0.8498 (t80) cc_final: 0.7980 (t80) REVERT: C 47 TYR cc_start: 0.8792 (t80) cc_final: 0.8303 (t80) REVERT: C 70 LEU cc_start: 0.9579 (tt) cc_final: 0.9371 (mt) REVERT: C 72 HIS cc_start: 0.8832 (OUTLIER) cc_final: 0.8516 (t70) REVERT: D 330 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.7845 (t70) outliers start: 15 outliers final: 11 residues processed: 66 average time/residue: 0.1672 time to fit residues: 18.2138 Evaluate side-chains 63 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 330 HIS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.049979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.035262 restraints weight = 70052.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.036109 restraints weight = 38253.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.036828 restraints weight = 27370.771| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 9971 Z= 0.428 Angle : 0.735 12.170 13505 Z= 0.357 Chirality : 0.042 0.146 1597 Planarity : 0.004 0.038 1677 Dihedral : 3.826 19.377 1328 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.72 % Allowed : 21.89 % Favored : 76.39 % 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: 1.76 (0.25), residues: 1228 helix: 2.51 (0.19), residues: 763 sheet: -1.45 (0.57), residues: 86 loop : -1.08 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 156 HIS 0.006 0.001 HIS C 72 PHE 0.026 0.002 PHE C 58 TYR 0.021 0.002 TYR F 190 ARG 0.014 0.001 ARG A 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1706.58 seconds wall clock time: 32 minutes 9.87 seconds (1929.87 seconds total)